{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/large-language-models-in-biomedical-natural","title":"Benchmarking large language models for biomedical natural language processing applications and recommendations","arxiv_id":"2305.16326","date":"2023-05-10","proceeding":null,"authors":["Qingyu Chen","Yan Hu","Xueqing Peng","Qianqian Xie","Qiao Jin","Aidan Gilson","Maxwell B. Singer","Xuguang Ai","Po-Ting Lai","Zhizheng Wang","Vipina Kuttichi Keloth","Kalpana Raja","Jiming Huang","Huan He","Fongci Lin","Jingcheng Du","Rui Zhang","W. Jim Zheng","Ron A. Adelman","Zhiyong Lu","Hua Xu"],"abstract":"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 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.","url_abs":"https://arxiv.org/abs/2305.16326v5","url_pdf":"https://arxiv.org/pdf/2305.16326v5.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"large-language-models-in-biomedical-natural","repo_url":"https://github.com/bids-xu-lab/biomedical-nlp-benchmarks","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"document-classification","task_name":"Document Classification"},{"task_slug":null,"task_name":"Medical Question Answering"},{"task_slug":"named-entity-recognition-1","task_name":"Named Entity Recognition"},{"task_slug":"question-answering","task_name":"Question Answering"},{"task_slug":"relation-extraction","task_name":"Relation Extraction"},{"task_slug":"semantic-similarity","task_name":"Semantic Similarity"},{"task_slug":"semantic-textual-similarity","task_name":"Semantic Textual Similarity"},{"task_slug":"text-simplification","task_name":"Text Simplification"},{"task_slug":"text-summarization","task_name":"Text Summarization"},{"task_slug":"named-entity-recognition","task_name":"named-entity-recognition"}],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"attention-dropout","method_name":"Attention Dropout"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"cosine-annealing","method_name":"Cosine Annealing"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"gpt-3","method_name":"GPT-3"},{"method_slug":"gpt-4","method_name":"GPT-4"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"linear-warmup-with-cosine-annealing","method_name":"Linear Warmup With Cosine Annealing"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"transformer","method_name":"Transformer"},{"method_slug":"weight-decay","method_name":"Weight Decay"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":"https://app.syntology.ai/?focus=2305.16326","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}