├── .gitignore ├── CoNIC ├── README.md ├── inference.py ├── misc_util.py ├── net_desc.py ├── requirements.txt └── visualisation.py ├── DSMIL ├── MIL_CV.py ├── attention_map.py ├── compute_feats.py ├── deepzoom_tiler.py ├── dsmil.py ├── env.yml ├── readme.md ├── simclr │ ├── config.yaml │ ├── data_aug │ │ ├── dataset_wrapper.py │ │ └── gaussian_blur.py │ ├── loss │ │ └── nt_xent.py │ ├── models │ │ ├── baseline_encoder.py │ │ └── resnet_simclr.py │ ├── run.py │ └── simclr.py └── t_test.py ├── HIPT ├── 1-Hierarchical-Pretraining │ ├── From ViT-16 to ViT-256.ipynb │ ├── eval_copy_detection.py │ ├── eval_image_retrieval.py │ ├── eval_knn.py │ ├── eval_linear.py │ ├── eval_video_segmentation.py │ ├── hubconf.py │ ├── main_dino.py │ ├── main_dino4k.py │ ├── run_with_submitit.py │ ├── utils.py │ ├── video_generation.py │ ├── vision_transformer.py │ ├── vision_transformer4k.py │ └── visualize_attention.py ├── 2-Weakly-Supervised-Subtyping │ ├── Evaluation-Classification.ipynb │ ├── Model Walkthrough.ipynb │ ├── generate_splits.py │ ├── main.py │ ├── models │ │ ├── model_clam.py │ │ ├── model_cluster.py │ │ ├── model_dgcn.py │ │ ├── model_dsmil.py │ │ ├── model_hierarchical_mil.py │ │ ├── model_mil.py │ │ ├── model_utils.py │ │ └── resnet_custom.py │ ├── utils │ │ ├── core_utils.py │ │ ├── eval_utils.py │ │ └── utils.py │ └── wsi_core │ │ ├── WholeSlideImage.py │ │ ├── batch_process_utils.py │ │ ├── util_classes.py │ │ └── wsi_utils.py ├── HIPT.py ├── HIPT_4K │ ├── HIPT_4K Inference + Attention Visualization.ipynb │ ├── attention_visualization_utils.py │ ├── hipt_4k.py │ ├── hipt_heatmap_utils.py │ ├── hipt_model_utils.py │ ├── vision_transformer.py │ └── vision_transformer4k.py ├── HIPT_inference.py ├── generate_heatmaps.py ├── generate_patch_embeddings.py ├── generate_region_embeddings.py ├── parse_4k.py ├── readme.md └── requirements.txt ├── QC_model └── README.md ├── README.md ├── imgs └── pipeline.png └── patch_extraction ├── README.md ├── config.yaml ├── modules 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