# Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge

arXiv: https://arxiv.org/abs/2307.08813 · HTML: https://mlsanity.com/paper/2307.08813/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 54 references that are in the map.
- First posted on arXiv 17 Jul 2023.

## Builds on (most cited first, 15 of 15)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Large Language Models are Zero-Shot Reasoners](https://mlsanity.com/paper/2205.11916/) (2022)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [A Survey of Large Language Models](https://mlsanity.com/paper/2303.18223/) (2023)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Guiding Large Language Models via Directional Stimulus Prompting](https://mlsanity.com/paper/2302.11520/) (2023)
- [BERTology Meets Biology: Interpreting Attention in Protein Language Models](https://mlsanity.com/paper/2006.15222/) (2020)
- [reStructured Pre-training](https://mlsanity.com/paper/2206.11147/) (2022)
- [Deep learning for extracting protein-protein interactions from biomedical literature](https://mlsanity.com/paper/1706.01556/) (2017)
- [Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response](https://mlsanity.com/paper/2301.01769/) (2023)

## Built on by (most cited first, 5 of 5)

- [BioMedLM: A 2.7B Parameter Language Model Trained On Biomedical Text](https://mlsanity.com/paper/2403.18421/) (2024)
- [BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments](https://mlsanity.com/paper/2405.17631/) (2024)
- [BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning](https://mlsanity.com/paper/2502.16660/) (2025)
- [Density Estimation via Measure Transport: Outlook for Applications in the Biological Sciences](https://mlsanity.com/paper/2309.15366/) (2023)
- [Knowledge-Augmented Long-CoT Generation for Complex Biomolecular Reasoning](https://mlsanity.com/paper/2511.08024/) (2025)

## Abstract (arXiv)

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection of such molecular interactions has heavily relied on expert curation in the past, making it labor-intensive and time-consuming. To mitigate these challenges, we propose leveraging the capabilities of large language models (LLMs) to automate genome-scale extraction of this crucial knowledge. Results: In this study, we investigate the efficacy of various LLMs in addressing biological tasks, such as the recognition of protein interactions, identification of genes linked to pathways affected by low-dose radiation, and the delineation of gene regulatory relationships. Overall, the larger models exhibited superior performance, indicating their potential for specific tasks that involve the extraction of complex interactions among genes and proteins. Although these models possessed detailed information for distinct gene and protein groups, they faced challenges in identifying groups with diverse functions and in recognizing highly correlated gene regulatory relationships. Conclusions: By conducting a comprehensive assessment of the state-of-the-art models using well-established molecular interaction and pathway databases, our study reveals that LLMs can identify genes/proteins associated with pathways of interest and predict their interactions to a certain extent. Furthermore, these models can provide important insights, marking a noteworthy stride toward advancing our understanding of biological systems through AI-assisted knowledge discovery.