├── CODEOWNERS ├── LICENSE.txt ├── README.md ├── assets ├── example.tif └── main_figure.png ├── conf.yaml ├── conf ├── extract_features │ ├── feature_extractor │ │ └── iBOTViTBasePANCAN.yaml │ ├── slide_config.yaml │ ├── slide_dataset │ │ ├── camelyon16_full.yaml │ │ ├── tcga_brca.yaml │ │ ├── tcga_coad.yaml │ │ ├── tcga_kich.yaml │ │ ├── tcga_kirc.yaml │ │ ├── tcga_kirp.yaml │ │ ├── tcga_luad.yaml │ │ ├── tcga_lusc.yaml │ │ ├── tcga_ov.yaml │ │ ├── tcga_paad.yaml │ │ ├── tcga_read.yaml │ │ └── tcga_stad.yaml │ ├── tile_config.yaml │ └── tile_dataset │ │ ├── camelyon17_wilds.yaml │ │ └── nct_crc.yaml ├── slide_level_task │ └── cross_validation │ │ ├── config.yaml │ │ ├── model │ │ ├── abmil.yaml │ │ ├── chowder.yaml │ │ ├── dsmil.yaml │ │ ├── hipt_mil.yaml │ │ ├── mean_pool.yaml │ │ └── trans_mil.yaml │ │ ├── task │ │ ├── camelyon16_train_tumor_prediction.yaml │ │ ├── tcga_brca_histological_subtype_prediction.yaml │ │ ├── tcga_brca_hrd_prediction.yaml │ │ ├── tcga_brca_molecular_subtype_prediction.yaml │ │ ├── tcga_brca_os_prediction.yaml │ │ ├── tcga_coad_os_prediction.yaml │ │ ├── tcga_crc_msi_prediction.yaml │ │ ├── tcga_luad_os_prediction.yaml │ │ ├── tcga_lusc_os_prediction.yaml │ │ ├── tcga_nsclc_cancer_subtype_prediction.yaml │ │ ├── tcga_ov_hrd_prediction.yaml │ │ ├── tcga_paad_os_prediction.yaml │ │ ├── tcga_rcc_cancer_subtype_prediction.yaml │ │ └── tcga_stad_msi_prediction.yaml │ │ └── test_ncv.yaml └── tile_level_task │ └── linear_evaluation │ └── config.yaml ├── dev_tools ├── linting.sh └── run_tests.sh ├── notebooks └── phikon_tutorial.ipynb ├── pylintrc ├── requirements-tests.txt ├── requirements.txt ├── rl_benchmarks ├── __init__.py ├── constants.py ├── datasets │ ├── __init__.py │ ├── slides_classification │ │ ├── __init__.py │ │ ├── camelyon16.py │ │ ├── core.py │ │ └── tcga.py │ └── tiles_classification │ │ ├── __init__.py │ │ ├── camelyon17_wilds.py │ │ └── nct_crc.py ├── losses │ ├── __init__.py │ ├── bce_with_logits_loss.py │ ├── cox_loss.py │ └── cross_entropy_loss.py ├── metrics │ ├── __init__.py │ ├── classification_metrics.py │ └── survival_metrics.py ├── models │ ├── __init__.py │ ├── feature_extractors │ │ ├── __init__.py │ │ ├── core.py │ │ ├── encoders │ │ │ ├── __init__.py │ │ │ ├── vision_transformer.py │ │ │ └── weight_init.py │ │ ├── ibot_vit.py │ │ └── utils.py │ └── slide_models │ │ ├── __init__.py │ │ ├── abmil.py │ │ ├── chowder.py │ │ ├── dsmil.py │ │ ├── hiptmil.py │ │ ├── meanpool.py │ │ ├── transmil.py │ │ └── utils │ │ ├── __init__.py │ │ ├── attention.py │ │ ├── extreme_layer.py │ │ ├── mlp.py │ │ └── tile_layers.py ├── trainers │ ├── __init__.py │ ├── base_trainer.py │ ├── torch_trainer.py │ └── utils.py ├── utils │ ├── __init__.py │ ├── cross_validation.py │ ├── features.py │ ├── functional.py │ ├── linear_evaluation.py │ ├── loading.py │ ├── logging.py │ ├── serialization.py │ └── testing.py └── val_schemes │ ├── __init__.py │ ├── nested_cross_validation.py │ └── utils.py ├── scripts ├── extract_slide_features.sh ├── extract_tile_features.sh ├── slides_classification.sh └── tiles_classification.sh ├── setup.cfg ├── setup.py ├── tests ├── .gitkeep ├── __init__.py ├── conftest.py ├── datasets │ ├── test_features_loading.py │ └── test_slides_and_images_loading.py ├── losses │ └── test_losses.py ├── models │ ├── __init__.py │ ├── test_feature_extractors.py │ └── test_slide_models.py ├── test_constants.py └── val_schemes │ ├── test_utils.py │ └── test_val_schemes.py └── tools ├── __init__.py ├── extract_features ├── __init__.py ├── extract_slide_features.py └── extract_tile_features.py ├── slide_level_tasks ├── __init__.py ├── cross_validation.py └── get_results.py └── tile_level_tasks ├── __init__.py └── linear_evaluation.py /CODEOWNERS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/owkin/HistoSSLscaling/HEAD/CODEOWNERS 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