Causality for Tabular Data Synthesis: A High-Order Structure Causal Benchmark Framework

Synthetic tabular data generation addresses data scarcity and privacy constraints in a variety of domains. Tabular Prior-Data Fitted Network (TabPFN), a recent foundation model for tabular data, has been shown capable of generating high-quality synthetic tabular data. However, TabPFN is autoregressive: features are generated sequentially by conditioning on the previous ones, depending on the order in which they appear in the input data. We demonstrate that when the feature order conflicts with causal structure, the model produces spurious correlations that impair its ability to generate synthetic data and preserve causal effects. We address this limitation by integrating causal structure into TabPFN's generation process through two complementary approaches: Directed Acyclic Graph (DAG)-aware conditioning, which samples each variable given its causal parents, and a partially directed acyclic graph (PDAG)-based strategy for scenarios with partial causal knowledge. We evaluate these approaches on controlled benchmarks and six CSuite datasets, assessing structural fidelity, distributional quality, and Average Treatment Effect (ATE) preservation. Across most settings, DAG-aware conditioning improves the quality and stability of synthetic data relative to vanilla TabPFN. Under partial causal knowledge, the oracle partially directed acyclic graph (oracle-PDAG), which orients only the edges into the colliders, shows moderate gains, while the benefit of a Completed Partially Directed Acyclic Graph (CPDAG) discovered from data depends on how well the causal structure is recovered. These results indicate that reliable causal structure, even partial, can be injected into TabPFN at inference time, without parameter updates, to improve synthetic data quality.

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.

Synthetic tabular data support use cases like data sharing, model development under access restrictions, and rapid prototyping of analytical workflows. Modern generative models are evaluated by their statistical similarity, correlation structure, privacy, and downstream machine-learning utility. However, such evaluations leave a gap: they rarely test the structure that matters for analytical queries. We present TabQueryBench, a query-centric benchmark that uses SQL-shaped analytical queries as structural assessors for synthetic data fidelity. It provides an extensible foundation for query-centric synthetic-data evaluation. From 12 public sources of analytical queries, TabQueryBench taxonomizes recurring cross-domain logic into 44 reusable query templates and grounds them to each dataset via a policy-guided template-to-SQL pipeline. This makes queries schema-aware while preserving comparability across generative models. Across 49 datasets and 11 generative models, it activates 10-12 templates per dataset, producing more than 100 executable SQL queries per dataset. Our systematic experiments show five main patterns. First, current tabular generative models can have good distance-based fidelity, but they still fall short on query-centric fidelity: RealTabFormer achieves the highest query-centric fidelity, but it only reaches 0.75 +/- 0.15 (REAL data score is 1.00). Second, tabular generative models struggle with very high-cardinality discrete support. Third, SOTA generative models preserve good global conditional query-centric fidelity, but fail more on local queries. Fourth, tail fidelity deteriorates as queries move toward the extreme tail; even the best model recovers only about 40.7% of real rare values. Finally, there is a fidelity-cost tradeoff in tabular generation: BayesNet offers the strongest tradeoff, with slightly lower query-centric fidelity but much lower generation cost.