Accelerating Reproducible Research in Synthetic EHR Generation

• URL: http://arxiv.org/abs/2606.06990v1
• Date: Fri, 05 Jun 2026 07:28:26 GMT
• Title: Accelerating Reproducible Research in Synthetic EHR Generation
• Abstract summary: We introduce a lightweight, end-to-end benchmarking framework for reproducible synthetic EHR evaluation.<n>Our current implementation targets the generation of ICD diagnosis codes.<n>We contribute a rigorous, architecture-agnostic privacy-utility evaluation suite.
• Score: 15.020554967749996
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: The generation of high-fidelity synthetic Electronic Health Records (EHR) is crucial for advancing medical research while preserving patient privacy. However, head-to-head comparison of existing generative models is hindered by disjointed codebases, incompatible data loaders, conflicting library dependencies, and inconsistent evaluation protocols. To address these gaps, we introduce a lightweight, end-to-end benchmarking framework for reproducible synthetic EHR evaluation, organized as a unified pipeline spanning data ingestion, standardized model training, and architecture-agnostic evaluation. Our current implementation targets the generation of longitudinal ICD diagnosis codes -- the most commonly studied modality in this literature -- and is built on the community-maintained PyHealth library. We reimplement and unify strong baselines (MedGAN, CorGAN, PromptEHR, HALO) under full ICD-9 vocabulary granularity, and add a lightweight GPT-2 baseline from the general-purpose sequence-modeling literature. We contribute a rigorous, architecture-agnostic privacy-utility evaluation suite that applies identically to GAN- and transformer-based generators, and report bootstrapped confidence intervals across all metrics. We further analyze the poor long-tailed performance of existing models and discuss the extensibility of our framework beyond diagnosis codes. By lowering the engineering barrier to running, extending, and evaluating under a single pipeline, we introduce a starting point for community-driven reproducibility and benchmarking synthetic EHR models.

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