Causal Discovery with Latent Confounding

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3 papers in the last four weeks, with none the four weeks before. 0.0% of all new papers.

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Latest papers 22

Sep 29, 2026cs.LG

Differentiable Structure Learning for Cyclic Linear Gaussian Models with Latent Confounders

We study causal structure learning from observational data in linear Gaussian structural causal models in the presence of directed cycles and an unknown number of exogenous latent confounders, bounded by a given maximum. We derive the covariance of the observed variables and introduce marginal quasi-equivalence, which characterizes when different causal models share a full-dimensional subset of the observational distributions they can generate. We formulate structure learning as minimization of the Gaussian negative log-likelihood with a logarithmically scaled complexity penalty that counts directed edges and latent variables. For a fixed number of observed variables and a fixed upper bound on latent variables, we establish consistency of global score minimizers up to marginal quasi-equivalence under algebraic faithfulness, structural minimality, and model-overlap assumptions. We parameterize the inclusion of directed edges and candidate latent variables using Bernoulli gates, whose continuous probabilities are optimized jointly with the structural coefficients. Averaging the penalized negative log-likelihood over these gates yields an objective with a closed-form differentiable complexity penalty. We prove that this expected objective has the same global infimum as the corresponding discrete structure-learning objective. Experimental results show that our approach achieves lower recovery error than previous methods in several experimental settings.

Sadegh Khorasani, Ali Najar, Saber Salehkaleybar +1

School of Computer and Communication Sciences, EPFL, Lausanne, Switzerland · Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands · College of Management of Technology, EPFL, Lausanne, Switzerland

Structural Causal Models Causal Discovery Causal Structure Learning Causal Identifiability Causal Discovery with Latent Confounding

Sep 21, 2026cs.LG

Hessian Rank Constraint for Learning Structure of Nonlinear Latent Variable Models

Uncovering latent variables and their causal relations from observed data is a fundamental yet challenging problem. Existing methods often rely on restrictive assumptions, such as linear relations or invertible mixing functions. To better address this problem under general nonlinear mixing procedures, we propose a condition called the cross-Hessian Rank Constraint (HRC), which serves as a primitive rank-based tool for nonlinear latent causal discovery. In particular, we show that a rank-based property arises from the cross-Hessian of the observed-data log-density in the nonlinear case, revealing information about the latent variables, and reduces to the Tetrad constraints in the linear Gaussian case. More specifically, when two groups of observed variables are d-separated by a set of lower-dimensional latent variables, the rank of this cross-Hessian is equal to the dimension of the latent variables, under a mild affine derivative assumption on the conditional log-density derivatives. This assumption can be naturally satisfied when the noise level is low or the relevant nonlinearity is moderate. As a downstream application, we instantiate HRC in the pure one-factor measurement setting for locating latent variables and recovering their causal structure up to Markov equivalence. Experimental results on synthetic and real-world datasets support the theoretical claims.

Zijian Li, Ruichu Cai, Feng Xie +7

Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, UAE · Carnegie Mellon University, Pittsburgh, PA, USA · Guangdong University of Technology, Guangzhou, China +3

Latent Variable Models Causal Discovery Causal Structure Learning Causal Discovery with Latent Confounding

Sep 16, 2026cs.LG

Provable Guarantees and Efficient Learning of Structural Equation Models with Latent Confounders

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.

Weijian Yu, Jean Honorio

CIS, The University of Melbourne

Structural Causal Models Low-Rank Matrix Decomposition Causal Structure Learning Causal Discovery with Latent Confounding

Jul 22, 2026cs.LG

Local Causal Structure Learning in the Presence of Latent Variables and Selection Bias

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.

Zheng Li, Hao Zhang, Ruxin Wang +3

Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China. · School of Computer Science, Guangdong University of Technology, Guangzhou, China. · Peng Cheng Laboratory, Shenzhen, China. +3

Causal Discovery Causal Structure Learning Causal Discovery with Latent Confounding

Jul 21, 2026math.OC

Equilibrium Causal Games: Separation, Identification, and the Identifiability of Cyclic Latent States

Power grids, markets, and interacting populations, settle into feedback driven equilibria observed through unknown sensors. Our Equilibrium Causal Game (ECG) joins a game to its cyclic causal model, hidden inputs, sensor map, and rules for interventions and equilibrium selection; interventions edit declared objects and recompute equilibrium. Under stated conditions, ECG-separation is sound but incomplete in our examples. Back-door/half-trek routes identify observed queries. Yet for an untouched rotationally symmetric Gaussian block, second moments determine only a source-frame rotation, across which distinct-variable effects generically change. Unknown sensing creates a separate ambiguity. In passive stable linear models without self-effects, unknown wiring and full-rank unknown sensing leave

B

completely unidentified for

d\ge2

. Under LiNG, non-Gaussianity removes the source rotation; mechanism interventions separate sensing from interactions. With unknown support, invariant sensing, aligned responses, and well-posed single-target interventions identify

(H,B)

up to declared equivalence. Of

d

targets,

d-1

suffice exactly when the sole untargeted node directly parents all others; otherwise

d

are needed. Acquisition probes are excluded; known wiring gives no universal count. With nonlinear sensing, isotropic Gaussian source blocks admit hidden twists within and across blocks in labelled environments preserving required radial laws. Conversely, under stated positivity, informative one-block changes, rank, and irreducibility conditions, the finest independent source-block representation is identified within the stated alternative class up to block permutation and blockwise coordinate changes, but not downstream mechanisms or the sensor/interaction split. Together, these results show which causal conclusions equilibrium data support and which require targeted experiments.

Faraz Dadgostari, Neda Nazemi

Department of Mechanical & Industrial Engineering, Montana State University · Gianforte School of Computing, Montana State University

Causal Representation Learning Causal Identifiability Causal Inference Causal Intervention Causal Discovery with Latent Confounding

Jul 10, 2026cs.AI

How Does Bayesian Causal Discovery Fail? Characterising Structural Consequences in Linear Gaussian Networks under Latent Confounding

Bayesian causal discovery is widely used for its ability to quantify epistemic uncertainty over directed acyclic graphs (DAGs) through posterior inference. However, its behaviour under latent confounding remains poorly understood, as existing work typically notes that confounding breaks identifiability without characterising how the posterior distribution over DAGs responds. In this work, we analyse posterior behaviour under latent confounding in linear Gaussian causal models, focusing on additive latent confounding between exactly two observed variables. We derive a critical correlation threshold above which the score function favours graphs with a spurious edge between the confounded variables, and show that this threshold decreases with sample size -- more data lowers the correlation required for the spurious edge to be favoured. Beyond this threshold, we characterize two distinct posterior failure regimes determined by the local structure around the confounded variables. Our findings are supported by exact posterior computations on multiple graph structures, demonstrating both the predicted failure regimes.

Debargha Ghosh, Silja Renooij, Anna V. Kononova

Department of Information and Computing Sciences, Utrecht University · Leiden Institute of Advanced Computer Science, Leiden University

Structural Causal Models Bayesian Networks Causal Discovery Causal Discovery with Latent Confounding

Jul 7, 2026cs.LG

Learning Sparsest Linear Causal DAGs with Latent Confounders via Higher-Order Cumulants

Recovering the exact directed acyclic graph (DAG) in linear non-Gaussian acyclic models with latent confounders (LvLiNGAM) remains a challenging problem. Although LvLiNGAM is identifiable only up to an observational equivalence class, each equivalence class is characterized by a unique sparsest DAG. Recovering the sparsest DAG from finite samples, however, remains difficult. Although existing methods are asymptotically consistent, they do not provide an explicit finite-sample procedure for recovering the unique sparsest DAG, nor do they handle models with an arbitrary number of latent confounders. In this paper, we propose a finite-sample method for recovering the sparsest DAG without imposing any restriction on the number of latent confounders. Simulation studies and real-data analyses demonstrate that the proposed method achieves superior finite-sample performance compared with existing approaches.

Ming Cai, Hisayuki Hara

Graduate School of Informatics, Kyoto University, Kyoto, Japan · Institute for Liberal Arts and Sciences, Kyoto University, Kyoto, Japan

Structural Causal Models Causal Discovery Causal Discovery with Latent Confounding

Jul 5, 2026cs.LG

MDL Meets Latent Confounders: LNML-based Causal Discovery

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.

Zhongyi Que, Shin Matsushima, Kenji Yamanishi

Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan · Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan

Minimum Description Length Causal Discovery Causal Discovery with Latent Confounding

Jun 18, 2026cs.LG

Temporal Causal Prior-Data Fitted Networks for Panel Data with Learned Reliability Signals

Estimating causal effects in industrial time series requires handling temporal dynamics, time-varying treatments, and unobserved confounders. Existing causal foundation models (CausalPFN, CausalFM) operate only on static cross-sectional data; neural temporal methods (CRN, G-Net) require per-dataset training; and concurrent temporal-PFN proposals have not been demonstrated at industrial scale. None output explicit per-pair reliability signals alongside their CATE estimates. We introduce Temporal Causal Prior-Data Fitted Networks (TCPFN), a foundation model for zero-shot temporal causal discovery with learned reliability signals. TCPFN makes four contributions: (1) a Causal Judgment Head that jointly predicts null-effect probability, confounding strength, identifiability, mediation fraction, and causal regime; (2) a mixed training prior covering six causal regimes (independent, direct, confounded, mediated, time-varying confounded, feedback) plus CausalFM-style front-door and instrumental-variable priors; (3) a discrete-token panel-data architecture with cross-attention masking that prevents inter-horizon leakage; (4) zero-shot inference at industrial scale via FAISS-based context selection and one-step posterior correction. On 19 benchmark datasets across five domains, TCPFN achieves competitive zero-shot causal discovery: AUROC 0.96 on Tennessee Eastman, 0.93 on SWaT, 0.98 on Causal Rivers, 0.97 on CAUSRCA. The null detector reaches NullF1 0.94, AUROC 0.99. TCPFN scales to V=1,275 on a proprietary Kraft pulp-and-paper dataset in 6 hours on a single GPU; PCMCI, a CPU-only library, on a V=666 sub-panel of the same data took 81.5 hours, extrapolating by O(V^2) to ~12.5 days at V=1,275. TCPFN's top edges identify cross-subsystem causal relationships while PCMCI's surface within-instrument controller-measurement coupling -- a scalability case study.

Shravan Talupula, Saurabh Sharma

ProfitOps Inc.

Causal Foundation Models Causal Effect Estimation Time-Series Causal Discovery Causal Identifiability Prior-Data Fitted Networks Causal Discovery with Latent Confounding

Jun 17, 2026cs.LG

Latent Confounded Causal Discovery via Lie Bracket Geometry

Recent work on Kan-Do-Calculus (KDC) has established that the boundary between passive observation and active intervention in causal inference is a category-theoretic bi-adjunction, with interventions modeled by left Kan extensions and conditioning by right Kan extensions. This paper introduces two causal discovery algorithms under latent confounding, building on the information-geometric and categorical consequences of KDC. In smooth statistical settings, Radon-Nikodym derivatives between observational and interventional measures induce local causal vector fields; failures of these fields to close under Lie brackets become computable Frobenius residuals, which we interpret as witnesses of failed visible integrability and possible latent or unmodeled structure. Our first algorithm, BRIDGE (Bracket Residuals for Interventional Discovery and Geometric Estimation), combines an interventional density or Radon-Nikodym-ratio engine with a geometric screen that proposes a high-recall family of admissible arrows, identifies non-closing visible pairs as latent-obstruction candidates, and passes the reduced family to downstream score-based or differentiable discovery routines. The second algorithmic contribution, Spectral Kan-Do Flow Matching (SKFM), learns amortized intervention fields and factors latent curvature spectrally, exposing the direct Lie-space endpoint toward which BRIDGE points. A detailed set of experiments show that both algorithms are capable of discovering causal models with latent confounders while collapsing the super-exponential space of possible DAGs by many orders of magnitude. This paper introduces a new paradigm in causal discovery, where latent structure is inferred directly from the geometry of intervention-induced flows.

Sridhar Mahadevan

Adobe Research and University of Massachusetts, Amherst

Causal Discovery Causal Intervention Causal Discovery with Latent Confounding

Jun 17, 2026cs.LG

Identifying Structural Biases from Causal Mechanism Shifts

Causal discovery methods commonly assume that all data is independently and identically distributed (i.i.d.) and that there are no unmeasured variables affecting the system. In practice, these assumptions are often violated, leading to inaccurate inference. In this paper, we study how to identify hidden confounding and selection biases from causal mechanism shifts. In particular, we show that structural biases lead to dependent mechanism shifts. That is, by considering for which variables the mechanisms change given data from different environments, we can tell which variables are unbiased, which are subject to hidden confounding, and which are undergoing selection bias. We formalize this into an empirically testable criterion based on mutual information, and show under which conditions it identifies structural biases. To tell which nodes are subject to what kind of bias, we introduce the StruBI algorithm. Experiments on synthetic and real-world data show that StruBI works well in practice, accurately recovering affected variable sets and types of biases, outperforming the state-of-the-art by a wide margin.

Praharsh Nanavati, Jilles Vreeken, David Kaltenpoth

CISPA Helmholtz Center for Information Security

Structural Causal Models Causal Discovery Causal Inference Selection Bias Causal Discovery with Latent Confounding

Jun 16, 2026cs.LG

FoundCause: Causal Discovery with Latent Confounders from Observational Data

Causal discovery from observational data remains challenging due to the need to recover directed structure and latent confounding without interventions. We propose FoundCause, an amortized causal discovery model trained entirely on synthetic data that maps datasets directly to causal graphs in a single forward pass. By learning from large collections of simulated structural causal models, FoundCause captures transferable statistical patterns that generalize beyond individual datasets. The architecture incorporates several key inductive biases for causal discovery. It uses a permutation-invariant transformer encoder with alternating attention over samples and variables to jointly model cross-variable dependence and per-variable distributions. Pairwise statistical features derived from classical asymmetry measures are injected through statistics-conditioned attention, guiding the model toward known causal signals. A factorized decoder separates edge existence from direction, while a triangular refinement module enables reasoning over higher-order causal motifs such as chains and colliders. In addition, a dedicated confounder module based on learnable latent tokens explicitly models hidden common causes, and the model explicitly handles missing data via its masked input representation. To our knowledge, FoundCause is the first amortized causal discovery approach to explicitly model latent confounding. FoundCause outperforms 11 classical non-amortized methods (e.g., PC, GES, NOTEARS-style optimization) and 4 amortized causal discovery methods on 15 real-world datasets, achieving +9.6% improvement in

F_1

, +1.2% in AUROC, and an 18.9% reduction in structural Hamming distance relative to the strongest non-amortized methods, while performing inference in a single forward pass.

Patrick Blöbaum, Krishnakumar Balasubramanian, Shiva Prasad Kasiviswanathan

Amazon Web Services · Department of Statistics, University of California, Davis

Structural Causal Models Amortized Inference Causal Discovery Causal Discovery with Latent Confounding

Jun 6, 2026stat.ML

Beyond Additivity: Causal Discovery in Location-Scale Noise Models with Hidden Variables

We study causal discovery from observational data when some variables are hidden and the data-generating process follows a location-scale noise model (LSNM). Existing methods that handle hidden confounders typically assume additive noise, but in practice, causes often modulate not just the mean but also the variance of their effects. We prove that acyclic directed mixed graphs (ADMGs) satisfying a bow-free condition are identifiable under LSNM with hidden variables, establishing the first identifiability result for causally insufficient models beyond noise additivity. We further provide sufficient conditions for identifying causal direction even when the bow-free assumption is violated. Our two-stage algorithm, LSNM-UV, is sound and complete, and experiments demonstrate improved performance over additive baselines on heteroscedastic data.

Mariyam Khan, Shohei Shimizu, Thong Pham

University of Bergen · *Work conducted while a student trainee at RIKEN AIP · 2The University of Osaka +2

Graph Structure Learning Causal Discovery Causal Identifiability Causal Discovery with Latent Confounding

May 19, 2026cs.LG

Score-Based Causal Discovery of Latent Variable Causal Models

Identifying latent variables and the causal structure involving them is essential across various scientific fields. While many existing works fall under the category of constraint-based methods (with e.g. conditional independence or rank deficiency tests), they may face empirical challenges such as testing-order dependency, error propagation, and choosing an appropriate significance level. These issues can potentially be mitigated by properly designed score-based methods, such as Greedy Equivalence Search (GES) (Chickering, 2002) in the specific setting without latent variables. Yet, formulating score-based methods with latent variables is highly challenging. In this work, we develop score-based methods that are capable of identifying causal structures containing causally-related latent variables with identifiability guarantees. Specifically, we show that a properly formulated scoring function can achieve score equivalence and consistency for structure learning of latent variable causal models. We further provide a characterization of the degrees of freedom for the marginal over the observed variables under multiple structural assumptions considered in the literature, and accordingly develop both exact and continuous score-based methods. This offers a unified view of several existing constraint-based methods with different structural assumptions. Experimental results validate the effectiveness of the proposed methods.

Ignavier Ng, Xinshuai Dong, Haoyue Dai +3

Carnegie Mellon University · University of California, San Diego · Mohamed bin Zayed University of Artificial Intelligence

Latent Variable Models Structural Causal Models Causal Discovery Causal Structure Learning Causal Identifiability Causal Discovery with Latent Confounding

May 11, 2026cs.LG

A Recursive Decomposition Framework for Causal Structure Learning in the Presence of Latent Variables

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.

Zheng Li, Feng Xie, Shenglan Nie +3

Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China · Department of Applied Statistics, Beijing Technology and Business University, Beijing, China · College of Computer Science and Artificial Intelligence, Fudan University, Shanghai, China

Causal Discovery Causal Structure Learning Causal Discovery with Latent Confounding

May 8, 2026cs.LG

Physical Simulators as Do-Operators: Causal Discovery under Latent Confounders for AI-for-Science

Existing interventional causal discovery methods -- IGSP, DCDI, ENCO -- assume causal sufficiency (no latent confounders) and rely on virtual interventions in synthetic simulators. In AI-for-Science settings such as molecular design and materials science, latent confounders are ubiquitous and real interventions (e.g., physics-based simulations) require hours to days per data point. We propose CFM-SD (Causal Flow Matching with Simulation Data), which uses first-principles physical simulators as do-operators in Pearl's interventional calculus to simultaneously handle latent confounders and real interventional data. Theoretically,

d

-variable causal structure is identifiable with

O(d)

single-variable interventions -- the minimum under physical realizability constraints. In Intrinsic Evaluation on synthetic data (

γ=0.2

--

0.8

), CFM-SD achieves average F1

=0.800

vs. F1

=0.127

--

0.562

for all baselines. In Extrinsic Evaluation on real scientific data, CFM-SD achieves 57--58% bias reduction in molecular toxicity prediction and battery electrolyte optimization, demonstrating practical value beyond synthetic benchmarks.

Tsuyoshi Okita

Kyushu Institute of Technology

AI for Science Causal Discovery Causal Intervention Causal Discovery with Latent Confounding

Apr 24, 2026cs.LG

From Local to Cluster: A Unified Framework for Causal Discovery with Latent Variables

Latent variables pose a fundamental challenge to causal discovery and inference. Conventional local methods focus on direct neighbors but fail to provide macro level insights. Cluster level methods enable macro causal reasoning but either assume clusters are known a priori or require causal sufficiency. Moreover, directly applying single variable causal discovery methods to cluster level problems violates causal sufficiency and leads to incorrect results. To overcome these limitations, this paper proposes L2C (Local to Cluster Causal Abstraction), a unified framework that bridges local structure learning and cluster level causal discovery. Unlike prior work that requires a complete manual assignment of micro variables to clusters, L2C discovers the partition automatically from local causal patterns. Our solution leverages a cluster reduction theorem to reduce any cluster to at most three nodes without loss of causal information, applies local causal discovery to identify direct causes, effects, and V structures in the presence of latent variables, and performs macro level causal inference via cluster level calculus on the learned cluster graph. L2C does not assume causal sufficiency, as latent variables are handled through local discovery. Theoretical analysis shows that L2C ensures soundness, atomic completeness, and computational efficiency. Extensive experiments on synthetic and real world data demonstrate that L2C accurately recovers ground truth clusters and achieves superior macro causal effect identification compared to existing baselines.

Zongyu Li

Causal Effect Estimation Causal Discovery Causal Abstraction Causal Discovery with Latent Confounding

Oct 22, 2025cs.LG

Learning Granger Causality under Latent Confounding via Intervention-Induced Heterogeneity

Granger causality characterizes directed predictive dependencies in multivariate time series, but recovering such dependencies becomes challenging in the presence of latent confounding. Cross-environment invariance provides a natural source of information in heterogeneous settings, yet invariance alone can be insufficient: when latent-to-observed mechanisms remain stable, hidden confounders can induce predictive dependencies that are just as invariant as genuine Granger-causal relations. We show that interventions provide an additional source of identifying information by inducing structured variation in observed mechanisms, while stable latent pathways need not exhibit the same cross-environment changes. In practice, however, neither the intervened environments nor the affected mechanisms are known. We propose GRACE, a framework for learning Granger causality under latent confounding from intervention-induced heterogeneity. GRACE decomposes multivariate dynamics into a shared Granger mechanism, sparse environment-specific deviations that capture edge-level interventions, and a latent component that accounts for confounding. Under a linear generative model, we show that GRACE can recover which environments intervene on a given edge when the edge is perturbed in at least one but fewer than half of the environments and the intervention effect is sufficiently large to survive sparsity shrinkage; the recovered intervention pattern then provides a certificate for the corresponding Granger causal edge. Experiments on synthetic and real-world time series demonstrate improved Granger causal structure recovery under latent confounding and unknown interventions.

Ziyi Zhang, Shaogang Ren, Xiaoning Qian +1

Texas A&M University · University of Tennessee at Chattanooga · Brookhaven National Laboratory

Time-Series Causal Discovery Causal Discovery Causal Discovery with Latent Confounding

Sep 2, 2025stat.ML

Design of Experiment for Discovering Directed Mixed Graph

We study the design of interventions for causal discovery in simple structural causal models whose causal graphs are directed mixed graphs (DMGs) that may contain directed cycles and bidirected edges representing latent confounding. In such case, observational conditional-independence (CI) information may not identify even the graph skeleton, while CI alone cannot generally detect a bidirected edge coexisting with a directed edge. To this end, we propose a stage-wise framework based on tailored separating systems. Separating-system interventions first recover descendant relations and strongly connected components (SCCs). The SCCs are then ordered by ancestry, and an SCC-Anc separating system recovers the directed subgraph. Given this subgraph, further systems use CI tests interpreted through

d

- or

σ

-separation to recover non-adjacent bidirected edges, whose endpoints share no directed edge, and do-see comparisons to recover those coexisting with exactly one directed edge. Under our assumptions, the framework recovers the directed subgraph and every bidirected edge except double-adjacent ones, whose endpoints are connected by a directed edge in each direction. We develop algorithms for unrestricted and

M

-bounded settings, with each experiment targeting at most

M

variables in the latter. For recovering the directed subgraph and non-adjacent bidirected edges, our upper bounds on the number and maximum size of experiments match corresponding worst-case lower bounds up to logarithmic factors.

Haijie Xu, Chen Zhang

Department of Industrial Engineering Tsinghua University

Graph Structure Learning Causal Discovery Causal Intervention Causal Discovery with Latent Confounding

Feb 11, 2025stat.ML

The observational partial order of causal structures with latent variables

For two causal structures with the same set of visible variables, one is said to observationally dominate the other if the set of distributions over the visible variables realizable by the first contains the set of distributions over the visible variables realizable by the second. Knowing such dominance relations is useful for adjudicating between these structures given observational data. Here, we consider the problem of determining the partial order of equivalence classes of causal structures with latent variables relative to observational dominance. We provide a complete characterization of the dominance order in the case of three visible variables, and a partial characterization in the case of four visible variables. Our techniques also help to identify which observational equivalence classes have a set of realizable distributions that is characterized by nontrivial inequality constraints, analogous to Bell inequalities and instrumental inequalities. We find evidence that as one increases the number of visible variables, the equivalence classes satisfying nontrivial inequality constraints become ubiquitous. (Because such classes are the ones for which there can be a difference in the distributions that are quantumly and classically realizable, this implies that the potential for quantum-classical gaps is also ubiquitous.) Furthermore, we find evidence that constraint-based causal discovery algorithms that rely solely on conditional independence constraints have a significantly weaker distinguishing power among observational equivalence classes than algorithms that go beyond these (i.e., algorithms that also leverage nested Markov constraints and inequality constraints).

Marina Maciel Ansanelli, Elie Wolfe, Robert W. Spekkens

Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo, Ontario Canada N2L 2Y5 · Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada, N2L 3G1

Latent Variable Models Causal Discovery Causal Structure Learning Causal Discovery with Latent Confounding

Jul 10, 2024stat.ML

Towards Complete Causal Explanation with Expert Knowledge

We study the problem of restricting a Markov equivalence class of maximal ancestral graphs (MAGs) to only those MAGs that contain certain edge marks, which we refer to as expert or orientation knowledge. Such a restriction of the Markov equivalence class can be uniquely represented by a restricted essential ancestral graph. Our contributions are several-fold. First, we prove certain properties for the entire Markov equivalence class including a conjecture from Ali et al. (2009). Second, we present several new sound graphical orientation rules for adding orientation knowledge to an essential ancestral graph. We also show that some orientation rules of Zhang (2008b) are not needed for restricting the Markov equivalence class with orientation knowledge. Third, we provide an algorithm for including this orientation knowledge and show that in certain settings the output of our algorithm is a restricted essential ancestral graph. Finally, outside of the specified settings, we provide an algorithm for checking whether a graph is a restricted essential graph and discuss its runtime. This work can be seen as a generalization of Meek (1995) to settings which allow for latent confounding.

Aparajithan Venkateswaran, Emilija Perković

Microsoft · Redmond, WA 98052, USA · Department of Statistics +2

Structural Causal Models Causal Discovery Causal Structure Learning Causal Identifiability Causal Discovery with Latent Confounding

Nov 13, 2023cs.LG

Causal Discovery in Mixtures of Populations

Causal discovery aims to learn causal structures up to certain symmetries. Diverse populations or changing environments give rise to heterogeneous data in the following sense: each population/environment is a ``source'' which idiosyncratically determines the forms of causal effects. From this perspective, the source is a latent common cause for every observed variable. While some methods for causal discovery can work around latent confounding in special cases, a global confounder poses a significant challenge. The only known ways to deal with latent global confounding involve making assumptions that limit structural equations and/or noise functions. We demonstrate that globally confounded causal structures can still be identified with arbitrary structural equations and noise functions, so long as the number of latent classes remains small relative to the size and sparsity of the underlying DAG. The approach relies on agglomerating variables into large-enough matrices of moments, whose ranks directly reveal graphical properties of the causal structure. We also provide a statistical test to test the rank of these matrices.

Bijan Mazaheri, Spencer Gordon, Yuval Rabani +1

Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA · Fragment Data Technologies, San Francisco, California, USA · Department of Computer Science, Hebrew Univeristy of Jerusalem, Jerusalem, Israel +1

Latent Variable Models Causal Discovery Causal Identifiability Causal Discovery with Latent Confounding