├── .gitignore ├── .vscode └── settings.json ├── README.md ├── assets └── model.png ├── classification ├── config │ ├── __init__.py │ ├── base_cfg.yaml │ ├── dataset │ │ └── mimic_lab.yaml │ ├── model │ │ └── multi_modal_pretrained_vit_lab.yaml │ └── scheduler │ │ ├── cosine_annealing.yaml │ │ ├── cosine_annealing_warm_restarts.yaml │ │ ├── none.yaml │ │ ├── plateau.yaml │ │ └── step.yaml ├── datasets │ ├── helper.py │ ├── med_lab_utils │ │ ├── README.md │ │ ├── discretizer_config.json │ │ ├── ph_ts0.8.input_str:previous.start_time:zero.normalizer │ │ ├── ph_ts1.0.input_str:previous.start_time:zero.normalizer │ │ └── preprocessor.py │ └── mimic_lab.py ├── metrics │ ├── __init__.py │ ├── partial_roc_auc_score.py │ ├── roc_auc_score.py │ └── screening_sens_at_spec.py ├── models │ ├── __init__.py │ └── multi_modal_pretrained_vit_lab.py └── training │ ├── best_checkpoint.py │ ├── dataset.py │ ├── lightning.py │ ├── model.py │ └── trainer.py ├── requirements.txt └── utils └── mimic4extract ├── LICENSE ├── README.md ├── count.py ├── mimic3benchmark ├── __init__.py ├── evaluation │ ├── README.md │ ├── __init__.py │ ├── evaluate_decomp.py │ ├── evaluate_ihm.py │ ├── evaluate_los.py │ └── evaluate_pheno.py ├── mimic3csv.py ├── more_on_readers.md ├── preprocessing.py ├── readers.py ├── resources │ ├── 2018 Code Descriptions │ │ ├── icd10OrderFiles.pdf │ │ ├── icd10cmCodesFile.pdf │ │ ├── icd10cm_codes_2018.txt │ │ ├── icd10cm_codes_addenda_2018.txt │ │ ├── icd10cm_order_2018.txt │ │ └── icd10cm_order_addenda_2018.txt │ ├── diagnosis_gems_2018 │ │ ├── 2018_I10gem.txt │ │ ├── 2018_I9gem.txt │ │ ├── Dxgem_guide_2018.pdf │ │ └── GemsTechDoc_2018.pdf │ ├── full_match.yaml │ ├── hcup_ccs_2015_definitions.yaml │ ├── icd_9_10_definitions.yaml │ ├── icd_9_10_definitions_2.yaml │ ├── itemid_to_variable_map.csv │ ├── subset.yaml │ ├── testset.csv │ ├── testset_iv.csv │ └── variable_ranges.csv ├── scripts │ ├── __init__.py │ ├── create_decompensation.py │ ├── create_in_hospital_mortality.py │ ├── create_length_of_stay.py │ ├── create_multitask.py │ ├── create_phenotyping.py │ ├── extract_episodes_from_subjects.py │ ├── extract_subjects_iv.py │ ├── more_on_validating_events.md │ ├── split_train_and_test.py │ └── validate_events.py ├── subject.py ├── tests │ ├── README.md │ ├── __init__.py │ ├── hash_tables.py │ └── resources │ │ ├── decomp.pkl │ │ ├── ihm.pkl │ │ ├── los.pkl │ │ ├── multitasking.pkl │ │ ├── pheno.pkl │ │ ├── root-after-validating.pkl │ │ └── root-final.pkl └── util.py └── mimic3models ├── __init__.py ├── common_utils.py ├── create_normalizer_state.py ├── decompensation ├── __init__.py ├── decomp_ts0.8.input_str:previous.n1e5.start_time:zero.normalizer ├── decomp_ts1.0.input_str:previous.n1e5.start_time:zero.normalizer ├── keras_logs │ └── k_lstm.n128.dep1.bs8.ts1.0.csv ├── logistic │ ├── __init__.py │ └── main.py ├── main.py ├── main_pytorch.py └── utils.py ├── feature_extractor.py ├── helpers.md ├── in_hospital_mortality ├── __init__.py ├── ihm_ts0.8.input_str:previous.start_time:zero.normalizer ├── ihm_ts1.0.input_str:previous.start_time:zero.normalizer ├── ihm_ts2.0.input_str:previous.start_time:zero.normalizer ├── logistic │ ├── __init__.py │ └── main.py ├── main.py └── utils.py ├── keras_models ├── __init__.py ├── channel_wise_lstms.py ├── lstm.py ├── multitask_channel_wise_lstms.py └── multitask_lstm.py ├── keras_utils.py ├── length_of_stay ├── __init__.py ├── logistic │ ├── __init__.py │ ├── main.py │ └── main_cf.py ├── los_ts0.8.input_str:previous.start_time:zero.n5e4.normalizer ├── los_ts1.0.input_str:previous.start_time:zero.n5e4.normalizer ├── main.py └── utils.py ├── metrics.py ├── multitask ├── __init__.py ├── main.py ├── mult_ts1.0.input_str:previous.start_time:zero.normalizer └── utils.py ├── parse_utils.py ├── phenotyping ├── __init__.py ├── keras_logs │ └── k_lstm.n256.d0.3.dep1.bs8.ts1.0.csv ├── logistic │ ├── __init__.py │ └── main.py ├── main.py ├── main_torch copy.py ├── 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