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arXiv · 2509.19319

FHIR-AgentBench: Benchmarking LLM Agents for Realistic Interoperable EHR Question Answering

Gyubok Lee·Elea Bach·Eric Yang·Tom Pollard·Alistair Johnson·Edward Choi·Yugang jia·Jong Ha Lee
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Abstract

The recent shift toward the Health Level Seven Fast Healthcare Interoperability Resources (HL7 FHIR) standard opens a new frontier for clinical AI, demanding LLM agents to navigate complex, resource-based data models instead of conventional structured health data. However, existing benchmarks have lagged behind this transition, lacking the realism needed to evaluate recent LLMs on interoperable clinical data. To bridge this gap, we introduce FHIR-AgentBench, a benchmark that grounds 2,931 real-world clinical questions in the HL7 FHIR standard. Using this benchmark, we systematically evaluate agentic frameworks, comparing different data retrieval strategies (direct FHIR API calls vs. specialized tools), interaction patterns (single-turn vs. multi-turn), and reasoning strategies (natural language vs. code generation). Our experiments highlight the practical challenges of retrieving data from intricate FHIR resources and the difficulty of reasoning over them, both of which critically affect question answering performance. We publicly release the FHIR-AgentBench dataset and evaluation suite (https://github.com/glee4810/FHIR-AgentBench) to promote reproducible research and the development of robust, reliable LLM agents for clinical applications.

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Gyubok Lee, Elea Bach, Eric Yang, Tom Pollard, Alistair Johnson, Edward Choi, Yugang jia, Jong Ha Lee. 2025-11-13. FHIR-AgentBench: Benchmarking LLM Agents for Realistic Interoperable EHR Question Answering. https://arxiv.org/abs/2509.19319

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