Self-Improving Zero-Shot Biomedical NER with LLMs

This repository contains the code for the DSC 253/CSE 291 Project "Self-Improving Zero-Shot Biomedical Named Entity Recognition with Large Language Models".

Setup

To setup the environment, run the following command:

bash setup.sh
conda create --name zero-shot-bioner-env python=3.10
conda activate zero-shot-bioner-env
pip install -r requirements.txt

Datasets

The datasets used in this project are:

1. NCBI Disease
2. I2B2 2010
3. BC2GM

References

• Code for Self-Evaluation Guided Decoding is adapted from SelfEval-Guided Decoding for Multi-step Reasoning
• Necessary changes have been made to the code to adapt it to the biomedical NER task.