Efficient Ensemble Conditional Independence Test Framework for Causal Discovery

Abstract

Constraint-based causal discovery relies on numerous conditional independence tests (CITs), but its practical applicability is severely constrained by the prohibitive computational cost, especially as CITs themselves have high time complexity with respect to the sample size. To address this key bottleneck, we introduce the Ensemble Conditional Independence Test (E-CIT), a general-purpose and plug-and-play framework. E-CIT operates on an intuitive divide-and-aggregate strategy: it partitions the data into subsets, applies a given base CIT independently to each subset, and aggregates the resulting p-values using a novel method grounded in the properties of stable distributions. This framework reduces the computational complexity of a base CIT to linear in the sample size when the subset size is fixed. Moreover, our tailored p-value combination method offers theoretical consistency guarantees under mild conditions on the subtests. Experimental results demonstrate that E-CIT not only significantly reduces the computational burden of CITs and causal discovery but also achieves competitive performance. Notably, it exhibits an improvement in complex testing scenarios, particularly on real-world datasets.