Integrated-EHR-Pipeline

• Pre-processing code refining project in UniHPF

Install Requirements

• NOTE: This repository requires python>=3.9 and Java>=8
• NOTE: Since there is a performance issue related to transformers library, it is recommended to use transformers==4.29.1.

pip install numpy pandas tqdm treelib transformers==4.29.1 pyspark

How to Use

main.py --ehr {eicu, mimiciii, mimiciv}

• It automatically download the corresponding dataset from physionet, but requires appropriate certification.
• You can also use the downloaded dataset with --data {data path} option
• You can check sample implementation of pytorch dataset on sample_dataset.py