Merge pull request #231 from InnopolisUni/med_fix

Med fix

config/experiments/demo_med/KA_130923_fbFMFDe1_lung_description_decision.yaml

@@ -0,0 +1,8 @@
+# @package _global_
+defaults:
+  - override /models: classification/lung_description_decision.yaml
+  - override /datasets: classification/lung_description_decision_datamodule.yaml
+  - override /callbacks: lung_description_decision
+
+project: "lung_description_decision"
+task: "table-classification"

config/experiments/demo_med/KG_100323_ianfq90_lion_test.yaml

@@ -0,0 +1,19 @@
+# @package _global_
+defaults:
+  - override /models: semantic-segmentation/unet
+  - override /datasets: semantic-segmentation/segmentation_brain.yaml
+  - override /optimizers: lion.yaml
+  - override /augmentations_train: none
+  - override /augmentations_val: none
+  - override /augmentations_test: none
+  - override /losses: segmentation_losses.yaml
+
+models:
+  in_channels: 1
+project: "segmentation"
+task: "image-segmentation"
+random_seed: 42
+stop_param: 10
+epochs: 10
+weights_freq: 1
+batch_size: 4

config/experiments/demo_med/KG_230323_sjdv8f20_segformer.yaml

@@ -0,0 +1,26 @@
+# @package _global_
+defaults:
+  - override /models: semantic-segmentation/segformer_for_segmentation.yaml
+  - override /datasets: semantic-segmentation/segmentation_brain.yaml
+  - override /augmentations_train: none
+  - override /optimizers: adam.yaml
+  - override /augmentations_val: none
+  - override /augmentations_test: none
+  - override /losses: segmentation_losses.yaml
+  - override /callbacks: segmentation
+
+
+models:
+  num_channels: 1
+  num_labels: 1
+  retain_dim: True
+project: "segmentation"
+task: "image-segmentation"
+random_seed: 42
+stop_param: 3
+epochs: 3
+weights_freq: 1
+batch_size: 8
+accelerator: cpu # gpu
+#override hydra/job_logging: stdout
+

config/experiments/demo_med/SK_100923_unet_brain_mri.yaml

@@ -0,0 +1,17 @@
+# @package _global_
+defaults:
+  - override /models: semantic-segmentation/unet
+  - override /datasets: semantic-segmentation/segmentation_brain.yaml
+  - override /augmentations_train: none #segmentation_stroke.yaml
+  - override /augmentations_val: none
+  - override /augmentations_test: none
+  - override /losses: segmentation_losses.yaml
+models:
+  in_channels: 1
+project: "segmentation"
+task: "image-segmentation-complexing"
+random_seed: 42
+stop_param: 10
+epochs: 300
+weights_freq: 1
+batch_size: 10

config/experiments/demo_med/SK_180822_qmciwj41_unet_brain.yaml

@@ -0,0 +1,17 @@
+# @package _global_
+defaults:
+  - override /models: semantic-segmentation/unet
+  - override /datasets: semantic-segmentation/segmentation_brain.yaml
+  - override /augmentations_train: none #segmentation_stroke.yaml
+  - override /augmentations_val: none
+  - override /augmentations_test: none
+  - override /losses: segmentation_losses.yaml
+models:
+  in_channels: 1
+project: "segmentation"
+task: "image-segmentation"
+random_seed: 42
+stop_param: 10
+epochs: 300
+weights_freq: 1
+batch_size: 10

config/experiments/demo_med/SK_180822_qwefnew31_yolov5_lungs.yaml

@@ -0,0 +1,12 @@
+# @package _global_
+defaults:
+  - override /models: detection/yolov5
+  - override /datasets: detection/detection_lungs
+
+
+project: "lungs"
+task: "image-detection"
+random_seed: 43
+epochs: 300
+batch_size: 2
+weights_freq: 1

config/experiments/demo_med/SK_180822_qwefnew31_yolov5_lungs_seg.yaml

@@ -0,0 +1,12 @@
+# @package _global_
+defaults:
+  - override /models: detection/yolov5_segmentation
+  - override /datasets: detection/detection_lungs
+
+
+project: "lungs"
+task: "image-detection"
+random_seed: 43
+epochs: 20
+batch_size: 2
+weights_freq: 1

config/experiments/demo_med/SK_210722_vfdkmls3_deeplabv3.yaml

@@ -0,0 +1,16 @@
+# @package _global_
+defaults:
+  - override /models: semantic-segmentation/deeplabv3plus.yaml
+  - override /datasets: semantic-segmentation/segmentation_arable.yaml
+  - override /optimizers: adam.yaml
+  - override /losses: segmentation_losses
+  - override /augmentations_train: none #segmentation_inference
+  - override /augmentations_val: none
+  - override /augmentations_test: none
+  - override /initializations: he
+
+project: "segmentation"
+task: "image-segmentation"
+random_seed: 42
+weights_freq: 1
+batch_size: 10

config/experiments/demo_med/SK_260722_frwmfrw4_faster_rcnn.yaml

@@ -0,0 +1,13 @@
+# @package _global_
+defaults:
+  - override /models: detection/faster_rcnn
+  - override /datasets: detection/detection_wheat
+  - override /optimizers: adam.yaml
+
+
+project: "wheat"
+task: "image-detection"
+random_seed: 42
+epochs: 300
+batch_size: 2
+weights_freq: 1

config/experiments/demo_med/example_image_segmentation_unet.yaml

@@ -6,13 +6,13 @@ defaults:
   - override /augmentations_val: none
   - override /augmentations_test: none
   - override /losses: segmentation_losses.yaml
+  - override /clear_ml: enabled
 models:
   in_channels: 1
 project: "segmentation"
 task: "image-segmentation"
 random_seed: 42
-stop_param: 10
 epochs: 35
 weights_freq: 1
 batch_size: 10
-ckpt_path: https://api.blackhole.ai.innopolis.university/pretrained/segmentation_unet_brain.pt
+ckpt_path: https://api.blackhole.ai.innopolis.university/pretrained/med/stroke/baseline/unet_fscore94.pt

config/experiments/demo_med/uwmadison/KG_150423_lsjdvnd8_segformer_uwmadison.yaml

@@ -0,0 +1,37 @@
+# @package _global_
+defaults:
+  - override /models: semantic-segmentation/segformer_for_segmentation.yaml
+  - override /datasets: semantic-segmentation/segmentation_uwmadison
+  - override /optimizers: lion.yaml
+  - override /augmentations_train: none
+  - override /augmentations_val: none
+  - override /augmentations_test: none
+  - override /callbacks: multiclass_segmentation
+  - override /losses: multiclass_segmentation_losses
+  - override /loggers: wandb
+
+models:
+  num_channels: 1
+  num_labels: 4
+  retain_dim: True
+
+optimizers:
+  lr: 0.0003
+
+project: "organs segmentation"
+task: "multiclass-image-segmentation"
+random_seed: 42
+weights_freq: 1
+batch_size: 16
+n_classes: 4
+epochs: 100
+accelerator: gpu
+override hydra/job_logging: stdout
+
+wandb:
+  enable: True
+  project: uw_madison
+  entity: "k-galliamov"
+  group: none
+  job_type: training
+

config/experiments/demo_med/uwmadison/KG_260423_boqe16_unet_uwmadison.yaml

@@ -0,0 +1,38 @@
+# @package _global_
+defaults:
+  - override /models: semantic-segmentation/unet
+  - override /datasets: semantic-segmentation/segmentation_uwmadison
+  - override /optimizers: adam.yaml
+  - override /augmentations_train: none
+  - override /augmentations_val: none
+  - override /augmentations_test: none
+  - override /callbacks: multiclass_segmentation
+  - override /losses: multiclass_segmentation_losses
+  - override /loggers: wandb
+
+n_classes: 4
+
+models:
+  in_channels: 1
+  classes: ${n_classes}
+  encoder_name: resnet34
+
+optimizers:
+  lr: 0.00477
+
+project: "organs segmentation"
+task: "multiclass-image-segmentation"
+random_seed: 42
+weights_freq: 1
+batch_size: 8
+epochs: 25
+accelerator: gpu
+devices: 1
+override hydra/job_logging: stdout
+
+wandb:
+ enable: True
+ project: uw_madison
+ entity: "k-galliamov"
+ job_type: training
+

config/experiments/demo_med/uwmadison/KG_260423_pgn135_deeplab_uwmadison.yaml

@@ -0,0 +1,41 @@
+# @package _global_
+defaults:
+  - override /models: semantic-segmentation/deeplabv3plus.yaml
+  - override /datasets: semantic-segmentation/segmentation_uwmadison
+  - override /optimizers: adam.yaml
+  - override /augmentations_train: ../augmentations/position/random_horizontal_flip.yaml
+  - override /augmentations_val: none
+  - override /augmentations_test: none
+  - override /callbacks: multiclass_segmentation
+  - override /losses: multiclass_segmentation_losses
+  - override /loggers: wandb
+
+models:
+  in_channels: 1
+  classes: 4
+  encoder_name: resnet34
+
+optimizers:
+  lr: 0.004313519324382217
+
+n_classes: 4
+project: "organs segmentation"
+task: "multiclass-image-segmentation"
+random_seed: 42
+weights_freq: 1
+ckpt_path: https://api.blackhole.ai.innopolis.university/pretrained/segmentation/uw_madison_deeplabv3plus.pickle
+
+# When tuning from the checkpoint, the number of epochs has to be set to at least
+#  the № of epoch on which the checkpoint was created + 1 (in this case, 39 + 1 = 40 would be a lower bound)
+epochs: 50
+batch_size: 128
+accelerator: gpu
+devices: 1
+override hydra/job_logging: stdout
+
+wandb:
+  enable: True
+  project: uw_madison
+  entity: "k-galliamov"
+  job_type: training
+

config/experiments/demo_nm/GR_050822_AGgrv2Dg_catboost_regressor_qm9.yaml

@@ -0,0 +1,10 @@
+# @package _global_
+defaults:
+  - override /models: regression/catboost_regression
+  - override /datasets: qm9
+  - override /callbacks: regression
+
+
+project: "qm9"
+task: "qsar-regression"
+random_seed: 42

config/experiments/demo_nm/GR_050822_AGgrv2Dg_catboost_regressor_qm9_non_pretrained.yaml

@@ -0,0 +1,18 @@
+# @package _global_
+defaults:
+  - override /initializations: random
+  - override /models: regression/catboost_regression
+  - override /datasets: qm9_2
+  - override /callbacks: regression
+
+
+
+project: "qm9"
+task: "qsar-regression"
+random_seed: 42
+
+# ckpt_path: https://api.blackhole.ai.innopolis.university/pretrained/catboost_regression_qm9.pickle
+
+
+models:
+    learning_rate: 0.1

config/experiments/demo_nm/GR_050822_AGgrv2Dg_catboost_regressor_qm9_pretrained.yaml

@@ -0,0 +1,13 @@
+# @package _global_
+defaults:
+  - initializations:
+  - override /models: regression/catboost_regression
+  - override /datasets: qm9_2
+  - override /callbacks: regression
+
+
+project: "qm9"
+task: "qsar-regression"
+random_seed: 42
+
+ckpt_path: https://api.blackhole.ai.innopolis.university/pretrained/catboost_regression_qm9.pickle

config/experiments/demo_nm/GR_061022_DkOLIn2s_vae_qm9_reverse.yaml

@@ -0,0 +1,18 @@
+# @package _global_
+defaults:
+  - override /models: text-vae/hier_vae.py
+  - override /datasets: qm9_selfies
+  - override /losses: vae
+
+
+experiment_name: "GR_061022_DkOLIn2s_vae_qm9_reverse"
+project: chem-vae
+task: text-vae-reverse
+random_seed: 42
+accelerator: cpu
+devices: 1
+batch_size: 128
+num_workers: 0
+
+datasets:
+  work_mode: reverse

config/experiments/demo_nm/GR_061022_skOLI42s_vae_qm9_forward.yaml

@@ -0,0 +1,18 @@
+# @package _global_
+defaults:
+  - override /models: text-vae/hier_vae.py
+  - override /datasets: qm9_selfies
+  - override /losses: vae
+
+
+experiment_name: "GR_061022_skOLI42s_vae_qm9_forward"
+project: chem-vae
+task: text-vae-forward
+random_seed: 42
+accelerator: cpu
+devices: 1
+batch_size: 128
+num_workers: 0
+
+datasets:
+  work_mode: forward

config/experiments/demo_nm/GR_070922_jLqZn8Wh_catboost_regressor_mcl1.yaml

@@ -0,0 +1,10 @@
+# @package _global_
+defaults:
+  - override /models: regression/catboost_regression
+  - override /datasets: mcl1
+  - override /callbacks: regression
+
+project: "mcl1"
+task: "qsar-regression"
+random_seed: 42
+# original_work_dir: ${hydra:runtime.cwd}

config/experiments/demo_nm/GR_160822_AsdDwgf2_catboost_active_learning_qm9.yaml

@@ -0,0 +1,16 @@
+# @package _global_
+defaults:
+  - override /models: regression/catboost_regression
+  - override /datasets: qm9
+  - override /callbacks: regression
+
+
+project: "qm9"
+task: "qsar-regression"
+random_seed: 42
+
+extra:
+  active_learning:
+    query_size: 100
+    epochs_num: 5
+    use_data_uncertainty: False