CrossPropertyTL

This repository contains the code for performing cross-property deep transfer learning to predict materials properties using elemental fractions (EF), physical attributes (PA) or extracted features as the model input. The code provides the following functions:

• Train a ElemNet model on a given dataset.
• Use a pre-trained ElemNet model to perform transfer learning on a given target dataset.
• Predict material properties of new compounds with a pre-trained ElemNet model.

It is recommended to train large dataset (e.g. OQMD, MP) from scratch (SC) and small datasets (DFT-computed or experimental datasets) using transfer learning methods.

Please look at the Nature Communications 2021 paper (reference below) for details of the cross-property deep transfer learning framework.

Installation Requirements

The basic requirement for using the files are a Python 3.6.3 Jupyter environment with the packages listed in requirements.txt. It is advisable to create an virtual environment with the correct dependencies.

The work related experiments was performed on Linux Fedora 7.9 Maipo. The code should be able to work on other Operating Systems as well but it has not been tested elsewhere.

Source Files

Here is a brief description about the folder content:

• elemnet: code for training ElemNet model from scratch or using a pretrained ElemNet model to perform transfer learning.

• data: 39 different datasets used for training ElemNet model.

• representation: Jupyter Notebook to perform feature extraction from a specific layer of pre-trained ElemNet model. We have also provided the code to convert chemical formula of a compound into elemental fractions and physical attributes.

• prediction: Jupyter Notebook to perform prediction using the pre-trained ElemNet model.

Example Use

Create a customized dataset

To use different representations (such as elemental fractions, physical attributes or extracted features) as input to ElemNet, you will need to create a customized dataset using a .csv file. You can prepare a customized dataset in the following manner:

1. Prepare a .csv file which contain two columns. The first column contains the compound, and the second column contains the value of target property as shown below:

pretty_comp	target property
KH2N	-0.40
NiTeO4	-0.82

2. Use the Jupyter Notebook in representation folder to pre-process and convert the first column of the .csv file into elemental fraction, physical attributes or to extract features using a pre-trained ElemNet model. Above example when converted into elemental fraction becomes as follows:

pretty_comp	H	...	Pu	target property
KH2N	0.5	...	0	-0.40
NiTeO4	0	...	0	-0.82

3. Split the customized dataset into train, validation and test set. We have used train_test_split function of the sklearn library with a random seed of 1234567 to perform the train\validation\test split in our work.

We have provided an example of customized datasets in the repository: data/sample. Here we have converted the first column of the .csv file into elemental fractions. Note that this is required for both training and predicting.

Run ElemNet model

The code to run the ElemNet model is provided in the elemnet folder. In order to run the model you can pass a sample config file to the dl_regressors_tf2.py from inside of your elemnet directory:

python dl_regressors_tf2.py --config_file sample/sample-run_example_tf2.config

The config file defines all the related hyperparameters associated with the model training and model testing such as loss_type, training_data_path, val_data_path, test_data_path, label, input_type, etc. If you want to randomly initialize the weight of the last layer of the trained model as done in the work, set the last_layer_with_weight hyperparameter of the config file as false.

For transfer learning, you need to set 'model_path' [e.g. model/sample_model].

To add customized input_type, please make changes to the data_utils.py as follows:

1. Add a new array with the required columns (preferably near the place where other arrays are defined). For example:

a	b	c	d	pred
0.1	0.3	0.5	0.7	0.9
0.2	0.4	0.6	0.8	1.0

If you have the following .csv file where you have to use columns a, b, c, d to predict pred, you can add new_input = ['a','b','c','d'] to the file.

2. Add the array variable to the input_atts dictionary so that it can be used with input_type of the config (and pred used with label). For example:

   input_atts = {'new_input':new_input, 'elements':elements, ... , 'input32':input32}

After training, you will get the following files:

• The output log from the training will be saved in the log folder as log/sample-run_example_tf2.log file.

• The trained model will be saved in model folder as model/sample-run_example_tf2.h5 and model/sample-run_example_tf2.json. .h5 file contains the weights values and .json contains the model's architecture.
  
  We also save the model in a newer version of the TensorFlow SavedModel format in sample folder as sample-run_example_tf2 folder. The model architecture, and training configuration (including the optimizer, losses, and metrics) are stored in saved_model.pb. The weights are saved in the variables/ directory. For more information see here
  
  You can try our code with the weights trained in our work on customized dataset/provided dataset from here

The above command runs a default task with an early stopping of 200 epochs on small dataset of target property (formation energy). This sample task can be used without any changes so that the user can get an idea of how the ElemNet model works. The sample task should take about 1-2 minute on an average when a GPU is available and give a test set MAE of 0.29-0.32 eV after the model training is finished.

Note: Your results may vary given the stochastic nature of the algorithm or evaluation procedure, the size of the dataset, the target property to perform the regression modelling for or differences in numerical precision. Consider running the example a few times and compare the average outcome.

Developer Team

The code was developed by Vishu Gupta from the CUCIS group at the Electrical and Computer Engineering Department at Northwestern University.

Publication

1. Vishu Gupta, Kamal Choudhary, Francesca Tavazza, Carelyn Campbell, Wei-keng Liao, Alok Choudhary, and Ankit Agrawal, “Cross-property deep transfer learning framework for enhanced predictive analytics on small materials data,” Nature Communications, 12, 6595 (2021) [DOI] [PDF]

@article{gupta2021crossproperty,
  title={Cross-property deep transfer learning framework for enhanced predictive analytics on small materials data},
  author={Gupta, Vishu and Choudhary, Kamal and Tavazza, Francesca and Campbell, Carelyn and Liao, Wei-keng and Choudhary, Alok and Agrawal, Ankit},
  journal={Nature Communications},
  volume={12},
  number={6595},
  year={2021},
  publisher={Nature Publishing Group}
}

Acknowledgements

The open-source implementation of ElemNet here provided significant initial inspiration for the structure of this code-base.

Disclaimer

The research code shared in this repository is shared without any support or guarantee on its quality. However, please do raise an issue if you find anything wrong and I will try my best to address it.

email: [email protected]

Copyright (C) 2021, Northwestern University.

See COPYRIGHT notice in top-level directory.

Funding Support

This work was performed under the following financial assistance award 70NANB19H005 from U.S. Department of Commerce, National Institute of Standards and Technology as part of the Center for Hierarchical Materials Design (CHiMaD). Partial support is also acknowledged from DOE awards DE-SC0014330, DE-SC0019358 and DE-SC0021399.