Automated Extraction of Molecular Interactions and Pathway Knowledge using Large Language Model, Galactica: Opportunities and Challenges

Abstract

Understanding protein interactions and pathway knowledge is essential for comprehending living systems and investigating the mechanisms underlying various biological functions and complex diseases. While numerous databases curate such biological data obtained from literature and other sources, they are not comprehensive and require considerable effort to maintain. One mitigation strategies can be utilizing large language models to automatically extract biological information and explore their potential in life science research. This study presents an initial investigation of the efficacy of utilizing a large language model, Galactica in life science research by assessing its performance on tasks involving protein interactions, pathways, and gene regulatory relation recognition. The paper details the results obtained from the model evaluation, highlights the findings, and discusses the opportunities and challenges. The code and data are available at: https://github.com/boxorange/BioIE-LLM.