├── README.md ├── create_patches.py ├── create_splits.py ├── data_BRIGHT_three.xlsx ├── dataset_csv ├── BRIGHT_subtyping_six.csv └── BRIGHT_subtyping_three.csv ├── datasets ├── BatchWSI.py ├── dataset_generic.py ├── dataset_h5.py └── wsi_dataset.py ├── eval.py ├── feature_extraction ├── patch_extraction.py ├── patch_extraction.sh ├── patch_extraction_utils.py └── resnet_trunc.py ├── image └── readme │ └── framework.png ├── main.py ├── models ├── __init__.py ├── configs.py ├── model_MG_Trans.py ├── model_mil.py ├── model_utils.py ├── resnet_custom.py └── vision_transformer.py ├── patch_alignment.py ├── presets ├── bwh_biopsy.csv ├── bwh_resection.csv └── tcga.csv ├── scripts ├── creat_splits.sh ├── create_patches.sh ├── eval_MG_Trans_BRIGHT.sh └── train_MG_Trans_BRIGHT_cls3.sh ├── utils ├── __init__.py ├── core_utils.py ├── eval_utils.py ├── file_utils.py ├── loss_utils.py └── utils.py └── wsi_core ├── WholeSlideImage.py ├── batch_process_utils.py ├── util_classes.py └── wsi_utils.py 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