SimonSuster / ELI

Extracting entities and relations from medical abstracts

ELI

Extracting entities and relations from medical abstracts

This repository contains the code necessary to run a pre-trained version of the models described in our publication Trialstreamer: Mapping and Browsing Medical Evidence in Real-Time.

Further details about the models and implementations are published in Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations.

Processing your own documents:

• Download the pre-trained models here
• Move the model checkpoints into the corresponding directories in this repo
• Save your documents as a .json file that contains a list of records in the format {"pmid": XXX, "text": "..."}
• cd to scripts and run python run_pipeline.py $INPUT_FILE_NAME $OUT_FILE_NAME