├── .github ├── ISSUE_TEMPLATE │ ├── add-a-dataset.md │ ├── add-a-model.md │ ├── add-a-task.md │ └── benchmark-result.yml └── workflows │ ├── aggregate_benchmark_results.yaml │ ├── code-quality-main.yaml │ ├── code-quality-pr.yaml │ ├── python-build.yaml │ ├── tests.yaml │ └── upload_benchmark_result.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── pyproject.toml ├── src └── MEDS_DEV │ ├── __init__.py │ ├── configs │ ├── __init__.py │ ├── _build_dataset.yaml │ ├── _evaluate_predictions.yaml │ ├── _extract_task.yaml │ ├── _package_result.yaml │ ├── _run_model.yaml │ └── _validate_result.yaml │ ├── datasets │ ├── AUMCdb │ │ ├── README.md │ │ └── predicates.yaml │ ├── MIMIC-IV │ │ ├── README.md │ │ ├── __init__.py │ │ ├── dataset.yaml │ │ ├── predicates.yaml │ │ ├── refs.bib │ │ └── requirements.txt │ ├── README.md │ ├── __init__.py │ └── __main__.py │ ├── evaluation │ ├── README.md │ ├── __init__.py │ └── __main__.py │ ├── models │ ├── __init__.py │ ├── __main__.py │ ├── cehrbert │ │ ├── README.md │ │ ├── __init__.py │ │ ├── _config.yaml │ │ ├── cehrbert_finetune_template.yaml │ │ ├── cehrbert_pretrain_template.yaml │ │ ├── finetune_cehrbert.py │ │ ├── generate_cehrbert_predictions.py │ │ ├── model.yaml │ │ ├── pretrain_cehrbert.py │ │ ├── refs.bib │ │ └── requirements.txt │ ├── genhpf │ │ ├── README.md │ │ ├── __init__.py │ │ ├── genhpf_predict.yaml │ │ ├── genhpf_train.yaml │ │ ├── model.yaml │ │ ├── refs.bib │ │ └── requirements.txt │ ├── meds_tab │ │ ├── README.md │ │ ├── refs.bib │ │ └── tiny │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── model.yaml │ │ │ └── requirements.txt │ └── random_predictor │ │ ├── README.md │ │ ├── __init__.py │ │ ├── _config.yaml │ │ ├── generate_random_predictions.py │ │ └── model.yaml │ ├── results │ ├── README.md │ ├── __init__.py │ └── __main__.py │ ├── tasks │ ├── README.md │ ├── __init__.py │ ├── __main__.py │ ├── abnormal_lab │ │ ├── README.md │ │ ├── blood_chemistry │ │ │ ├── elevated_creatinine │ │ │ │ └── first_24h.yaml │ │ │ ├── hyponatremia │ │ │ │ └── first_24h.yaml │ │ │ └── metabolic_acidosis │ │ │ │ └── first_24h.yaml │ │ ├── cbc │ │ │ ├── anemia │ │ │ │ └── first_24h.yaml │ │ │ ├── leukocytosis │ │ │ │ └── first_24h.yaml │ │ │ └── thrombocytopenia │ │ │ │ └── first_24h.yaml │ │ └── vital │ │ │ └── hypotension │ │ │ └── first_24h.yaml │ ├── mortality │ │ ├── README.md │ │ └── in_icu │ │ │ ├── README.md │ │ │ └── first_24h.yaml │ └── readmission │ │ ├── README.md │ │ └── general_hospital │ │ ├── 30d.yaml │ │ └── README.md │ └── utils.py ├── templates ├── README.md ├── dataset.md ├── model.md ├── results.md └── task.md └── tests ├── __init__.py ├── conftest.py ├── test_0_datasets.py ├── test_1_tasks.py ├── test_1_unsupervised_models.py ├── test_2_supervised_models.py ├── test_3_evaluation.py ├── test_4_result_packaging.py └── utils.py /.github/ISSUE_TEMPLATE/add-a-dataset.md: 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