├── .gitignore ├── Additional ├── MakeDictionaries.py ├── MimicAdmSummary.py ├── MimicAdmToUMLS.py └── MimicClauseExample.py ├── Data └── README.md ├── MIMIC-tools ├── ExploreMimic.ipynb ├── MimicDesc.py ├── MimicEvent.py ├── MimicPatient.py ├── ParseMimic.py ├── README.md ├── Utils.py └── split_scripts │ ├── SplitMimicOthers.py │ └── SplitMimicText.py ├── MLN ├── MimicAdmSummary.py ├── MimicAdmToUMLS.py └── MimicClauseExample.py ├── Preprocessing ├── ConceptCRFMatch │ ├── ExtractConcepts.py │ ├── MakeCRFData.py │ ├── README.md │ ├── ReadCRFOutput.py │ ├── ReadUMLS.py │ ├── StanNLPInterface.py │ ├── crf_model │ │ └── model_overlaps.dat │ ├── example_inputs │ │ ├── patient_01.txt │ │ ├── patient_02.txt │ │ ├── patient_03.txt │ │ ├── patient_04.txt │ │ ├── patient_05.txt │ │ ├── patient_06.txt │ │ ├── patient_07.txt │ │ ├── patient_08.txt │ │ └── patient_09.txt │ └── example_outputs │ │ ├── patient_01.pk │ │ ├── patient_02.pk │ │ ├── patient_03.pk │ │ ├── patient_04.pk │ │ ├── patient_05.pk │ │ ├── patient_06.pk │ │ ├── patient_07.pk │ │ ├── patient_08.pk │ │ ├── patient_09.pk │ │ ├── spans_patient_01.txt │ │ ├── spans_patient_02.txt │ │ ├── spans_patient_03.txt │ │ ├── spans_patient_04.txt │ │ ├── spans_patient_05.txt │ │ ├── spans_patient_06.txt │ │ ├── spans_patient_07.txt │ │ ├── spans_patient_08.txt │ │ ├── spans_patient_09.txt │ │ ├── text_patient_01.txt │ │ ├── text_patient_02.txt │ │ ├── text_patient_03.txt │ │ ├── text_patient_04.txt │ │ ├── text_patient_05.txt │ │ ├── text_patient_06.txt │ │ ├── text_patient_07.txt │ │ ├── text_patient_08.txt │ │ └── text_patient_09.txt ├── ConceptStringMatch │ ├── FindConcepts.py │ └── README.md ├── README.md ├── ReadXmlVisits.py └── TODO.md ├── README.md └── UMLS ├── MakeDictionaries.py ├── ParseUMLS.py ├── README.md ├── README.rst ├── UMLS ├── UMLSUtils.py └── __init__.py ├── examples ├── .ipynb_checkpoints │ └── UMLS_Example-checkpoint.ipynb └── UMLS_Example.ipynb └── setup.py /.gitignore: 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