ICBERT

Getting Started

Create a Python virtual environment and install the packages from the requirements.txt file

python -m venv venv
source ./venv/bin/activate
pip install -r requirements.txt

Download the MIMIC-IV dataset from PysioNet. The paper uses version 2.2 of the dataset. Insert the dataset into the mimic-iv folder at ./data/mimic-iv

The full dataset is not required to reproduce the results from the paper but only the following files:

• admissions.csv.gz
• diagnoses_icd.csv.gz
• procedures_icd.csv.gz
• d_icd_diagnoses.csv.gz
• d_icd_procedures.csv.gz

These files should be placed in ./data/mimic-iv/hosp

Download the EHRSHOT dataset and person.csv table from redivis. Insert EHRSHOT_ASSETS into the ./data folder and person.csv into that folder ./data/EHRSHOT_ASSETS

Finally run numbered scripts in ./src in order.