├── .gitignore ├── LICENSE ├── PH_NLP_annotation_guidelines.md ├── README.md ├── cohort ├── 1. PE Cohort Sanity Checks.py ├── 2. Define Cohort.py ├── 3. Link and anonymize rad notes.py ├── 4. Extract DICOM metadata.py ├── 5. Get Cohort Demographics.py ├── README.md └── environments.yml ├── data ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-38.pyc │ ├── data_module.cpython-38.pyc │ ├── dataset_1d.cpython-38.pyc │ ├── dataset_2d.cpython-38.pyc │ └── dataset_base.cpython-38.pyc ├── data_module.py ├── dataset_1d.py ├── dataset_2d.py └── dataset_base.py ├── ehr ├── 1_csv_to_database.py ├── 2_generate_labels_and_features.py ├── 3_train_gbm.py ├── 4_compute_pesi_score.py ├── requirements.txt ├── run_all_ehr.py └── utils.py ├── get_label_counts.py ├── get_model_performance.py ├── image ├── README.md ├── convert_to_hdf5.py ├── demo │ └── ___main_figure.png ├── environments.yml ├── radfusion3 │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-38.pyc │ │ ├── builder.cpython-38.pyc │ │ ├── constants.cpython-38.pyc │ │ └── utils.cpython-38.pyc │ ├── builder.py │ ├── configs │ │ ├── classify.yaml │ │ ├── dataset │ │ │ ├── rsna.yaml │ │ │ ├── rsna_featurized.yaml │ │ │ ├── stanford.yaml │ │ │ └── stanford_featurized.yaml │ │ ├── extract.yaml │ │ └── model │ │ │ ├── clip_convnext.yaml │ │ │ ├── clip_vit.yaml │ │ │ ├── dinov1.yaml │ │ │ ├── dinov1_ct.yaml │ │ │ ├── dinov2.yaml │ │ │ ├── model_1d.yaml │ │ │ ├── resnetv2.yaml │ │ │ ├── resnetv2_ct.yaml │ │ │ ├── sup.yaml │ │ │ └── swinv2.yaml │ ├── constants.py │ ├── data │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── data_module.cpython-38.pyc │ │ │ ├── dataset_1d.cpython-38.pyc │ │ │ ├── dataset_2d.cpython-38.pyc │ │ │ └── dataset_base.cpython-38.pyc │ │ ├── data_module.py │ │ ├── dataset_1d.py │ │ ├── dataset_2d.py │ │ └── dataset_base.py │ ├── lightning │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── classification_lightning_model.cpython-38.pyc │ │ │ └── featurize_lightning_model.cpython-38.pyc │ │ ├── classification_lightning_model.py │ │ └── featurize_lightning_model.py │ ├── models │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── models_1d.cpython-38.pyc │ │ │ ├── models_2d.cpython-38.pyc │ │ │ └── vision_backbones.cpython-38.pyc │ │ ├── models_1d.py │ │ ├── models_2d.py │ │ └── vision_backbones.py │ ├── transforms │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-38.pyc │ │ │ ├── dinov1.cpython-38.pyc │ │ │ ├── dinov2.cpython-38.pyc │ │ │ └── supervised.cpython-38.pyc │ │ ├── dinov1.py │ │ ├── dinov2.py │ │ └── supervised.py │ └── utils.py ├── run_classify.py ├── run_classify.sh ├── run_classify_12m_mort.sh ├── run_classify_1m_mort.sh ├── run_classify_6m_mort.sh ├── run_classify_all.sh ├── run_classify_pe.sh ├── run_classify_ph.sh ├── run_classify_read_12m.sh ├── run_classify_read_1m.sh ├── run_classify_read_6m.sh ├── run_featurize.py ├── run_featurize.sh ├── run_rsna.sh ├── run_sweep.py └── sweep.yaml └── reports ├── R1. Anonymize CTPA Notes.py ├── R2. 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