Understanding protein interactions and pathway knowledge is crucial for unraveling the complexities of living systems and investigating the underlying mechanisms of biological functions and complex diseases. While existing databases provide curated biological data from literature and other sources, they are often incomplete and their maintenance is labor-intensive, necessitating alternative approaches. In this study, we propose to harness the capabilities of large language models to address these issues by automatically extracting such knowledge from the relevant scientific literature. Toward this goal, in this work, we investigate the effectiveness of different large language models in tasks that involve recognizing protein interactions, identifying genes associated with pathways affected by low-dose radiation, and gene regulatory relations. We thoroughly evaluate the performance of various models, highlight the significant findings, and discuss both the future opportunities and the remaining challenges associated with this approach. The code and data are available at: https://github.com/boxorange/BioIE-LLM

This study aimed to evaluate the proficiency of prominent Large Language Models (LLMs), namely OpenAI's ChatGPT 3.5 and 4.0, Google's Bard(LaMDA), and Microsoft's Bing AI in discerning the truthfulness of news items using black box testing. A total of 100 fact-checked news items, all sourced from independent fact-checking agencies, were presented to each of these LLMs under controlled conditions. Their responses were classified into one of three categories: True, False, and Partially True/False. The effectiveness of the LLMs was gauged based on the accuracy of their classifications against the verified facts provided by the independent agencies. The results showed a moderate proficiency across all models, with an average score of 65.25 out of 100. Among the models, OpenAI's GPT-4.0 stood out with a score of 71, suggesting an edge in newer LLMs' abilities to differentiate fact from deception. However, when juxtaposed against the performance of human fact-checkers, the AI models, despite showing promise, lag in comprehending the subtleties and contexts inherent in news information. The findings highlight the potential of AI in the domain of fact-checking while underscoring the continued importance of human cognitive skills and the necessity for persistent advancements in AI capabilities. Finally, the experimental data produced from the simulation of this work is openly available on Kaggle.