├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── data_configs ├── pure_tcga │ ├── train_pure_tcga.csv │ └── val_pure_tcga.csv ├── test_adeno.csv ├── test_alldata.csv ├── test_refined.csv ├── test_small_lesion.csv ├── test_squamous.csv ├── test_tcga.csv ├── test_tcga_tissue.csv ├── train_adeno.csv ├── train_alldata.csv ├── train_eighth.csv ├── train_half.csv ├── train_quarter.csv ├── train_refined.csv ├── train_squamous.csv ├── val_adeno.csv ├── val_alldata.csv ├── val_dummy.csv ├── val_refined.csv └── val_squamous.csv ├── misc ├── tcga_vahadane.pkl └── tmuh_vahadane.pkl ├── poetry.lock ├── pyproject.toml ├── slide_data └── .gitignore ├── tools ├── calc_auc.R ├── compare_auc.R ├── draw_roc.py ├── gen_bootstrap_aucs.R └── print_scores.py ├── train_configs ├── config_mil_em_4x.yaml ├── config_mil_k1_10x.yaml ├── config_mil_k1_2x.yaml ├── config_mil_k1_4x.yaml ├── config_mil_k3_4x.yaml ├── config_mil_k5_4x.yaml ├── config_wholeslide_10x.yaml ├── config_wholeslide_1x.yaml ├── config_wholeslide_2x.yaml ├── config_wholeslide_4x.yaml ├── config_wholeslide_4x_adeno.yaml ├── config_wholeslide_4x_eighth.yaml ├── config_wholeslide_4x_gap.yaml ├── config_wholeslide_4x_half.yaml ├── config_wholeslide_4x_quarter.yaml ├── config_wholeslide_4x_resnet34.yaml ├── config_wholeslide_4x_squamous.yaml ├── pure_tcga │ └── config_pure_tcga_wholeslide_4x.yaml └── throughput │ ├── config_throughput_11000_r50_mil.yaml │ ├── config_throughput_11000_r50_wholeslide.yaml │ ├── config_throughput_11000_r50_wholeslide_noopt.yaml │ ├── config_throughput_21500_r50_mil.yaml │ ├── config_throughput_21500_r50_wholeslide.yaml │ └── config_throughput_21500_r50_wholeslide_noopt.yaml └── whole_slide_cnn ├── __init__.py ├── dataloader.py ├── dataset.py ├── huge_layer_wrapper.py ├── model.py ├── post_train.py ├── post_train_model.py ├── resnet.py ├── test.py ├── train.py ├── utils.py └── vahadane.py /.gitattributes: -------------------------------------------------------------------------------- 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