CoMedBench: A Multi-Source Benchmark of Synthetic Medical Data Fidelity and Downstream Utility

Abstract:Access to clinical data is essential for developing reliable healthcare machine learning systems, but direct use of electronic health records is constrained by privacy regulation, institutional review, data-use agreements, and the risk of re-identification. Synthetic data promises a practical alternative: it can preserve useful statistical and clinical structure while reducing exposure of sensitive patient records. Prior studies often evaluate a single generator, one dataset, or a narrow downstream task, making it difficult to know when synthetic data can support model development and when it fails to preserve task-critical signal. We introduce CoMedBench, a reproducible benchmark that evaluates a family of generators under a common clinical-validity framework and one shared training and evaluation engine, spanning static tabular and temporal downstream tasks on established critical-care datasets. In total the benchmark spans 37 dataset-task pairs across two modalities consists of 20 static tabular and 17 temporal ICU time-series-drawn from seven public data sources: three intensive-care databases (MIMIC-III, MIMIC-IV, and eICU) together with the UCI Machine Learning Repository, the CDC BRFSS diabetes cohort (2015), NHANES (1999-2014), and the pycox survival datasets (GBSG and METABRIC). The benchmark evaluates both statistical fidelity and task utility by comparing models trained and tested across real and synthetic data. In these settings, synthetic training data preserves most of the downstream signal: on tabular tasks the reference generator CoMed-CTGAN retains a mean AUROC utility (the synthetic-to-real performance ratio) of 90.6%, rising to 97.3% for the strongest generator, CoMed-TVAE. Temporal ICU tasks are harder and more generator-sensitive: CoMed-CTGAN retains 81.6% (AUROC) and only 64.0% under the imbalance-sensitive AUPRC, whereas CoMed-TVAE still retains ~95% (AUROC).

Machine Learning (cs.LG)

arXiv:2608.12805 [cs.LG]

(or arXiv:2608.12805v2 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2608.12805 Focus to learn more arXiv-issued DOI via DataCite

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