Improving TabPFN's Synthetic Data Generation by Integrating Causal Structure

Abstract

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 Completed Partially Directed Acyclic Graph (CPDAG)-based strategy for scenarios with partial causal knowledge. We evaluate these approaches on controlled benchmarks and six CSuite datasets, assessing structural fidelity, distributional alignment, privacy preservation, and Average Treatment Effect (ATE) preservation. Across most settings, DAG-aware conditioning improves the quality and stability of synthetic data relative to vanilla TabPFN. The CPDAG-based strategy shows moderate improvements, with effectiveness depending on the number of oriented edges. These results indicate that injecting causal structure into autoregressive generation enhances the reliability of synthetic tabular data.