Information Extraction From Clinical Notes: Are We Ready to Switch to Large Language Models?

Authors

• Yan Hu
• Xu Zuo
• Yujia Zhou
• Xueqing Peng
• Jimin Huang
• Vipina K Keloth
• Vincent J Zhang
• Ruey-Ling Weng
• Cathy Shyr
• Qingyu Chen
• Xiaoqian Jiang
• Kirk E Roberts
• Hua Xu

Language

English

Publication Date

3-1-2026

Journal

Journal of the American Medical Informatics Association

DOI

10.1093/jamia/ocaf213

PMID

41533750

PMCID

PMC12981642

PubMedCentral® Posted Date

1-14-2026

PubMedCentral® Full Text Version

Post-print

Abstract

Objectives: To assess the performance, generalizability, and computational efficiency of instruction-tuned Large Language Model Meta AI (LLaMA)-2 and LLaMA-3 models compared to bidirectional encoder representations from transformers (BERT) for clinical information extraction (IE) tasks, specifically named entity recognition (NER) and relation extraction (RE).

Materials and methods: We developed a comprehensive annotated corpus of 1588 clinical notes from 4 data sources-UT Physicians (UTP) (1342 notes), Transcribed Medical Transcription Sample Reports and Examples (MTSamples) (146), Medical Information Mart for Intensive Care (MIMIC)-III (50), and Informatics for Integrating Biology and the Bedside (i2b2) (50), capturing 4 clinical entities (problems, tests, medications, other treatments) and 16 modifiers (eg, negation, certainty). Large Language Model Meta AI-2 and LLaMA-3 were instruction-tuned for clinical NER and RE, and their performance was benchmarked against BERT.

Results: Large Language Model Meta AI models consistently outperformed BERT across datasets. In data-rich settings (eg, UTP), LLaMA achieved marginal gains (approximately 1% improvement for NER and 1.5%-3.7% for RE). Under limited data conditions (eg, MTSamples, MIMIC-III) and on the unseen i2b2 dataset, LLaMA-3-70B improved F1 scores by over 7% for NER and 4% for RE. However, performance gains came with increased computational costs, with LLaMA models requiring more memory and Graphics Processing Unit (GPU) hours and running up to 28 times slower than BERT.

Discussion: While LLaMA models offer enhanced performance, their higher computational demands and slower throughput highlight the need to balance performance with practical resource constraints. Application-specific considerations are essential when choosing between LLMs and BERT for clinical IE.

Conclusion: Instruction-tuned LLaMA models show promise for clinical NER and RE tasks. However, the tradeoff between improved performance and increased computational cost must be carefully evaluated. We release our Kiwi package (https://kiwi.clinicalnlp.org/) to facilitate the application of both LLaMA and BERT models in clinical IE applications.

Keywords

Large Language Models, Humans, Electronic Health Records, Information Storage and Retrieval, Natural Language Processing, Data Mining, large language model, information extraction, instruction-tuning

Published Open-Access

yes

Recommended Citation

Hu, Yan; Zuo, Xu; Zhou, Yujia; et al., "Information Extraction From Clinical Notes: Are We Ready to Switch to Large Language Models?" (2026). Faculty, Staff and Student Publications. 987.
https://digitalcommons.library.tmc.edu/uthshis_docs/987