Large Language Models for Automating Clinical Data Standardization: HL7 FHIR Use Case

TL;DR

This paper demonstrates that large language models like GPT-4o and Llama 3.2 can effectively automate the conversion of clinical data into HL7 FHIR format, improving interoperability in healthcare data exchange.

Contribution

It introduces a semi-automated, prompt-based method leveraging LLMs for clinical data standardization into HL7 FHIR, with high accuracy demonstrated on the MIMIC-IV dataset.

Findings

Resource identification achieved perfect F1-score with GPT-4o.

Accuracy remained high at 94% under real-world conditions.

Prompt refinement mitigated hallucinations and mismatches.

Abstract

For years, semantic interoperability standards have sought to streamline the exchange of clinical data, yet their deployment remains time-consuming, resource-intensive, and technically challenging. To address this, we introduce a semi-automated approach that leverages large language models specifically GPT-4o and Llama 3.2 405b to convert structured clinical datasets into HL7 FHIR format while assessing accuracy, reliability, and security. Applying our method to the MIMIC-IV database, we combined embedding techniques, clustering algorithms, and semantic retrieval to craft prompts that guide the models in mapping each tabular field to its corresponding FHIR resource. In an initial benchmark, resource identification achieved a perfect F1-score, with GPT-4o outperforming Llama 3.2 thanks to the inclusion of FHIR resource schemas within the prompt. Under real-world conditions, accuracy dipped slightly to 94 %, but refinements to the prompting strategy restored robust mappings. Error analysis revealed occasional hallucinations of non-existent attributes and mismatches in granularity, which more detailed prompts can mitigate. Overall, our study demonstrates the feasibility of context-aware, LLM-driven transformation of clinical data into HL7 FHIR, laying the groundwork for semi-automated interoperability workflows. Future work will focus on fine-tuning models with specialized medical corpora, extending support to additional standards such as HL7 CDA and OMOP, and developing an interactive interface to enable expert validation and iterative refinement.