├── .gitignore ├── CLAM ├── LICENSE.md ├── build_preset.py ├── create_heatmaps.py ├── create_patches.py ├── create_patches_fp.py ├── create_splits_seq.py ├── dataset_csv │ ├── tumor_subtyping_dummy_clean.csv │ └── tumor_vs_normal_dummy_clean.csv ├── dataset_modules │ ├── __init__.py │ ├── dataset_generic.py │ ├── dataset_h5.py │ └── wsi_dataset.py ├── docs │ ├── CLAM1.jpg │ ├── CLAM1.tiff │ ├── CLAM2.jpg │ ├── INSTALLATION.md │ ├── README.md │ ├── README_old.md │ ├── ani.gif │ ├── clam-logo.png │ ├── fig-gh3.jpg │ └── fig-git-hm.jpg ├── env.yml ├── eval.py ├── extract_features.py ├── extract_features_fp.py ├── heatmaps │ ├── configs │ │ └── config_template.yaml │ ├── demo │ │ ├── ckpts │ │ │ └── s_0_checkpoint.pt │ │ └── slides │ │ │ ├── C3L-01663-21.svs │ │ │ └── C3L-03262-22.svs │ └── process_lists │ │ └── heatmap_demo_dataset.csv ├── index.html ├── index.html.1 ├── main.py ├── models │ ├── __init__.py │ ├── builder.py │ ├── model_clam.py │ ├── model_mil.py │ ├── resnet_custom_dep.py │ └── timm_wrapper.py ├── presets │ ├── bwh_biopsy.csv │ ├── bwh_resection.csv │ ├── tcga.csv │ └── tcga_nsclc.csv ├── save_patches.py ├── splits │ ├── task_1_tumor_vs_normal_75 │ │ ├── splits_0.csv │ │ ├── splits_0_bool.csv │ │ ├── splits_0_descriptor.csv │ │ ├── splits_1.csv │ │ ├── splits_1_bool.csv │ │ ├── splits_1_descriptor.csv │ │ ├── splits_2.csv │ │ ├── splits_2_bool.csv │ │ ├── splits_2_descriptor.csv │ │ ├── splits_3.csv │ │ ├── splits_3_bool.csv │ │ ├── splits_3_descriptor.csv │ │ ├── splits_4.csv │ │ ├── splits_4_bool.csv │ │ ├── splits_4_descriptor.csv │ │ ├── splits_5.csv │ │ ├── splits_5_bool.csv │ │ ├── splits_5_descriptor.csv │ │ ├── splits_6.csv │ │ ├── splits_6_bool.csv │ │ ├── splits_6_descriptor.csv │ │ ├── splits_7.csv │ │ ├── splits_7_bool.csv │ │ ├── splits_7_descriptor.csv │ │ ├── splits_8.csv │ │ ├── splits_8_bool.csv │ │ ├── splits_8_descriptor.csv │ │ ├── splits_9.csv │ │ ├── splits_9_bool.csv │ │ └── splits_9_descriptor.csv │ └── task_2_tumor_subtyping_50 │ │ ├── splits_0.csv │ │ ├── splits_0_bool.csv │ │ ├── splits_0_descriptor.csv │ │ ├── splits_1.csv │ │ ├── splits_1_bool.csv │ │ ├── splits_1_descriptor.csv │ │ ├── splits_2.csv │ │ ├── splits_2_bool.csv │ │ ├── splits_2_descriptor.csv │ │ ├── splits_3.csv │ │ ├── splits_3_bool.csv │ │ ├── splits_3_descriptor.csv │ │ ├── splits_4.csv │ │ ├── splits_4_bool.csv │ │ ├── splits_4_descriptor.csv │ │ ├── splits_5.csv │ │ ├── splits_5_bool.csv │ │ ├── splits_5_descriptor.csv │ │ ├── splits_6.csv │ │ ├── splits_6_bool.csv │ │ ├── splits_6_descriptor.csv │ │ ├── splits_7.csv │ │ ├── splits_7_bool.csv │ │ ├── splits_7_descriptor.csv │ │ ├── splits_8.csv │ │ ├── splits_8_bool.csv │ │ ├── splits_8_descriptor.csv │ │ ├── splits_9.csv │ │ ├── splits_9_bool.csv │ │ └── splits_9_descriptor.csv ├── test.py ├── utils │ ├── __init__.py │ ├── constants.py │ ├── core_utils.py │ ├── eval_utils.py │ ├── file_utils.py │ ├── transform_utils.py │ └── utils.py ├── vis_utils │ ├── __init__.py │ └── heatmap_utils.py └── wsi_core │ ├── WholeSlideImage.py │ ├── __init__.py │ ├── batch_process_utils.py │ ├── util_classes.py │ └── wsi_utils.py ├── README.md ├── config ├── e2e │ ├── r18_brca_subtyping.yaml │ ├── r18_brca_survival.yaml │ ├── r18_panda.yaml │ ├── r50_brca_subtyping.yaml │ └── r50_panda.yaml └── feat │ ├── fm_panda.yaml │ ├── fm_subtyping.yaml │ └── fm_survival.yaml ├── datasets ├── __init__.py ├── data_utils.py ├── dataloader.py ├── dataset_feat.py └── dataset_img.py ├── doc ├── abx.png └── intro.png ├── engines ├── __init__.py ├── base_engine.py ├── common_mil.py ├── e2e.py └── metrics.py ├── labels ├── panda.csv ├── subtyping_tcga_brca.csv ├── subtyping_tcga_brca_resample.csv └── survival_tcga_brca_3fold │ ├── fold_0.csv │ ├── fold_1.csv │ └── fold_2.csv ├── main.py ├── modules ├── __init__.py ├── abmil.py ├── abmilx.py ├── chief.py ├── clam.py ├── dsmil.py ├── dtfd.py ├── e2e.py ├── e2e_pooling.py ├── emb_position.py ├── encoders.py ├── gigap.py ├── longnet │ ├── __init__.py │ ├── architecture │ │ ├── __init__.py │ │ ├── config.py │ │ ├── decoder.py │ │ ├── encoder.py │ │ ├── encoder_decoder.py │ │ ├── retnet.py │ │ └── utils.py │ ├── component │ │ ├── __init__.py │ │ ├── custom_dilated_attention.py │ │ ├── custom_flash_attention.py │ │ ├── custom_multihead_attention.py │ │ ├── dilated_attention.py │ │ ├── droppath.py │ │ ├── embedding.py │ │ ├── feedforward_network.py │ │ ├── flash_attention.py │ │ ├── gate_linear_unit.py │ │ ├── multihead_attention.py │ │ ├── multiscale_retention.py │ │ ├── multiway_network.py │ │ ├── relative_position_bias.py │ │ ├── rms_norm.py │ │ ├── utils.py │ │ ├── xmoe │ │ │ ├── __init__.py │ │ │ ├── global_groups.py │ │ │ ├── moe_layer.py │ │ │ └── routing.py │ │ └── xpos_relative_position.py │ └── model │ │ ├── BEiT3.py │ │ ├── LongNet.py │ │ ├── LongNetConfig.py │ │ └── __init__.py ├── mean_max.py ├── nystrom_attention.py ├── rrt.py ├── topk │ ├── __init__.py │ ├── functional.py │ ├── logarithm.py │ ├── polynomial │ 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