LLM-drug-discovery

Automating Biomedical Literature Review for Rapid Drug Discovery: Leveraging GPT-4 to Expedite Pandemic Response.

Introduction

This repository contains the code and resources for our research project aimed at curtailing the time and resources traditionally associated with manual reviews in drug discovery and repurposing. Our automated framework identifies papers with potential drug targets, aiding researchers in maintaining an up-to-date map of current readiness for priority pathogens.

Getting Started

Setting Up the Virtual Environment

To set up the virtual environment and install the required libraries, execute the following commands:

conda env create -f environment.yml

conda activate drug

OpenAI API Key

Before using the scripts in this repository, you need to obtain an API key from OpenAI and replace your API key in the scripts.

Note: Keep your API key secure and do not share it publicly.

Usage

This section provides detailed instructions on how to run the scripts in this repository.

Data Preparation

Step 1: Data Collection

python data_preparation/PubMed_abstract_extraction.py

Step 2: Explanation Generation

python data_preparation/concatenate_sections.py

python data_preparation/generate_explanation.py

Step 3: Embedding Fetching

python data_preparation/generate_embedding.py

Step 4: Data Split

python data_preparation/run_cross_validation.py

python data_preparation/run_cross_validation_embeddings.py

Query Response

Zero-Shot

python model/run_zero.py --cot 0

Zero-Shot-CoT

python model/run_zero.py --cot 1

Few-Shot

python model/run_few_random.py --cot 0

Few-Shot-CoT

python model/run_few_random.py --cot 1

Similar-Shot

python model/run_few_similar.py --cot 0

Similar-Shot-CoT

python model/run_few_similar.py --cot 1

Authors or Acknowledgments

Title: Automating Biomedical Literature Review for Rapid Drug Discovery: Leveraging GPT-4 to Expedite Pandemic Response

Authors:

• Jingmei Yang
• Kenji C. Walker
• Ayse A. Bekar-Cesaretli
• Boran Hao
• Nahid Bhadelia, M.D.
• Diane Joseph-McCarthy, Ph.D.
• Ioannis Ch. Paschalidis, Ph.D

Cite US

  title={Automating biomedical literature review for rapid drug discovery: Leveraging GPT-4 to expedite pandemic response},
  author={Yang, Jingmei and Walker, Kenji C and Bekar-Cesaretli, Ayse A and Hao, Boran and Bhadelia, Nahid and Joseph-McCarthy, Diane and Paschalidis, Ioannis Ch},
  journal={International Journal of Medical Informatics},
  pages={105500},
  year={2024},
  publisher={Elsevier}
}

License

This project is open source and available under the MIT License.

Contact Information

• Email: [email protected].