Source code for paper "A GPT-based EHR Modeling System for Unsupervised Novel Disease Detection".
Basic environment:
conda env create -f environment.yml
Code:
"data/" includes the main code for EHR data pre-processing.
"model/" includes the main code for GPT model building, training and inference.
NOTE: the BERT (or other LM modules apart from GPT) in anomaly.py was used during the development process and partially used as class placeholders in the script, which will not be actually loaded/trained.
Due to a restrictive data use agreement and HIPAA rules, part of the code for data pre-processing is not provided.