Fourier Feature Methods for Nonlinear Causal Discovery: FFML Scoring, TRFF Scoring, and FFCI Testing in Mixed Data

Causal discovery with nonlinear mechanisms and latent confounders remains challenging. Existing methods often rely on either linear assumptions or causal sufficiency, limiting their applicability. We propose an MDL-based causal discovery framework that explicitly accounts for latent confounders while allowing flexible nonlinear mechanisms by minimizing the luckiness normalized maximum likelihood (LNML) code-length. The causal relationship between each variable pair is determined by selecting the shortest code-length of the causal model, and we introduce the notion of $Δ$-pseudo-collinearity to identify dependencies induced by latent confounders. Based on these ideas, we develop a greedy algorithm, termed Pseudo-Collinearity Guided Causal Discovery (PCG-CD). Experiments on synthetic and real-world datasets demonstrate that the proposed method accurately recovers directed causal relationships and effectively detects latent confounders.

Constraint-based causal discovery relies on repeated conditional independence tests, but fast nonparametric tests often sacrifice calibration, especially when variables depend on the conditioning set through nonlinear relationships. We introduce BLITZ (Broad-to-Local Independence Testing via residualiZation), a nonparametric conditional independence test designed to run well under a second while maintaining the accuracy needed for the thousands of queries performed by constraint-based causal discovery algorithms. BLITZ first removes broad smooth dependence on the conditioning set using low-order polynomial regression, then applies a small nonlinear feature map and residualizes those features with shallow tree regressions. The resulting statistic tests residual cross-covariance, with a moment-matched chi-square approximation to the null distribution. We show theoretically that the two-stage design reduces the effective complexity faced by the tree residualizers, allowing shallow trees to control residual conditional-mean bias while avoiding excessive overfitting. In simulations, BLITZ provides better null calibration than fast kernel, random-feature, and regression-based competitors while remaining among the fastest methods tested. In causal discovery experiments on synthetic graphs and flow-cytometry data, BLITZ yields more reliable endpoint orientations among retained adjacencies and competitive structural recovery. These results suggest that broad-to-local residualization is a practical route to calibrated, scalable nonparametric conditional independence testing for causal discovery.

In this paper we study linear non-Gaussian acyclic models (LiNGAM) when used in federated environments. These causal models allow one to go beyond Markov equivalence. However, in many domains data are scarce, and increasing the sample size by centralising data from different clients is not advisable due to regulations such as the GDPR. The federated environment offers an attractive option to balance privacy and causal discovery accuracy. Unfortunately, the standard centralised estimator in the LiNGAM setting, i.e., DirectLiNGAM, cannot be straightforwardly federated. Higher-order cumulant tensors offer a way around this obstacle: they depend only on the joint distribution of the variables involved and add exactly across independent sample groups, so a single communication round suffices in horizontal, vertical, and hybrid partitions. However, FedISHC, i.e., the current federated method along these lines, breaks down under near-symmetric noise. To overcome the above limitation, we introduce the FedRCD family of causal discovery algorithms, and investigate three variants that trade off communication rounds against algebraic noise; two of them are exact federated counterparts of the centralised high-order cumulant (HC) and HC-LiNGAM algorithms, and the single-round variants further effectively support exact unlearning at any granularity, from a single observation to a whole client. Numerical experiments show that at sample sizes typical of real deployments, the entire cumulant-based federated family does not actually rank variables by the population asymmetry that the scores encode at zero. It ranks them by a variance ladder induced by the DAG along its directed paths, the cumulant counterpart of varsortability. Marginal standardisation collapses every cumulant method to near-random ordering, while scale-invariant DirectLiNGAM, not federable under this protocol, is unaffected.