LLMs in Biomedicine: A study on clinical Named Entity Recognition
Masoud Monajatipoor, Jiaxin Yang, Joel Stremmel, Melika Emami, Fazlolah Mohaghegh, Mozhdeh Rouhsedaghat, Kai-Wei Chang
Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedicine due to medical language complexities and data scarcity. This paper investigates the application of LLMs in the medical domain by exploring strategies to enhance their performance for the Named-Entity Recognition (NER) task. Specifically, our study reveals the importance of meticulously designed prompts in biomedicine. Strategic selection of in-context examples yields a notable improvement, showcasing ~15-20\% increase in F1 score across all benchmark datasets for few-shot clinical NER. Additionally, our findings suggest that integrating external resources through prompting strategies can bridge the gap between general-purpose LLM proficiency and the specialized demands of medical NER. Leveraging a medical knowledge base, our proposed method inspired by Retrieval-Augmented Generation (RAG) can boost the F1 score of LLMs for zero-shot clinical NER. We will release the code upon publication.