├── .gitignore ├── CITATION.cff ├── DATA ├── Cohort │ ├── basic.py │ ├── data.py │ ├── location.py │ └── utils.py ├── Database │ ├── data_aug.py │ ├── dataset.py │ ├── stain_norm.py │ └── utils.py ├── FileIO │ ├── h5_worker.py │ ├── pkl_worker.py │ ├── table_backends.py │ ├── utils.py │ └── wsi_backends.py └── Slide │ ├── collector │ ├── data_collector.py │ └── items.py │ └── concepts │ ├── WholeSlideImage.py │ ├── feature.py │ ├── patch.py │ ├── tissue.py │ └── utils.py ├── EXP ├── paras │ ├── cohort.py │ ├── dataset.py │ ├── env.py │ ├── optloss.py │ ├── slides.py │ └── trainer.py ├── pre_defined_settings │ └── scheduler.py ├── trainer │ ├── base.py │ ├── slide.py │ └── ssl.py └── workspace │ ├── env.py │ └── experiment.py ├── LICENSE ├── MODEL ├── Image │ ├── MIL │ │ ├── ABMIL │ │ │ ├── model.py │ │ │ ├── paras.py │ │ │ └── pl.py │ │ ├── DSMIL │ │ │ ├── model.py │ │ │ ├── paras.py │ │ │ └── pl.py │ │ ├── TransMIL │ │ │ ├── model.py │ │ │ ├── paras.py │ │ │ └── pl.py │ │ ├── init.py │ │ └── utils.py │ ├── Modules │ │ ├── CTransPath.py │ │ ├── NormalizationLayers.py │ │ └── NystromAttention.py │ ├── PL_protocol │ │ ├── MIL.py │ │ ├── basic.py │ │ └── utils.py │ ├── SSL │ │ ├── base_model.py │ │ ├── example.py │ │ ├── modules.py │ │ ├── paras.py │ │ ├── pl.py │ │ └── utils.py │ └── init.py ├── Metrics │ └── init.py └── OptLoss │ ├── LossModules │ ├── ND_Crossentropy.py │ ├── boundary_loss.py │ ├── coxloss.py │ ├── dice_loss.py │ ├── focal_loss.py │ ├── hausdorff.py │ ├── init.py │ └── lovasz_loss.py │ ├── OptModules │ ├── adafactor.py │ ├── adahessian.py │ ├── adamp.py │ ├── adamw.py │ ├── init.py │ ├── lookahead.py │ ├── nadam.py │ ├── novograd.py │ ├── radam.py │ ├── rmsprop_tf.py │ └── sgdp.py │ └── init.py ├── Notebooks ├── 0_machine_config.ipynb ├── 1_preprocessing.ipynb ├── 2_ssl.ipynb ├── 3_mil.ipynb ├── data_example.csv ├── machine_config.py ├── mil_run.py ├── pre_processing.py └── ssl_run.py ├── README.md ├── __init__.py ├── env.txt ├── env.yaml ├── 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