A Study of Large Language Models for Patient Information Extraction: Model Architecture, Fine-Tuning Strategy, and Multi-task Instruction Tuning

Natural language processing (NLP) is a key technology to extract important patient information from clinical narratives to support healthcare applications. The rapid development of large language models (LLMs) has revolutionized many NLP tasks in the clinical domain, yet their optimal use in patient information extraction tasks requires further exploration. This study examines LLMs' effectiveness in patient information extraction, focusing on LLM architectures, fine-tuning strategies, and multi-task instruction tuning techniques for developing robust and generalizable patient information extraction systems. This study aims to explore key concepts of using LLMs for clinical concept and relation extraction tasks, including: (1) encoder-only or decoder-only LLMs, (2) prompt-based parameter-efficient fine-tuning (PEFT) algorithms, and (3) multi-task instruction tuning on few-shot learning performance. We benchmarked a suite of LLMs, including encoder-based LLMs (BERT, GatorTron) and decoder-based LLMs (GatorTronGPT, Llama 3.1, GatorTronLlama), across five datasets. We compared traditional full-size fine-tuning and prompt-based PEFT. We explored a multi-task instruction tuning framework that combines both tasks across four datasets to evaluate the zero-shot and few-shot learning performance using the leave-one-dataset-out strategy.