├── LICENSE ├── README.md ├── ROAM ├── compute_metric.py ├── configs │ ├── int_glioma_tumor_subtyping.ini │ └── int_glioma_tumor_subtyping_test.ini ├── dataset │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── patchdataset.cpython-37.pyc │ │ ├── patchdataset.cpython-38.pyc │ │ ├── roidataset.cpython-37.pyc │ │ ├── roidataset.cpython-38.pyc │ │ ├── roidataset.cpython-39.pyc │ │ ├── vis_dataset.cpython-38.pyc │ │ └── wsi_dataset.cpython-38.pyc │ ├── roidataset.py │ └── vis_dataset.py ├── gen_visheatmaps_roi_batch.py ├── gen_visheatmaps_slide_batch.py ├── main.py ├── models │ ├── ROAM.py │ └── __init__.py ├── models_embed │ ├── ResNet.py │ ├── ccl.py │ ├── ctran.py │ ├── extractor.py │ └── simclr_ciga.py ├── parse_config.py ├── position_embedding.py ├── predict_cascade.py ├── prediction_results │ └── s1 │ │ ├── cascade_int_oli_grade_split.npy │ │ └── int_glioma_tumor_subtyping │ │ ├── predictions.json │ │ └── results.json ├── results │ └── int_glioma_tumor_subtyping │ │ └── int_glioma_tumor_subtyping_[2, 2, 2, 2, 2]_ImageNet_4_True_True_1.0_4_0_ms_0_False │ │ └── s1 │ │ ├── results.json │ │ └── visual_res │ │ ├── cm_mean.png │ │ ├── metrics.json │ │ └── normal_cm_mean.png ├── scripts │ ├── cascade_pred_int_glioma_tumor_subtyping.sh │ ├── int_glioma_tumor_subtyping.sh │ └── int_glioma_tumor_subtyping_test.sh ├── utils │ ├── __pycache__ │ │ ├── core_utils.cpython-37.pyc │ │ ├── file_utils.cpython-37.pyc │ │ ├── file_utils.cpython-38.pyc │ │ ├── utils.cpython-37.pyc │ │ └── utils.cpython-38.pyc │ ├── eval_utils.py │ ├── file_utils.py │ └── utils.py ├── vahadane.py ├── vis_utils │ ├── __pycache__ │ │ ├── heatmap_utils.cpython-38.pyc │ │ ├── vit_grad_rollout.cpython-38.pyc │ │ └── vit_rollout.cpython-38.pyc │ ├── heatmap_utils.py │ ├── vit_explain.py │ ├── vit_grad_rollout.py │ └── vit_rollout.py ├── visheatmaps │ ├── roi_vis │ │ ├── configs │ │ │ └── int_glioma_tumor_subtyping_vis_roi.ini │ │ └── high │ │ │ └── int_glioma_tumor_subtyping_[2, 2, 2, 2, 2]_ImageNet_4_True_True_1.0_4_0_ms_0_False │ │ │ └── grad_rollout │ │ │ └── oligodendroglioma │ │ │ └── d0ab09865c3b467 │ │ │ └── top1_seeds1_0_d2_l2_r0.0_avg.png │ ├── slide_vis │ │ ├── configs │ │ │ ├── config_int_glioma_tumor_subtyping.yaml │ │ │ └── config_int_glioma_tumor_subtyping_roi.yaml │ │ ├── process_list │ │ │ ├── int_glioma_tumor_subtyping.csv │ │ │ └── int_glioma_tumor_subtyping_roi.csv │ │ └── results │ │ │ ├── heatmap_production_results │ │ │ └── int_glioma_tumor_subtyping_[2, 2, 2, 2, 2]_ImageNet_4_True_True_1.0_4_0_ms_0_False │ │ │ │ └── oligodendroglioma │ │ │ │ ├── d0ab09865c3b467_0.95_roi_1_blur_1_rs_1_bc_0_a_0.4_l_4_bi_0_-1.0.jpg │ │ │ │ ├── d0ab09865c3b467_0.9_roi_0_blur_1_rs_1_bc_0_a_0.4_l_5_bi_0_-1.0.jpg │ │ │ │ ├── d0ab09865c3b467_orig_4.jpg │ │ │ │ └── d0ab09865c3b467_orig_5.jpg │ │ │ └── int_glioma_tumor_subtyping_roi.csv │ └── target_roi_6e3.jpg └── wsi_core │ ├── WholeSlideImage.py │ ├── batch_process_utils.py │ ├── util_classes.py │ └── wsi_utils.py ├── data_prepare ├── create_patches_fp.py ├── create_splits.ipynb ├── data_csv │ └── example_xiangya_data_info_pro.csv ├── data_split │ └── xiangya_split_subtype │ │ └── example_test_split.npy ├── extract_feature_patch.py ├── models │ ├── ResNet.py │ ├── ccl.py │ ├── ctran.py │ ├── extractor.py │ └── simclr_ciga.py ├── patchdataset.py ├── target_images │ ├── target_image_6e3_1024.jpg │ ├── target_image_6e3_256.jpg │ ├── target_image_6e3_512.jpg │ └── target_roi_6e3.jpg ├── utils │ ├── __pycache__ │ │ ├── file_utils.cpython-38.pyc │ │ └── utils.cpython-38.pyc │ ├── file_utils.py │ └── utils.py ├── vahadane.py └── wsi_core │ ├── WholeSlideImage.py │ ├── __pycache__ │ ├── WholeSlideImage.cpython-37.pyc │ ├── WholeSlideImage.cpython-38.pyc │ ├── batch_process_utils.cpython-37.pyc │ ├── batch_process_utils.cpython-38.pyc │ ├── util_classes.cpython-37.pyc │ ├── util_classes.cpython-38.pyc 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