EHRStruct: A Comprehensive Benchmark Framework for Evaluating Large Language Models on Structured Electronic Health Record Tasks

Structured Electronic Health Record (EHR) data stores patient information in relational tables and plays a central role in clinical decision-making. Recent advances have explored the use of large language models (LLMs) to process such data, showing promise across various clinical tasks. However, the absence of standardized evaluation frameworks and clearly defined tasks makes it difficult to systematically assess and compare LLM performance on structured EHR data. To address these evaluation challenges, we introduce EHRStruct, a benchmark specifically designed to evaluate LLMs on structured EHR tasks. EHRStruct defines 11 representative tasks spanning diverse clinical needs and includes 2,200 task-specific evaluation samples derived from two widely used EHR datasets. We use EHRStruct to evaluate 20 advanced and representative LLMs, covering both general and medical models. We further analyze key factors influencing model performance, including input formats, few-shot generalisation, and finetuning strategies, and compare results with 11 state-of-the-art LLM-based enhancement methods for structured data reasoning. Our results indicate that many structured EHR tasks place high demands on the understanding and reasoning capabilities of LLMs. In response, we propose SEMaster, a code-augmented method that achieves state-of-the-art performance and offers practical insights to guide future research.