├── AttentionMap.png ├── CS-MIL_Docker ├── CS-MIL_docker_commandline.txt ├── Dockerfile ├── requirements.txt └── src │ ├── DeepAttnMISL_CS_MIL.py │ ├── GCA512_0411_train4w.yaml │ ├── MIL_dataloader_csv_MAg_clustering_pair_stack.py │ ├── arguments.py │ ├── augmentations │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── byol_aug.cpython-36.pyc │ │ ├── byol_aug.cpython-38.pyc │ │ ├── eval_aug.cpython-36.pyc │ │ ├── eval_aug.cpython-38.pyc │ │ ├── simclr_aug.cpython-36.pyc │ │ ├── simclr_aug.cpython-38.pyc │ │ ├── simsiam_aug.cpython-36.pyc │ │ └── simsiam_aug.cpython-38.pyc │ ├── byol_aug.py │ ├── eval_aug.py │ ├── gaussian_blur.py │ ├── simclr_aug.py │ ├── simsiam_aug.py │ └── swav_aug.py │ ├── datasets │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── random_dataset.cpython-36.pyc │ │ └── random_dataset.cpython-38.pyc │ └── random_dataset.py │ ├── models │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── byol.cpython-36.pyc │ │ ├── byol.cpython-38.pyc │ │ ├── simclr.cpython-36.pyc │ │ ├── simclr.cpython-38.pyc │ │ ├── simsiam.cpython-36.pyc │ │ └── simsiam.cpython-38.pyc │ ├── backbones │ │ ├── TCGA_eval_onehot.py │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-36.pyc │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── cifar_resnet_1.cpython-36.pyc │ │ │ ├── cifar_resnet_1.cpython-38.pyc │ │ │ ├── cifar_resnet_2.cpython-36.pyc │ │ │ └── cifar_resnet_2.cpython-38.pyc │ │ ├── cifar_resnet_1.py │ │ └── cifar_resnet_2.py │ ├── byol.py │ ├── simclr.py │ ├── simsiam.py │ └── swav.py │ ├── optimizers │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── larc.cpython-36.pyc │ │ ├── larc.cpython-38.pyc │ │ ├── lars.cpython-36.pyc │ │ ├── lars.cpython-38.pyc │ │ ├── lars_simclr.cpython-36.pyc │ │ ├── lars_simclr.cpython-38.pyc │ │ ├── lr_scheduler.cpython-36.pyc │ │ └── lr_scheduler.cpython-38.pyc │ ├── larc.py │ ├── lars.py │ ├── lars_simclr.py │ └── lr_scheduler.py │ ├── run_inference.py │ └── tools │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── __init__.cpython-38.pyc │ ├── accuracy.cpython-36.pyc │ ├── accuracy.cpython-38.pyc │ ├── average_meter.cpython-36.pyc │ ├── average_meter.cpython-38.pyc │ ├── file_exist_fn.cpython-36.pyc │ ├── file_exist_fn.cpython-38.pyc │ ├── knn_monitor.cpython-36.pyc │ ├── knn_monitor.cpython-38.pyc │ ├── logger.cpython-36.pyc │ ├── logger.cpython-38.pyc │ ├── plotter.cpython-36.pyc │ └── plotter.cpython-38.pyc │ ├── accuracy.py │ ├── average_meter.py │ ├── file_exist_fn.py │ ├── knn_monitor.py │ ├── logger.py │ └── plotter.py ├── Cross-modality.png ├── Cross-scale.png ├── Cross_modality.png ├── Emb_Clustering_Code ├── LICENSE ├── MicrosoftVision.ResNet50.tar ├── arguments.py ├── configs │ └── GCA512_0411_train4w.yaml ├── create_kmeans_features_local_multi-resolution.py ├── create_kmeans_features_local_singleresolution.py ├── datasets │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-36.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── random_dataset.cpython-36.pyc │ │ └── random_dataset.cpython-38.pyc │ └── random_dataset.py ├── get_features_simsiam_1024.py ├── get_features_simsiam_256.py ├── get_features_simsiam_512.py ├── get_features_simsiam_multi-resolution.py ├── main_mixprecision.py └── optimizers │ ├── __init__.py │ ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── __init__.cpython-38.pyc │ ├── larc.cpython-36.pyc │ ├── larc.cpython-38.pyc │ ├── lars.cpython-36.pyc │ ├── lars.cpython-38.pyc │ ├── lars_simclr.cpython-36.pyc │ ├── lars_simclr.cpython-38.pyc │ ├── lr_scheduler.cpython-36.pyc │ └── lr_scheduler.cpython-38.pyc │ ├── larc.py │ ├── lars.py │ ├── lars_simclr.py │ └── lr_scheduler.py ├── LICENSE ├── Pipeline.png ├── README.md ├── Toydataset.png ├── ToydatasetResults.png ├── Toydataset_Code ├── cs-mil-toydataset │ ├── AttentionMapping_dataset1.py │ ├── AttentionMapping_dataset2.py │ ├── Background_filter.py │ ├── Boxplot_dataset1.py │ ├── Boxplot_dataset1_classmark.py │ ├── Boxplot_dataset2_classmark.py │ ├── Classifier_model_MAg.py │ ├── DeepAttnMISL_model.py │ ├── DeepAttnMISL_model_no21.py │ ├── DeepAttnMISL_model_no21_attentionscore.py │ ├── DeepAttnMISL_model_no21_withResnet.py │ ├── GetDataList.py │ ├── LICENSE │ ├── MILDataset.py │ ├── MIL_dataloader_csv_data1.py │ ├── MIL_dataloader_csv_data2.py │ ├── MIL_dataloader_csv_image.py │ ├── MIL_dataloader_image.py │ ├── MIL_global_Stage1_Testing_all.py │ ├── MIL_main.py │ ├── MIL_main_DeepSurv.py │ ├── MIL_main_DeepSurv_batch_dataset1_getattention.py │ ├── MIL_main_DeepSurv_batch_dataset2_getattention.py │ ├── MIL_main_DeepSurv_dataset1.py │ ├── MIL_main_DeepSurv_dataset2.py │ ├── Patch_select_MIL_dataloader_csv_MAg_clustering_check_stack.py │ ├── Patch_select_MIL_global_Stage1_attention_cross.py │ ├── ROCAUC_dataset1_classmark.py │ ├── ROCAUC_dataset2_classmark.py │ ├── __init__.py │ ├── create_kmeans.py │ ├── data_split.py │ ├── data_split_tranvalbalanced.py │ ├── dataloader.py │ └── mnist_bags_loader.py └── data_processing │ ├── MIL_bag_generation.py │ ├── MIL_bag_generation_forattention_data1.py │ ├── MIL_bag_generation_forattention_data2.py │ ├── MIL_main_DeepSurv_batch_dataset1_getattention.py │ └── MIL_main_DeepSurv_batch_dataset2_getattention.py └── Train_Test_Code ├── Background_filter.py ├── Classifier_model_MAg.py ├── DeepAttnMISL_model.py ├── DeepAttnMISL_model_no21.py ├── GetDataList.py ├── MILDataset.py ├── MIL_dataloader.py ├── MIL_dataloader_csv.py ├── MIL_dataloader_csv_MAg.py ├── MIL_dataloader_csv_MAg_clustering.py ├── MIL_dataloader_csv_MAg_clustering_pair_stack.py ├── MIL_dataloader_csv_clustering.py ├── MIL_dataloader_csv_clustering_pair_stack.py ├── MIL_global_Stage1_Testing.py ├── MIL_global_Stage1_Training.py ├── 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