High-throughput Biomedical Relation Extraction for Semi-Structured Web Articles Empowered by Large Language Models

Objective: To develop a high-throughput biomedical relation extraction system that takes advantage of the large language models' (LLMs) reading comprehension ability and biomedical world knowledge in a scalable and evidential manner. Methods: We formulate the relation extraction task as a simple binary classification problem for large language models such as ChatGPT. Specifically, LLMs make the decision based on the external corpus and its world knowledge, giving the reason for the judgment to factual verification. This method is tailored for semi-structured web articles, wherein we designate the main title as the tail entity and explicitly incorporate it into the context, and the potential head entities are matched based on a biomedical thesaurus. Moreover, lengthy contents are sliced into text chunks, embedded, and retrieved with additional embedding models, ensuring compatibility with the context window size constraints of available open-source LLMs. Results: Using an open-source LLM, we extracted 304315 relation triplets of three distinct relation types from four reputable biomedical websites. To assess the efficacy of the basic pipeline employed for biomedical relation extraction, we curated a benchmark dataset annotated by a medical expert. Evaluation results indicate that the pipeline exhibits performance comparable to that of GPT-4. Case studies further illuminate challenges faced by contemporary LLMs in the context of biomedical relation extraction for semi-structured web articles. Conclusion: The proposed method has demonstrated its effectiveness in leveraging the strengths of LLMs for high-throughput biomedical relation extraction. Its adaptability is evident, as it can be seamlessly extended to diverse semi-structured biomedical websites, facilitating the extraction of various types of biomedical relations with ease.