Improving TabPFN's Synthetic Data Generation by Integrating Causal Structure

Synthetic tabular data are often evaluated by distributional similarity, privacy distance, or train-on-synthetic-test-on-real predictive performance, but these criteria do not ensure validity for causal inference. We show that fully generative tabular synthesizers, including GAN- and LLM-based models, can preserve predictive utility while distorting average treatment effect (ATE) estimates. The failure is structural: ATE preservation requires both a realistic covariate law and an accurate treatment-effect contrast, whereas prediction loss penalizes treatment-effect error only through an overlap-weighted term. Thus, under imbalance or limited overlap, a generator may reproduce dominant observed outcomes while underlearning intervention-relevant contrasts. We formalize this mismatch through sensitivity and loss-decomposition results. Motivated by this causal analysis and intuition, we propose a hybrid synthetic-data framework for causal inference that generates covariates while modeling treatment and outcome mechanisms separately. We evaluate the framework in three settings: ATE preservation under fully generative versus hybrid synthesis, augmentation for practical positivity problems, and diagnostic simulation engines for comparing OR, IPW, AIPW, and TMLE before real-data analysis. We also stress-test the hybrid construction across settings that vary overlap, covariate dimension, seed sample size, and treatment-effect complexity, including a logistic outcome-model misspecification check. Across controlled simulation experiments, hybrid synthesis improves causal fidelity relative to fully generative baselines; the ACTG application shows improved predictive fidelity and potential for finite-sample estimator benchmarking. LLM-based hybrid synthesis is often more faithful than CTGAN in settings where causal fidelity can be assessed.

Existing evaluations of tabular synthesis models rely primarily on low-order statistics and downstream task performance, leaving multivariate causal relationships that go beyond pairwise correlations largely unmeasured. We argue that a systematic evaluation on high-order structural information is a crucial first step in addressing this issue in tabular data synthesis. In this paper, we present high-order structural causal information as a natural form of prior knowledge and introduce a benchmark framework to evaluate tabular synthesis models. This framework allows us to generate benchmark datasets through a flexible range of data generation processes, allowing for the training of tabular synthesis models using these datasets for further evaluation. We propose multiple benchmark tasks, high-order metrics, and causal inference tasks as downstream tasks for evaluating the quality of synthetic data generated by the trained models. Our experiments demonstrate the effectiveness of the benchmark framework in evaluating the model's ability to capture high-order structural causal information. Furthermore, our benchmarking results provide an initial assessment of state-of-the-art tabular synthesis models. These results reveal significant gaps between ideal and actual performance and highlight how baseline methods differ. We position the framework as a controlled diagnostic benchmark for causal fidelity, complementing existing low-order and downstream evaluations. We open source the benchmark framework, including both code and data along with documentation, to support further research in this area.

Most tabular-data generators match marginal statistics yet ignore causal structure, leading downstream models to learn spurious or unfair patterns. We present TabSCM, a mixed-type generator that preserves those causal dependencies. Starting from a Completed Partially Directed Acyclic Graph (CPDAG) found by any causal structure discovery algorithm, TabSCM (i) orients edges to a DAG, (ii) fits root-node marginals with KDE or categorical frequencies, and (iii) learns topologically ordered structural assignments. Such assignments are achieved using conditional diffusion models for continuous variables as child nodes and gradient-boosted trees for categorical ones. Ancestral sampling yields semantically valid records and enables exact counterfactual queries. On seven public datasets, encompassing healthcare, finance, housing, environment, TabSCM matches or surpasses state-of-the-art GAN, diffusion, and LLM baselines in statistical fidelity, downstream utility, and privacy risk, while also cutting rule-violation rates and providing causally meaningful and robust conditional interventions. Because generation is decomposed into explicit equations, it runs up to 583$\times$ faster than diffusion-only models and exposes interpretable knobs for fairness auditing and policy simulation, making TabSCM a practical choice for realism, explainability, and causal soundness.