Score-Based Causal Discovery of Latent Variable Causal Models

Constraint-based causal discovery is widely used for learning causal structures, but heavy reliance on conditional independence (CI) testing makes it computationally expensive in high-dimensional settings. To mitigate this limitation, many divide-and-conquer frameworks have been proposed, but most assume causal sufficiency, i.e., no latent variables. In this paper, we show that divide-and-conquer strategies can be theoretically generalized beyond causal sufficiency to settings with latent variables. Specifically, we propose a recursive decomposition framework, termed DiCoLa, that enables divide-and-conquer causal discovery in the presence of latent variables. It recursively decomposes the global learning task into smaller subproblems and integrates their solutions through a principled reconstruction step to recover the global structure. We theoretically establish the soundness and completeness of the proposed framework. Extensive experiments on synthetic data demonstrate that our approach significantly improves computational efficiency across a range of causal discovery algorithms, while experiments on a real-world dataset further illustrate its practical effectiveness.

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.

Discovering the direct causes and effects of a target variable from observational data is a fundamental problem in causal discovery, with broad applications in domains such as gene regulatory analysis and biomedical research. Existing causal discovery methods either learn a global causal structure, which incurs substantial computational cost, or assume the absence of latent variables and selection bias, assumptions that are often violated in real-world settings. Motivated by these challenges, we study local causal structure learning in the presence of latent variables and selection bias. Specifically, we first characterize a local region that enables target-specific causal discovery without recovering the entire global structure. We then establish a theoretical bridge between causal information learned from the observed distribution induced on this local region and the corresponding information in the global causal structure. Building on these foundations, we propose LoCaLS, a local causal structure learning algorithm that is sound and complete under standard assumptions and identifies the same direct causes and effects of a target variable as those identifiable by global causal discovery methods, while allowing for latent variables and selection bias. Extensive experiments on random and real-world structures demonstrate that the proposed method consistently achieves higher structural accuracy than existing local methods while requiring substantially less computational effort than state-of-the-art global methods. Furthermore, applications to two real-world gene expression datasets reveal biologically plausible target-specific causal structures, demonstrating its practical applicability in large-scale biological data analysis.