A comprehensive evaluation of large language models in mining gene relations and pathway knowledge

Abstract Understanding complex biological pathways, including gene–gene interactions and gene regulatory networks, is critical for exploring disease mechanisms and drug development. Manual literature curation of biological pathways cannot keep up with the exponential growth of new discoveries in the literature. Large‐scale language models (LLMs) trained on extensive text corpora contain rich biological information, and they can be mined as a biological knowledge graph. This study assesses 21 LLMs, including both application programming interface (API)‐based models and open‐source models in their capacities of retrieving biological knowledge. The evaluation focuses on predicting gene regulatory relations (activation, inhibition, and phosphorylation) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway components. Results indicated a significant disparity in model performance. API‐based models GPT‐4 and Claude‐Pro showed superior performance, with an F1 score of 0.4448 and 0.4386 for the gene regulatory relation prediction, and a Jaccard similarity index of 0.2778 and 0.2657 for the KEGG pathway prediction, respectively. Open‐source models lagged behind their API‐based counterparts, whereas Falcon‐180b and llama2‐7b had the highest F1 scores of 0.2787 and 0.1923 in gene regulatory relations, respectively. The KEGG pathway recognition had a Jaccard similarity index of 0.2237 for Falcon‐180b and 0.2207 for llama2‐7b. Our study suggests that LLMs are informative in gene network analysis and pathway mapping, but their effectiveness varies, necessitating careful model selection. This work also provides a case study and insight into using LLMs das knowledge graphs. Our code is publicly available at the website of GitHub (Muh‐aza).