Sequential versus fully conditional specification for tree-based synthesis of health data

There is no consensus in the field of synthetic data on concise metrics for quality evaluations or benchmarks on large health datasets, such as historical epidemiological data. This study presents an evaluation of seven recent models from major machine learning families. The models were evaluated using four different datasets, each with a distinct scale. To ensure a fair comparison, we systematically tuned the hyperparameters of each model for each dataset. We propose a methodology for evaluating the fidelity of synthesized joint distributions, aligning metrics with visualization on a single plot. This method is applicable to any dataset and is complemented by a domain-specific analysis of the German Cancer Registries' epidemiological dataset. The analysis reveals the challenges models face in strictly adhering to the medical domain. We hope this approach will serve as a foundational framework for guiding the selection of synthesizers and remain accessible to all stakeholders involved in releasing synthetic datasets.

Synthetic data is widely used in healthcare to create datasets that preserve statistical properties of real data without exposing sensitive patient information. Generating and evaluating synthetic data across privacy, utility, and fairness dimensions is crucial for enabling high-quality data availability in downstream prediction tasks and clinical decision making. We present Memisis, a tool that orchestrates and evaluates synthetic data by leveraging existing synthesis libraries, large language models (LLMs), and state-of-the-art evaluation metrics. Our tool creates a unified workflow for data generation, validation, and evaluation. Users can control training size, training epochs, and the number of synthetic rows to sample. Beyond manual configuration, an interactive agent mode allows users to specify data generation goals in natural language, and the tool orchestrates the full pipeline by invoking existing synthesizers while performing the requisite evaluation. For the demo, we use an open-source schizophrenia dataset with protected attributes related to race and gender, evaluate six synthesizers spanning GANs, VAEs, diffusion models, and normalizing flows, and use a local LLM to orchestrate the workflow. The system affords users flexibility and control over the data generation and evaluation process.

Synthetic healthcare data are widely proposed as privacy-preserving substitutes for real patient data, yet their evaluation remains dominated by statistical similarity and predictive performance that do not reflect clinical validity. We introduce a multi-dimensional evaluation framework grounded in epidemiology, assessing descriptive fidelity, clinical utility, and structural validity, corresponding to descriptive, predictive, and causal questions. We evaluate four representative generative paradigms - GAN-based, VAE-boosted, diffusion-based, and masked modelling - using PRIME-CVD, a 50,000-person cohort with known ground-truth structure. While all models reproduce marginal distributions, none simultaneously preserve subgroup structure, effect estimates, and dependency structure. Notably, models with strong distributional fidelity can exhibit poor calibration and distorted relationships, leading to unreliable inference. These results show that current evaluation practices can overestimate synthetic data quality and motivate domain-informed assessment based on the ability to support valid clinical and scientific conclusions.