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README.md

Medical Code Assignment

Data

Sign the data use agreement and download MIMIC-III dataset from PhysioNet.

Organize your data using the following structure

data
|   D_ICD_DIAGNOSES.csv
|   D_ICD_PROCEDURES.csv
|   ICD9_descriptions
└───mimic3/
|   |   NOTEEVENTS.csv
|   |   DIAGNOSES_ICD.csv
|   |   PROCEDURES_ICD.csv
|   |   *_hadm_ids.csv

ICD9_descriptions is available here, and *_hadm_ids.csv are available here. MIMIC_RAW_DSUMS is available here, while the rest file for MIMIC2 can be generated with their code. If you use Python3 consctruct_datasest.py in ICD9_Coding_of_Discharge_Summaries to create data files, remember to convert dict object to list (line 82&83) and use dict.items() instead of dict.iteritems(). Assign the directories of MIMIC data using MIMIC_3_DIR.

Run

python3 main.py

Configs available at options.py.

Requirements:

  • python 3.7
  • pytorch>=1.5.0

Acknowledgements

The code is based on the following two great repositories.