Journal Article

Benchmarking large language models for biomedical natural language processing applications and recommendations

Gilson, Aidan, Xu, Hua, Hu, Yan, Peng, Xueqing, Jin, Qiao, Lin, Fongci, Lu, Zhiyong, Adelman, Ron A., He, Huan, Du, Jingcheng, Singer, Maxwell B., Huang, Jimin, Keloth, Vipina K., Ai, Xuguang, Raja, Kalpana, Xie, Qianqian, Chen, Qingyu, Zhang, Rui, Zheng, W. Jim, Wang, Zhizheng, Lai, Po-Ting

2025

Overview

The rapid growth of biomedical literature poses challenges for manual knowledge curation and synthesis. Biomedical Natural Language Processing (BioNLP) automates the process. While Large Language Models (LLMs) have shown promise in general domains, their effectiveness in BioNLP tasks remains unclear due to limited benchmarks and practical guidelines. We perform a systematic evaluation of four LLMs—GPT and LLaMA representatives—on 12 BioNLP benchmarks across six applications. We compare their zero-shot, few-shot, and fine-tuning performance with the traditional fine-tuning of BERT or BART models. We examine inconsistencies, missing information, hallucinations, and perform cost analysis. Here, we show that traditional fine-tuning outperforms zero- or few-shot LLMs in most tasks. However, closed-source LLMs like GPT-4 excel in reasoning-related tasks such as medical question answering. Open-source LLMs still require fine-tuning to close performance gaps. We find issues like missing information and hallucinations in LLM outputs. These results offer practical insights for applying LLMs in BioNLP. Baseline performance, benchmarks, and guidance for LLMs in biomedicine are limited. The authors assess four LLMs on 12 tasks, establish baselines, examine hallucinations, and provide recommendations for optimal LLM use.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/114/2164 / 692/700 / Benchmarking / Benchmarks / Cost analysis / Hallucinations / Humanities and Social Sciences / Humans / Large Language Models / multidisciplinary / Natural Language Processing / Science / Science (multidisciplinary)