├── .DS_Store ├── README.md ├── mean_and_var_pool_arch.png ├── run_all_fits.py ├── run_viz_top_patches.py ├── scripts ├── .DS_Store ├── agg_val_tune.py ├── baseline_cox.py ├── eval.py ├── redo_save_preds.py ├── run_tune.py ├── train.py └── visualize.py ├── setup.py ├── tcga_scripts ├── .DS_Store ├── aggregate_surv_cv_folds.py ├── download_tcga_clinical_data.py ├── make_discr_suvr_splits.py ├── make_subtype_clf_splits.py ├── make_surv_yaml.py ├── stat_sig_c_index_cutoff.py ├── viz_top_patches-extremes_only.py └── viz_top_patches.py └── var_pool ├── .DS_Store ├── __init__.py ├── file_utils.py ├── gpu_utils.py ├── mhist ├── .DS_Store ├── __init__.py ├── clinical_data_porpoise.py ├── get_model.py ├── get_model_from_args.py ├── get_model_with_switch.py ├── patch_gcn_arch.py ├── tcga_agg_slides_to_patient_level.py └── tcga_clinical_data.py ├── nn ├── .DS_Store ├── ComparablePairSampler.py ├── CoxLoss.py ├── NLLSurvLoss.py ├── SurvRankingLoss.py ├── __init__.py ├── arch │ ├── .DS_Store │ ├── AttnMIL.py │ ├── AttnMIL_utils.py │ ├── GlobalPoolMIL.py │ ├── PatchGCN.py │ ├── SumMIL.py │ ├── VarPool.py │ ├── VarPool_switch.py │ ├── __init__.py │ └── utils.py ├── datasets │ ├── .DS_Store │ ├── BagDatasets.py │ ├── GraphDatasets.py │ ├── __init__.py │ └── fixed_bag_size.py ├── seeds.py ├── stream_evaler.py ├── train │ ├── .DS_Store │ ├── EarlyStopper.py │ ├── GradAccum.py │ ├── __init__.py │ ├── loops.py │ └── tests │ │ ├── .DS_Store │ │ ├── __init__.py │ │ ├── test_GradAccum.py │ │ └── utils_grad_accum.py ├── tune_utils.py └── utils.py ├── processing ├── .DS_Store ├── __init__.py ├── clf_utils.py ├── data_split.py └── discr_surv_utils.py ├── script_utils.py ├── utils.py └── viz ├── .DS_Store ├── __init__.py ├── top_attn.py ├── utils.py └── var_pool_extremes.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mahmoodlab/varpool/HEAD/.DS_Store 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