diff --git a/.DS_Store b/.DS_Store index 33eb081..1a20b43 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/README.md b/README.md index 832edb3..35e1a15 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# QPTUNA: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ) +# QSARtuna 𓆛: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ) Build predictive models for CompChem with hyperparameters optimized by [Optuna](https://optuna.org/). @@ -14,16 +14,16 @@ for the given data. The search itself is done using [Optuna](https://optuna.org/). -Devloped models employ +Developed models employ the latest state-of-the-art -uncertinaty estimation and +uncertainty estimation and explainability python packages Further documentation in the GitHub pages [here](https://molecularai.github.io/Qptuna/). ### The three-step process -QPTUNA is structured around three steps: +QSARtuna is structured around three steps: 1. *Hyperparameter Optimization:* Train many models with different parameters using Optuna. @@ -135,7 +135,7 @@ When we have our data and our configuration, it is time to start the optimizatio ### Running via singulartity -QPTUNA can be deployed using [Singularity](https://sylabs.io/guides/3.7/user-guide/index.html) container. +QSARtuna can be deployed using [Singularity](https://sylabs.io/guides/3.7/user-guide/index.html) container. To run commands inside the container, Singularity uses the following syntax: ```shell @@ -145,12 +145,12 @@ singularity exec We can run three-step-process from command line with the following command: ```shell -singularity exec /projects/cc/mai/containers/Qptuna_latest.sif \ - /opt/qptuna/.venv/bin/qptuna-optimize \ +singularity exec /projects/cc/mai/containers/QSARtuna_latest.sif \ + /opt/qsartuna/.venv/bin/qsartuna-optimize \ --config examples/optimization/regression_drd2_50.json \ - --best-buildconfig-outpath ~/qptuna-target/best.json \ - --best-model-outpath ~/qptuna-target/best.pkl \ - --merged-model-outpath ~/qptuna-target/merged.pkl + --best-buildconfig-outpath ~/qsartuna-target/best.json \ + --best-model-outpath ~/qsartuna-target/best.pkl \ + --merged-model-outpath ~/qsartuna-target/merged.pkl ``` Since optimization can be a long process, @@ -171,53 +171,53 @@ We can submit our script to the queue by giving `sbatch` the following script: #SBATCH --time=100:0:0 #SBATCH --partition core -# This script illustrates how to run one configuration from Qptuna examples. +# This script illustrates how to run one configuration from QSARtuna examples. # The example we use is in examples/optimization/regression_drd2_50.json. # The example we chose uses relative paths to data files, change directory. cd /{project_folder}/OptunaAZ-versions/OptunaAZ_latest singularity exec \ - /{project_folder}/containers/Qptuna_latest.sif \ - /opt/qptuna/.venv/bin/qptuna-optimize \ + /{project_folder}/containers/QSARtuna_latest.sif \ + /opt/qsartuna/.venv/bin/qsartuna-optimize \ --config{project_folder}/examples/optimization/regression_drd2_50.json \ - --best-buildconfig-outpath ~/qptuna-target/best.json \ - --best-model-outpath ~/qptuna-target/best.pkl \ - --merged-model-outpath ~/qptuna-target/merged.pkl + --best-buildconfig-outpath ~/qsartuna-target/best.json \ + --best-model-outpath ~/qsartuna-target/best.pkl \ + --merged-model-outpath ~/qsartuna-target/merged.pkl ``` -When the script is complete, it will create pickled model files inside your home directory under `~/qptuna-target/`. +When the script is complete, it will create pickled model files inside your home directory under `~/qsartuna-target/`. ### Using the model When the model is built, run inference: ```shell -singularity exec /{project_folder}/containers/Qptuna_latest.sif \ - /opt/qptuna/.venv/bin/qptuna-predict \ +singularity exec /{project_folder}/containers/QSARtuna_latest.sif \ + /opt/qsartuna/.venv/bin/qsartuna-predict \ --model-file target/merged.pkl \ --input-smiles-csv-file tests/data/DRD2/subset-50/test.csv \ --input-smiles-csv-column "canonical" \ --output-prediction-csv-file target/prediction.csv ``` -Note that Qptuna_latest.sif points to the most recent version of Qptuna. +Note that QSARtuna_latest.sif points to the most recent version of QSARtuna. -Legacy models require the inference with the same Qptuna version used to train the model. +Legacy models require the inference with the same QSARtuna version used to train the model. This can be specified by modifying the above command and supplying -`/projects/cc/mai/containers/Qptuna_.sif` (replace with the version of Qptuna). +`/projects/cc/mai/containers/QSARtuna_.sif` (replace with the version of QSARtuna). E.g: ```shell -singularity exec /{project_folder}/containers/Qptuna_2.5.1.sif \ - /opt/qptuna/.venv/bin/qptuna-predict \ +singularity exec /{project_folder}/containers/QSARtuna_2.5.1.sif \ + /opt/qsartuna/.venv/bin/qsartuna-predict \ --model-file 2.5.1_model.pkl \ --input-smiles-csv-file tests/data/DRD2/subset-50/test.csv \ --input-smiles-csv-column "canonical" \ --output-prediction-csv-file target/prediction.csv ``` -would generate predictions for a model trained with Qptuna 2.5.1. +would generate predictions for a model trained with QSARtuna 2.5.1. ### Optional: inspect To inspect performance of different models tried during optimization, @@ -258,27 +258,27 @@ There you can access run/trial build (training) configuration. ## Run from Python/Jupyter Notebook -Create conda environment with Jupyter and Install Qptuna there: +Create conda environment with Jupyter and Install QSARtuna there: ```shell module purge module load Miniconda3 -conda create --name my_env_with_qptuna python=3.10.10 jupyter pip -conda activate my_env_with_qptuna +conda create --name my_env_with_qsartuna python=3.10.10 jupyter pip +conda activate my_env_with_qsartuna module purge # Just in case. -which python # Check. Should output path that contains "my_env_with_qptuna". -python -m pip install http://pages.scp.astrazeneca.net/mai/qptuna/releases/Qptuna_latest.tar.gz +which python # Check. Should output path that contains "my_env_with_qsartuna". +python -m pip install ``` -Then you can use Qptuna inside your Notebook: +Then you can use QSARtuna inside your Notebook: ```python -from qptuna.three_step_opt_build_merge import ( +from qsartuna.three_step_opt_build_merge import ( optimize, buildconfig_best, build_best, build_merged, ) -from qptuna.config import ModelMode, OptimizationDirection -from qptuna.config.optconfig import ( +from qsartuna.config import ModelMode, OptimizationDirection +from qsartuna.config.optconfig import ( OptimizationConfig, SVR, RandomForest, @@ -287,8 +287,8 @@ from qptuna.config.optconfig import ( PLS, XGBregressor, ) -from qptuna.datareader import Dataset -from qptuna.descriptors import ECFP, MACCS_keys, ECFP_counts +from qsartuna.datareader import Dataset +from qsartuna.descriptors import ECFP, MACCS_keys, ECFP_counts ## # Prepare hyperparameter optimization configuration. diff --git a/docs/.DS_Store b/docs/.DS_Store index 1021ea7..e9481d6 100644 Binary files a/docs/.DS_Store and b/docs/.DS_Store differ diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QPTUNA_Tutorial.ipynb b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QPTUNA_Tutorial.ipynb index c9fc52e..59265ed 100644 --- a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QPTUNA_Tutorial.ipynb +++ b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/QPTUNA_Tutorial.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# QPTUNA CLI Tutorial" + "# QSARtuna CLI Tutorial" ] }, { @@ -18,9 +18,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This tutorial is intended to provide a new user with the necessary background to start using Qptuna through a command line interface (CLI).\n", + "This tutorial is intended to provide a new user with the necessary background to start using QSARtuna through a command line interface (CLI).\n", "\n", - "A separate tutorial is available describing the use of the Qptuna GUI." + "A separate tutorial is available describing the use of the QSARtuna GUI." ] }, { @@ -34,9 +34,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA is a python package to automate the model building process for *REINVENT*. These models can use a variety of algorithms to fit to your input data and most of them have one or more so-called hyper-parameters (e.g. the maximum number of trees using a *Random Forest* or the C parameter in SVRs, controlling the influence of every support vector).\n", + "QSARtuna is a python package to automate the model building process for *REINVENT*. These models can use a variety of algorithms to fit to your input data and most of them have one or more so-called hyper-parameters (e.g. the maximum number of trees using a *Random Forest* or the C parameter in SVRs, controlling the influence of every support vector).\n", "\n", - "For both regression and classification tasks, QPTUNA allows you to specify input data for which the optimal hyper-parameters and a model can obtained automatically. If you want to get an idea on how the package is structured, read on otherwise you might want to skip it and The following examples should give you an idea how.\n" + "For both regression and classification tasks, QSARtuna allows you to specify input data for which the optimal hyper-parameters and a model can obtained automatically. If you want to get an idea on how the package is structured, read on otherwise you might want to skip it and The following examples should give you an idea how.\n" ] }, { @@ -50,7 +50,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna is structured around three steps:\n", + "QSARtuna is structured around three steps:\n", "1. **Hyperparameter Optimization:** \n", " Train many models with different parameters using Optuna.\n", " Only the training dataset is used here. \n", @@ -76,9 +76,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "To use QPTUNA from Jupyter Notebook, install it with:\n", + "To use QSARtuna from Jupyter Notebook, install it with:\n", "```\n", - "python -m pip install http://pages.scp.astrazeneca.net/mai/qptuna/releases/Qptuna_latest.tar.gz\n", + "python -m pip install http://pages.scp.astrazeneca.net/mai/qsartuna/releases/QSARtuna_latest.tar.gz\n", "```" ] }, @@ -91,7 +91,7 @@ "\n", "Training dataset is a CSV file. It has SMILES strings in a column named \"canonical\". It has the value that we will try to predict in column \"molwt\".\n", "\n", - "This example has train and test (holdout) dataset ready. If you have single dataset and would like QPTUNA to split it into train and test (holdout) datasets, see the next section." + "This example has train and test (holdout) dataset ready. If you have single dataset and would like QSARtuna to split it into train and test (holdout) datasets, see the next section." ] }, { @@ -142,7 +142,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA configuration can be read from a JSON file or created in Python. Here we create it in Python." + "QSARtuna configuration can be read from a JSON file or created in Python. Here we create it in Python." ] }, { @@ -164,7 +164,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", " from .autonotebook import tqdm as notebook_tqdm\n" ] } @@ -359,17 +359,17 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.731e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.731e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,452] Trial 54 finished with value: -437.4551843552628 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.0988827083418571, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.728e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.728e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,513] Trial 55 finished with value: -437.7905045218911 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.10275551704677868, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 8.093e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 8.093e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 9.647e+01, tolerance: 2.262e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 9.647e+01, tolerance: 2.262e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 7.442e+01, tolerance: 2.313e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 7.442e+01, tolerance: 2.313e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,588] Trial 56 finished with value: -460.9949341873208 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.02258838612145872, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", "[I 2024-02-15 17:30:38,673] Trial 57 finished with value: -437.2063895411025 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.001303005653721337, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", @@ -797,7 +797,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA can split data into train and test (holdout) datasets. To do so, send all data in as training_dataset_file, and choose a splitting strategy. Currently QPTUNA supports three splitting strategies: random, temporal and stratified. \n", + "QSARtuna can split data into train and test (holdout) datasets. To do so, send all data in as training_dataset_file, and choose a splitting strategy. Currently QSARtuna supports three splitting strategies: random, temporal and stratified. \n", "\n", "Random strategy splits data randomly, taking a specified fraction of observations to be test dataset. \n", "\n", @@ -817,7 +817,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "All the algorithms QPTUNA supports do not work with duplicates. Duplicates can come from multiple measurements for the same compound, or from the fact that the molecular descriptors we use are all disregard stereochemistry, so even if compounds are different, descriptors make them into duplicates. QPTUNA provides several strategies to remove duplicates:\n", + "All the algorithms QSARtuna supports do not work with duplicates. Duplicates can come from multiple measurements for the same compound, or from the fact that the molecular descriptors we use are all disregard stereochemistry, so even if compounds are different, descriptors make them into duplicates. QSARtuna provides several strategies to remove duplicates:\n", "* keep median - factors experimental deviation using all replicates into one median value (robust to outliers - recommended)\n", "* keep average - use all experimental data acorss all replicates (less robust to outliers vs. median)\n", "* keep first / keep last - when the first or the last measurement is the trusted one\n", @@ -885,15 +885,15 @@ "text": [ "[I 2024-02-15 17:30:42,956] A new study created in memory with name: my_study_stratified_split\n", "[I 2024-02-15 17:30:42,992] A new study created in memory with name: study_name_0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", "[I 2024-02-15 17:30:43,100] Trial 0 finished with value: -1916.9080190588304 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.6455264533858698, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 0 with value: -1916.9080190588304.\n", "[I 2024-02-15 17:30:43,165] Trial 1 finished with value: -2756.046839500092 and parameters: {'algorithm_name': 'PLSRegression', 'PLSRegression_algorithm_hash': '9f2f76e479633c0bf18cf2912fed9eda', 'n_components': 2, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 0 with value: -1916.9080190588304.\n", @@ -1052,7 +1052,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "By default, QPTUNA uses `neg_mean_squared_error` for regression and `roc_auc` for classification. It is possible to change to other scoring functions that supported by scikit-learn (https://scikit-learn.org/stable/modules/model_evaluation.html) amongst others:" + "By default, QSARtuna uses `neg_mean_squared_error` for regression and `roc_auc` for classification. It is possible to change to other scoring functions that supported by scikit-learn (https://scikit-learn.org/stable/modules/model_evaluation.html) amongst others:" ] }, { @@ -1189,11 +1189,11 @@ "[I 2024-02-15 17:30:50,908] Trial 12 finished with value: 0.3125909835602004 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 1.2601024383222263, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:50,962] Trial 13 finished with value: 0.35938304159920104 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.704926958538193, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:51,047] Trial 14 finished with value: -0.139217147681443 and parameters: {'algorithm_name': 'RandomForestRegressor', 'RandomForestRegressor_algorithm_hash': 'f1ac01e1bba332215ccbd0c29c9ac3c3', 'max_depth': 5, 'n_estimators': 7, 'max_features': , 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.831e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.831e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 5.012e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 5.012e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 4.308e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 4.308e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:51,100] Trial 15 finished with value: -0.3520572381552265 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.003736146475899149, 'descriptor': '{\"name\": \"MACCS_keys\", \"parameters\": {}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:51,156] Trial 16 finished with value: 0.3097224153934907 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 1.3643850817675436, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", @@ -1250,11 +1250,11 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.208e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.208e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 2.075e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 2.075e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.665e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.665e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:52,349] Trial 38 finished with value: 0.33582943996366277 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.03037397374709805, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:52,441] Trial 39 finished with value: -0.014200255758600178 and parameters: {'algorithm_name': 'RandomForestRegressor', 'RandomForestRegressor_algorithm_hash': 'f1ac01e1bba332215ccbd0c29c9ac3c3', 'max_depth': 12, 'n_estimators': 6, 'max_features': , 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", @@ -1303,11 +1303,11 @@ "[I 2024-02-15 17:30:54,404] Trial 76 finished with value: 0.8203032617778302 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.02814913529858031, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:54,453] Trial 77 finished with value: 0.8203033764469106 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.028018087885969566, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:54,506] Trial 78 finished with value: 0.8203229095425186 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.005685911509939887, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.109e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.109e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.002e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.002e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.165e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.165e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n" ] }, @@ -1316,11 +1316,11 @@ "output_type": "stream", "text": [ "[I 2024-02-15 17:30:54,617] Trial 79 finished with value: 0.8611747184538611 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.00427216024040911, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 79 with value: 0.8611747184538611.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.220e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.220e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.321e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.321e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.497e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.497e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:54,731] Trial 80 finished with value: 0.8613400144535142 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.02833136367189578, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 80 with value: 0.8613400144535142.\n", "[I 2024-02-15 17:30:54,843] Trial 81 finished with value: 0.8869607357185316 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.0008522399475568362, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 81 with value: 0.8869607357185316.\n", @@ -1387,7 +1387,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Various algorithms are available in Qptuna:" + "Various algorithms are available in QSARtuna:" ] }, { @@ -1445,13 +1445,13 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "PRF is a modification of the long-established Random Forest (RF) algorithm and takes into account uncertainties in features and/or labels (though only uncertainty in labels are currently implemented in Qptuna), which was first described in[1]. It can be seen as a probabilistic method to factor experimental uncertainty during training, and is considered a hybrid between regression and classification algorithms.\n", + "PRF is a modification of the long-established Random Forest (RF) algorithm and takes into account uncertainties in features and/or labels (though only uncertainty in labels are currently implemented in QSARtuna), which was first described in[1]. It can be seen as a probabilistic method to factor experimental uncertainty during training, and is considered a hybrid between regression and classification algorithms.\n", "\n", "In more detail; PRF treats labels as probability distribution functions [PDFs] (denoted as `∆y`), rather than deterministic quantities. In comparison, the traditional RF uses discrete variables for activity (binary y-labels, also referred to as `y`) from the discretised bioactivity scale defining active/inactive sets. \n", "\n", - "PTR integration was added to Qptuna to afford this probabilistic approach towards modelling, and is particularly useful combined with the PTR (See the preprocessing notebook for details). In this combination, PRF takes as input real-valued probabilities (similar to regression), from a Probabilistic Threshold Representation (PTR). However, similar to classification algorithms, PRF outputs the probability of activity for the active class.\n", + "PTR integration was added to QSARtuna to afford this probabilistic approach towards modelling, and is particularly useful combined with the PTR (See the preprocessing notebook for details). In this combination, PRF takes as input real-valued probabilities (similar to regression), from a Probabilistic Threshold Representation (PTR). However, similar to classification algorithms, PRF outputs the probability of activity for the active class.\n", "\n", - "Note that Qptuna runs the PRFClassifier in a regression setting, since the model only outputs class liklihood membership based on `∆y`\n", + "Note that QSARtuna runs the PRFClassifier in a regression setting, since the model only outputs class liklihood membership based on `∆y`\n", "\n", "[1] https://iopscience.iop.org/article/10.3847/1538-3881/aaf101/meta\n", "\n", @@ -1498,7 +1498,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Note that Qptuna is run in regression mode (`ModelMode.REGRESSION`), as outputs from the algorithm are always continuous values.\n", + "Note that QSARtuna is run in regression mode (`ModelMode.REGRESSION`), as outputs from the algorithm are always continuous values.\n", "\n", "Next we can run the PRF/PTR study:" ] @@ -1632,7 +1632,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "N.B It is not possible to train on response column values outside the likelihood for y-label memberships (ranging from 0-1), as expected for `∆y`. Doing so will result in the following error from Qptuna:" + "N.B It is not possible to train on response column values outside the likelihood for y-label memberships (ranging from 0-1), as expected for `∆y`. Doing so will result in the following error from QSARtuna:" ] }, { @@ -1648,7 +1648,7 @@ "[I 2024-02-15 17:31:35,748] A new study created in memory with name: study_name_0\n", "[W 2024-02-15 17:31:35,749] Trial 0 failed with parameters: {} because of the following error: ValueError('PRFClassifier supplied but response column outside [0.0-1.0] acceptable range. Response max: 9.7, response min: 5.3 ').\n", "Traceback (most recent call last):\n", - " File \"/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/optuna/study/_optimize.py\", line 200, in _run_trial\n", + " File \"/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/optuna/study/_optimize.py\", line 200, in _run_trial\n", " value_or_values = func(trial)\n", " File \"/Users/kljk345/PycharmProjects/optuna_az/optunaz/objective.py\", line 124, in __call__\n", " self._validate_algos()\n", @@ -1717,7 +1717,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA has the functionaility to train `ChemProp` deep learning models. These are message passing neural networks (MPNNs) based on a graph representation of training molecules. They are considered by many to offer the state-of-the-art approach for property prediction.\n", + "QSARtuna has the functionaility to train `ChemProp` deep learning models. These are message passing neural networks (MPNNs) based on a graph representation of training molecules. They are considered by many to offer the state-of-the-art approach for property prediction.\n", "\n", "`ChemProp` was first described in the paper Analyzing Learned Molecular Representations for Property Prediction: https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237\n", "\n", @@ -1779,25 +1779,25 @@ "INFO:root:Enqueued ChemProp manual trial with sensible defaults: {'activation': 'ReLU', 'aggregation': 'mean', 'aggregation_norm': 100, 'batch_size': 50, 'depth': 3, 'dropout': 0.0, 'features_generator': 'none', 'ffn_hidden_size': 300, 'ffn_num_layers': 3, 'final_lr_ratio_exp': -1, 'hidden_size': 300, 'init_lr_ratio_exp': -1, 'max_lr_exp': -3, 'warmup_epochs_ratio': 0.1, 'algorithm_name': 'ChemPropRegressor'}\n", "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 59.407933 on epoch 1\n", "Model 0 best validation rmse = 102.010993 on epoch 4\n", @@ -1912,23 +1912,23 @@ "text": [ "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 97.581963 on epoch 0\n", "Model 0 provided with no test set, no metric evaluation will be performed.\n", @@ -1937,7 +1937,7 @@ "\tSeed 0 ==> test rmse = nan\n", "Overall test rmse = nan +/- nan\n", "Elapsed time = 0:00:04\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 67.110851 on epoch 4\n", "Model 0 provided with no test set, no metric evaluation will be performed.\n", @@ -2063,9 +2063,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "You may safely ignore `ChemProp` warnings such as `Model 0 provided with no test set, no metric evaluation will be performed`, `\"rmse = nan\"` and `1-fold cross validation`, as they are information prompts printed from `ChemProp` due to some (deactivated) CV functionaility (ChemProp can perform it's own cross validation - details for this are still printed despite its deactivation within `Qptuna`).\n", + "You may safely ignore `ChemProp` warnings such as `Model 0 provided with no test set, no metric evaluation will be performed`, `\"rmse = nan\"` and `1-fold cross validation`, as they are information prompts printed from `ChemProp` due to some (deactivated) CV functionaility (ChemProp can perform it's own cross validation - details for this are still printed despite its deactivation within `QSARtuna`).\n", "\n", - "NB: Qptuna will first trial the sensible defaults for the MPNN architecture (where possible given the user config). This is communicated to the user, e.g. see the output which advises:\n", + "NB: QSARtuna will first trial the sensible defaults for the MPNN architecture (where possible given the user config). This is communicated to the user, e.g. see the output which advises:\n", "\n", "`A new study created in memory with name: study_name_0\n", "INFO:root:Enqueued ChemProp manual trial with sensible defaults: {'activation': 'ReLU', 'aggregation': 'mean', 'aggregation_norm': 100, 'batch_size': 50, 'depth': 3, 'dropout': 0.0, 'features_generator': 'none', 'ffn_hidden_size': 300, 'ffn_num_layers': 3, 'final_lr_ratio_exp': -1, 'hidden_size': 300, 'init_lr_ratio_exp': -1, 'max_lr_exp': -3, 'warmup_epochs_ratio': 0.1, 'algorithm_name': 'ChemPropRegressor'}`.\n", @@ -2084,7 +2084,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "By default, `Qptuna` separates `ChemProp` from the other shallow methods using the `split_chemprop` flag. When this setting is set, the user must specify the number of `ChemProp` trials using the `n_chemprop_trials` flag if more than 1 (default) trial is desired:" + "By default, `QSARtuna` separates `ChemProp` from the other shallow methods using the `split_chemprop` flag. When this setting is set, the user must specify the number of `ChemProp` trials using the `n_chemprop_trials` flag if more than 1 (default) trial is desired:" ] }, { @@ -2135,7 +2135,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna optimises all aspects of the ChemProp architecture when using ChemPropRegressor or ChemPropClassifier, however, users can activate the [original hyperparameter-optimization implementation](https://github.com/chemprop/chemprop#hyperparameter-optimization) in the `ChemProp` package, which performs automated Bayesian hyperparameter optimization using the `Hyperopt` package within each trial, at large computational cost.\n", + "QSARtuna optimises all aspects of the ChemProp architecture when using ChemPropRegressor or ChemPropClassifier, however, users can activate the [original hyperparameter-optimization implementation](https://github.com/chemprop/chemprop#hyperparameter-optimization) in the `ChemProp` package, which performs automated Bayesian hyperparameter optimization using the `Hyperopt` package within each trial, at large computational cost.\n", "\n", "NB: The principal way for users to expand and perform more advanced runs is to extend the available non-network hyperparameters, such as the `features_generator` option or e.g. to trial differnt side information weighting (if side information is available).\n", "\n", @@ -2190,9 +2190,9 @@ "\n", "#### A note on MPNN Hyperopt search space\n", "\n", - "`ChemProp` models trained using Hyperopt use the [original implementation](https://chemprop.readthedocs.io/en/latest/hyperopt.html), but one key difference is the `search_parameter_level` setting created for `Qptuna`; Instead of using pre-defined search spaces as in the original package, `Qptuna` can (and will by the default since `search_parameter_level`=`auto` unless changed) alter the space depending on the characteristics of user input data. For example, no. training set compounds, hyperparameter trials (`num_iters`) & epochs (`epochs`) are used by the `auto` setting to ensure search spaces are not too large for limited data/epochs, and _vice-versa_, an extensive search space is trailed when applicable.\n", + "`ChemProp` models trained using Hyperopt use the [original implementation](https://chemprop.readthedocs.io/en/latest/hyperopt.html), but one key difference is the `search_parameter_level` setting created for `QSARtuna`; Instead of using pre-defined search spaces as in the original package, `QSARtuna` can (and will by the default since `search_parameter_level`=`auto` unless changed) alter the space depending on the characteristics of user input data. For example, no. training set compounds, hyperparameter trials (`num_iters`) & epochs (`epochs`) are used by the `auto` setting to ensure search spaces are not too large for limited data/epochs, and _vice-versa_, an extensive search space is trailed when applicable.\n", "\n", - "N.B: Users can also manually define `Hyperopt` search spaces by altering `search_parameter_level` from `auto` to a different level between `[0-8]`, representing the increasing search space size (see the [Qptuna documentation](https://pages.scp.astrazeneca.net/mai/qptuna/optunaz.config.html#optunaz.config.optconfig.ChemPropSearch_Parameter_Level) for details)." + "N.B: Users can also manually define `Hyperopt` search spaces by altering `search_parameter_level` from `auto` to a different level between `[0-8]`, representing the increasing search space size (see the [QSARtuna documentation](https://pages.scp.astrazeneca.net/mai/qsartuna/optunaz.config.html#optunaz.config.optconfig.ChemPropSearch_Parameter_Level) for details)." ] }, { @@ -2208,7 +2208,7 @@ "source": [ "_“Even if you are only optimizing one loss as is the typical case, chances are there is an auxiliary task that will help you improve upon your main task”_ [Caruana, 1998]\n", "\n", - "`Qptuna` typically optimizes for one particular metric for a given molecule property. While we can generally achieve acceptable performance this way, these single task (ST) models ignore information that may improve the prediction of main task of intent. See option `a.` in the figure below.\n", + "`QSARtuna` typically optimizes for one particular metric for a given molecule property. While we can generally achieve acceptable performance this way, these single task (ST) models ignore information that may improve the prediction of main task of intent. See option `a.` in the figure below.\n", "\n", "Signals from relevant related tasks (aka \"auxiliary tasks\" or \"side information\") could come from the training signals of other molecular properties and by sharing representations between related tasks, we can enable a neural network to generalize better on our original task of intent. This approach is called Multi-Task Learning (MTL) See option `b.` in the figure below.\n", "\n", @@ -2217,7 +2217,7 @@ "_(above) Differences between optimizing one vs. more than one loss function. a.) Single-task (ST): one model trained to predict one task one model optimised until performance no longer increases b.) Multi-task (MT/MTL): training one model to predict multiple tasks one model optimising more than one loss function at once enables representations to be shared between trained tasks training signals of related tasks shared between all tasks._\n", "\n", "\n", - "`ChemProp` performs MTL by using the knowledge learnt during training one task to reduce the loss of other tasks included in training. In order to use this function in `Qptuna`, a user should provide side information in a separate file, and it should have the same ordering and length as the input/response columns (i.e. length of y should = length of side information for y).\n", + "`ChemProp` performs MTL by using the knowledge learnt during training one task to reduce the loss of other tasks included in training. In order to use this function in `QSARtuna`, a user should provide side information in a separate file, and it should have the same ordering and length as the input/response columns (i.e. length of y should = length of side information for y).\n", "\n", "E.g: consider the DRD2 example input from earlier:" ] @@ -2322,7 +2322,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The contribution or _weight_ of all side information tasks in their contribution to the loss function during training a network is a parameter that can be optimised within Qptuna, e.g:" + "The contribution or _weight_ of all side information tasks in their contribution to the loss function during training a network is a parameter that can be optimised within QSARtuna, e.g:" ] }, { @@ -2338,101 +2338,101 @@ "[I 2024-02-15 17:31:47,393] A new study created in memory with name: study_name_0\n", "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n" ] }, @@ -2440,43 +2440,43 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", @@ -7146,7 +7146,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Above described how ChemProp is by default split from shallow methods. Users can override this using the advanced functionaility when `split_chemprop`=False. In this situation `Qptuna` will optimise `ChemProp` with the other shallow methods:" + "Above described how ChemProp is by default split from shallow methods. Users can override this using the advanced functionaility when `split_chemprop`=False. In this situation `QSARtuna` will optimise `ChemProp` with the other shallow methods:" ] }, { @@ -7186,7 +7186,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Combining ChemProp and traditional methods in this way means the potential search possible in `Qptuna` comprises some incompatible sub-spaces; for example, `ChemProp` is only compatible with SMILES-based descriptors, whilst traditional methods are incompatible with SMILES. In the following examples, we consider the following search space: \"Valid" + "Combining ChemProp and traditional methods in this way means the potential search possible in `QSARtuna` comprises some incompatible sub-spaces; for example, `ChemProp` is only compatible with SMILES-based descriptors, whilst traditional methods are incompatible with SMILES. In the following examples, we consider the following search space: \"Valid" ] }, { @@ -7201,9 +7201,9 @@ "\n", "Pruning is an `Optuna` feature [originally designed](https://optuna.readthedocs.io/en/v2.0.0/tutorial/pruning.html) to automatically stop unpromising trials early in training.\n", "\n", - "_How/why is pruning implemented in Qptuna?_\n", + "_How/why is pruning implemented in QSARtuna?_\n", "\n", - "Instead of the original intention of pruning _unpromising trials_ due to poor performance, `Qptuna` ensures `Optuna` prunes _incompatible algorithm-desciptor pairs_, so the sampler will not trial incomptaible settings again. Duplicated trials are also pruned, to avoid repeatedly suggesting the same hyerparameters. Pruning the trial (instead of returning a cached result) explicitly tasks the sampler to avoid identical parameters.\n", + "Instead of the original intention of pruning _unpromising trials_ due to poor performance, `QSARtuna` ensures `Optuna` prunes _incompatible algorithm-desciptor pairs_, so the sampler will not trial incomptaible settings again. Duplicated trials are also pruned, to avoid repeatedly suggesting the same hyerparameters. Pruning the trial (instead of returning a cached result) explicitly tasks the sampler to avoid identical parameters.\n", "\n", "Now let us consider the following run:" ] @@ -7292,7 +7292,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Consulting the `Qptuna` output, we observe cases of e.g. \"`Trial 3 pruned. Incompatible subspace`\", which indicates an instance when the sampler has sampled an incompitble algo-descriptor pair. \n", + "Consulting the `QSARtuna` output, we observe cases of e.g. \"`Trial 3 pruned. Incompatible subspace`\", which indicates an instance when the sampler has sampled an incompitble algo-descriptor pair. \n", "\n", "\"`Trial 13 pruned. Duplicate parameter set`\" is an example of pruning a duplicated trial parameter suggestion.\n", "\n", @@ -7342,7 +7342,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "When performing classification you often want not only to predict the class label, but also obtain a probability of the respective label. This probability gives you some kind of confidence on the prediction. Some models can give you poor estimates of the class probabilities. The `CalibratedClassifierCV` Qptuna models allow better calibration for the probabilities of a given model.\n", + "When performing classification you often want not only to predict the class label, but also obtain a probability of the respective label. This probability gives you some kind of confidence on the prediction. Some models can give you poor estimates of the class probabilities. The `CalibratedClassifierCV` QSARtuna models allow better calibration for the probabilities of a given model.\n", "\n", "First, we should understand that well calibrated classifiers are probabilistic classifiers for which the output of the predict_proba method can be directly interpreted as a confidence level. For instance, a well calibrated (binary) classifier should classify the samples such that among the samples to which it gave a predict_proba value close to 0.8, approximately 80% actually belong to the positive class.\n", "\n", @@ -7735,7 +7735,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna offers three different ways to calculate uncertainty estimates. \n", + "QSARtuna offers three different ways to calculate uncertainty estimates. \n", "\n", "1. VennABERS calibration (a probability calibration covered in the section above).\n", "2. Ensemble uncertainty (ChemProp models trained with random initialisations).\n", @@ -11827,7 +11827,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "For regression uncertainty, the MAPIE package is available within Qptuna for regression algorithms, and is selected like so:" + "For regression uncertainty, the MAPIE package is available within QSARtuna for regression algorithms, and is selected like so:" ] }, { @@ -12013,7 +12013,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Model explainability is incorporated into Qptuna using two different approaches, depending on the algorithm chosen:\n", + "Model explainability is incorporated into QSARtuna using two different approaches, depending on the algorithm chosen:\n", "1. **SHAP:** \n", " Any shallow algorithm is compatible with the SHAP package (even traditionally unsupported packages use the `KernelExplainer`)\n", "2. **ChemProp interpret:**\n", @@ -12031,7 +12031,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "[SHAP](https://proceedings.neurips.cc/paper_files/paper/2017/hash/8a20a8621978632d76c43dfd28b67767-Abstract.html) (SHapley Additive exPlanations) are available in `Qptuna` based on the implementation available at https://github.com/slundberg/shap. The method uses a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions (see [here](https://shap.readthedocs.io/en/latest/index.html) for more details on the published tool and [here](https://github.com/slundberg/shap#methods-unified-by-shap) for papers using the approach).\n", + "[SHAP](https://proceedings.neurips.cc/paper_files/paper/2017/hash/8a20a8621978632d76c43dfd28b67767-Abstract.html) (SHapley Additive exPlanations) are available in `QSARtuna` based on the implementation available at https://github.com/slundberg/shap. The method uses a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions (see [here](https://shap.readthedocs.io/en/latest/index.html) for more details on the published tool and [here](https://github.com/slundberg/shap#methods-unified-by-shap) for papers using the approach).\n", "\n", "In the following example, a `RIDGE` regressor is trained using the a comopsite descriptor based on the `ECFP`, `MACCS` keys and `PhysChem` descriptors:" ] @@ -13296,14 +13296,14 @@ "source": [ "chemprop.predictor.chemprop_fingerprint(\n", " df[config.data.input_column].head(5),\n", - " fingerprint_type=\"MPN\") # MPN specified for illustration purposes - this is the default method in Qptuna" + " fingerprint_type=\"MPN\") # MPN specified for illustration purposes - this is the default method in QSARtuna" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "The output is n compounds as the input query in the rows by n latent representation features from the MPN in the columns. This output can then be used for any semi-supervise learning approach outside of Qptuna, as required. Alternatively the last layer of the FFN can be used as so:" + "The output is n compounds as the input query in the rows by n latent representation features from the MPN in the columns. This output can then be used for any semi-supervise learning approach outside of QSARtuna, as required. Alternatively the last layer of the FFN can be used as so:" ] }, { @@ -13588,7 +13588,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna can be used to transform input labels so that log-scaled or irregularly distributed data can be transformed to a normal distribution as required for most Machine Learning inputs. The following example shows how XC50 values can be scaled to pXC50 values by using the -Log10 to the 6th unit conversion, like so:" + "QSARtuna can be used to transform input labels so that log-scaled or irregularly distributed data can be transformed to a normal distribution as required for most Machine Learning inputs. The following example shows how XC50 values can be scaled to pXC50 values by using the -Log10 to the 6th unit conversion, like so:" ] }, { @@ -13815,7 +13815,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In comparison, Qptuna does not normally transform the data:" + "In comparison, QSARtuna does not normally transform the data:" ] }, { @@ -14116,7 +14116,7 @@ "source": [ "NB: Please note that outputs have automatically been reversed transformed at inference, back onto the original XC50 scale, as shown by large values outside the log pXC50.\n", "\n", - "This is the default behaviour of Qptuna; reverse transform is performed at inference when log transformation was applied, so that users can action on prediction the original input data scale. Importantly, a user can easily override this behaviour by providing the transform parameter as `None`:" + "This is the default behaviour of QSARtuna; reverse transform is performed at inference when log transformation was applied, so that users can action on prediction the original input data scale. Importantly, a user can easily override this behaviour by providing the transform parameter as `None`:" ] }, { @@ -14143,7 +14143,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This will instruct Qptuna to avoid the reverse transform on the predictions. This transform parameter is ignored if no transformation was applied in the user config.\n", + "This will instruct QSARtuna to avoid the reverse transform on the predictions. This transform parameter is ignored if no transformation was applied in the user config.\n", "\n", "Log transformation can also be combined with the PTR transform. In this situation, all user inputs are expected to be on the untransformed scale. For example, if a user wishes to create a PTR model, trained on pXC50 data and a cut-off for pXC50 values of 5 (10um), the following config can be used:" ] @@ -14444,7 +14444,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Advanced options for Qptuna runs" + "## Advanced options for QSARtuna runs" ] }, { @@ -14458,7 +14458,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna can optimize for the minimzation of the standard deviation of performance across the folds. This should in theory prioritize hyperparameters that are consistently performative across different splits of the data, and so should be more generalizable/performative in production. This can be performed with the `minimize_std_dev` in the example below:" + "QSARtuna can optimize for the minimzation of the standard deviation of performance across the folds. This should in theory prioritize hyperparameters that are consistently performative across different splits of the data, and so should be more generalizable/performative in production. This can be performed with the `minimize_std_dev` in the example below:" ] }, { @@ -16444,7 +16444,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Further visualization of Qptuna runs" + "### Further visualization of QSARtuna runs" ] }, { diff --git a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/preprocess_data.ipynb b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/preprocess_data.ipynb index 5d586e8..398f9d0 100644 --- a/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/preprocess_data.ipynb +++ b/docs/sphinx-builddir/doctrees/nbsphinx/notebooks/preprocess_data.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Preprocessing data for Qptuna" + "# Preprocessing data for QSARtuna" ] }, { @@ -15,7 +15,7 @@ "\n", "Probably the most important step in using the automated parameter optimization is the preprocessing of the data prior to training the model. Common considerations include how to deal with duplicates SMILES having different read-out values, if and how to split the data into a training and (holdout) test set, and how to prepare input files in a proper way (e.g. transform SDF files into a dataframe with SMILE string- and read-out-columns).\n", "\n", - "The Qptuna (`Optuna_AZ`) packages have some built-in functionality to facilitate that process." + "The QSARtuna (`Optuna_AZ`) packages have some built-in functionality to facilitate that process." ] }, { @@ -108,11 +108,11 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna can use either SMILES strings (no stereochemistry!) or SDF as input molecular representation.\n", + "QSARtuna can use either SMILES strings (no stereochemistry!) or SDF as input molecular representation.\n", "\n", "SMILES input is a comma-separated values (CSV) file with a SMILES column and a read-out (response) column. Read-out (response) column can be either numeric values (for regression) or labels (for classification). Note, that labels can be in the form of integer/boolean values - as long as the optimization process is specified as `classification`, they will be translated into nominal data values. SDF files should have the response column provided within the SDF file.\n", "\n", - "Data provided in SDF format can (optionally - since Qptuna can accept SDF files) be converted to a SMILES file (so that any optional more advanced preprocessing can be conducted) using the following code." + "Data provided in SDF format can (optionally - since QSARtuna can accept SDF files) be converted to a SMILES file (so that any optional more advanced preprocessing can be conducted) using the following code." ] }, { @@ -433,9 +433,9 @@ "* `KeepRandom(seed)`: keep a random observation for each duplicate. Note, that the order of observations is not preserved. Use the `seed` parameter to vary results or to reproduce them.\n", "* `KeepMin()` and `KeepMax()`: keep min or max value.\n", "* `KeepAvg()`: take the average for all duplicates.\n", - "* `KeepMedian()`: (default in Qptuna) take the median for all duplicates.\n", + "* `KeepMedian()`: (default in QSARtuna) take the median for all duplicates.\n", "\n", - "The default deduplication method in Qptuna is KeepMedian, which is recommended best practice due the ability to utilise all experimental data into one value (account for experimental variability across replicated), whilst being robust to outliers.\n", + "The default deduplication method in QSARtuna is KeepMedian, which is recommended best practice due the ability to utilise all experimental data into one value (account for experimental variability across replicated), whilst being robust to outliers.\n", "\n", "Each of the deduplication methods returns a unique version of the stored dataframe." ] @@ -874,7 +874,7 @@ "metadata": {}, "source": [ "## Transform of data inputs \n", - "Qptuna can perform two types of transforms on input labels either a probabilistic transformation named Probabilistic Threshold Representation (PTR) or simple logarithmic scaling. The latter is a required step for data that is not normally distributed for most Machine Learning inputs. These approaches are discussed in more detail in the following sections." + "QSARtuna can perform two types of transforms on input labels either a probabilistic transformation named Probabilistic Threshold Representation (PTR) or simple logarithmic scaling. The latter is a required step for data that is not normally distributed for most Machine Learning inputs. These approaches are discussed in more detail in the following sections." ] }, { @@ -890,7 +890,7 @@ "\n", "Most algorithms assume numerical co-variates have a Gaussian (normally distributed) probability distribution. In reality, input data may or may not have a normal distribution. Some may have a Gaussian-like distribution (e.g. nearly Gaussian but with outliers or a skew) whilst other may exhibit totally different distribution (e.g. exponential scale). For this reason, superior performance for a wide range of machine learning algorithms is obtained by performing a transformation to user inputs and/or output variables to have a Gaussian or Gaussian-like distribution.\n", "\n", - "A good example of this is the conversion of principal (IC50) activity results to the pXC50 (negative log base), which have already been precomputed outside of Qptuna in the following example:" + "A good example of this is the conversion of principal (IC50) activity results to the pXC50 (negative log base), which have already been precomputed outside of QSARtuna in the following example:" ] }, { @@ -958,10 +958,10 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Qptuna logarithmic transformation \n", + "### QSARtuna logarithmic transformation \n", "\n", "\n", - "Qptuna implements a 'ModelDataTransform' transormation method for converting numerical input or output variables to have a Gaussian or more-Gaussian-like distribution, which can be performed like so:" + "QSARtuna implements a 'ModelDataTransform' transormation method for converting numerical input or output variables to have a Gaussian or more-Gaussian-like distribution, which can be performed like so:" ] }, { @@ -1003,9 +1003,9 @@ " conversion=6\n", ")\n", "\n", - "comparison['Qptuna pXC50 ModelDataTransform'] = transform.transform(comparison['XC50'])\n", + "comparison['QSARtuna pXC50 ModelDataTransform'] = transform.transform(comparison['XC50'])\n", "\n", - "g = sns.jointplot(data=comparison, x=\"Qptuna pXC50 ModelDataTransform\", y=\"pXC50\")\n", + "g = sns.jointplot(data=comparison, x=\"QSARtuna pXC50 ModelDataTransform\", y=\"pXC50\")\n", "g.plot_marginals(sns.rugplot, color=\"crimson\", height=-.15, clip_on=False, alpha=.2)" ] }, @@ -1096,7 +1096,7 @@ "\n", "NB: the log transformation is reversed at inference. I.e. only the model is trained with the transformed values, any predictions will be output to the original scale as provided in user input data.\n", "\n", - "Qptuna also implements the reverse of the transform using `reverse_transform`, so that users can obtain values on the original scale at inference, like so:" + "QSARtuna also implements the reverse of the transform using `reverse_transform`, so that users can obtain values on the original scale at inference, like so:" ] }, { @@ -1158,7 +1158,7 @@ "\n", "PTR hence represents the activity in a framework in-between the classification and regression architecture, with philosophical differences from either approach. Compared to classification, this approach enables better representation of factors increasing/decreasing inactivity. Conversely, one can utilize all data (even delimited/operand/censored data far from a cut-off) at the same time as taking into account the granularity around the cut-off, compared to a conventional regression framework. Thereby, PTR combines characteristics from both classification and regression settings.\n", "\n", - "NB: Qptuna treats the PTR values as the ‘ideal y-label’, i.e. they become the new response column values for train/test/validation performance evaluation, since it represents the ideal case, where experimental error is taken into account and model outputs most closely reflect this.\n", + "NB: QSARtuna treats the PTR values as the ‘ideal y-label’, i.e. they become the new response column values for train/test/validation performance evaluation, since it represents the ideal case, where experimental error is taken into account and model outputs most closely reflect this.\n", "\n", "\n", "[1] https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00539-7#Sec12" @@ -1168,9 +1168,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Qptuna implementation of the PTR\n", + "### QSARtuna implementation of the PTR\n", "\n", - "PTR is also easily applied within the Datareader class by specifying the PTR options to the Qptuna datareader. E.g:" + "PTR is also easily applied within the Datareader class by specifying the PTR options to the QSARtuna datareader. E.g:" ] }, { @@ -1392,7 +1392,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In this section, we next also look at how the PTR within the Qptuna datareader is implemented, and show how a user can assess the experimental reproducability/uncertainty for their query dataset.\n", + "In this section, we next also look at how the PTR within the QSARtuna datareader is implemented, and show how a user can assess the experimental reproducability/uncertainty for their query dataset.\n", "\n", "First we start with imports and define the PTR function using `stats.norm.cdf` from scipy" ] @@ -1637,9 +1637,9 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.\n", " warnings.warn(msg, UserWarning)\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.\n", " warnings.warn(msg, UserWarning)\n" ] }, diff --git a/docs/sphinx-builddir/html/README.html b/docs/sphinx-builddir/html/README.html index 0db388b..fec7f7b 100644 --- a/docs/sphinx-builddir/html/README.html +++ b/docs/sphinx-builddir/html/README.html @@ -4,7 +4,7 @@ - QPTUNA: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ) — QPTUNA 2.7.11 documentation + QSARtuna: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ) — QSARtuna 2.7.11 documentation @@ -21,8 +21,8 @@ - - + + @@ -34,7 +34,7 @@ - QPTUNA + QSARtuna
@@ -62,8 +62,8 @@
  • Run from Python/Jupyter Notebook
  • -
  • Jupyter Notebook: Preprocessing Data for Qptuna
  • -
  • Jupyter Notebook: Qptuna CLI Tutorial
  • +
  • Jupyter Notebook: Preprocessing Data for QSARtuna
  • +
  • Jupyter Notebook: QSARtuna CLI Tutorial
  • List of available ML algorithms
  • List of available molecular descriptors
  • List of available evaluation splits
  • @@ -75,7 +75,7 @@
    @@ -83,7 +83,7 @@
    • - +
    • View page source
    • @@ -117,8 +117,8 @@ text-align: unset; } -
      -

      QPTUNA: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ)

      +
      +

      QSARtuna: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ)

      Build predictive models for CompChem with hyperparameters optimized by Optuna.

      Developed with Uncertainty Quantification and model explainability in mind.

      @@ -135,7 +135,7 @@

      Background

      The three-step process

      -

      QPTUNA is structured around three steps:

      +

      QSARtuna is structured around three steps:

      1. Hyperparameter Optimization: Train many models with different parameters using Optuna. @@ -242,18 +242,18 @@

        Configuration file

        Running via singulartity

        -

        QPTUNA can be deployed using Singularity container.

        +

        QSARtuna can be deployed using Singularity container.

        To run commands inside the container, Singularity uses the following syntax:

        singularity exec <container.sif> <command>
         

        We can run three-step-process from command line with the following command:

        -
        singularity exec /projects/cc/mai/containers/Qptuna_latest.sif \
        -  /opt/qptuna/.venv/bin/qptuna-optimize \
        +
        singularity exec /projects/cc/mai/containers/QSARtuna_latest.sif \
        +  /opt/qsartuna/.venv/bin/qsartuna-optimize \
           --config examples/optimization/regression_drd2_50.json \
        -  --best-buildconfig-outpath ~/qptuna-target/best.json \
        -  --best-model-outpath ~/qptuna-target/best.pkl \
        -  --merged-model-outpath ~/qptuna-target/merged.pkl
        +  --best-buildconfig-outpath ~/qsartuna-target/best.json \
        +  --best-model-outpath ~/qsartuna-target/best.pkl \
        +  --merged-model-outpath ~/qsartuna-target/merged.pkl
         

        Since optimization can be a long process, @@ -271,48 +271,48 @@

        Submitting to SLURM#SBATCH --time=100:0:0 #SBATCH --partition core -# This script illustrates how to run one configuration from Qptuna examples. +# This script illustrates how to run one configuration from QSARtuna examples. # The example we use is in examples/optimization/regression_drd2_50.json. # The example we chose uses relative paths to data files, change directory. cd /{project_folder}/OptunaAZ-versions/OptunaAZ_latest singularity exec \ - /{project_folder}/containers/Qptuna_latest.sif \ - /opt/qptuna/.venv/bin/qptuna-optimize \ + /{project_folder}/containers/QSARtuna_latest.sif \ + /opt/qsartuna/.venv/bin/qsartuna-optimize \ --config{project_folder}/examples/optimization/regression_drd2_50.json \ - --best-buildconfig-outpath ~/qptuna-target/best.json \ - --best-model-outpath ~/qptuna-target/best.pkl \ - --merged-model-outpath ~/qptuna-target/merged.pkl + --best-buildconfig-outpath ~/qsartuna-target/best.json \ + --best-model-outpath ~/qsartuna-target/best.pkl \ + --merged-model-outpath ~/qsartuna-target/merged.pkl

        -

        When the script is complete, it will create pickled model files inside your home directory under ~/qptuna-target/.

        +

        When the script is complete, it will create pickled model files inside your home directory under ~/qsartuna-target/.

      Using the model

      When the model is built, run inference:

      -
      singularity exec /{project_folder}/containers/Qptuna_latest.sif \
      -  /opt/qptuna/.venv/bin/qptuna-predict \
      +
      singularity exec /{project_folder}/containers/QSARtuna_latest.sif \
      +  /opt/qsartuna/.venv/bin/qsartuna-predict \
         --model-file target/merged.pkl \
         --input-smiles-csv-file tests/data/DRD2/subset-50/test.csv \
         --input-smiles-csv-column "canonical" \
         --output-prediction-csv-file target/prediction.csv
       
      -

      Note that Qptuna_latest.sif points to the most recent version of Qptuna.

      -

      Legacy models require the inference with the same Qptuna version used to train the model. +

      Note that QSARtuna_latest.sif points to the most recent version of QSARtuna.

      +

      Legacy models require the inference with the same QSARtuna version used to train the model. This can be specified by modifying the above command and supplying -/projects/cc/mai/containers/Qptuna_<version>.sif (replace with the version of Qptuna).

      +/projects/cc/mai/containers/QSARtuna_<version>.sif (replace with the version of QSARtuna).

      E.g:

      -
      singularity exec /{project_folder}/containers/Qptuna_2.5.1.sif \
      -  /opt/qptuna/.venv/bin/qptuna-predict \
      +
      singularity exec /{project_folder}/containers/QSARtuna_2.5.1.sif \
      +  /opt/qsartuna/.venv/bin/qsartuna-predict \
         --model-file 2.5.1_model.pkl \
         --input-smiles-csv-file tests/data/DRD2/subset-50/test.csv \
         --input-smiles-csv-column "canonical" \
         --output-prediction-csv-file target/prediction.csv
       
      -

      would generate predictions for a model trained with Qptuna 2.5.1.

      +

      would generate predictions for a model trained with QSARtuna 2.5.1.

      Optional: inspect

      @@ -347,25 +347,25 @@

      Optional: inspect

      Run from Python/Jupyter Notebook

      -

      Create conda environment with Jupyter and Install Qptuna there:

      +

      Create conda environment with Jupyter and Install QSARtuna there:

      module purge
       module load Miniconda3
      -conda create --name my_env_with_qptuna python=3.10.10 jupyter pip
      -conda activate my_env_with_qptuna
      +conda create --name my_env_with_qsartuna python=3.10.10 jupyter pip
      +conda activate my_env_with_qsartuna
       module purge  # Just in case.
      -which python  # Check. Should output path that contains "my_env_with_qptuna".
      -python -m pip install http://pages.scp.astrazeneca.net/mai/qptuna/releases/Qptuna_latest.tar.gz
      +which python  # Check. Should output path that contains "my_env_with_qsartuna".
      +python -m pip install http://pages.scp.astrazeneca.net/mai/qsartuna/releases/QSARtuna_latest.tar.gz
       
      -

      Then you can use Qptuna inside your Notebook:

      -
      from qptuna.three_step_opt_build_merge import (
      +

      Then you can use QSARtuna inside your Notebook:

      +
      from qsartuna.three_step_opt_build_merge import (
           optimize,
           buildconfig_best,
           build_best,
           build_merged,
       )
      -from qptuna.config import ModelMode, OptimizationDirection
      -from qptuna.config.optconfig import (
      +from qsartuna.config import ModelMode, OptimizationDirection
      +from qsartuna.config.optconfig import (
           OptimizationConfig,
           SVR,
           RandomForest,
      @@ -374,8 +374,8 @@ 

      Run from Python/Jupyter NotebookPLS, XGBregressor, ) -from qptuna.datareader import Dataset -from qptuna.descriptors import ECFP, MACCS_keys, ECFP_counts +from qsartuna.datareader import Dataset +from qsartuna.descriptors import ECFP, MACCS_keys, ECFP_counts ## # Prepare hyperparameter optimization configuration. @@ -429,8 +429,8 @@

      Run from Python/Jupyter Notebook - - + +


      diff --git a/docs/sphinx-builddir/html/_modules/index.html b/docs/sphinx-builddir/html/_modules/index.html index a12f677..6322549 100644 --- a/docs/sphinx-builddir/html/_modules/index.html +++ b/docs/sphinx-builddir/html/_modules/index.html @@ -3,7 +3,7 @@ - Overview: module code — QPTUNA 2.7.11 documentation + Overview: module code — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
      @@ -44,8 +44,8 @@

      Documentation:

      • Intro and Quick Start
      • -
      • Jupyter Notebook: Preprocessing Data for Qptuna
      • -
      • Jupyter Notebook: Qptuna CLI Tutorial
      • +
      • Jupyter Notebook: Preprocessing Data for QSARtuna
      • +
      • Jupyter Notebook: QSARtuna CLI Tutorial
      • List of available ML algorithms
      • List of available molecular descriptors
      • List of available evaluation splits
      • @@ -57,7 +57,7 @@
        diff --git a/docs/sphinx-builddir/html/_modules/optunaz/builder.html b/docs/sphinx-builddir/html/_modules/optunaz/builder.html index 03fecbb..3d81272 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/builder.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/builder.html @@ -3,7 +3,7 @@ - optunaz.builder — QPTUNA 2.7.11 documentation + optunaz.builder — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
        @@ -44,8 +44,8 @@

        Documentation:

        • Intro and Quick Start
        • -
        • Jupyter Notebook: Preprocessing Data for Qptuna
        • -
        • Jupyter Notebook: Qptuna CLI Tutorial
        • +
        • Jupyter Notebook: Preprocessing Data for QSARtuna
        • +
        • Jupyter Notebook: QSARtuna CLI Tutorial
        • List of available ML algorithms
        • List of available molecular descriptors
        • List of available evaluation splits
        • @@ -57,7 +57,7 @@
          diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config.html b/docs/sphinx-builddir/html/_modules/optunaz/config.html index 456d412..07c3736 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/config.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/config.html @@ -3,7 +3,7 @@ - optunaz.config — QPTUNA 2.7.11 documentation + optunaz.config — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
          @@ -44,8 +44,8 @@

          Documentation:

          • Intro and Quick Start
          • -
          • Jupyter Notebook: Preprocessing Data for Qptuna
          • -
          • Jupyter Notebook: Qptuna CLI Tutorial
          • +
          • Jupyter Notebook: Preprocessing Data for QSARtuna
          • +
          • Jupyter Notebook: QSARtuna CLI Tutorial
          • List of available ML algorithms
          • List of available molecular descriptors
          • List of available evaluation splits
          • @@ -57,7 +57,7 @@
            diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html b/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html index dc25d23..bd6fae5 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/config/build_from_opt.html @@ -3,7 +3,7 @@ - optunaz.config.build_from_opt — QPTUNA 2.7.11 documentation + optunaz.config.build_from_opt — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
            @@ -44,8 +44,8 @@

            Documentation:

            • Intro and Quick Start
            • -
            • Jupyter Notebook: Preprocessing Data for Qptuna
            • -
            • Jupyter Notebook: Qptuna CLI Tutorial
            • +
            • Jupyter Notebook: Preprocessing Data for QSARtuna
            • +
            • Jupyter Notebook: QSARtuna CLI Tutorial
            • List of available ML algorithms
            • List of available molecular descriptors
            • List of available evaluation splits
            • @@ -57,7 +57,7 @@
              diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html b/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html index 51269db..dedf290 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/config/buildconfig.html @@ -3,7 +3,7 @@ - optunaz.config.buildconfig — QPTUNA 2.7.11 documentation + optunaz.config.buildconfig — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
              @@ -44,8 +44,8 @@

              Documentation:

              • Intro and Quick Start
              • -
              • Jupyter Notebook: Preprocessing Data for Qptuna
              • -
              • Jupyter Notebook: Qptuna CLI Tutorial
              • +
              • Jupyter Notebook: Preprocessing Data for QSARtuna
              • +
              • Jupyter Notebook: QSARtuna CLI Tutorial
              • List of available ML algorithms
              • List of available molecular descriptors
              • List of available evaluation splits
              • @@ -57,7 +57,7 @@
                diff --git a/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html b/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html index 287325b..5d874b3 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/config/optconfig.html @@ -3,7 +3,7 @@ - optunaz.config.optconfig — QPTUNA 2.7.11 documentation + optunaz.config.optconfig — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                @@ -44,8 +44,8 @@

                Documentation:

                • Intro and Quick Start
                • -
                • Jupyter Notebook: Preprocessing Data for Qptuna
                • -
                • Jupyter Notebook: Qptuna CLI Tutorial
                • +
                • Jupyter Notebook: Preprocessing Data for QSARtuna
                • +
                • Jupyter Notebook: QSARtuna CLI Tutorial
                • List of available ML algorithms
                • List of available molecular descriptors
                • List of available evaluation splits
                • @@ -57,7 +57,7 @@
                  @@ -1251,7 +1251,7 @@

                  Source code for optunaz.config.optconfig

                   
                   
                  [docs]class ChemPropSearch_Parameter_Level(str, Enum): """ - `Qptuna` implements a hyperparameter search space level for ChemProp in order to define Hyperopt search space + `QSARtuna` implements a hyperparameter search space level for ChemProp in order to define Hyperopt search space to optimise. Increasing levels correspond to increasing the search space. """ diff --git a/docs/sphinx-builddir/html/_modules/optunaz/datareader.html b/docs/sphinx-builddir/html/_modules/optunaz/datareader.html index 5abc055..ec1cca6 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/datareader.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/datareader.html @@ -3,7 +3,7 @@ - optunaz.datareader — QPTUNA 2.7.11 documentation + optunaz.datareader — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                  @@ -44,8 +44,8 @@

                  Documentation:

                  • Intro and Quick Start
                  • -
                  • Jupyter Notebook: Preprocessing Data for Qptuna
                  • -
                  • Jupyter Notebook: Qptuna CLI Tutorial
                  • +
                  • Jupyter Notebook: Preprocessing Data for QSARtuna
                  • +
                  • Jupyter Notebook: QSARtuna CLI Tutorial
                  • List of available ML algorithms
                  • List of available molecular descriptors
                  • List of available evaluation splits
                  • @@ -57,7 +57,7 @@
                    diff --git a/docs/sphinx-builddir/html/_modules/optunaz/descriptors.html b/docs/sphinx-builddir/html/_modules/optunaz/descriptors.html index 23589cf..ca11c1b 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/descriptors.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/descriptors.html @@ -3,7 +3,7 @@ - optunaz.descriptors — QPTUNA 2.7.11 documentation + optunaz.descriptors — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                    @@ -44,8 +44,8 @@

                    Documentation:

                    • Intro and Quick Start
                    • -
                    • Jupyter Notebook: Preprocessing Data for Qptuna
                    • -
                    • Jupyter Notebook: Qptuna CLI Tutorial
                    • +
                    • Jupyter Notebook: Preprocessing Data for QSARtuna
                    • +
                    • Jupyter Notebook: QSARtuna CLI Tutorial
                    • List of available ML algorithms
                    • List of available molecular descriptors
                    • List of available evaluation splits
                    • @@ -57,7 +57,7 @@
                      diff --git a/docs/sphinx-builddir/html/_modules/optunaz/evaluate.html b/docs/sphinx-builddir/html/_modules/optunaz/evaluate.html index 02af68c..8997249 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/evaluate.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/evaluate.html @@ -3,7 +3,7 @@ - optunaz.evaluate — QPTUNA 2.7.11 documentation + optunaz.evaluate — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                      @@ -44,8 +44,8 @@

                      Documentation:

                      • Intro and Quick Start
                      • -
                      • Jupyter Notebook: Preprocessing Data for Qptuna
                      • -
                      • Jupyter Notebook: Qptuna CLI Tutorial
                      • +
                      • Jupyter Notebook: Preprocessing Data for QSARtuna
                      • +
                      • Jupyter Notebook: QSARtuna CLI Tutorial
                      • List of available ML algorithms
                      • List of available molecular descriptors
                      • List of available evaluation splits
                      • @@ -57,7 +57,7 @@
                        diff --git a/docs/sphinx-builddir/html/_modules/optunaz/explainability.html b/docs/sphinx-builddir/html/_modules/optunaz/explainability.html index 51fd993..9703188 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/explainability.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/explainability.html @@ -3,7 +3,7 @@ - optunaz.explainability — QPTUNA 2.7.11 documentation + optunaz.explainability — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                        @@ -44,8 +44,8 @@

                        Documentation:

                        • Intro and Quick Start
                        • -
                        • Jupyter Notebook: Preprocessing Data for Qptuna
                        • -
                        • Jupyter Notebook: Qptuna CLI Tutorial
                        • +
                        • Jupyter Notebook: Preprocessing Data for QSARtuna
                        • +
                        • Jupyter Notebook: QSARtuna CLI Tutorial
                        • List of available ML algorithms
                        • List of available molecular descriptors
                        • List of available evaluation splits
                        • @@ -57,7 +57,7 @@
                          diff --git a/docs/sphinx-builddir/html/_modules/optunaz/metircs.html b/docs/sphinx-builddir/html/_modules/optunaz/metircs.html index 299ea48..a0da99a 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/metircs.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/metircs.html @@ -3,7 +3,7 @@ - optunaz.metircs — QPTUNA 2.7.11 documentation + optunaz.metircs — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                          @@ -44,8 +44,8 @@

                          Documentation:

                          • Intro and Quick Start
                          • -
                          • Jupyter Notebook: Preprocessing Data for Qptuna
                          • -
                          • Jupyter Notebook: Qptuna CLI Tutorial
                          • +
                          • Jupyter Notebook: Preprocessing Data for QSARtuna
                          • +
                          • Jupyter Notebook: QSARtuna CLI Tutorial
                          • List of available ML algorithms
                          • List of available molecular descriptors
                          • List of available evaluation splits
                          • @@ -57,7 +57,7 @@
                            diff --git a/docs/sphinx-builddir/html/_modules/optunaz/model_writer.html b/docs/sphinx-builddir/html/_modules/optunaz/model_writer.html index fd4c9e1..f11e3d7 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/model_writer.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/model_writer.html @@ -3,7 +3,7 @@ - optunaz.model_writer — QPTUNA 2.7.11 documentation + optunaz.model_writer — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                            @@ -44,8 +44,8 @@

                            Documentation:

                            • Intro and Quick Start
                            • -
                            • Jupyter Notebook: Preprocessing Data for Qptuna
                            • -
                            • Jupyter Notebook: Qptuna CLI Tutorial
                            • +
                            • Jupyter Notebook: Preprocessing Data for QSARtuna
                            • +
                            • Jupyter Notebook: QSARtuna CLI Tutorial
                            • List of available ML algorithms
                            • List of available molecular descriptors
                            • List of available evaluation splits
                            • @@ -57,7 +57,7 @@
                              @@ -124,7 +124,7 @@

                              Source code for optunaz.model_writer

                               
                                   Returns: 1d numpy array, with numpy.nan for invalid SMILES.
                               
                              -    Deprecated, use 'QptunaModel.predict_from_smiles()' instead.
                              +    Deprecated, use 'QSARtunaModel.predict_from_smiles()' instead.
                                   """
                               
                                   if isinstance(smiles, str):  # Single SMILES string - wrap into list.
                              @@ -195,7 +195,7 @@ 

                              Source code for optunaz.model_writer

                               
                                   This function will become a method of the predictive model.
                               
                              -    Deprecated, use 'QptunaModel.predict_from_smiles()' instead.
                              +    Deprecated, use 'QSARtunaModel.predict_from_smiles()' instead.
                                   """
                               
                                   return predict(self, mode, self.mol_descriptor, smiles, uncert, explain)
                              @@ -204,7 +204,7 @@

                              Source code for optunaz.model_writer

                               
                              [docs]def add_predict_from_smiles(model: Any, descriptor: AnyDescriptor, mode: ModelMode): """Adds method 'predict_from_smiles' to a predictive model. - Deprecated, use 'QptunaModel.predict_from_smiles()' instead. + Deprecated, use 'QSARtunaModel.predict_from_smiles()' instead. """ # side info replaced so side info not required for inference @@ -260,8 +260,8 @@

                              Source code for optunaz.model_writer

                                       ...
                              -
                              [docs]@dataclass -class QptunaModel(abc.ABC): +
                              [docs]@dataclass +class QSARtunaModel(abc.ABC): predictor: Predictor descriptor: AnyDescriptor mode: ModelMode @@ -269,7 +269,7 @@

                              Source code for optunaz.model_writer

                                   aux_transform: Optional[AnyAuxTransformer] = None
                                   metadata: Optional[Dict] = None
                               
                              -
                              [docs] def predict_from_smiles( +
                              [docs] def predict_from_smiles( self, smiles: Union[str, List[str]], aux=None, @@ -384,8 +384,8 @@

                              Source code for optunaz.model_writer

                                   transform: Optional[ModelDataTransform] = None,
                                   aux_transform: Optional[AnyAuxTransformer] = None,
                                   metadata: Optional[Dict] = None,
                              -) -> QptunaModel:
                              -    return QptunaModel(model, descriptor, mode, transform, aux_transform, metadata)
                              +) -> QSARtunaModel: + return QSARtunaModel(model, descriptor, mode, transform, aux_transform, metadata)
                              [docs]def save_model( diff --git a/docs/sphinx-builddir/html/_modules/optunaz/objective.html b/docs/sphinx-builddir/html/_modules/optunaz/objective.html index 8457252..c1f09d9 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/objective.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/objective.html @@ -3,7 +3,7 @@ - optunaz.objective — QPTUNA 2.7.11 documentation + optunaz.objective — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                              @@ -44,8 +44,8 @@

                              Documentation:

                              • Intro and Quick Start
                              • -
                              • Jupyter Notebook: Preprocessing Data for Qptuna
                              • -
                              • Jupyter Notebook: Qptuna CLI Tutorial
                              • +
                              • Jupyter Notebook: Preprocessing Data for QSARtuna
                              • +
                              • Jupyter Notebook: QSARtuna CLI Tutorial
                              • List of available ML algorithms
                              • List of available molecular descriptors
                              • List of available evaluation splits
                              • @@ -57,7 +57,7 @@
                                diff --git a/docs/sphinx-builddir/html/_modules/optunaz/optbuild.html b/docs/sphinx-builddir/html/_modules/optunaz/optbuild.html index 938779f..30c14e7 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/optbuild.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/optbuild.html @@ -3,7 +3,7 @@ - optunaz.optbuild — QPTUNA 2.7.11 documentation + optunaz.optbuild — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                @@ -44,8 +44,8 @@

                                Documentation:

                                • Intro and Quick Start
                                • -
                                • Jupyter Notebook: Preprocessing Data for Qptuna
                                • -
                                • Jupyter Notebook: Qptuna CLI Tutorial
                                • +
                                • Jupyter Notebook: Preprocessing Data for QSARtuna
                                • +
                                • Jupyter Notebook: QSARtuna CLI Tutorial
                                • List of available ML algorithms
                                • List of available molecular descriptors
                                • List of available evaluation splits
                                • @@ -57,7 +57,7 @@
                                  diff --git a/docs/sphinx-builddir/html/_modules/optunaz/predict.html b/docs/sphinx-builddir/html/_modules/optunaz/predict.html index 27c49d8..e27eef1 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/predict.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/predict.html @@ -3,7 +3,7 @@ - optunaz.predict — QPTUNA 2.7.11 documentation + optunaz.predict — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                  @@ -44,8 +44,8 @@

                                  Documentation:

                                  • Intro and Quick Start
                                  • -
                                  • Jupyter Notebook: Preprocessing Data for Qptuna
                                  • -
                                  • Jupyter Notebook: Qptuna CLI Tutorial
                                  • +
                                  • Jupyter Notebook: Preprocessing Data for QSARtuna
                                  • +
                                  • Jupyter Notebook: QSARtuna CLI Tutorial
                                  • List of available ML algorithms
                                  • List of available molecular descriptors
                                  • List of available evaluation splits
                                  • @@ -57,7 +57,7 @@
                                    diff --git a/docs/sphinx-builddir/html/_modules/optunaz/schemagen.html b/docs/sphinx-builddir/html/_modules/optunaz/schemagen.html index 550c132..bfc68a1 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/schemagen.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/schemagen.html @@ -3,7 +3,7 @@ - optunaz.schemagen — QPTUNA 2.7.11 documentation + optunaz.schemagen — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                    @@ -44,8 +44,8 @@

                                    Documentation:

                                    • Intro and Quick Start
                                    • -
                                    • Jupyter Notebook: Preprocessing Data for Qptuna
                                    • -
                                    • Jupyter Notebook: Qptuna CLI Tutorial
                                    • +
                                    • Jupyter Notebook: Preprocessing Data for QSARtuna
                                    • +
                                    • Jupyter Notebook: QSARtuna CLI Tutorial
                                    • List of available ML algorithms
                                    • List of available molecular descriptors
                                    • List of available evaluation splits
                                    • @@ -57,7 +57,7 @@
                                      @@ -386,7 +386,7 @@

                                      Source code for optunaz.schemagen

                                               .get("training_dataset_file", {})
                                           )[
                                               "format"
                                      -    ] = "qptuna-file"  # this format emphasized csv and sdf support with basic validation and automated column handling
                                      +    ] = "qsartuna-file"  # this format emphasized csv and sdf support with basic validation and automated column handling
                                       
                                           (
                                               schema.get("$defs", {})
                                      @@ -404,7 +404,7 @@ 

                                      Source code for optunaz.schemagen

                                               .get("input_column", {})
                                           )[
                                               "format"
                                      -    ] = "single-string-select"  # for Qptuna model this field is string, but in GUI we generate values for it based on qptuna-file
                                      +    ] = "single-string-select"  # for QSARtuna model this field is string, but in GUI we generate values for it based on qsartuna-file
                                       
                                           (
                                               schema.get("$defs", {})
                                      @@ -413,7 +413,7 @@ 

                                      Source code for optunaz.schemagen

                                               .get("response_column", {})
                                           )[
                                               "format"
                                      -    ] = "single-string-select"  # for Qptuna model this field is string, but in GUI we generate values for it based on qptuna-file
                                      +    ] = "single-string-select"  # for QSARtuna model this field is string, but in GUI we generate values for it based on qsartuna-file
                                       
                                           (
                                               schema.get("$defs", {})
                                      diff --git a/docs/sphinx-builddir/html/_modules/optunaz/three_step_opt_build_merge.html b/docs/sphinx-builddir/html/_modules/optunaz/three_step_opt_build_merge.html
                                      index 2aeb073..e7745fd 100644
                                      --- a/docs/sphinx-builddir/html/_modules/optunaz/three_step_opt_build_merge.html
                                      +++ b/docs/sphinx-builddir/html/_modules/optunaz/three_step_opt_build_merge.html
                                      @@ -3,7 +3,7 @@
                                       
                                         
                                         
                                      -  optunaz.three_step_opt_build_merge — QPTUNA 2.7.11 documentation
                                      +  optunaz.three_step_opt_build_merge — QSARtuna 2.7.11 documentation
                                             
                                             
                                             
                                      @@ -31,7 +31,7 @@
                                                 
                                                 
                                                 
                                      -            QPTUNA
                                      +            QSARtuna
                                                 
                                       
                                      @@ -44,8 +44,8 @@

                                      Documentation:

                                      • Intro and Quick Start
                                      • -
                                      • Jupyter Notebook: Preprocessing Data for Qptuna
                                      • -
                                      • Jupyter Notebook: Qptuna CLI Tutorial
                                      • +
                                      • Jupyter Notebook: Preprocessing Data for QSARtuna
                                      • +
                                      • Jupyter Notebook: QSARtuna CLI Tutorial
                                      • List of available ML algorithms
                                      • List of available molecular descriptors
                                      • List of available evaluation splits
                                      • @@ -57,7 +57,7 @@
                                        diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils.html b/docs/sphinx-builddir/html/_modules/optunaz/utils.html index 1c4bb24..fe9583d 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils.html @@ -3,7 +3,7 @@ - optunaz.utils — QPTUNA 2.7.11 documentation + optunaz.utils — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                        @@ -44,8 +44,8 @@

                                        Documentation:

                                        • Intro and Quick Start
                                        • -
                                        • Jupyter Notebook: Preprocessing Data for Qptuna
                                        • -
                                        • Jupyter Notebook: Qptuna CLI Tutorial
                                        • +
                                        • Jupyter Notebook: Preprocessing Data for QSARtuna
                                        • +
                                        • Jupyter Notebook: QSARtuna CLI Tutorial
                                        • List of available ML algorithms
                                        • List of available molecular descriptors
                                        • List of available evaluation splits
                                        • @@ -57,7 +57,7 @@
                                          diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums.html index af5bf0b..0f8ce79 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums.html @@ -3,7 +3,7 @@ - optunaz.utils.enums — QPTUNA 2.7.11 documentation + optunaz.utils.enums — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                          @@ -44,8 +44,8 @@

                                          Documentation:

                                          • Intro and Quick Start
                                          • -
                                          • Jupyter Notebook: Preprocessing Data for Qptuna
                                          • -
                                          • Jupyter Notebook: Qptuna CLI Tutorial
                                          • +
                                          • Jupyter Notebook: Preprocessing Data for QSARtuna
                                          • +
                                          • Jupyter Notebook: QSARtuna CLI Tutorial
                                          • List of available ML algorithms
                                          • List of available molecular descriptors
                                          • List of available evaluation splits
                                          • @@ -57,7 +57,7 @@
                                            diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/building_configuration_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/building_configuration_enum.html index 7c1afce..1f458a2 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/building_configuration_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/building_configuration_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.building_configuration_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.building_configuration_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                            @@ -44,8 +44,8 @@

                                            Documentation:

                                            • Intro and Quick Start
                                            • -
                                            • Jupyter Notebook: Preprocessing Data for Qptuna
                                            • -
                                            • Jupyter Notebook: Qptuna CLI Tutorial
                                            • +
                                            • Jupyter Notebook: Preprocessing Data for QSARtuna
                                            • +
                                            • Jupyter Notebook: QSARtuna CLI Tutorial
                                            • List of available ML algorithms
                                            • List of available molecular descriptors
                                            • List of available evaluation splits
                                            • @@ -57,7 +57,7 @@
                                              diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/configuration_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/configuration_enum.html index 18889b4..ab989bb 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/configuration_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/configuration_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.configuration_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.configuration_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                              @@ -44,8 +44,8 @@

                                              Documentation:

                                              • Intro and Quick Start
                                              • -
                                              • Jupyter Notebook: Preprocessing Data for Qptuna
                                              • -
                                              • Jupyter Notebook: Qptuna CLI Tutorial
                                              • +
                                              • Jupyter Notebook: Preprocessing Data for QSARtuna
                                              • +
                                              • Jupyter Notebook: QSARtuna CLI Tutorial
                                              • List of available ML algorithms
                                              • List of available molecular descriptors
                                              • List of available evaluation splits
                                              • @@ -57,7 +57,7 @@
                                                diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/interface_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/interface_enum.html index 4d78376..72cb3f7 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/interface_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/interface_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.interface_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.interface_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                @@ -44,8 +44,8 @@

                                                Documentation:

                                                • Intro and Quick Start
                                                • -
                                                • Jupyter Notebook: Preprocessing Data for Qptuna
                                                • -
                                                • Jupyter Notebook: Qptuna CLI Tutorial
                                                • +
                                                • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                • +
                                                • Jupyter Notebook: QSARtuna CLI Tutorial
                                                • List of available ML algorithms
                                                • List of available molecular descriptors
                                                • List of available evaluation splits
                                                • @@ -57,7 +57,7 @@
                                                  diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/model_runner_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/model_runner_enum.html index 8173978..e0c861d 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/model_runner_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/model_runner_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.model_runner_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.model_runner_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                  @@ -44,8 +44,8 @@

                                                  Documentation:

                                                  • Intro and Quick Start
                                                  • -
                                                  • Jupyter Notebook: Preprocessing Data for Qptuna
                                                  • -
                                                  • Jupyter Notebook: Qptuna CLI Tutorial
                                                  • +
                                                  • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                  • +
                                                  • Jupyter Notebook: QSARtuna CLI Tutorial
                                                  • List of available ML algorithms
                                                  • List of available molecular descriptors
                                                  • List of available evaluation splits
                                                  • @@ -57,7 +57,7 @@
                                                    diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/objective_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/objective_enum.html index d90062a..235a268 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/objective_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/objective_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.objective_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.objective_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                    @@ -44,8 +44,8 @@

                                                    Documentation:

                                                    • Intro and Quick Start
                                                    • -
                                                    • Jupyter Notebook: Preprocessing Data for Qptuna
                                                    • -
                                                    • Jupyter Notebook: Qptuna CLI Tutorial
                                                    • +
                                                    • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                    • +
                                                    • Jupyter Notebook: QSARtuna CLI Tutorial
                                                    • List of available ML algorithms
                                                    • List of available molecular descriptors
                                                    • List of available evaluation splits
                                                    • @@ -57,7 +57,7 @@
                                                      diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/optimization_configuration_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/optimization_configuration_enum.html index 8dcc41f..ecb0e5a 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/optimization_configuration_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/optimization_configuration_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.optimization_configuration_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.optimization_configuration_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                      @@ -44,8 +44,8 @@

                                                      Documentation:

                                                      • Intro and Quick Start
                                                      • -
                                                      • Jupyter Notebook: Preprocessing Data for Qptuna
                                                      • -
                                                      • Jupyter Notebook: Qptuna CLI Tutorial
                                                      • +
                                                      • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                      • +
                                                      • Jupyter Notebook: QSARtuna CLI Tutorial
                                                      • List of available ML algorithms
                                                      • List of available molecular descriptors
                                                      • List of available evaluation splits
                                                      • @@ -57,7 +57,7 @@
                                                        diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/prediction_configuration_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/prediction_configuration_enum.html index 92e4950..d99934f 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/prediction_configuration_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/prediction_configuration_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.prediction_configuration_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.prediction_configuration_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                        @@ -44,8 +44,8 @@

                                                        Documentation:

                                                        • Intro and Quick Start
                                                        • -
                                                        • Jupyter Notebook: Preprocessing Data for Qptuna
                                                        • -
                                                        • Jupyter Notebook: Qptuna CLI Tutorial
                                                        • +
                                                        • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                        • +
                                                        • Jupyter Notebook: QSARtuna CLI Tutorial
                                                        • List of available ML algorithms
                                                        • List of available molecular descriptors
                                                        • List of available evaluation splits
                                                        • @@ -57,7 +57,7 @@
                                                          diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/return_values_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/return_values_enum.html index e83e1ca..54cceb7 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/return_values_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/return_values_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.return_values_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.return_values_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                          @@ -44,8 +44,8 @@

                                                          Documentation:

                                                          • Intro and Quick Start
                                                          • -
                                                          • Jupyter Notebook: Preprocessing Data for Qptuna
                                                          • -
                                                          • Jupyter Notebook: Qptuna CLI Tutorial
                                                          • +
                                                          • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                          • +
                                                          • Jupyter Notebook: QSARtuna CLI Tutorial
                                                          • List of available ML algorithms
                                                          • List of available molecular descriptors
                                                          • List of available evaluation splits
                                                          • @@ -57,7 +57,7 @@
                                                            diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/visualization_enum.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/visualization_enum.html index f61e1a6..049a000 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/visualization_enum.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/enums/visualization_enum.html @@ -3,7 +3,7 @@ - optunaz.utils.enums.visualization_enum — QPTUNA 2.7.11 documentation + optunaz.utils.enums.visualization_enum — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                            @@ -44,8 +44,8 @@

                                                            Documentation:

                                                            • Intro and Quick Start
                                                            • -
                                                            • Jupyter Notebook: Preprocessing Data for Qptuna
                                                            • -
                                                            • Jupyter Notebook: Qptuna CLI Tutorial
                                                            • +
                                                            • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                            • +
                                                            • Jupyter Notebook: QSARtuna CLI Tutorial
                                                            • List of available ML algorithms
                                                            • List of available molecular descriptors
                                                            • List of available evaluation splits
                                                            • @@ -57,7 +57,7 @@
                                                              diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/files_paths.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/files_paths.html index 5a7069a..0e990ef 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/files_paths.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/files_paths.html @@ -3,7 +3,7 @@ - optunaz.utils.files_paths — QPTUNA 2.7.11 documentation + optunaz.utils.files_paths — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                              @@ -44,8 +44,8 @@

                                                              Documentation:

                                                              • Intro and Quick Start
                                                              • -
                                                              • Jupyter Notebook: Preprocessing Data for Qptuna
                                                              • -
                                                              • Jupyter Notebook: Qptuna CLI Tutorial
                                                              • +
                                                              • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                              • +
                                                              • Jupyter Notebook: QSARtuna CLI Tutorial
                                                              • List of available ML algorithms
                                                              • List of available molecular descriptors
                                                              • List of available evaluation splits
                                                              • @@ -57,7 +57,7 @@
                                                                diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/load_json.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/load_json.html index 2f64dbb..176741c 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/load_json.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/load_json.html @@ -3,7 +3,7 @@ - optunaz.utils.load_json — QPTUNA 2.7.11 documentation + optunaz.utils.load_json — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                                @@ -44,8 +44,8 @@

                                                                Documentation:

                                                                • Intro and Quick Start
                                                                • -
                                                                • Jupyter Notebook: Preprocessing Data for Qptuna
                                                                • -
                                                                • Jupyter Notebook: Qptuna CLI Tutorial
                                                                • +
                                                                • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                                • +
                                                                • Jupyter Notebook: QSARtuna CLI Tutorial
                                                                • List of available ML algorithms
                                                                • List of available molecular descriptors
                                                                • List of available evaluation splits
                                                                • @@ -57,7 +57,7 @@
                                                                  diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/mlflow.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/mlflow.html index b9b73d5..2304716 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/mlflow.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/mlflow.html @@ -3,7 +3,7 @@ - optunaz.utils.mlflow — QPTUNA 2.7.11 documentation + optunaz.utils.mlflow — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                                  @@ -44,8 +44,8 @@

                                                                  Documentation:

                                                                  • Intro and Quick Start
                                                                  • -
                                                                  • Jupyter Notebook: Preprocessing Data for Qptuna
                                                                  • -
                                                                  • Jupyter Notebook: Qptuna CLI Tutorial
                                                                  • +
                                                                  • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                                  • +
                                                                  • Jupyter Notebook: QSARtuna CLI Tutorial
                                                                  • List of available ML algorithms
                                                                  • List of available molecular descriptors
                                                                  • List of available evaluation splits
                                                                  • @@ -57,7 +57,7 @@
                                                                    diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/deduplicator.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/deduplicator.html index 254fad3..86d78d6 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/deduplicator.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/deduplicator.html @@ -3,7 +3,7 @@ - optunaz.utils.preprocessing.deduplicator — QPTUNA 2.7.11 documentation + optunaz.utils.preprocessing.deduplicator — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                                    @@ -44,8 +44,8 @@

                                                                    Documentation:

                                                                    • Intro and Quick Start
                                                                    • -
                                                                    • Jupyter Notebook: Preprocessing Data for Qptuna
                                                                    • -
                                                                    • Jupyter Notebook: Qptuna CLI Tutorial
                                                                    • +
                                                                    • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                                    • +
                                                                    • Jupyter Notebook: QSARtuna CLI Tutorial
                                                                    • List of available ML algorithms
                                                                    • List of available molecular descriptors
                                                                    • List of available evaluation splits
                                                                    • @@ -57,7 +57,7 @@
                                                                      diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/splitter.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/splitter.html index 50b6e52..cfc6042 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/splitter.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/splitter.html @@ -3,7 +3,7 @@ - optunaz.utils.preprocessing.splitter — QPTUNA 2.7.11 documentation + optunaz.utils.preprocessing.splitter — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                                      @@ -44,8 +44,8 @@

                                                                      Documentation:

                                                                      • Intro and Quick Start
                                                                      • -
                                                                      • Jupyter Notebook: Preprocessing Data for Qptuna
                                                                      • -
                                                                      • Jupyter Notebook: Qptuna CLI Tutorial
                                                                      • +
                                                                      • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                                      • +
                                                                      • Jupyter Notebook: QSARtuna CLI Tutorial
                                                                      • List of available ML algorithms
                                                                      • List of available molecular descriptors
                                                                      • List of available evaluation splits
                                                                      • @@ -57,7 +57,7 @@
                                                                        diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/transform.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/transform.html index 35c272f..1c54337 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/transform.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/preprocessing/transform.html @@ -3,7 +3,7 @@ - optunaz.utils.preprocessing.transform — QPTUNA 2.7.11 documentation + optunaz.utils.preprocessing.transform — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                                        @@ -44,8 +44,8 @@

                                                                        Documentation:

                                                                        • Intro and Quick Start
                                                                        • -
                                                                        • Jupyter Notebook: Preprocessing Data for Qptuna
                                                                        • -
                                                                        • Jupyter Notebook: Qptuna CLI Tutorial
                                                                        • +
                                                                        • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                                        • +
                                                                        • Jupyter Notebook: QSARtuna CLI Tutorial
                                                                        • List of available ML algorithms
                                                                        • List of available molecular descriptors
                                                                        • List of available evaluation splits
                                                                        • @@ -57,7 +57,7 @@
                                                                          diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/schema.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/schema.html index faf8759..188fc44 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/schema.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/schema.html @@ -3,7 +3,7 @@ - optunaz.utils.schema — QPTUNA 2.7.11 documentation + optunaz.utils.schema — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                                          @@ -44,8 +44,8 @@

                                                                          Documentation:

                                                                          • Intro and Quick Start
                                                                          • -
                                                                          • Jupyter Notebook: Preprocessing Data for Qptuna
                                                                          • -
                                                                          • Jupyter Notebook: Qptuna CLI Tutorial
                                                                          • +
                                                                          • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                                          • +
                                                                          • Jupyter Notebook: QSARtuna CLI Tutorial
                                                                          • List of available ML algorithms
                                                                          • List of available molecular descriptors
                                                                          • List of available evaluation splits
                                                                          • @@ -57,7 +57,7 @@
                                                                            diff --git a/docs/sphinx-builddir/html/_modules/optunaz/utils/tracking.html b/docs/sphinx-builddir/html/_modules/optunaz/utils/tracking.html index 122bd48..e659546 100644 --- a/docs/sphinx-builddir/html/_modules/optunaz/utils/tracking.html +++ b/docs/sphinx-builddir/html/_modules/optunaz/utils/tracking.html @@ -3,7 +3,7 @@ - optunaz.utils.tracking — QPTUNA 2.7.11 documentation + optunaz.utils.tracking — QSARtuna 2.7.11 documentation @@ -31,7 +31,7 @@ - QPTUNA + QSARtuna
                                                                            @@ -44,8 +44,8 @@

                                                                            Documentation:

                                                                            • Intro and Quick Start
                                                                            • -
                                                                            • Jupyter Notebook: Preprocessing Data for Qptuna
                                                                            • -
                                                                            • Jupyter Notebook: Qptuna CLI Tutorial
                                                                            • +
                                                                            • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                                            • +
                                                                            • Jupyter Notebook: QSARtuna CLI Tutorial
                                                                            • List of available ML algorithms
                                                                            • List of available molecular descriptors
                                                                            • List of available evaluation splits
                                                                            • @@ -57,7 +57,7 @@
                                                                              @@ -200,9 +200,9 @@

                                                                              Source code for optunaz.utils.tracking

                                                                               
                                                                                   mode = buildconfig.settings.mode
                                                                                   descriptor = buildconfig.descriptor
                                                                              -    qptuna_model = wrap_model(model, descriptor=descriptor, mode=mode)
                                                                              +    qsartuna_model = wrap_model(model, descriptor=descriptor, mode=mode)
                                                                               
                                                                              -    predicted = qptuna_model.predict_from_smiles(smiles)
                                                                              +    predicted = qsartuna_model.predict_from_smiles(smiles)
                                                                               
                                                                                   test_points = [
                                                                                       Datapoint(
                                                                              diff --git a/docs/sphinx-builddir/html/_modules/optunaz/visualizer.html b/docs/sphinx-builddir/html/_modules/optunaz/visualizer.html
                                                                              index b6db63c..f5a1ddc 100644
                                                                              --- a/docs/sphinx-builddir/html/_modules/optunaz/visualizer.html
                                                                              +++ b/docs/sphinx-builddir/html/_modules/optunaz/visualizer.html
                                                                              @@ -3,7 +3,7 @@
                                                                               
                                                                                 
                                                                                 
                                                                              -  optunaz.visualizer — QPTUNA 2.7.11 documentation
                                                                              +  optunaz.visualizer — QSARtuna 2.7.11 documentation
                                                                                     
                                                                                     
                                                                                     
                                                                              @@ -31,7 +31,7 @@
                                                                                         
                                                                                         
                                                                                         
                                                                              -            QPTUNA
                                                                              +            QSARtuna
                                                                                         
                                                                               
                                                                              @@ -44,8 +44,8 @@

                                                                              Documentation:

                                                                              • Intro and Quick Start
                                                                              • -
                                                                              • Jupyter Notebook: Preprocessing Data for Qptuna
                                                                              • -
                                                                              • Jupyter Notebook: Qptuna CLI Tutorial
                                                                              • +
                                                                              • Jupyter Notebook: Preprocessing Data for QSARtuna
                                                                              • +
                                                                              • Jupyter Notebook: QSARtuna CLI Tutorial
                                                                              • List of available ML algorithms
                                                                              • List of available molecular descriptors
                                                                              • List of available evaluation splits
                                                                              • @@ -57,7 +57,7 @@
                                                                                diff --git a/docs/sphinx-builddir/html/_sources/README.md.txt b/docs/sphinx-builddir/html/_sources/README.md.txt index 179b249..a5e04e8 100644 --- a/docs/sphinx-builddir/html/_sources/README.md.txt +++ b/docs/sphinx-builddir/html/_sources/README.md.txt @@ -1,4 +1,4 @@ -# QPTUNA: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ) +# QSARtuna: QSAR using Optimization for Hyperparameter Tuning (formerly Optuna AZ) Build predictive models for CompChem with hyperparameters optimized by [Optuna](https://optuna.org/). @@ -21,7 +21,7 @@ explainability python packages ### The three-step process -QPTUNA is structured around three steps: +QSARtuna is structured around three steps: 1. *Hyperparameter Optimization:* Train many models with different parameters using Optuna. @@ -133,7 +133,7 @@ When we have our data and our configuration, it is time to start the optimizatio ### Running via singulartity -QPTUNA can be deployed using [Singularity](https://sylabs.io/guides/3.7/user-guide/index.html) container. +QSARtuna can be deployed using [Singularity](https://sylabs.io/guides/3.7/user-guide/index.html) container. To run commands inside the container, Singularity uses the following syntax: ```shell @@ -143,12 +143,12 @@ singularity exec We can run three-step-process from command line with the following command: ```shell -singularity exec /projects/cc/mai/containers/Qptuna_latest.sif \ - /opt/qptuna/.venv/bin/qptuna-optimize \ +singularity exec /projects/cc/mai/containers/QSARtuna_latest.sif \ + /opt/qsartuna/.venv/bin/qsartuna-optimize \ --config examples/optimization/regression_drd2_50.json \ - --best-buildconfig-outpath ~/qptuna-target/best.json \ - --best-model-outpath ~/qptuna-target/best.pkl \ - --merged-model-outpath ~/qptuna-target/merged.pkl + --best-buildconfig-outpath ~/qsartuna-target/best.json \ + --best-model-outpath ~/qsartuna-target/best.pkl \ + --merged-model-outpath ~/qsartuna-target/merged.pkl ``` Since optimization can be a long process, @@ -169,53 +169,53 @@ We can submit our script to the queue by giving `sbatch` the following script: #SBATCH --time=100:0:0 #SBATCH --partition core -# This script illustrates how to run one configuration from Qptuna examples. +# This script illustrates how to run one configuration from QSARtuna examples. # The example we use is in examples/optimization/regression_drd2_50.json. # The example we chose uses relative paths to data files, change directory. cd /{project_folder}/OptunaAZ-versions/OptunaAZ_latest singularity exec \ - /{project_folder}/containers/Qptuna_latest.sif \ - /opt/qptuna/.venv/bin/qptuna-optimize \ + /{project_folder}/containers/QSARtuna_latest.sif \ + /opt/qsartuna/.venv/bin/qsartuna-optimize \ --config{project_folder}/examples/optimization/regression_drd2_50.json \ - --best-buildconfig-outpath ~/qptuna-target/best.json \ - --best-model-outpath ~/qptuna-target/best.pkl \ - --merged-model-outpath ~/qptuna-target/merged.pkl + --best-buildconfig-outpath ~/qsartuna-target/best.json \ + --best-model-outpath ~/qsartuna-target/best.pkl \ + --merged-model-outpath ~/qsartuna-target/merged.pkl ``` -When the script is complete, it will create pickled model files inside your home directory under `~/qptuna-target/`. +When the script is complete, it will create pickled model files inside your home directory under `~/qsartuna-target/`. ### Using the model When the model is built, run inference: ```shell -singularity exec /{project_folder}/containers/Qptuna_latest.sif \ - /opt/qptuna/.venv/bin/qptuna-predict \ +singularity exec /{project_folder}/containers/QSARtuna_latest.sif \ + /opt/qsartuna/.venv/bin/qsartuna-predict \ --model-file target/merged.pkl \ --input-smiles-csv-file tests/data/DRD2/subset-50/test.csv \ --input-smiles-csv-column "canonical" \ --output-prediction-csv-file target/prediction.csv ``` -Note that Qptuna_latest.sif points to the most recent version of Qptuna. +Note that QSARtuna_latest.sif points to the most recent version of QSARtuna. -Legacy models require the inference with the same Qptuna version used to train the model. +Legacy models require the inference with the same QSARtuna version used to train the model. This can be specified by modifying the above command and supplying -`/projects/cc/mai/containers/Qptuna_.sif` (replace with the version of Qptuna). +`/projects/cc/mai/containers/QSARtuna_.sif` (replace with the version of QSARtuna). E.g: ```shell -singularity exec /{project_folder}/containers/Qptuna_2.5.1.sif \ - /opt/qptuna/.venv/bin/qptuna-predict \ +singularity exec /{project_folder}/containers/QSARtuna_2.5.1.sif \ + /opt/qsartuna/.venv/bin/qsartuna-predict \ --model-file 2.5.1_model.pkl \ --input-smiles-csv-file tests/data/DRD2/subset-50/test.csv \ --input-smiles-csv-column "canonical" \ --output-prediction-csv-file target/prediction.csv ``` -would generate predictions for a model trained with Qptuna 2.5.1. +would generate predictions for a model trained with QSARtuna 2.5.1. ### Optional: inspect To inspect performance of different models tried during optimization, @@ -256,27 +256,27 @@ There you can access run/trial build (training) configuration. ## Run from Python/Jupyter Notebook -Create conda environment with Jupyter and Install Qptuna there: +Create conda environment with Jupyter and Install QSARtuna there: ```shell module purge module load Miniconda3 -conda create --name my_env_with_qptuna python=3.10.10 jupyter pip -conda activate my_env_with_qptuna +conda create --name my_env_with_qsartuna python=3.10.10 jupyter pip +conda activate my_env_with_qsartuna module purge # Just in case. -which python # Check. Should output path that contains "my_env_with_qptuna". -python -m pip install http://pages.scp.astrazeneca.net/mai/qptuna/releases/Qptuna_latest.tar.gz +which python # Check. Should output path that contains "my_env_with_qsartuna". +python -m pip install http://pages.scp.astrazeneca.net/mai/qsartuna/releases/QSARtuna_latest.tar.gz ``` -Then you can use Qptuna inside your Notebook: +Then you can use QSARtuna inside your Notebook: ```python -from qptuna.three_step_opt_build_merge import ( +from qsartuna.three_step_opt_build_merge import ( optimize, buildconfig_best, build_best, build_merged, ) -from qptuna.config import ModelMode, OptimizationDirection -from qptuna.config.optconfig import ( +from qsartuna.config import ModelMode, OptimizationDirection +from qsartuna.config.optconfig import ( OptimizationConfig, SVR, RandomForest, @@ -285,8 +285,8 @@ from qptuna.config.optconfig import ( PLS, XGBregressor, ) -from qptuna.datareader import Dataset -from qptuna.descriptors import ECFP, MACCS_keys, ECFP_counts +from qsartuna.datareader import Dataset +from qsartuna.descriptors import ECFP, MACCS_keys, ECFP_counts ## # Prepare hyperparameter optimization configuration. diff --git a/docs/sphinx-builddir/html/_sources/index.rst.txt b/docs/sphinx-builddir/html/_sources/index.rst.txt index 714e991..bdf92b1 100644 --- a/docs/sphinx-builddir/html/_sources/index.rst.txt +++ b/docs/sphinx-builddir/html/_sources/index.rst.txt @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -Welcome to QPTUNA Documentation! +Welcome to QSARtuna Documentation! ===================================== -Welcome to QPTUNA: QSAR using Optimization for Hyperparameter Tuning. +Welcome to QSARtuna: QSAR using Optimization for Hyperparameter Tuning. Build QSAR models with hyperparameters optimized by `Optuna `_. @@ -15,8 +15,8 @@ Build QSAR models with hyperparameters optimized by `Optuna - Jupyter Notebook: Preprocessing Data for Qptuna - Jupyter Notebook: Qptuna CLI Tutorial + Jupyter Notebook: Preprocessing Data for QSARtuna + Jupyter Notebook: QSARtuna CLI Tutorial List of available ML algorithms List of available molecular descriptors List of available evaluation splits @@ -28,4 +28,4 @@ Development * `Test coverage <_static/pytest/coverage/index.html>`_ * `Source code (GitHub) `_ * `Issues (Jira) `_ -* `Public release (3.0.0) `_ \ No newline at end of file +* `Public release (3.0.0) `_ \ No newline at end of file diff --git a/docs/sphinx-builddir/html/_sources/notebooks/QPTUNA_Tutorial.ipynb.txt b/docs/sphinx-builddir/html/_sources/notebooks/QPTUNA_Tutorial.ipynb.txt index 6979b11..98eca5d 100644 --- a/docs/sphinx-builddir/html/_sources/notebooks/QPTUNA_Tutorial.ipynb.txt +++ b/docs/sphinx-builddir/html/_sources/notebooks/QPTUNA_Tutorial.ipynb.txt @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# QPTUNA CLI Tutorial" + "# QSARtuna CLI Tutorial" ] }, { @@ -18,9 +18,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This tutorial is intended to provide a new user with the necessary background to start using Qptuna through a command line interface (CLI).\n", + "This tutorial is intended to provide a new user with the necessary background to start using QSARtuna through a command line interface (CLI).\n", "\n", - "A separate tutorial is available describing the use of the Qptuna GUI." + "A separate tutorial is available describing the use of the QSARtuna GUI." ] }, { @@ -34,9 +34,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA is a python package to automate the model building process for *REINVENT*. These models can use a variety of algorithms to fit to your input data and most of them have one or more so-called hyper-parameters (e.g. the maximum number of trees using a *Random Forest* or the C parameter in SVRs, controlling the influence of every support vector).\n", + "QSARtuna is a python package to automate the model building process for *REINVENT*. These models can use a variety of algorithms to fit to your input data and most of them have one or more so-called hyper-parameters (e.g. the maximum number of trees using a *Random Forest* or the C parameter in SVRs, controlling the influence of every support vector).\n", "\n", - "For both regression and classification tasks, QPTUNA allows you to specify input data for which the optimal hyper-parameters and a model can obtained automatically. If you want to get an idea on how the package is structured, read on otherwise you might want to skip it and The following examples should give you an idea how.\n" + "For both regression and classification tasks, QSARtuna allows you to specify input data for which the optimal hyper-parameters and a model can obtained automatically. If you want to get an idea on how the package is structured, read on otherwise you might want to skip it and The following examples should give you an idea how.\n" ] }, { @@ -50,7 +50,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna is structured around three steps:\n", + "QSARtuna is structured around three steps:\n", "1. **Hyperparameter Optimization:** \n", " Train many models with different parameters using Optuna.\n", " Only the training dataset is used here. \n", @@ -76,9 +76,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "To use QPTUNA from Jupyter Notebook, install it with:\n", + "To use QSARtuna from Jupyter Notebook, install it with:\n", "```\n", - "python -m pip install http://pages.scp.astrazeneca.net/mai/qptuna/releases/Qptuna_latest.tar.gz\n", + "python -m pip install http://pages.scp.astrazeneca.net/mai/qsartuna/releases/QSARtuna_latest.tar.gz\n", "```" ] }, @@ -91,7 +91,7 @@ "\n", "Training dataset is a CSV file. It has SMILES strings in a column named \"canonical\". It has the value that we will try to predict in column \"molwt\".\n", "\n", - "This example has train and test (holdout) dataset ready. If you have single dataset and would like QPTUNA to split it into train and test (holdout) datasets, see the next section." + "This example has train and test (holdout) dataset ready. If you have single dataset and would like QSARtuna to split it into train and test (holdout) datasets, see the next section." ] }, { @@ -142,7 +142,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA configuration can be read from a JSON file or created in Python. Here we create it in Python." + "QSARtuna configuration can be read from a JSON file or created in Python. Here we create it in Python." ] }, { @@ -164,7 +164,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", " from .autonotebook import tqdm as notebook_tqdm\n" ] } @@ -359,17 +359,17 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.731e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.731e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,452] Trial 54 finished with value: -437.4551843552628 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.0988827083418571, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.728e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.728e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,513] Trial 55 finished with value: -437.7905045218911 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.10275551704677868, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 8.093e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 8.093e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 9.647e+01, tolerance: 2.262e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 9.647e+01, tolerance: 2.262e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 7.442e+01, tolerance: 2.313e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 7.442e+01, tolerance: 2.313e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,588] Trial 56 finished with value: -460.9949341873208 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.02258838612145872, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", "[I 2024-02-15 17:30:38,673] Trial 57 finished with value: -437.2063895411025 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.001303005653721337, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", @@ -797,7 +797,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA can split data into train and test (holdout) datasets. To do so, send all data in as training_dataset_file, and choose a splitting strategy. Currently QPTUNA supports three splitting strategies: random, temporal and stratified. \n", + "QSARtuna can split data into train and test (holdout) datasets. To do so, send all data in as training_dataset_file, and choose a splitting strategy. Currently QSARtuna supports three splitting strategies: random, temporal and stratified. \n", "\n", "Random strategy splits data randomly, taking a specified fraction of observations to be test dataset. \n", "\n", @@ -817,7 +817,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "All the algorithms QPTUNA supports do not work with duplicates. Duplicates can come from multiple measurements for the same compound, or from the fact that the molecular descriptors we use are all disregard stereochemistry, so even if compounds are different, descriptors make them into duplicates. QPTUNA provides several strategies to remove duplicates:\n", + "All the algorithms QSARtuna supports do not work with duplicates. Duplicates can come from multiple measurements for the same compound, or from the fact that the molecular descriptors we use are all disregard stereochemistry, so even if compounds are different, descriptors make them into duplicates. QSARtuna provides several strategies to remove duplicates:\n", "* keep median - factors experimental deviation using all replicates into one median value (robust to outliers - recommended)\n", "* keep average - use all experimental data acorss all replicates (less robust to outliers vs. median)\n", "* keep first / keep last - when the first or the last measurement is the trusted one\n", @@ -885,15 +885,15 @@ "text": [ "[I 2024-02-15 17:30:42,956] A new study created in memory with name: my_study_stratified_split\n", "[I 2024-02-15 17:30:42,992] A new study created in memory with name: study_name_0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", "[I 2024-02-15 17:30:43,100] Trial 0 finished with value: -1916.9080190588304 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.6455264533858698, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 0 with value: -1916.9080190588304.\n", "[I 2024-02-15 17:30:43,165] Trial 1 finished with value: -2756.046839500092 and parameters: {'algorithm_name': 'PLSRegression', 'PLSRegression_algorithm_hash': '9f2f76e479633c0bf18cf2912fed9eda', 'n_components': 2, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 0 with value: -1916.9080190588304.\n", @@ -1052,7 +1052,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "By default, QPTUNA uses `neg_mean_squared_error` for regression and `roc_auc` for classification. It is possible to change to other scoring functions that supported by scikit-learn (https://scikit-learn.org/stable/modules/model_evaluation.html) amongst others:" + "By default, QSARtuna uses `neg_mean_squared_error` for regression and `roc_auc` for classification. It is possible to change to other scoring functions that supported by scikit-learn (https://scikit-learn.org/stable/modules/model_evaluation.html) amongst others:" ] }, { @@ -1189,11 +1189,11 @@ "[I 2024-02-15 17:30:50,908] Trial 12 finished with value: 0.3125909835602004 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 1.2601024383222263, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:50,962] Trial 13 finished with value: 0.35938304159920104 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.704926958538193, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:51,047] Trial 14 finished with value: -0.139217147681443 and parameters: {'algorithm_name': 'RandomForestRegressor', 'RandomForestRegressor_algorithm_hash': 'f1ac01e1bba332215ccbd0c29c9ac3c3', 'max_depth': 5, 'n_estimators': 7, 'max_features': , 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.831e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.831e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 5.012e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 5.012e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 4.308e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 4.308e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:51,100] Trial 15 finished with value: -0.3520572381552265 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.003736146475899149, 'descriptor': '{\"name\": \"MACCS_keys\", \"parameters\": {}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:51,156] Trial 16 finished with value: 0.3097224153934907 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 1.3643850817675436, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", @@ -1250,11 +1250,11 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.208e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.208e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 2.075e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 2.075e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.665e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.665e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:52,349] Trial 38 finished with value: 0.33582943996366277 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.03037397374709805, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:52,441] Trial 39 finished with value: -0.014200255758600178 and parameters: {'algorithm_name': 'RandomForestRegressor', 'RandomForestRegressor_algorithm_hash': 'f1ac01e1bba332215ccbd0c29c9ac3c3', 'max_depth': 12, 'n_estimators': 6, 'max_features': , 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", @@ -1303,11 +1303,11 @@ "[I 2024-02-15 17:30:54,404] Trial 76 finished with value: 0.8203032617778302 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.02814913529858031, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:54,453] Trial 77 finished with value: 0.8203033764469106 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.028018087885969566, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:54,506] Trial 78 finished with value: 0.8203229095425186 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.005685911509939887, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.109e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.109e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.002e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.002e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.165e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.165e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n" ] }, @@ -1316,11 +1316,11 @@ "output_type": "stream", "text": [ "[I 2024-02-15 17:30:54,617] Trial 79 finished with value: 0.8611747184538611 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.00427216024040911, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 79 with value: 0.8611747184538611.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.220e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.220e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.321e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.321e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.497e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.497e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:54,731] Trial 80 finished with value: 0.8613400144535142 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.02833136367189578, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 80 with value: 0.8613400144535142.\n", "[I 2024-02-15 17:30:54,843] Trial 81 finished with value: 0.8869607357185316 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.0008522399475568362, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 81 with value: 0.8869607357185316.\n", @@ -1387,7 +1387,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Various algorithms are available in Qptuna:" + "Various algorithms are available in QSARtuna:" ] }, { @@ -1445,13 +1445,13 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "PRF is a modification of the long-established Random Forest (RF) algorithm and takes into account uncertainties in features and/or labels (though only uncertainty in labels are currently implemented in Qptuna), which was first described in[1]. It can be seen as a probabilistic method to factor experimental uncertainty during training, and is considered a hybrid between regression and classification algorithms.\n", + "PRF is a modification of the long-established Random Forest (RF) algorithm and takes into account uncertainties in features and/or labels (though only uncertainty in labels are currently implemented in QSARtuna), which was first described in[1]. It can be seen as a probabilistic method to factor experimental uncertainty during training, and is considered a hybrid between regression and classification algorithms.\n", "\n", "In more detail; PRF treats labels as probability distribution functions [PDFs] (denoted as `∆y`), rather than deterministic quantities. In comparison, the traditional RF uses discrete variables for activity (binary y-labels, also referred to as `y`) from the discretised bioactivity scale defining active/inactive sets. \n", "\n", - "PTR integration was added to Qptuna to afford this probabilistic approach towards modelling, and is particularly useful combined with the PTR (See the preprocessing notebook for details). In this combination, PRF takes as input real-valued probabilities (similar to regression), from a Probabilistic Threshold Representation (PTR). However, similar to classification algorithms, PRF outputs the probability of activity for the active class.\n", + "PTR integration was added to QSARtuna to afford this probabilistic approach towards modelling, and is particularly useful combined with the PTR (See the preprocessing notebook for details). In this combination, PRF takes as input real-valued probabilities (similar to regression), from a Probabilistic Threshold Representation (PTR). However, similar to classification algorithms, PRF outputs the probability of activity for the active class.\n", "\n", - "Note that Qptuna runs the PRFClassifier in a regression setting, since the model only outputs class liklihood membership based on `∆y`\n", + "Note that QSARtuna runs the PRFClassifier in a regression setting, since the model only outputs class liklihood membership based on `∆y`\n", "\n", "[1] https://iopscience.iop.org/article/10.3847/1538-3881/aaf101/meta\n", "\n", @@ -1498,7 +1498,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Note that Qptuna is run in regression mode (`ModelMode.REGRESSION`), as outputs from the algorithm are always continuous values.\n", + "Note that QSARtuna is run in regression mode (`ModelMode.REGRESSION`), as outputs from the algorithm are always continuous values.\n", "\n", "Next we can run the PRF/PTR study:" ] @@ -1632,7 +1632,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "N.B It is not possible to train on response column values outside the likelihood for y-label memberships (ranging from 0-1), as expected for `∆y`. Doing so will result in the following error from Qptuna:" + "N.B It is not possible to train on response column values outside the likelihood for y-label memberships (ranging from 0-1), as expected for `∆y`. Doing so will result in the following error from QSARtuna:" ] }, { @@ -1648,7 +1648,7 @@ "[I 2024-02-15 17:31:35,748] A new study created in memory with name: study_name_0\n", "[W 2024-02-15 17:31:35,749] Trial 0 failed with parameters: {} because of the following error: ValueError('PRFClassifier supplied but response column outside [0.0-1.0] acceptable range. Response max: 9.7, response min: 5.3 ').\n", "Traceback (most recent call last):\n", - " File \"/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/optuna/study/_optimize.py\", line 200, in _run_trial\n", + " File \"/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/optuna/study/_optimize.py\", line 200, in _run_trial\n", " value_or_values = func(trial)\n", " File \"/Users/kljk345/PycharmProjects/optuna_az/optunaz/objective.py\", line 124, in __call__\n", " self._validate_algos()\n", @@ -1717,7 +1717,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA has the functionaility to train `ChemProp` deep learning models. These are message passing neural networks (MPNNs) based on a graph representation of training molecules. They are considered by many to offer the state-of-the-art approach for property prediction.\n", + "QSARtuna has the functionaility to train `ChemProp` deep learning models. These are message passing neural networks (MPNNs) based on a graph representation of training molecules. They are considered by many to offer the state-of-the-art approach for property prediction.\n", "\n", "`ChemProp` was first described in the paper Analyzing Learned Molecular Representations for Property Prediction: https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237\n", "\n", @@ -1779,25 +1779,25 @@ "INFO:root:Enqueued ChemProp manual trial with sensible defaults: {'activation': 'ReLU', 'aggregation': 'mean', 'aggregation_norm': 100, 'batch_size': 50, 'depth': 3, 'dropout': 0.0, 'features_generator': 'none', 'ffn_hidden_size': 300, 'ffn_num_layers': 3, 'final_lr_ratio_exp': -1, 'hidden_size': 300, 'init_lr_ratio_exp': -1, 'max_lr_exp': -3, 'warmup_epochs_ratio': 0.1, 'algorithm_name': 'ChemPropRegressor'}\n", "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 59.407933 on epoch 1\n", "Model 0 best validation rmse = 102.010993 on epoch 4\n", @@ -1912,23 +1912,23 @@ "text": [ "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 97.581963 on epoch 0\n", "Model 0 provided with no test set, no metric evaluation will be performed.\n", @@ -1937,7 +1937,7 @@ "\tSeed 0 ==> test rmse = nan\n", "Overall test rmse = nan +/- nan\n", "Elapsed time = 0:00:04\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 67.110851 on epoch 4\n", "Model 0 provided with no test set, no metric evaluation will be performed.\n", @@ -2063,9 +2063,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "You may safely ignore `ChemProp` warnings such as `Model 0 provided with no test set, no metric evaluation will be performed`, `\"rmse = nan\"` and `1-fold cross validation`, as they are information prompts printed from `ChemProp` due to some (deactivated) CV functionaility (ChemProp can perform it's own cross validation - details for this are still printed despite its deactivation within `Qptuna`).\n", + "You may safely ignore `ChemProp` warnings such as `Model 0 provided with no test set, no metric evaluation will be performed`, `\"rmse = nan\"` and `1-fold cross validation`, as they are information prompts printed from `ChemProp` due to some (deactivated) CV functionaility (ChemProp can perform it's own cross validation - details for this are still printed despite its deactivation within `QSARtuna`).\n", "\n", - "NB: Qptuna will first trial the sensible defaults for the MPNN architecture (where possible given the user config). This is communicated to the user, e.g. see the output which advises:\n", + "NB: QSARtuna will first trial the sensible defaults for the MPNN architecture (where possible given the user config). This is communicated to the user, e.g. see the output which advises:\n", "\n", "`A new study created in memory with name: study_name_0\n", "INFO:root:Enqueued ChemProp manual trial with sensible defaults: {'activation': 'ReLU', 'aggregation': 'mean', 'aggregation_norm': 100, 'batch_size': 50, 'depth': 3, 'dropout': 0.0, 'features_generator': 'none', 'ffn_hidden_size': 300, 'ffn_num_layers': 3, 'final_lr_ratio_exp': -1, 'hidden_size': 300, 'init_lr_ratio_exp': -1, 'max_lr_exp': -3, 'warmup_epochs_ratio': 0.1, 'algorithm_name': 'ChemPropRegressor'}`.\n", @@ -2084,7 +2084,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "By default, `Qptuna` separates `ChemProp` from the other shallow methods using the `split_chemprop` flag. When this setting is set, the user must specify the number of `ChemProp` trials using the `n_chemprop_trials` flag if more than 1 (default) trial is desired:" + "By default, `QSARtuna` separates `ChemProp` from the other shallow methods using the `split_chemprop` flag. When this setting is set, the user must specify the number of `ChemProp` trials using the `n_chemprop_trials` flag if more than 1 (default) trial is desired:" ] }, { @@ -2135,7 +2135,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna optimises all aspects of the ChemProp architecture when using ChemPropRegressor or ChemPropClassifier, however, users can activate the [original hyperparameter-optimization implementation](https://github.com/chemprop/chemprop#hyperparameter-optimization) in the `ChemProp` package, which performs automated Bayesian hyperparameter optimization using the `Hyperopt` package within each trial, at large computational cost.\n", + "QSARtuna optimises all aspects of the ChemProp architecture when using ChemPropRegressor or ChemPropClassifier, however, users can activate the [original hyperparameter-optimization implementation](https://github.com/chemprop/chemprop#hyperparameter-optimization) in the `ChemProp` package, which performs automated Bayesian hyperparameter optimization using the `Hyperopt` package within each trial, at large computational cost.\n", "\n", "NB: The principal way for users to expand and perform more advanced runs is to extend the available non-network hyperparameters, such as the `features_generator` option or e.g. to trial differnt side information weighting (if side information is available).\n", "\n", @@ -2190,9 +2190,9 @@ "\n", "#### A note on MPNN Hyperopt search space\n", "\n", - "`ChemProp` models trained using Hyperopt use the [original implementation](https://chemprop.readthedocs.io/en/latest/hyperopt.html), but one key difference is the `search_parameter_level` setting created for `Qptuna`; Instead of using pre-defined search spaces as in the original package, `Qptuna` can (and will by the default since `search_parameter_level`=`auto` unless changed) alter the space depending on the characteristics of user input data. For example, no. training set compounds, hyperparameter trials (`num_iters`) & epochs (`epochs`) are used by the `auto` setting to ensure search spaces are not too large for limited data/epochs, and _vice-versa_, an extensive search space is trailed when applicable.\n", + "`ChemProp` models trained using Hyperopt use the [original implementation](https://chemprop.readthedocs.io/en/latest/hyperopt.html), but one key difference is the `search_parameter_level` setting created for `QSARtuna`; Instead of using pre-defined search spaces as in the original package, `QSARtuna` can (and will by the default since `search_parameter_level`=`auto` unless changed) alter the space depending on the characteristics of user input data. For example, no. training set compounds, hyperparameter trials (`num_iters`) & epochs (`epochs`) are used by the `auto` setting to ensure search spaces are not too large for limited data/epochs, and _vice-versa_, an extensive search space is trailed when applicable.\n", "\n", - "N.B: Users can also manually define `Hyperopt` search spaces by altering `search_parameter_level` from `auto` to a different level between `[0-8]`, representing the increasing search space size (see the [Qptuna documentation](https://pages.scp.astrazeneca.net/mai/qptuna/optunaz.config.html#optunaz.config.optconfig.ChemPropSearch_Parameter_Level) for details)." + "N.B: Users can also manually define `Hyperopt` search spaces by altering `search_parameter_level` from `auto` to a different level between `[0-8]`, representing the increasing search space size (see the [QSARtuna documentation](https://pages.scp.astrazeneca.net/mai/qsartuna/optunaz.config.html#optunaz.config.optconfig.ChemPropSearch_Parameter_Level) for details)." ] }, { @@ -2208,7 +2208,7 @@ "source": [ "_“Even if you are only optimizing one loss as is the typical case, chances are there is an auxiliary task that will help you improve upon your main task”_ [Caruana, 1998]\n", "\n", - "`Qptuna` typically optimizes for one particular metric for a given molecule property. While we can generally achieve acceptable performance this way, these single task (ST) models ignore information that may improve the prediction of main task of intent. See option `a.` in the figure below.\n", + "`QSARtuna` typically optimizes for one particular metric for a given molecule property. While we can generally achieve acceptable performance this way, these single task (ST) models ignore information that may improve the prediction of main task of intent. See option `a.` in the figure below.\n", "\n", "Signals from relevant related tasks (aka \"auxiliary tasks\" or \"side information\") could come from the training signals of other molecular properties and by sharing representations between related tasks, we can enable a neural network to generalize better on our original task of intent. This approach is called Multi-Task Learning (MTL) See option `b.` in the figure below.\n", "\n", @@ -2217,7 +2217,7 @@ "_(above) Differences between optimizing one vs. more than one loss function. a.) Single-task (ST): one model trained to predict one task one model optimised until performance no longer increases b.) Multi-task (MT/MTL): training one model to predict multiple tasks one model optimising more than one loss function at once enables representations to be shared between trained tasks training signals of related tasks shared between all tasks._\n", "\n", "\n", - "`ChemProp` performs MTL by using the knowledge learnt during training one task to reduce the loss of other tasks included in training. In order to use this function in `Qptuna`, a user should provide side information in a separate file, and it should have the same ordering and length as the input/response columns (i.e. length of y should = length of side information for y).\n", + "`ChemProp` performs MTL by using the knowledge learnt during training one task to reduce the loss of other tasks included in training. In order to use this function in `QSARtuna`, a user should provide side information in a separate file, and it should have the same ordering and length as the input/response columns (i.e. length of y should = length of side information for y).\n", "\n", "E.g: consider the DRD2 example input from earlier:" ] @@ -2322,7 +2322,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The contribution or _weight_ of all side information tasks in their contribution to the loss function during training a network is a parameter that can be optimised within Qptuna, e.g:" + "The contribution or _weight_ of all side information tasks in their contribution to the loss function during training a network is a parameter that can be optimised within QSARtuna, e.g:" ] }, { @@ -2338,101 +2338,101 @@ "[I 2024-02-15 17:31:47,393] A new study created in memory with name: study_name_0\n", "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n" ] }, @@ -2440,101 +2440,101 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n" ] }, @@ -2542,99 +2542,99 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n" ] }, @@ -2642,68 +2642,68 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - " 0%| | 0/1 [00:00 test rmse = nan\n", "Overall test rmse = nan +/- nan\n", "Elapsed time = 0:00:03\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n" ] }, @@ -2856,7 +2856,7 @@ "output_type": "stream", "text": [ "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", @@ -7146,7 +7146,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Above described how ChemProp is by default split from shallow methods. Users can override this using the advanced functionaility when `split_chemprop`=False. In this situation `Qptuna` will optimise `ChemProp` with the other shallow methods:" + "Above described how ChemProp is by default split from shallow methods. Users can override this using the advanced functionaility when `split_chemprop`=False. In this situation `QSARtuna` will optimise `ChemProp` with the other shallow methods:" ] }, { @@ -7186,7 +7186,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Combining ChemProp and traditional methods in this way means the potential search possible in `Qptuna` comprises some incompatible sub-spaces; for example, `ChemProp` is only compatible with SMILES-based descriptors, whilst traditional methods are incompatible with SMILES. In the following examples, we consider the following search space: \"Valid" + "Combining ChemProp and traditional methods in this way means the potential search possible in `QSARtuna` comprises some incompatible sub-spaces; for example, `ChemProp` is only compatible with SMILES-based descriptors, whilst traditional methods are incompatible with SMILES. In the following examples, we consider the following search space: \"Valid" ] }, { @@ -7201,9 +7201,9 @@ "\n", "Pruning is an `Optuna` feature [originally designed](https://optuna.readthedocs.io/en/v2.0.0/tutorial/pruning.html) to automatically stop unpromising trials early in training.\n", "\n", - "_How/why is pruning implemented in Qptuna?_\n", + "_How/why is pruning implemented in QSARtuna?_\n", "\n", - "Instead of the original intention of pruning _unpromising trials_ due to poor performance, `Qptuna` ensures `Optuna` prunes _incompatible algorithm-desciptor pairs_, so the sampler will not trial incomptaible settings again. Duplicated trials are also pruned, to avoid repeatedly suggesting the same hyerparameters. Pruning the trial (instead of returning a cached result) explicitly tasks the sampler to avoid identical parameters.\n", + "Instead of the original intention of pruning _unpromising trials_ due to poor performance, `QSARtuna` ensures `Optuna` prunes _incompatible algorithm-desciptor pairs_, so the sampler will not trial incomptaible settings again. Duplicated trials are also pruned, to avoid repeatedly suggesting the same hyerparameters. Pruning the trial (instead of returning a cached result) explicitly tasks the sampler to avoid identical parameters.\n", "\n", "Now let us consider the following run:" ] @@ -7292,7 +7292,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Consulting the `Qptuna` output, we observe cases of e.g. \"`Trial 3 pruned. Incompatible subspace`\", which indicates an instance when the sampler has sampled an incompitble algo-descriptor pair. \n", + "Consulting the `QSARtuna` output, we observe cases of e.g. \"`Trial 3 pruned. Incompatible subspace`\", which indicates an instance when the sampler has sampled an incompitble algo-descriptor pair. \n", "\n", "\"`Trial 13 pruned. Duplicate parameter set`\" is an example of pruning a duplicated trial parameter suggestion.\n", "\n", @@ -7342,7 +7342,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "When performing classification you often want not only to predict the class label, but also obtain a probability of the respective label. This probability gives you some kind of confidence on the prediction. Some models can give you poor estimates of the class probabilities. The `CalibratedClassifierCV` Qptuna models allow better calibration for the probabilities of a given model.\n", + "When performing classification you often want not only to predict the class label, but also obtain a probability of the respective label. This probability gives you some kind of confidence on the prediction. Some models can give you poor estimates of the class probabilities. The `CalibratedClassifierCV` QSARtuna models allow better calibration for the probabilities of a given model.\n", "\n", "First, we should understand that well calibrated classifiers are probabilistic classifiers for which the output of the predict_proba method can be directly interpreted as a confidence level. For instance, a well calibrated (binary) classifier should classify the samples such that among the samples to which it gave a predict_proba value close to 0.8, approximately 80% actually belong to the positive class.\n", "\n", @@ -7735,7 +7735,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna offers three different ways to calculate uncertainty estimates. \n", + "QSARtuna offers three different ways to calculate uncertainty estimates. \n", "\n", "1. VennABERS calibration (a probability calibration covered in the section above).\n", "2. Ensemble uncertainty (ChemProp models trained with random initialisations).\n", @@ -11827,7 +11827,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "For regression uncertainty, the MAPIE package is available within Qptuna for regression algorithms, and is selected like so:" + "For regression uncertainty, the MAPIE package is available within QSARtuna for regression algorithms, and is selected like so:" ] }, { @@ -12013,7 +12013,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Model explainability is incorporated into Qptuna using two different approaches, depending on the algorithm chosen:\n", + "Model explainability is incorporated into QSARtuna using two different approaches, depending on the algorithm chosen:\n", "1. **SHAP:** \n", " Any shallow algorithm is compatible with the SHAP package (even traditionally unsupported packages use the `KernelExplainer`)\n", "2. **ChemProp interpret:**\n", @@ -12031,7 +12031,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "[SHAP](https://proceedings.neurips.cc/paper_files/paper/2017/hash/8a20a8621978632d76c43dfd28b67767-Abstract.html) (SHapley Additive exPlanations) are available in `Qptuna` based on the implementation available at https://github.com/slundberg/shap. The method uses a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions (see [here](https://shap.readthedocs.io/en/latest/index.html) for more details on the published tool and [here](https://github.com/slundberg/shap#methods-unified-by-shap) for papers using the approach).\n", + "[SHAP](https://proceedings.neurips.cc/paper_files/paper/2017/hash/8a20a8621978632d76c43dfd28b67767-Abstract.html) (SHapley Additive exPlanations) are available in `QSARtuna` based on the implementation available at https://github.com/slundberg/shap. The method uses a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions (see [here](https://shap.readthedocs.io/en/latest/index.html) for more details on the published tool and [here](https://github.com/slundberg/shap#methods-unified-by-shap) for papers using the approach).\n", "\n", "In the following example, a `RIDGE` regressor is trained using the a comopsite descriptor based on the `ECFP`, `MACCS` keys and `PhysChem` descriptors:" ] @@ -13296,14 +13296,14 @@ "source": [ "chemprop.predictor.chemprop_fingerprint(\n", " df[config.data.input_column].head(5),\n", - " fingerprint_type=\"MPN\") # MPN specified for illustration purposes - this is the default method in Qptuna" + " fingerprint_type=\"MPN\") # MPN specified for illustration purposes - this is the default method in QSARtuna" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "The output is n compounds as the input query in the rows by n latent representation features from the MPN in the columns. This output can then be used for any semi-supervise learning approach outside of Qptuna, as required. Alternatively the last layer of the FFN can be used as so:" + "The output is n compounds as the input query in the rows by n latent representation features from the MPN in the columns. This output can then be used for any semi-supervise learning approach outside of QSARtuna, as required. Alternatively the last layer of the FFN can be used as so:" ] }, { @@ -13588,7 +13588,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna can be used to transform input labels so that log-scaled or irregularly distributed data can be transformed to a normal distribution as required for most Machine Learning inputs. The following example shows how XC50 values can be scaled to pXC50 values by using the -Log10 to the 6th unit conversion, like so:" + "QSARtuna can be used to transform input labels so that log-scaled or irregularly distributed data can be transformed to a normal distribution as required for most Machine Learning inputs. The following example shows how XC50 values can be scaled to pXC50 values by using the -Log10 to the 6th unit conversion, like so:" ] }, { @@ -13815,7 +13815,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In comparison, Qptuna does not normally transform the data:" + "In comparison, QSARtuna does not normally transform the data:" ] }, { @@ -14116,7 +14116,7 @@ "source": [ "NB: Please note that outputs have automatically been reversed transformed at inference, back onto the original XC50 scale, as shown by large values outside the log pXC50.\n", "\n", - "This is the default behaviour of Qptuna; reverse transform is performed at inference when log transformation was applied, so that users can action on prediction the original input data scale. Importantly, a user can easily override this behaviour by providing the transform parameter as `None`:" + "This is the default behaviour of QSARtuna; reverse transform is performed at inference when log transformation was applied, so that users can action on prediction the original input data scale. Importantly, a user can easily override this behaviour by providing the transform parameter as `None`:" ] }, { @@ -14143,7 +14143,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This will instruct Qptuna to avoid the reverse transform on the predictions. This transform parameter is ignored if no transformation was applied in the user config.\n", + "This will instruct QSARtuna to avoid the reverse transform on the predictions. This transform parameter is ignored if no transformation was applied in the user config.\n", "\n", "Log transformation can also be combined with the PTR transform. In this situation, all user inputs are expected to be on the untransformed scale. For example, if a user wishes to create a PTR model, trained on pXC50 data and a cut-off for pXC50 values of 5 (10um), the following config can be used:" ] @@ -14444,7 +14444,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Advanced options for Qptuna runs" + "## Advanced options for QSARtuna runs" ] }, { @@ -14458,7 +14458,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna can optimize for the minimzation of the standard deviation of performance across the folds. This should in theory prioritize hyperparameters that are consistently performative across different splits of the data, and so should be more generalizable/performative in production. This can be performed with the `minimize_std_dev` in the example below:" + "QSARtuna can optimize for the minimzation of the standard deviation of performance across the folds. This should in theory prioritize hyperparameters that are consistently performative across different splits of the data, and so should be more generalizable/performative in production. This can be performed with the `minimize_std_dev` in the example below:" ] }, { @@ -16444,7 +16444,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Further visualization of Qptuna runs" + "### Further visualization of QSARtuna runs" ] }, { diff --git a/docs/sphinx-builddir/html/_sources/notebooks/preprocess_data.ipynb.txt b/docs/sphinx-builddir/html/_sources/notebooks/preprocess_data.ipynb.txt index 5d586e8..398f9d0 100644 --- a/docs/sphinx-builddir/html/_sources/notebooks/preprocess_data.ipynb.txt +++ b/docs/sphinx-builddir/html/_sources/notebooks/preprocess_data.ipynb.txt @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# Preprocessing data for Qptuna" + "# Preprocessing data for QSARtuna" ] }, { @@ -15,7 +15,7 @@ "\n", "Probably the most important step in using the automated parameter optimization is the preprocessing of the data prior to training the model. Common considerations include how to deal with duplicates SMILES having different read-out values, if and how to split the data into a training and (holdout) test set, and how to prepare input files in a proper way (e.g. transform SDF files into a dataframe with SMILE string- and read-out-columns).\n", "\n", - "The Qptuna (`Optuna_AZ`) packages have some built-in functionality to facilitate that process." + "The QSARtuna (`Optuna_AZ`) packages have some built-in functionality to facilitate that process." ] }, { @@ -108,11 +108,11 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna can use either SMILES strings (no stereochemistry!) or SDF as input molecular representation.\n", + "QSARtuna can use either SMILES strings (no stereochemistry!) or SDF as input molecular representation.\n", "\n", "SMILES input is a comma-separated values (CSV) file with a SMILES column and a read-out (response) column. Read-out (response) column can be either numeric values (for regression) or labels (for classification). Note, that labels can be in the form of integer/boolean values - as long as the optimization process is specified as `classification`, they will be translated into nominal data values. SDF files should have the response column provided within the SDF file.\n", "\n", - "Data provided in SDF format can (optionally - since Qptuna can accept SDF files) be converted to a SMILES file (so that any optional more advanced preprocessing can be conducted) using the following code." + "Data provided in SDF format can (optionally - since QSARtuna can accept SDF files) be converted to a SMILES file (so that any optional more advanced preprocessing can be conducted) using the following code." ] }, { @@ -433,9 +433,9 @@ "* `KeepRandom(seed)`: keep a random observation for each duplicate. Note, that the order of observations is not preserved. Use the `seed` parameter to vary results or to reproduce them.\n", "* `KeepMin()` and `KeepMax()`: keep min or max value.\n", "* `KeepAvg()`: take the average for all duplicates.\n", - "* `KeepMedian()`: (default in Qptuna) take the median for all duplicates.\n", + "* `KeepMedian()`: (default in QSARtuna) take the median for all duplicates.\n", "\n", - "The default deduplication method in Qptuna is KeepMedian, which is recommended best practice due the ability to utilise all experimental data into one value (account for experimental variability across replicated), whilst being robust to outliers.\n", + "The default deduplication method in QSARtuna is KeepMedian, which is recommended best practice due the ability to utilise all experimental data into one value (account for experimental variability across replicated), whilst being robust to outliers.\n", "\n", "Each of the deduplication methods returns a unique version of the stored dataframe." ] @@ -874,7 +874,7 @@ "metadata": {}, "source": [ "## Transform of data inputs \n", - "Qptuna can perform two types of transforms on input labels either a probabilistic transformation named Probabilistic Threshold Representation (PTR) or simple logarithmic scaling. The latter is a required step for data that is not normally distributed for most Machine Learning inputs. These approaches are discussed in more detail in the following sections." + "QSARtuna can perform two types of transforms on input labels either a probabilistic transformation named Probabilistic Threshold Representation (PTR) or simple logarithmic scaling. The latter is a required step for data that is not normally distributed for most Machine Learning inputs. These approaches are discussed in more detail in the following sections." ] }, { @@ -890,7 +890,7 @@ "\n", "Most algorithms assume numerical co-variates have a Gaussian (normally distributed) probability distribution. In reality, input data may or may not have a normal distribution. Some may have a Gaussian-like distribution (e.g. nearly Gaussian but with outliers or a skew) whilst other may exhibit totally different distribution (e.g. exponential scale). For this reason, superior performance for a wide range of machine learning algorithms is obtained by performing a transformation to user inputs and/or output variables to have a Gaussian or Gaussian-like distribution.\n", "\n", - "A good example of this is the conversion of principal (IC50) activity results to the pXC50 (negative log base), which have already been precomputed outside of Qptuna in the following example:" + "A good example of this is the conversion of principal (IC50) activity results to the pXC50 (negative log base), which have already been precomputed outside of QSARtuna in the following example:" ] }, { @@ -958,10 +958,10 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Qptuna logarithmic transformation \n", + "### QSARtuna logarithmic transformation \n", "\n", "\n", - "Qptuna implements a 'ModelDataTransform' transormation method for converting numerical input or output variables to have a Gaussian or more-Gaussian-like distribution, which can be performed like so:" + "QSARtuna implements a 'ModelDataTransform' transormation method for converting numerical input or output variables to have a Gaussian or more-Gaussian-like distribution, which can be performed like so:" ] }, { @@ -1003,9 +1003,9 @@ " conversion=6\n", ")\n", "\n", - "comparison['Qptuna pXC50 ModelDataTransform'] = transform.transform(comparison['XC50'])\n", + "comparison['QSARtuna pXC50 ModelDataTransform'] = transform.transform(comparison['XC50'])\n", "\n", - "g = sns.jointplot(data=comparison, x=\"Qptuna pXC50 ModelDataTransform\", y=\"pXC50\")\n", + "g = sns.jointplot(data=comparison, x=\"QSARtuna pXC50 ModelDataTransform\", y=\"pXC50\")\n", "g.plot_marginals(sns.rugplot, color=\"crimson\", height=-.15, clip_on=False, alpha=.2)" ] }, @@ -1096,7 +1096,7 @@ "\n", "NB: the log transformation is reversed at inference. I.e. only the model is trained with the transformed values, any predictions will be output to the original scale as provided in user input data.\n", "\n", - "Qptuna also implements the reverse of the transform using `reverse_transform`, so that users can obtain values on the original scale at inference, like so:" + "QSARtuna also implements the reverse of the transform using `reverse_transform`, so that users can obtain values on the original scale at inference, like so:" ] }, { @@ -1158,7 +1158,7 @@ "\n", "PTR hence represents the activity in a framework in-between the classification and regression architecture, with philosophical differences from either approach. Compared to classification, this approach enables better representation of factors increasing/decreasing inactivity. Conversely, one can utilize all data (even delimited/operand/censored data far from a cut-off) at the same time as taking into account the granularity around the cut-off, compared to a conventional regression framework. Thereby, PTR combines characteristics from both classification and regression settings.\n", "\n", - "NB: Qptuna treats the PTR values as the ‘ideal y-label’, i.e. they become the new response column values for train/test/validation performance evaluation, since it represents the ideal case, where experimental error is taken into account and model outputs most closely reflect this.\n", + "NB: QSARtuna treats the PTR values as the ‘ideal y-label’, i.e. they become the new response column values for train/test/validation performance evaluation, since it represents the ideal case, where experimental error is taken into account and model outputs most closely reflect this.\n", "\n", "\n", "[1] https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00539-7#Sec12" @@ -1168,9 +1168,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Qptuna implementation of the PTR\n", + "### QSARtuna implementation of the PTR\n", "\n", - "PTR is also easily applied within the Datareader class by specifying the PTR options to the Qptuna datareader. E.g:" + "PTR is also easily applied within the Datareader class by specifying the PTR options to the QSARtuna datareader. E.g:" ] }, { @@ -1392,7 +1392,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In this section, we next also look at how the PTR within the Qptuna datareader is implemented, and show how a user can assess the experimental reproducability/uncertainty for their query dataset.\n", + "In this section, we next also look at how the PTR within the QSARtuna datareader is implemented, and show how a user can assess the experimental reproducability/uncertainty for their query dataset.\n", "\n", "First we start with imports and define the PTR function using `stats.norm.cdf` from scipy" ] @@ -1637,9 +1637,9 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.\n", " warnings.warn(msg, UserWarning)\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.\n", " warnings.warn(msg, UserWarning)\n" ] }, diff --git a/docs/sphinx-builddir/html/algorithms.html b/docs/sphinx-builddir/html/algorithms.html index a8d6fef..7289f8a 100644 --- a/docs/sphinx-builddir/html/algorithms.html +++ b/docs/sphinx-builddir/html/algorithms.html @@ -4,7 +4,7 @@ - Available algorithms — QPTUNA 2.7.11 documentation + Available algorithms — QSARtuna 2.7.11 documentation @@ -22,7 +22,7 @@ - + @@ -34,7 +34,7 @@ - QPTUNA + QSARtuna
                                                                              -
                                                                            • predict_from_smiles() (optunaz.model_writer.QptunaModel method) +
                                                                            • predict_from_smiles() (optunaz.model_writer.QSARtunaModel method)
                                                                            • predict_from_smiles_and_descriptor() (in module optunaz.model_writer)
                                                                            • @@ -2562,7 +2562,7 @@

                                                                              P

                                                                            • Predictor (class in optunaz.model_writer)
                                                                            • -
                                                                            • predictor (optunaz.model_writer.QptunaModel attribute) +
                                                                            • predictor (optunaz.model_writer.QSARtunaModel attribute)
                                                                            • PRELU (optunaz.config.optconfig.ChemPropActivation attribute)
                                                                            • @@ -2642,7 +2642,7 @@

                                                                              Q

                                                                          @@ -3076,7 +3076,7 @@

                                                                          T

                                                                        • training_dataset_file (optunaz.datareader.Dataset attribute)
                                                                        • -
                                                                        • transform (optunaz.model_writer.QptunaModel attribute) +
                                                                        • transform (optunaz.model_writer.QSARtunaModel attribute)
                                                                        • transform() (optunaz.utils.preprocessing.transform.AuxTransformer method) diff --git a/docs/sphinx-builddir/html/index.html b/docs/sphinx-builddir/html/index.html index 19a679f..278f5df 100644 --- a/docs/sphinx-builddir/html/index.html +++ b/docs/sphinx-builddir/html/index.html @@ -4,7 +4,7 @@ - Welcome to QPTUNA Documentation! — QPTUNA 2.7.11 documentation + Welcome to QSARtuna Documentation! — QSARtuna 2.7.11 documentation @@ -21,7 +21,7 @@ - + @@ -33,7 +33,7 @@ - QPTUNA + QSARtuna
                                                                          @@ -46,8 +46,8 @@

                                                                          Documentation:

                                                                        • @@ -203,7 +203,7 @@

                                                                          Development - +


                                                                        diff --git a/docs/sphinx-builddir/html/modules.html b/docs/sphinx-builddir/html/modules.html index 8586248..dcdbd81 100644 --- a/docs/sphinx-builddir/html/modules.html +++ b/docs/sphinx-builddir/html/modules.html @@ -4,7 +4,7 @@ - optunaz — QPTUNA 2.7.11 documentation + optunaz — QSARtuna 2.7.11 documentation @@ -32,7 +32,7 @@ - QPTUNA + QSARtuna
                                                                        @@ -45,8 +45,8 @@

                                                                        Documentation:

                                                                        -../_images/notebooks_QPTUNA_Tutorial_118_0.png +../_images/notebooks_QSARtuna_Tutorial_118_0.png

                                                                        Plotting the (sigmoid) calibrated predictions as a function of uncalibrated (default) values further highlights the behaviour of the probability calibration scaling:

                                                                        @@ -8419,7 +8419,7 @@

                                                                        Probability calibration (classification)

                                                                      -../_images/notebooks_QPTUNA_Tutorial_120_0.png +../_images/notebooks_QSARtuna_Tutorial_120_0.png

                                                                      We can now visualize how well calibrated the predicted probabilities are using calibration curves. A calibration curve, also known as a reliability diagram, uses inputs from a binary classifier and plots the average predicted probability for each bin against the fraction of positive classes, on the y-axis. See here for more info.

                                                                      @@ -8466,7 +8466,7 @@

                                                                      Probability calibration (classification)

                                                                    -../_images/notebooks_QPTUNA_Tutorial_122_0.png +../_images/notebooks_QSARtuna_Tutorial_122_0.png

                                                                    The diagonal line on the calibration (scatter) plot indicates the situation when a classifier is perfectly calibrationed, when the proportion of active instances annotated by the model are perfectly captured by the probability generated by the model. Deviation above this line indicates when a classifier is under-confident, since the proportion of actives obtaining that score is higher than the score itself, and vice-versa, lines below indicate over-confident estimators, when the proportion of @@ -8577,7 +8577,7 @@

                                                                    Probability calibration (classification)

                                                                    Uncertainty estimation

                                                                    -

                                                                    Qptuna offers three different ways to calculate uncertainty estimates.

                                                                    +

                                                                    QSARtuna offers three different ways to calculate uncertainty estimates.

                                                                    1. VennABERS calibration (a probability calibration covered in the section above).

                                                                    2. Ensemble uncertainty (ChemProp models trained with random initialisations).

                                                                    3. @@ -8696,7 +8696,7 @@

                                                                      VennABERS uncertainty

                                                                  -../_images/notebooks_QPTUNA_Tutorial_133_0.png +../_images/notebooks_QSARtuna_Tutorial_133_0.png

                                                                  Similar to the findings in the referenced scaling evaluation paper above, the lower and upper probability boundary intervals are shown to produce large discordance for test set molecules that are neither very similar nor very dissimilar to the active training set, which were hence difficult to predict.

                                                                  @@ -11186,7 +11186,7 @@

                                                                  Ensemble uncertainty (ChemProp Only)

                                                                -../_images/notebooks_QPTUNA_Tutorial_138_0.png +../_images/notebooks_QSARtuna_Tutorial_138_0.png

                                                                Similar to the VA uncertainty, the largest ensemble uncertainty is observed for test set molecules that are neither very similar nor very dissimilar to the active training set, which are hence difficult to predict. Larger uncertainty is also seen toward the midpoint of the ChemProp predictions, for cases when the probabilistic output from models is also neither very high nor very low.

                                                                @@ -12847,7 +12847,7 @@

                                                                ChemProp dropout uncertainty

                                                              -../_images/notebooks_QPTUNA_Tutorial_145_0.png +../_images/notebooks_QSARtuna_Tutorial_145_0.png

                                                              Comparison of dropout vs. ensemble uncertainties can be performed as follows:

                                                              @@ -12879,14 +12879,14 @@

                                                              ChemProp dropout uncertainty

                                                            -../_images/notebooks_QPTUNA_Tutorial_147_1.png +../_images/notebooks_QSARtuna_Tutorial_147_1.png

                                                            Findings show that a limited correlation between dropout and ensemble uncertainty for the toy example (real world examples with more epochs/more predictive models will be different)

                                                            MAPIE (regression uncertainty)

                                                            -

                                                            For regression uncertainty, the MAPIE package is available within Qptuna for regression algorithms, and is selected like so:

                                                            +

                                                            For regression uncertainty, the MAPIE package is available within QSARtuna for regression algorithms, and is selected like so:

                                                            [57]:
                                                             
                                                            @@ -12973,7 +12973,7 @@

                                                            MAPIE (regression uncertainty)

                                                            -../_images/notebooks_QPTUNA_Tutorial_155_0.png +../_images/notebooks_QSARtuna_Tutorial_155_0.png

                                                            Further analysis of the uncertainty using error bars is shown here:

                                                            @@ -12993,7 +12993,7 @@

                                                            MAPIE (regression uncertainty)

                                                          -../_images/notebooks_QPTUNA_Tutorial_157_0.png +../_images/notebooks_QSARtuna_Tutorial_157_0.png

                                                          where more certain predictions have smaller error bars.

                                                          @@ -13014,17 +13014,17 @@

                                                          MAPIE (regression uncertainty)

                                                        -../_images/notebooks_QPTUNA_Tutorial_159_0.png +../_images/notebooks_QSARtuna_Tutorial_159_0.png

                                                      Explainability

                                                      -

                                                      Model explainability is incorporated into Qptuna using two different approaches, depending on the algorithm chosen: 1. SHAP: Any shallow algorithm is compatible with the SHAP package (even traditionally unsupported packages use the KernelExplainer) 2. ChemProp interpret: This explainability approach is based on the interpret function in the original ChemProp package

                                                      +

                                                      Model explainability is incorporated into QSARtuna using two different approaches, depending on the algorithm chosen: 1. SHAP: Any shallow algorithm is compatible with the SHAP package (even traditionally unsupported packages use the KernelExplainer) 2. ChemProp interpret: This explainability approach is based on the interpret function in the original ChemProp package

                                                      SHAP

                                                      -

                                                      SHAP (SHapley Additive exPlanations) are available in Qptuna based on the implementation available at https://github.com/slundberg/shap. The method uses a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions (see +

                                                      SHAP (SHapley Additive exPlanations) are available in QSARtuna based on the implementation available at https://github.com/slundberg/shap. The method uses a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions (see here for more details on the published tool and here for papers using the approach).

                                                      In the following example, a RIDGE regressor is trained using the a comopsite descriptor based on the ECFP, MACCS keys and PhysChem descriptors:

                                                      @@ -14227,7 +14227,7 @@

                                                      ChemProp fingerprints (encode latent representation as descriptors)5 rows × 300 columns

                                                  -

                                                  The output is n compounds as the input query in the rows by n latent representation features from the MPN in the columns. This output can then be used for any semi-supervise learning approach outside of Qptuna, as required. Alternatively the last layer of the FFN can be used as so:

                                                  +

                                                  The output is n compounds as the input query in the rows by n latent representation features from the MPN in the columns. This output can then be used for any semi-supervise learning approach outside of QSARtuna, as required. Alternatively the last layer of the FFN can be used as so:

                                                  [67]:
                                                   
                                                  @@ -14471,7 +14471,7 @@

                                                  ChemProp fingerprints (encode latent representation as descriptors)

                                                  Log transformation

                                                  -

                                                  Qptuna can be used to transform input labels so that log-scaled or irregularly distributed data can be transformed to a normal distribution as required for most Machine Learning inputs. The following example shows how XC50 values can be scaled to pXC50 values by using the -Log10 to the 6th unit conversion, like so:

                                                  +

                                                  QSARtuna can be used to transform input labels so that log-scaled or irregularly distributed data can be transformed to a normal distribution as required for most Machine Learning inputs. The following example shows how XC50 values can be scaled to pXC50 values by using the -Log10 to the 6th unit conversion, like so:

                                                  [68]:
                                                   
                                                  @@ -14698,7 +14698,7 @@

                                                  Log transformation
                                                  -../_images/notebooks_QPTUNA_Tutorial_185_0.png +../_images/notebooks_QSARtuna_Tutorial_185_0.png

                                                  This example shows the influence of scaling the pXC50 values to the log scale. The non-noramlised distribution of the unlogged data yields very large (negative) model evaluation scores, since evaluation metrics such as MSE are relative, and the scale of the error is reported in performance values.

                                                  @@ -14979,7 +14979,7 @@

                                                  Log transformationNone:

                                                  +

                                                  This is the default behaviour of QSARtuna; reverse transform is performed at inference when log transformation was applied, so that users can action on prediction the original input data scale. Importantly, a user can easily override this behaviour by providing the transform parameter as None:

                                                  [72]:
                                                   
                                                  @@ -14997,7 +14997,7 @@

                                                  Log transformation

                                                  In comparison to log scaled models trained without the PRF transform, log-transformed models trained with PTR functions will always output the probabilistic class membership likelihoods from the PTR function:

                                                  @@ -15272,11 +15272,11 @@

                                                  Log transformation -

                                                  Advanced options for Qptuna runs

                                                  +
                                                  +

                                                  Advanced options for QSARtuna runs

                                                  Multi-objective prioritization of performance and standard deviation

                                                  -

                                                  Qptuna can optimize for the minimzation of the standard deviation of performance across the folds. This should in theory prioritize hyperparameters that are consistently performative across different splits of the data, and so should be more generalizable/performative in production. This can be performed with the minimize_std_dev in the example below:

                                                  +

                                                  QSARtuna can optimize for the minimzation of the standard deviation of performance across the folds. This should in theory prioritize hyperparameters that are consistently performative across different splits of the data, and so should be more generalizable/performative in production. This can be performed with the minimize_std_dev in the example below:

                                                  [76]:
                                                   
                                                  @@ -16205,7 +16205,7 @@

                                                  Multi-objective prioritization of performance and standard deviation

                                                  -../_images/notebooks_QPTUNA_Tutorial_202_1.png +../_images/notebooks_QSARtuna_Tutorial_202_1.png

                                                  We may plot the Pareto front of this multi-objective study using the Optuna plotting functionaility directly:

                                                  @@ -16275,8 +16275,8 @@

                                                  Multi-objective prioritization of performance and standard deviation

                                                  -
                                                  -

                                                  Further visualization of Qptuna runs

                                                  +
                                                  +

                                                  Further visualization of QSARtuna runs

                                                  It is possible to evaluate the parameter importances on regression metric performance across descriptor vs. algorithm choice, based on the completed trials in our study:

                                                  [79]:
                                                  @@ -16483,7 +16483,7 @@ 

                                                  Further visualization of Qptuna runs - +

                                                  diff --git a/docs/sphinx-builddir/html/notebooks/QPTUNA_Tutorial.ipynb b/docs/sphinx-builddir/html/notebooks/QPTUNA_Tutorial.ipynb index c9fc52e..6c89616 100644 --- a/docs/sphinx-builddir/html/notebooks/QPTUNA_Tutorial.ipynb +++ b/docs/sphinx-builddir/html/notebooks/QPTUNA_Tutorial.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "# QPTUNA CLI Tutorial" + "# QSARtuna CLI Tutorial" ] }, { @@ -18,9 +18,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This tutorial is intended to provide a new user with the necessary background to start using Qptuna through a command line interface (CLI).\n", + "This tutorial is intended to provide a new user with the necessary background to start using QSARtuna through a command line interface (CLI).\n", "\n", - "A separate tutorial is available describing the use of the Qptuna GUI." + "A separate tutorial is available describing the use of the QSARtuna GUI." ] }, { @@ -34,9 +34,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA is a python package to automate the model building process for *REINVENT*. These models can use a variety of algorithms to fit to your input data and most of them have one or more so-called hyper-parameters (e.g. the maximum number of trees using a *Random Forest* or the C parameter in SVRs, controlling the influence of every support vector).\n", + "QSARtuna is a python package to automate the model building process for *REINVENT*. These models can use a variety of algorithms to fit to your input data and most of them have one or more so-called hyper-parameters (e.g. the maximum number of trees using a *Random Forest* or the C parameter in SVRs, controlling the influence of every support vector).\n", "\n", - "For both regression and classification tasks, QPTUNA allows you to specify input data for which the optimal hyper-parameters and a model can obtained automatically. If you want to get an idea on how the package is structured, read on otherwise you might want to skip it and The following examples should give you an idea how.\n" + "For both regression and classification tasks, QSARtuna allows you to specify input data for which the optimal hyper-parameters and a model can obtained automatically. If you want to get an idea on how the package is structured, read on otherwise you might want to skip it and The following examples should give you an idea how.\n" ] }, { @@ -50,7 +50,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna is structured around three steps:\n", + "QSARtuna is structured around three steps:\n", "1. **Hyperparameter Optimization:** \n", " Train many models with different parameters using Optuna.\n", " Only the training dataset is used here. \n", @@ -76,9 +76,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "To use QPTUNA from Jupyter Notebook, install it with:\n", + "To use QSARtuna from Jupyter Notebook, install it with:\n", "```\n", - "python -m pip install http://pages.scp.astrazeneca.net/mai/qptuna/releases/Qptuna_latest.tar.gz\n", + "python -m pip install http://pages.scp.astrazeneca.net/mai/qsartuna/releases/QSARtuna_latest.tar.gz\n", "```" ] }, @@ -91,7 +91,7 @@ "\n", "Training dataset is a CSV file. It has SMILES strings in a column named \"canonical\". It has the value that we will try to predict in column \"molwt\".\n", "\n", - "This example has train and test (holdout) dataset ready. If you have single dataset and would like QPTUNA to split it into train and test (holdout) datasets, see the next section." + "This example has train and test (holdout) dataset ready. If you have single dataset and would like QSARtuna to split it into train and test (holdout) datasets, see the next section." ] }, { @@ -142,7 +142,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA configuration can be read from a JSON file or created in Python. Here we create it in Python." + "QSARtuna configuration can be read from a JSON file or created in Python. Here we create it in Python." ] }, { @@ -164,7 +164,7 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n", " from .autonotebook import tqdm as notebook_tqdm\n" ] } @@ -359,17 +359,17 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.731e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.731e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,452] Trial 54 finished with value: -437.4551843552628 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.0988827083418571, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.728e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.728e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,513] Trial 55 finished with value: -437.7905045218911 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.10275551704677868, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 8.093e+01, tolerance: 2.450e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 8.093e+01, tolerance: 2.450e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 9.647e+01, tolerance: 2.262e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 9.647e+01, tolerance: 2.262e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 7.442e+01, tolerance: 2.313e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 7.442e+01, tolerance: 2.313e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:38,588] Trial 56 finished with value: -460.9949341873208 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.02258838612145872, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", "[I 2024-02-15 17:30:38,673] Trial 57 finished with value: -437.2063895411025 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.001303005653721337, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 11 with value: -359.5346503101038.\n", @@ -797,7 +797,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA can split data into train and test (holdout) datasets. To do so, send all data in as training_dataset_file, and choose a splitting strategy. Currently QPTUNA supports three splitting strategies: random, temporal and stratified. \n", + "QSARtuna can split data into train and test (holdout) datasets. To do so, send all data in as training_dataset_file, and choose a splitting strategy. Currently QSARtuna supports three splitting strategies: random, temporal and stratified. \n", "\n", "Random strategy splits data randomly, taking a specified fraction of observations to be test dataset. \n", "\n", @@ -817,7 +817,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "All the algorithms QPTUNA supports do not work with duplicates. Duplicates can come from multiple measurements for the same compound, or from the fact that the molecular descriptors we use are all disregard stereochemistry, so even if compounds are different, descriptors make them into duplicates. QPTUNA provides several strategies to remove duplicates:\n", + "All the algorithms QSARtuna supports do not work with duplicates. Duplicates can come from multiple measurements for the same compound, or from the fact that the molecular descriptors we use are all disregard stereochemistry, so even if compounds are different, descriptors make them into duplicates. QSARtuna provides several strategies to remove duplicates:\n", "* keep median - factors experimental deviation using all replicates into one median value (robust to outliers - recommended)\n", "* keep average - use all experimental data acorss all replicates (less robust to outliers vs. median)\n", "* keep first / keep last - when the first or the last measurement is the trusted one\n", @@ -885,15 +885,15 @@ "text": [ "[I 2024-02-15 17:30:42,956] A new study created in memory with name: my_study_stratified_split\n", "[I 2024-02-15 17:30:42,992] A new study created in memory with name: study_name_0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/joblib/memory.py:655: JobLibCollisionWarning: Possible name collisions between functions 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:-1) and 'calculate_from_smi' (/Users/kljk345/PycharmProjects/optuna_az/optunaz/descriptors.py:172)\n", " return self._cached_call(args, kwargs)[0]\n", "[I 2024-02-15 17:30:43,100] Trial 0 finished with value: -1916.9080190588304 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.6455264533858698, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 0 with value: -1916.9080190588304.\n", "[I 2024-02-15 17:30:43,165] Trial 1 finished with value: -2756.046839500092 and parameters: {'algorithm_name': 'PLSRegression', 'PLSRegression_algorithm_hash': '9f2f76e479633c0bf18cf2912fed9eda', 'n_components': 2, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 0 with value: -1916.9080190588304.\n", @@ -1052,7 +1052,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "By default, QPTUNA uses `neg_mean_squared_error` for regression and `roc_auc` for classification. It is possible to change to other scoring functions that supported by scikit-learn (https://scikit-learn.org/stable/modules/model_evaluation.html) amongst others:" + "By default, QSARtuna uses `neg_mean_squared_error` for regression and `roc_auc` for classification. It is possible to change to other scoring functions that supported by scikit-learn (https://scikit-learn.org/stable/modules/model_evaluation.html) amongst others:" ] }, { @@ -1189,11 +1189,11 @@ "[I 2024-02-15 17:30:50,908] Trial 12 finished with value: 0.3125909835602004 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 1.2601024383222263, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:50,962] Trial 13 finished with value: 0.35938304159920104 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.704926958538193, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:51,047] Trial 14 finished with value: -0.139217147681443 and parameters: {'algorithm_name': 'RandomForestRegressor', 'RandomForestRegressor_algorithm_hash': 'f1ac01e1bba332215ccbd0c29c9ac3c3', 'max_depth': 5, 'n_estimators': 7, 'max_features': , 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.831e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.831e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 5.012e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 5.012e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 4.308e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 4.308e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:51,100] Trial 15 finished with value: -0.3520572381552265 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.003736146475899149, 'descriptor': '{\"name\": \"MACCS_keys\", \"parameters\": {}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:51,156] Trial 16 finished with value: 0.3097224153934907 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 1.3643850817675436, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", @@ -1250,11 +1250,11 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.208e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.208e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 2.075e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 2.075e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.665e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.665e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:52,349] Trial 38 finished with value: 0.33582943996366277 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.03037397374709805, 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:52,441] Trial 39 finished with value: -0.014200255758600178 and parameters: {'algorithm_name': 'RandomForestRegressor', 'RandomForestRegressor_algorithm_hash': 'f1ac01e1bba332215ccbd0c29c9ac3c3', 'max_depth': 12, 'n_estimators': 6, 'max_features': , 'descriptor': '{\"name\": \"ECFP\", \"parameters\": {\"radius\": 3, \"nBits\": 2048, \"returnRdkit\": false}}'}. Best is trial 9 with value: 0.8415543537460097.\n", @@ -1303,11 +1303,11 @@ "[I 2024-02-15 17:30:54,404] Trial 76 finished with value: 0.8203032617778302 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.02814913529858031, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:54,453] Trial 77 finished with value: 0.8203033764469106 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.028018087885969566, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", "[I 2024-02-15 17:30:54,506] Trial 78 finished with value: 0.8203229095425186 and parameters: {'algorithm_name': 'Ridge', 'Ridge_algorithm_hash': 'cfa1990d5153c8812982f034d788d7ee', 'alpha': 0.005685911509939887, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 9 with value: 0.8415543537460097.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.109e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.109e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.002e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.002e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.165e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.165e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n" ] }, @@ -1316,11 +1316,11 @@ "output_type": "stream", "text": [ "[I 2024-02-15 17:30:54,617] Trial 79 finished with value: 0.8611747184538611 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.00427216024040911, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 79 with value: 0.8611747184538611.\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.220e+02, tolerance: 4.977e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.220e+02, tolerance: 4.977e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.321e+02, tolerance: 4.782e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 3.321e+02, tolerance: 4.782e+01\n", " model = cd_fast.enet_coordinate_descent(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.497e+02, tolerance: 4.906e+01\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/linear_model/_coordinate_descent.py:678: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations, check the scale of the features or consider increasing regularisation. Duality gap: 1.497e+02, tolerance: 4.906e+01\n", " model = cd_fast.enet_coordinate_descent(\n", "[I 2024-02-15 17:30:54,731] Trial 80 finished with value: 0.8613400144535142 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.02833136367189578, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 80 with value: 0.8613400144535142.\n", "[I 2024-02-15 17:30:54,843] Trial 81 finished with value: 0.8869607357185316 and parameters: {'algorithm_name': 'Lasso', 'Lasso_algorithm_hash': '5457f609662e44f04dcc9423066d2f58', 'alpha': 0.0008522399475568362, 'descriptor': '{\"name\": \"ECFP_counts\", \"parameters\": {\"radius\": 3, \"useFeatures\": true, \"nBits\": 2048}}'}. Best is trial 81 with value: 0.8869607357185316.\n", @@ -1387,7 +1387,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Various algorithms are available in Qptuna:" + "Various algorithms are available in QSARtuna:" ] }, { @@ -1445,13 +1445,13 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "PRF is a modification of the long-established Random Forest (RF) algorithm and takes into account uncertainties in features and/or labels (though only uncertainty in labels are currently implemented in Qptuna), which was first described in[1]. It can be seen as a probabilistic method to factor experimental uncertainty during training, and is considered a hybrid between regression and classification algorithms.\n", + "PRF is a modification of the long-established Random Forest (RF) algorithm and takes into account uncertainties in features and/or labels (though only uncertainty in labels are currently implemented in QSARtuna), which was first described in[1]. It can be seen as a probabilistic method to factor experimental uncertainty during training, and is considered a hybrid between regression and classification algorithms.\n", "\n", "In more detail; PRF treats labels as probability distribution functions [PDFs] (denoted as `∆y`), rather than deterministic quantities. In comparison, the traditional RF uses discrete variables for activity (binary y-labels, also referred to as `y`) from the discretised bioactivity scale defining active/inactive sets. \n", "\n", - "PTR integration was added to Qptuna to afford this probabilistic approach towards modelling, and is particularly useful combined with the PTR (See the preprocessing notebook for details). In this combination, PRF takes as input real-valued probabilities (similar to regression), from a Probabilistic Threshold Representation (PTR). However, similar to classification algorithms, PRF outputs the probability of activity for the active class.\n", + "PTR integration was added to QSARtuna to afford this probabilistic approach towards modelling, and is particularly useful combined with the PTR (See the preprocessing notebook for details). In this combination, PRF takes as input real-valued probabilities (similar to regression), from a Probabilistic Threshold Representation (PTR). However, similar to classification algorithms, PRF outputs the probability of activity for the active class.\n", "\n", - "Note that Qptuna runs the PRFClassifier in a regression setting, since the model only outputs class liklihood membership based on `∆y`\n", + "Note that QSARtuna runs the PRFClassifier in a regression setting, since the model only outputs class liklihood membership based on `∆y`\n", "\n", "[1] https://iopscience.iop.org/article/10.3847/1538-3881/aaf101/meta\n", "\n", @@ -1498,7 +1498,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Note that Qptuna is run in regression mode (`ModelMode.REGRESSION`), as outputs from the algorithm are always continuous values.\n", + "Note that QSARtuna is run in regression mode (`ModelMode.REGRESSION`), as outputs from the algorithm are always continuous values.\n", "\n", "Next we can run the PRF/PTR study:" ] @@ -1632,7 +1632,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "N.B It is not possible to train on response column values outside the likelihood for y-label memberships (ranging from 0-1), as expected for `∆y`. Doing so will result in the following error from Qptuna:" + "N.B It is not possible to train on response column values outside the likelihood for y-label memberships (ranging from 0-1), as expected for `∆y`. Doing so will result in the following error from QSARtuna:" ] }, { @@ -1648,7 +1648,7 @@ "[I 2024-02-15 17:31:35,748] A new study created in memory with name: study_name_0\n", "[W 2024-02-15 17:31:35,749] Trial 0 failed with parameters: {} because of the following error: ValueError('PRFClassifier supplied but response column outside [0.0-1.0] acceptable range. Response max: 9.7, response min: 5.3 ').\n", "Traceback (most recent call last):\n", - " File \"/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/optuna/study/_optimize.py\", line 200, in _run_trial\n", + " File \"/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/optuna/study/_optimize.py\", line 200, in _run_trial\n", " value_or_values = func(trial)\n", " File \"/Users/kljk345/PycharmProjects/optuna_az/optunaz/objective.py\", line 124, in __call__\n", " self._validate_algos()\n", @@ -1717,7 +1717,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "QPTUNA has the functionaility to train `ChemProp` deep learning models. These are message passing neural networks (MPNNs) based on a graph representation of training molecules. They are considered by many to offer the state-of-the-art approach for property prediction.\n", + "QSARtuna has the functionaility to train `ChemProp` deep learning models. These are message passing neural networks (MPNNs) based on a graph representation of training molecules. They are considered by many to offer the state-of-the-art approach for property prediction.\n", "\n", "`ChemProp` was first described in the paper Analyzing Learned Molecular Representations for Property Prediction: https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00237\n", "\n", @@ -1779,25 +1779,25 @@ "INFO:root:Enqueued ChemProp manual trial with sensible defaults: {'activation': 'ReLU', 'aggregation': 'mean', 'aggregation_norm': 100, 'batch_size': 50, 'depth': 3, 'dropout': 0.0, 'features_generator': 'none', 'ffn_hidden_size': 300, 'ffn_num_layers': 3, 'final_lr_ratio_exp': -1, 'hidden_size': 300, 'init_lr_ratio_exp': -1, 'max_lr_exp': -3, 'warmup_epochs_ratio': 0.1, 'algorithm_name': 'ChemPropRegressor'}\n", "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 59.407933 on epoch 1\n", "Model 0 best validation rmse = 102.010993 on epoch 4\n", @@ -1912,23 +1912,23 @@ "text": [ "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 97.581963 on epoch 0\n", "Model 0 provided with no test set, no metric evaluation will be performed.\n", @@ -1937,7 +1937,7 @@ "\tSeed 0 ==> test rmse = nan\n", "Overall test rmse = nan +/- nan\n", "Elapsed time = 0:00:04\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "Model 0 best validation rmse = 67.110851 on epoch 4\n", "Model 0 provided with no test set, no metric evaluation will be performed.\n", @@ -2063,9 +2063,9 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "You may safely ignore `ChemProp` warnings such as `Model 0 provided with no test set, no metric evaluation will be performed`, `\"rmse = nan\"` and `1-fold cross validation`, as they are information prompts printed from `ChemProp` due to some (deactivated) CV functionaility (ChemProp can perform it's own cross validation - details for this are still printed despite its deactivation within `Qptuna`).\n", + "You may safely ignore `ChemProp` warnings such as `Model 0 provided with no test set, no metric evaluation will be performed`, `\"rmse = nan\"` and `1-fold cross validation`, as they are information prompts printed from `ChemProp` due to some (deactivated) CV functionaility (ChemProp can perform it's own cross validation - details for this are still printed despite its deactivation within `QSARtuna`).\n", "\n", - "NB: Qptuna will first trial the sensible defaults for the MPNN architecture (where possible given the user config). This is communicated to the user, e.g. see the output which advises:\n", + "NB: QSARtuna will first trial the sensible defaults for the MPNN architecture (where possible given the user config). This is communicated to the user, e.g. see the output which advises:\n", "\n", "`A new study created in memory with name: study_name_0\n", "INFO:root:Enqueued ChemProp manual trial with sensible defaults: {'activation': 'ReLU', 'aggregation': 'mean', 'aggregation_norm': 100, 'batch_size': 50, 'depth': 3, 'dropout': 0.0, 'features_generator': 'none', 'ffn_hidden_size': 300, 'ffn_num_layers': 3, 'final_lr_ratio_exp': -1, 'hidden_size': 300, 'init_lr_ratio_exp': -1, 'max_lr_exp': -3, 'warmup_epochs_ratio': 0.1, 'algorithm_name': 'ChemPropRegressor'}`.\n", @@ -2084,7 +2084,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "By default, `Qptuna` separates `ChemProp` from the other shallow methods using the `split_chemprop` flag. When this setting is set, the user must specify the number of `ChemProp` trials using the `n_chemprop_trials` flag if more than 1 (default) trial is desired:" + "By default, `QSARtuna` separates `ChemProp` from the other shallow methods using the `split_chemprop` flag. When this setting is set, the user must specify the number of `ChemProp` trials using the `n_chemprop_trials` flag if more than 1 (default) trial is desired:" ] }, { @@ -2135,7 +2135,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna optimises all aspects of the ChemProp architecture when using ChemPropRegressor or ChemPropClassifier, however, users can activate the [original hyperparameter-optimization implementation](https://github.com/chemprop/chemprop#hyperparameter-optimization) in the `ChemProp` package, which performs automated Bayesian hyperparameter optimization using the `Hyperopt` package within each trial, at large computational cost.\n", + "QSARtuna optimises all aspects of the ChemProp architecture when using ChemPropRegressor or ChemPropClassifier, however, users can activate the [original hyperparameter-optimization implementation](https://github.com/chemprop/chemprop#hyperparameter-optimization) in the `ChemProp` package, which performs automated Bayesian hyperparameter optimization using the `Hyperopt` package within each trial, at large computational cost.\n", "\n", "NB: The principal way for users to expand and perform more advanced runs is to extend the available non-network hyperparameters, such as the `features_generator` option or e.g. to trial differnt side information weighting (if side information is available).\n", "\n", @@ -2190,9 +2190,9 @@ "\n", "#### A note on MPNN Hyperopt search space\n", "\n", - "`ChemProp` models trained using Hyperopt use the [original implementation](https://chemprop.readthedocs.io/en/latest/hyperopt.html), but one key difference is the `search_parameter_level` setting created for `Qptuna`; Instead of using pre-defined search spaces as in the original package, `Qptuna` can (and will by the default since `search_parameter_level`=`auto` unless changed) alter the space depending on the characteristics of user input data. For example, no. training set compounds, hyperparameter trials (`num_iters`) & epochs (`epochs`) are used by the `auto` setting to ensure search spaces are not too large for limited data/epochs, and _vice-versa_, an extensive search space is trailed when applicable.\n", + "`ChemProp` models trained using Hyperopt use the [original implementation](https://chemprop.readthedocs.io/en/latest/hyperopt.html), but one key difference is the `search_parameter_level` setting created for `QSARtuna`; Instead of using pre-defined search spaces as in the original package, `QSARtuna` can (and will by the default since `search_parameter_level`=`auto` unless changed) alter the space depending on the characteristics of user input data. For example, no. training set compounds, hyperparameter trials (`num_iters`) & epochs (`epochs`) are used by the `auto` setting to ensure search spaces are not too large for limited data/epochs, and _vice-versa_, an extensive search space is trailed when applicable.\n", "\n", - "N.B: Users can also manually define `Hyperopt` search spaces by altering `search_parameter_level` from `auto` to a different level between `[0-8]`, representing the increasing search space size (see the [Qptuna documentation](https://pages.scp.astrazeneca.net/mai/qptuna/optunaz.config.html#optunaz.config.optconfig.ChemPropSearch_Parameter_Level) for details)." + "N.B: Users can also manually define `Hyperopt` search spaces by altering `search_parameter_level` from `auto` to a different level between `[0-8]`, representing the increasing search space size (see the [QSARtuna documentation](https://pages.scp.astrazeneca.net/mai/qsartuna/optunaz.config.html#optunaz.config.optconfig.ChemPropSearch_Parameter_Level) for details)." ] }, { @@ -2208,7 +2208,7 @@ "source": [ "_“Even if you are only optimizing one loss as is the typical case, chances are there is an auxiliary task that will help you improve upon your main task”_ [Caruana, 1998]\n", "\n", - "`Qptuna` typically optimizes for one particular metric for a given molecule property. While we can generally achieve acceptable performance this way, these single task (ST) models ignore information that may improve the prediction of main task of intent. See option `a.` in the figure below.\n", + "`QSARtuna` typically optimizes for one particular metric for a given molecule property. While we can generally achieve acceptable performance this way, these single task (ST) models ignore information that may improve the prediction of main task of intent. See option `a.` in the figure below.\n", "\n", "Signals from relevant related tasks (aka \"auxiliary tasks\" or \"side information\") could come from the training signals of other molecular properties and by sharing representations between related tasks, we can enable a neural network to generalize better on our original task of intent. This approach is called Multi-Task Learning (MTL) See option `b.` in the figure below.\n", "\n", @@ -2217,7 +2217,7 @@ "_(above) Differences between optimizing one vs. more than one loss function. a.) Single-task (ST): one model trained to predict one task one model optimised until performance no longer increases b.) Multi-task (MT/MTL): training one model to predict multiple tasks one model optimising more than one loss function at once enables representations to be shared between trained tasks training signals of related tasks shared between all tasks._\n", "\n", "\n", - "`ChemProp` performs MTL by using the knowledge learnt during training one task to reduce the loss of other tasks included in training. In order to use this function in `Qptuna`, a user should provide side information in a separate file, and it should have the same ordering and length as the input/response columns (i.e. length of y should = length of side information for y).\n", + "`ChemProp` performs MTL by using the knowledge learnt during training one task to reduce the loss of other tasks included in training. In order to use this function in `QSARtuna`, a user should provide side information in a separate file, and it should have the same ordering and length as the input/response columns (i.e. length of y should = length of side information for y).\n", "\n", "E.g: consider the DRD2 example input from earlier:" ] @@ -2322,7 +2322,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The contribution or _weight_ of all side information tasks in their contribution to the loss function during training a network is a parameter that can be optimised within Qptuna, e.g:" + "The contribution or _weight_ of all side information tasks in their contribution to the loss function during training a network is a parameter that can be optimised within QSARtuna, e.g:" ] }, { @@ -2338,101 +2338,101 @@ "[I 2024-02-15 17:31:47,393] A new study created in memory with name: study_name_0\n", "Fold 0\n", "Fold 0\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n" ] }, @@ -2440,81 +2440,81 @@ "name": "stderr", "output_type": "stream", "text": [ - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", - "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", + "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", "/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/sklearn/metrics/_regression.py:483: FutureWarning: 'squared' is deprecated in version 1.4 and will be removed in 1.6. To calculate the root mean squared error, use the function'root_mean_squared_error'.\n", " warnings.warn(\n", @@ -7146,7 +7146,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Above described how ChemProp is by default split from shallow methods. Users can override this using the advanced functionaility when `split_chemprop`=False. In this situation `Qptuna` will optimise `ChemProp` with the other shallow methods:" + "Above described how ChemProp is by default split from shallow methods. Users can override this using the advanced functionaility when `split_chemprop`=False. In this situation `QSARtuna` will optimise `ChemProp` with the other shallow methods:" ] }, { @@ -7186,7 +7186,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Combining ChemProp and traditional methods in this way means the potential search possible in `Qptuna` comprises some incompatible sub-spaces; for example, `ChemProp` is only compatible with SMILES-based descriptors, whilst traditional methods are incompatible with SMILES. In the following examples, we consider the following search space: \"Valid" + "Combining ChemProp and traditional methods in this way means the potential search possible in `QSARtuna` comprises some incompatible sub-spaces; for example, `ChemProp` is only compatible with SMILES-based descriptors, whilst traditional methods are incompatible with SMILES. In the following examples, we consider the following search space: \"Valid" ] }, { @@ -7201,9 +7201,9 @@ "\n", "Pruning is an `Optuna` feature [originally designed](https://optuna.readthedocs.io/en/v2.0.0/tutorial/pruning.html) to automatically stop unpromising trials early in training.\n", "\n", - "_How/why is pruning implemented in Qptuna?_\n", + "_How/why is pruning implemented in QSARtuna?_\n", "\n", - "Instead of the original intention of pruning _unpromising trials_ due to poor performance, `Qptuna` ensures `Optuna` prunes _incompatible algorithm-desciptor pairs_, so the sampler will not trial incomptaible settings again. Duplicated trials are also pruned, to avoid repeatedly suggesting the same hyerparameters. Pruning the trial (instead of returning a cached result) explicitly tasks the sampler to avoid identical parameters.\n", + "Instead of the original intention of pruning _unpromising trials_ due to poor performance, `QSARtuna` ensures `Optuna` prunes _incompatible algorithm-desciptor pairs_, so the sampler will not trial incomptaible settings again. Duplicated trials are also pruned, to avoid repeatedly suggesting the same hyerparameters. Pruning the trial (instead of returning a cached result) explicitly tasks the sampler to avoid identical parameters.\n", "\n", "Now let us consider the following run:" ] @@ -7292,7 +7292,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Consulting the `Qptuna` output, we observe cases of e.g. \"`Trial 3 pruned. Incompatible subspace`\", which indicates an instance when the sampler has sampled an incompitble algo-descriptor pair. \n", + "Consulting the `QSARtuna` output, we observe cases of e.g. \"`Trial 3 pruned. Incompatible subspace`\", which indicates an instance when the sampler has sampled an incompitble algo-descriptor pair. \n", "\n", "\"`Trial 13 pruned. Duplicate parameter set`\" is an example of pruning a duplicated trial parameter suggestion.\n", "\n", @@ -7342,7 +7342,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "When performing classification you often want not only to predict the class label, but also obtain a probability of the respective label. This probability gives you some kind of confidence on the prediction. Some models can give you poor estimates of the class probabilities. The `CalibratedClassifierCV` Qptuna models allow better calibration for the probabilities of a given model.\n", + "When performing classification you often want not only to predict the class label, but also obtain a probability of the respective label. This probability gives you some kind of confidence on the prediction. Some models can give you poor estimates of the class probabilities. The `CalibratedClassifierCV` QSARtuna models allow better calibration for the probabilities of a given model.\n", "\n", "First, we should understand that well calibrated classifiers are probabilistic classifiers for which the output of the predict_proba method can be directly interpreted as a confidence level. For instance, a well calibrated (binary) classifier should classify the samples such that among the samples to which it gave a predict_proba value close to 0.8, approximately 80% actually belong to the positive class.\n", "\n", @@ -7735,7 +7735,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna offers three different ways to calculate uncertainty estimates. \n", + "QSARtuna offers three different ways to calculate uncertainty estimates. \n", "\n", "1. VennABERS calibration (a probability calibration covered in the section above).\n", "2. Ensemble uncertainty (ChemProp models trained with random initialisations).\n", @@ -11827,7 +11827,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "For regression uncertainty, the MAPIE package is available within Qptuna for regression algorithms, and is selected like so:" + "For regression uncertainty, the MAPIE package is available within QSARtuna for regression algorithms, and is selected like so:" ] }, { @@ -12013,7 +12013,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Model explainability is incorporated into Qptuna using two different approaches, depending on the algorithm chosen:\n", + "Model explainability is incorporated into QSARtuna using two different approaches, depending on the algorithm chosen:\n", "1. **SHAP:** \n", " Any shallow algorithm is compatible with the SHAP package (even traditionally unsupported packages use the `KernelExplainer`)\n", "2. **ChemProp interpret:**\n", @@ -12031,7 +12031,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "[SHAP](https://proceedings.neurips.cc/paper_files/paper/2017/hash/8a20a8621978632d76c43dfd28b67767-Abstract.html) (SHapley Additive exPlanations) are available in `Qptuna` based on the implementation available at https://github.com/slundberg/shap. The method uses a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions (see [here](https://shap.readthedocs.io/en/latest/index.html) for more details on the published tool and [here](https://github.com/slundberg/shap#methods-unified-by-shap) for papers using the approach).\n", + "[SHAP](https://proceedings.neurips.cc/paper_files/paper/2017/hash/8a20a8621978632d76c43dfd28b67767-Abstract.html) (SHapley Additive exPlanations) are available in `QSARtuna` based on the implementation available at https://github.com/slundberg/shap. The method uses a game theoretic approach to explain the output of any machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley values from game theory and their related extensions (see [here](https://shap.readthedocs.io/en/latest/index.html) for more details on the published tool and [here](https://github.com/slundberg/shap#methods-unified-by-shap) for papers using the approach).\n", "\n", "In the following example, a `RIDGE` regressor is trained using the a comopsite descriptor based on the `ECFP`, `MACCS` keys and `PhysChem` descriptors:" ] @@ -13296,14 +13296,14 @@ "source": [ "chemprop.predictor.chemprop_fingerprint(\n", " df[config.data.input_column].head(5),\n", - " fingerprint_type=\"MPN\") # MPN specified for illustration purposes - this is the default method in Qptuna" + " fingerprint_type=\"MPN\") # MPN specified for illustration purposes - this is the default method in QSARtuna" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "The output is n compounds as the input query in the rows by n latent representation features from the MPN in the columns. This output can then be used for any semi-supervise learning approach outside of Qptuna, as required. Alternatively the last layer of the FFN can be used as so:" + "The output is n compounds as the input query in the rows by n latent representation features from the MPN in the columns. This output can then be used for any semi-supervise learning approach outside of QSARtuna, as required. Alternatively the last layer of the FFN can be used as so:" ] }, { @@ -13588,7 +13588,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna can be used to transform input labels so that log-scaled or irregularly distributed data can be transformed to a normal distribution as required for most Machine Learning inputs. The following example shows how XC50 values can be scaled to pXC50 values by using the -Log10 to the 6th unit conversion, like so:" + "QSARtuna can be used to transform input labels so that log-scaled or irregularly distributed data can be transformed to a normal distribution as required for most Machine Learning inputs. The following example shows how XC50 values can be scaled to pXC50 values by using the -Log10 to the 6th unit conversion, like so:" ] }, { @@ -13815,7 +13815,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "In comparison, Qptuna does not normally transform the data:" + "In comparison, QSARtuna does not normally transform the data:" ] }, { @@ -14116,7 +14116,7 @@ "source": [ "NB: Please note that outputs have automatically been reversed transformed at inference, back onto the original XC50 scale, as shown by large values outside the log pXC50.\n", "\n", - "This is the default behaviour of Qptuna; reverse transform is performed at inference when log transformation was applied, so that users can action on prediction the original input data scale. Importantly, a user can easily override this behaviour by providing the transform parameter as `None`:" + "This is the default behaviour of QSARtuna; reverse transform is performed at inference when log transformation was applied, so that users can action on prediction the original input data scale. Importantly, a user can easily override this behaviour by providing the transform parameter as `None`:" ] }, { @@ -14143,7 +14143,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This will instruct Qptuna to avoid the reverse transform on the predictions. This transform parameter is ignored if no transformation was applied in the user config.\n", + "This will instruct QSARtuna to avoid the reverse transform on the predictions. This transform parameter is ignored if no transformation was applied in the user config.\n", "\n", "Log transformation can also be combined with the PTR transform. In this situation, all user inputs are expected to be on the untransformed scale. For example, if a user wishes to create a PTR model, trained on pXC50 data and a cut-off for pXC50 values of 5 (10um), the following config can be used:" ] @@ -14444,7 +14444,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Advanced options for Qptuna runs" + "## Advanced options for QSARtuna runs" ] }, { @@ -14458,7 +14458,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Qptuna can optimize for the minimzation of the standard deviation of performance across the folds. This should in theory prioritize hyperparameters that are consistently performative across different splits of the data, and so should be more generalizable/performative in production. This can be performed with the `minimize_std_dev` in the example below:" + "QSARtuna can optimize for the minimzation of the standard deviation of performance across the folds. This should in theory prioritize hyperparameters that are consistently performative across different splits of the data, and so should be more generalizable/performative in production. This can be performed with the `minimize_std_dev` in the example below:" ] }, { @@ -16444,7 +16444,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Further visualization of Qptuna runs" + "### Further visualization of QSARtuna runs" ] }, { diff --git a/docs/sphinx-builddir/html/notebooks/preprocess_data.html b/docs/sphinx-builddir/html/notebooks/preprocess_data.html index 7d26ec6..b70a34c 100644 --- a/docs/sphinx-builddir/html/notebooks/preprocess_data.html +++ b/docs/sphinx-builddir/html/notebooks/preprocess_data.html @@ -4,7 +4,7 @@ - Preprocessing data for Qptuna — QPTUNA 2.7.11 documentation + Preprocessing data for QSARtuna — QSARtuna 2.7.11 documentation @@ -21,8 +21,8 @@ - - + + @@ -34,7 +34,7 @@ - QPTUNA + QSARtuna
                                                  @@ -47,7 +47,7 @@

                                                  Documentation:

                                      @@ -1197,7 +1197,7 @@

                                      Performing data transform within the Datareaderlog_transform_base set to perform a Log10, log_transform_negative=LogNegative.TRUE, and a log_transform_unit_conversion of 6 reproduces the pXC50 conversion we had pre-computed in the file.

                                      NB: the log transformation is reversed at inference. I.e. only the model is trained with the transformed values, any predictions will be output to the original scale as provided in user input data.

                                      -

                                      Qptuna also implements the reverse of the transform using reverse_transform, so that users can obtain values on the original scale at inference, like so:

                                      +

                                      QSARtuna also implements the reverse of the transform using reverse_transform, so that users can obtain values on the original scale at inference, like so:

                                      [18]:
                                       
                                      @@ -1245,12 +1245,12 @@

                                      Definition of the PTRResponse column values (e.g. pXC50) are converted into the ideal y-label probability using cdf with different bioactivity thresholds and standard deviation (SD) values. E.g. a response column of 5.1, would be assigned a PTR of 0.63 given a cutoff of 5.0 and σ (SD) of 0.3. The case when SD is 0 corresponds to the traditional classification at a cutoff scenario.

                                      PTR hence represents the activity in a framework in-between the classification and regression architecture, with philosophical differences from either approach. Compared to classification, this approach enables better representation of factors increasing/decreasing inactivity. Conversely, one can utilize all data (even delimited/operand/censored data far from a cut-off) at the same time as taking into account the granularity around the cut-off, compared to a conventional regression framework. Thereby, PTR combines characteristics from both classification and regression settings.

                                      -

                                      NB: Qptuna treats the PTR values as the ‘ideal y-label’, i.e. they become the new response column values for train/test/validation performance evaluation, since it represents the ideal case, where experimental error is taken into account and model outputs most closely reflect this.

                                      +

                                      NB: QSARtuna treats the PTR values as the ‘ideal y-label’, i.e. they become the new response column values for train/test/validation performance evaluation, since it represents the ideal case, where experimental error is taken into account and model outputs most closely reflect this.

                                      [1] https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00539-7#Sec12

                                      -
                                      -

                                      Qptuna implementation of the PTR

                                      -

                                      PTR is also easily applied within the Datareader class by specifying the PTR options to the Qptuna datareader. E.g:

                                      +
                                      +

                                      QSARtuna implementation of the PTR

                                      +

                                      PTR is also easily applied within the Datareader class by specifying the PTR options to the QSARtuna datareader. E.g:

                                      [19]:
                                       
                                      @@ -1420,7 +1420,7 @@

                                      Qptuna implementation of the PTR

                                      Conclusion: PTR calculation, evaluation of experimental reproducability & best practices

                                      -

                                      In this section, we next also look at how the PTR within the Qptuna datareader is implemented, and show how a user can assess the experimental reproducability/uncertainty for their query dataset.

                                      +

                                      In this section, we next also look at how the PTR within the QSARtuna datareader is implemented, and show how a user can assess the experimental reproducability/uncertainty for their query dataset.

                                      First we start with imports and define the PTR function using stats.norm.cdf from scipy

                                      [23]:
                                      @@ -1651,9 +1651,9 @@ 

                                      Conclusion: PTR calculation, evaluation of experimental reproducability &

                                      -/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.
                                      +/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.
                                         warnings.warn(msg, UserWarning)
                                      -/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qptuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.
                                      +/Users/kljk345/Library/Caches/pypoetry/virtualenvs/qsartuna-_QsKTRFT-py3.10/lib/python3.10/site-packages/seaborn/distributions.py:316: UserWarning: Dataset has 0 variance; skipping density estimate. Pass `warn_singular=False` to disable this warning.
                                         warnings.warn(msg, UserWarning)
                                       
                                      @@ -1676,8 +1676,8 @@

                                      Conclusion: PTR calculation, evaluation of experimental reproducability &