Learning Granger Causality under Latent Confounding via Intervention-Induced Heterogeneity

Causal discovery aims to recover causal relationships from observed data. In various fields, exploring causal relationships among variables remains an important topic, but this task becomes challenging due to the existence of latent confounders. Ignoring such confounders can lead to false associations and incorrect edge directions. In this paper, we study the linear structural equation model with latent confounders. We propose an algorithm that iteratively identifies terminal (observed) nodes and reconstructs the directed acyclic graph of the observed variables. To do this, we recover the precision matrix of the observed variables as a sparse plus low-rank matrix: a sparse matrix captures the conditional dependencies among observed variables, while a low-rank matrix captures the combined influence of a few latent confounders. We establish that for $p$ observed variables, $r$ latent confounders and $s$ edges, our procedure correctly identifies the directed causal relationship among observed variables, for $n \gtrsim \max\{s\log p,\ r p\}$ samples. Experimental results validate our theoretical contributions.

From climate teleconnections to gene regulation, modern time-series datasets encompass tens or hundreds of interacting variables, making causal discovery increasingly challenging. Constraint-based methods offer statistical rigor but their nonlinear CI tests are infeasible at scale, while score-based alternatives avoid CI testing but require arbitrary thresholds to binarize continuous edge scores. We propose GRACE ($\textbf{G}$ated $\textbf{R}$efinement for $\textbf{A}$ccurate $\textbf{C}$ausal $\textbf{E}$dge discovery), which refines constraint-based discovery using Hard Concrete gates with $L_0$ regularization: each candidate edge has an independent gate whose values concentrate near 0 or 1, yielding a clean bimodal separation that makes the binary decision robust, unlike the narrow, overlapping score distributions produced by $L_1$ and attention-based methods. A fast linear CI skeleton provides high-recall candidates; a single gated model then prunes false positives by learning which edges genuinely improve prediction, with automatic regularization adapted to problem dimensions and skeleton density. Systematic experiments on synthetic benchmarks, spanning diverse graph topologies (scale-free, Erdős-R'enyi, small-world) and dimensionalities up to $d=100$, show that GRACE substantially improves F1 over its base CI method while maintaining high precision, and outperforms attention-based and score-based alternatives. GRACE matches or exceeds expensive nonlinear CI tests at a fraction of the cost ($75\times$ faster). On a real-world river flow dataset, where rainfall confounders, variable propagation lags, and distributional shifts violate standard assumptions, a temporal bootstrap variant of GRACE recovers 9 of 11 causal edges along the Elbe River with only 1 false positive ($F_1 = 0.86$, AUROC${} = 0.99$), reducing the skeleton's 106 false positives by 99%.

Finding which variables cause which others in multivariate time series, and at what lags, is central to science and policy, yet existing methods force a choice between flexible confounder adjustment, data-driven lag selection, and inference that controls the false discovery rate (FDR). ORACLE-VARX does all three in one pipeline. First, double/debiased machine learning (DML) removes nonlinear confounder effects from the outcomes and the lagged series. Second, adaptive causal lag estimation (ACLE) picks the lag order at each time step by sequential significance tests, tracking regime changes. Third, entry-wise $z$-tests with Benjamini--Hochberg correction select directed edges at a target FDR. We prove that in each rolling window, the debiased coefficients are asymptotically normal around a window-averaged target, so their $z$-tests are asymptotically valid. On a synthetic benchmark with time-varying structure and nonlinear confounding, ORACLE-VARX (LightGBM) tracks the true lag order best (RMSE $0.96$ vs $1.1$--$1.5$), has edge FDR $0.047$, close to PCMCI ($0.045$) and below VAR ($0.129$) and VAR-LiNGAM ($0.187$), and forecasts better than all three. On nine U.S. sector ETFs with macroeconomic confounders, it yields interpretable causal graphs whose lag order rises in high-volatility regimes.