Electronic Health Records (EHRs) offer rich potential for clinical prediction, yet their inherent complexity and heterogeneity pose significant challenges for traditional machine learning approaches. Domain-specific EHR foundation models trained on large collections of unlabeled EHR data have demonstrated promising improvements in predictive accuracy and generalization; however, their training is constrained by limited access to diverse, high-quality datasets and inconsistencies in coding standards and healthcare practices. In this study, we explore the possibility of using general-purpose Large Language Models (LLMs) based embedding methods as EHR encoders. By serializing patient records into structured Markdown text, transforming codes into human-readable descriptors, we leverage the extensive generalization capabilities of LLMs pretrained on vast public corpora, thereby bypassing the need for proprietary medical datasets. We systematically evaluate two state-of-the-art LLM-embedding models, GTE-Qwen2-7B-Instruct and LLM2Vec-Llama3.1-8B-Instruct, across 15 diverse clinical prediction tasks from the EHRSHOT benchmark, comparing their performance to an EHRspecific foundation model, CLIMBR-T-Base, and traditional machine learning baselines. Our results demonstrate that LLM-based embeddings frequently match or exceed the performance of specialized models, even in few-shot settings, and that their effectiveness scales with the size of the underlying LLM and the available context window. Overall, our findings demonstrate that repurposing LLMs for EHR encoding offers a scalable and effective approach for clinical prediction, capable of overcoming the limitations of traditional EHR modeling and facilitating more interoperable and generalizable healthcare applications.
View on arXiv@article{hegselmann2025_2502.17403,
title={ Large Language Models are Powerful EHR Encoders },
author={ Stefan Hegselmann and Georg von Arnim and Tillmann Rheude and Noel Kronenberg and David Sontag and Gerhard Hindricks and Roland Eils and Benjamin Wild },
journal={arXiv preprint arXiv:2502.17403},
year={ 2025 }
}