├── .gitignore ├── LICENSE ├── README.md ├── assert ├── blca-test-WSI-TCGA-XF-A9ST.pt └── blca-train-VLSA │ ├── config.yaml │ └── train_model-last.pth ├── config └── IFMLE │ ├── tcga_blca │ ├── cfg_sa_base_conch.yaml │ ├── cfg_vlsa_conch.yaml │ └── cfg_zero_shot_conch.yaml │ ├── tcga_brca │ ├── cfg_sa_base_conch.yaml │ ├── cfg_vlsa_conch.yaml │ └── cfg_zero_shot_conch.yaml │ ├── tcga_gbmlgg │ ├── cfg_sa_base_conch.yaml │ ├── cfg_vlsa_conch.yaml │ └── cfg_zero_shot_conch.yaml │ ├── tcga_luad │ ├── cfg_sa_base_conch.yaml │ ├── cfg_vlsa_conch.yaml │ └── cfg_zero_shot_conch.yaml │ └── tcga_ucec │ ├── cfg_sa_base_conch.yaml │ ├── cfg_vlsa_conch.yaml │ └── cfg_zero_shot_conch.yaml ├── data_split └── 5foldcv │ ├── README.md │ ├── tcga_blca │ ├── mahmoodlab_tcga_blca_survival.csv │ ├── splits_0.csv │ ├── splits_1.csv │ ├── splits_2.csv │ ├── splits_3.csv │ └── splits_4.csv │ ├── tcga_brca │ ├── mahmoodlab_tcga_brca_survival.csv │ ├── splits_0.csv │ ├── splits_1.csv │ ├── splits_2.csv │ ├── splits_3.csv │ └── splits_4.csv │ ├── tcga_gbmlgg │ ├── mahmoodlab_tcga_gbmlgg_survival.csv │ ├── splits_0.csv │ ├── splits_1.csv │ ├── splits_2.csv │ ├── splits_3.csv │ └── splits_4.csv │ ├── tcga_luad │ ├── mahmoodlab_tcga_luad_survival.csv │ ├── splits_0.csv │ ├── splits_1.csv │ ├── splits_2.csv │ ├── splits_3.csv │ └── splits_4.csv │ └── tcga_ucec │ ├── mahmoodlab_tcga_ucec_survival.csv │ ├── splits_0.csv │ ├── splits_1.csv │ ├── splits_2.csv │ ├── splits_3.csv │ └── splits_4.csv ├── dataset ├── GraphBatchWSI.py ├── PatchWSI.py ├── __init__.py ├── label_converter.py └── utils.py ├── docs ├── VLSA.webp └── fig-vlsa-overview.png ├── eval ├── SurvivalEVAL │ ├── Evaluations │ │ ├── AreaUnderCurve.py │ │ ├── BrierScore.py │ │ ├── Concordance.py │ │ ├── D_Calibration.py │ │ ├── KM_Calibration.py │ │ ├── MeanError.py │ │ ├── OneCalibration.py │ │ ├── __init__.py │ │ ├── custom_types.py │ │ └── util.py │ ├── Evaluator.py │ ├── Examples │ │ ├── Calibration_for_CrossValidation_Example.ipynb │ │ ├── Compare_Interpolation_Methods.ipynb │ │ ├── Dealing_Non-Monotonic_Curves.ipynb │ │ ├── Lifelines_Example.ipynb │ │ ├── PySurvival_auton-survival_Example.ipynb │ │ ├── Pycox_Example.ipynb │ │ └── Scikit-survival_Example.ipynb │ ├── LICENSE │ ├── README.md │ └── __init__.py ├── __init__.py ├── cindex.py ├── evaluator_clf.py ├── evaluator_surv.py ├── utils.py └── utils_coxph.py ├── loss ├── __init__.py ├── loss_clf.py ├── loss_surv.py ├── loss_surv_ext.py └── utils.py ├── main.py ├── model ├── __init__.py ├── clip │ ├── __init__.py │ ├── bpe_simple_vocab_16e6.txt.gz │ ├── clip.py │ ├── model.py │ └── simple_tokenizer.py ├── conch │ ├── __init__.py │ ├── coca_model.py │ ├── constants.py │ ├── custom_tokenizer.py │ ├── factory.py │ ├── model_configs │ │ └── conch_ViT-B-16.json │ ├── tokenizers │ │ └── conch_byte_level_bpe_uncased.json │ ├── transform.py │ ├── transformer.py │ ├── utils.py │ └── vision_tower.py ├── deepmil.py ├── layers.py ├── prompt_encoder.py ├── prompt_learners │ ├── __init__.py │ ├── plain_prompt_learner.py │ ├── prompt_adapter.py │ └── rank_prompt_learner.py ├── utils.py ├── utils_vl.py └── vlsa.py ├── notebook └── VLSA-Walkthrough.ipynb ├── optim ├── __init__.py ├── adafactor.py ├── adahessian.py ├── adamp.py ├── adamw.py ├── ema.py ├── lookahead.py ├── nadam.py ├── novograd.py ├── nvnovograd.py ├── optim_factory.py ├── radam.py ├── rmsprop_tf.py └── sgdp.py ├── requirements.txt ├── runner ├── __init__.py ├── base_handler.py ├── global_cfg.py ├── sa_handler.py └── vlsa_handler.py ├── tools ├── sa_rank_names.txt ├── survival_prompts.json ├── survival_template_prompts.json └── survival_text_prototypes.json └── utils ├── __init__.py ├── func.py ├── io.py ├── model_inference.py └── visualization.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/liupei101/VLSA/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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