Causal Discovery

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17 papers in the last four weeks, up 183% on the four weeks before. 0.2% of all new papers.

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Latest papers 148

May 26, 2026stat.ML

Iterative Causal Discovery: Per-Edge Impossibility Certificates, Tier-Aware Oracle Queries, and the $1+K$ Lower Bound

Causal-discovery algorithms return a directed graph, yet provide no principled means of distinguishing edge directions identified by the data from those assigned without an identifying assumption. Under the standard Markov and faithfulness conditions, the observational distribution identifies only a Markov equivalence class; orientations within that class are not determined by the joint distribution and cannot be recovered from additional samples alone, but require either a functional restriction or an intervention. We introduce a protocol for observational causal discovery on continuous data that attaches to each candidate edge a discrete impossibility certificate: a RESOLVED code records the identifiability theorem under which the direction was committed, while an IMPOSSIBLE code records the failure mode together with the specific question a domain expert must answer to resolve it. The bivariate cascade is extended with five gated identifiability tiers LSNM, IGCI, Stein, MDL, and PEIT that abstain when their precondition test rejects. Two oracle primitives, the meta-hub query and the node-children query, jointly establish an upper bound of

1+K

expert interactions sufficient to recover any DAG, where

K

denotes the number of non-leaf vertices. Under an ideal-oracle assumption, the bound is met exactly on the asia, sachs, child, and alarm benchmarks.

Eichi Uehara

aflo, Inc., Tokyo, Japan

Bayesian Networks Causal Discovery Causal Structure Learning Causal Identifiability

May 25, 2026cs.AI

CausaLab: A Scalable Environment for Interactive Causal Discovery Toward AI Scientists

We introduce CausaLab, a scalable environment for evaluating interactive causal discovery by LLM agents. Unlike prior evaluations, CausaLab evaluates both whether an agent can solve a problem using causal evidence and whether its answer is grounded in a faithful recovered causal mechanism. Each episode places an agent in a synthetic laboratory: it receives prior measurement records, intervenes on a manipulator crystal, and predicts the resonance frequency of a held-out reactor crystal governed by the same mechanism. The hidden data-generating process is a randomly sampled structural causal model (SCM), so success requires recovering both a causal graph and structural equations rather than recalling prior knowledge. Experiments show a persistent gap between prediction and mechanism recovery: in the purely observational 6-node setting, GPT-5.2-high reaches 92% task accuracy but only 0.471 all-edge

F_1

. Mixed observation-intervention strategies improve structural fidelity, while pure intervention remains difficult even for strong agents. We identify premature stopping as a major weakness and show that consistency verification mitigates it. CausaLab therefore separates predictive success from causal understanding and exposes current LLM agents' limits as experimental causal reasoners.

Junlin Yang, Dylan Zhang, Xiangchen Song +7

Tsinghua University · University of Illinois Urbana-Champaign · Carnegie Mellon University +2

Structural Causal Models LLM Agent Evaluation Causal Discovery AI Agent Benchmarks Causal Reasoning in Language Models

May 24, 2026cs.LG

Evolving Causal Regulatory Networks (ECR-Net)

Modern machine learning models excel at pattern recognition but remain brittle, often failing to generalize out of distribution (OOD) because they capture spurious correlations rather than the underlying causal data-generating process. Current causal discovery methods, while powerful, typically assume a static graph structure, rendering them unable to model systems that adapt or undergo structural changes across different environments. We introduce ECR-Net, Evolving Causal Regulatory Networks, a novel, bio-inspired framework for adaptive causal mechanism discovery. Our approach models the data-generating process not as a static graph, but as a dynamic system analogous to a Gene Regulatory Network (GRN), composed of localized, recursive functions where variables can activate and inhibit one another. To discover the latent structure of this network, we employ an evolutionary search algorithm that evolves a population of candidate regulatory graphs, optimizing for a fitness function that measures how well the simulated system dynamics reconstruct the observed data. The key innovation of ECR-Net is its ability to model structural adaptation, it explicitly ingests shifts in the data's statistical properties as signals of an environmental shock. In response, the evolutionary search identifies parsimonious modifications to the causal graph topology, such as link inhibitions or activations that explain the new data regime. We posit that ECR-Net represents a new class of adaptive Structural Causal Models capable of discovering how and why a system's fundamental rules change, offering a path toward robust generalization in complex, non-stationary systems.

Govind Vallabhasseri Binish, Abdhul Ahadh, Rano Roy Kavanal +1

Structural Causal Models Causal Discovery Causal Structure Learning Dynamic Graph Learning

May 22, 2026cs.CV

From Activation to Causality: Discovery of Causal Visual Representations in the Human Brain

Identifying which brain regions represent a visual concept in the human brain is a central challenge in neuroscience. Existing approaches have localized coarse functional regions (e.g., faces, places) through activation maximization, identifying regions that activate strongly for a target concept relative to other concepts. Yet strong activation alone does not establish that a region represents the concept itself, as responses may instead be driven by correlated visual or semantic cues. We introduce BrainCause, an automated framework that combines generative and brain models to synthesize controlled stimuli and validate neural representations through targeted causal testing. Given a query specifying a concept of interest, our framework constructs targeted stimulus sets comprising concept images, counterfactual edits that remove the target concept while preserving other image content, and images with candidate correlated distractors. It then uses an image-to-fMRI encoding model to predict brain responses and searches for representations that respond specifically to the target concept over correlated alternatives. BrainCause returns validated candidate representations and proposes follow-up fMRI experiments to further test or extend its discoveries. Our approach successfully recovers known functional localizations and identifies new candidate representations across dozens of concepts, validated on both predicted and measured fMRI data. Critically, we show that without causal validation, a large fraction of localizations would be false positives, confirming that activation alone is insufficient evidence of representation.

Yuval Golbari, Navve Wasserman, Matias Cosarinsky +5

Weizmann Institute of Science · Massachusetts Institute of Technology

Causal Representation Learning Causal Discovery Visual Neuroscience Neuroimaging

May 22, 2026cs.LG

Leveraging Foundation Models for Causal Generative Modeling

Causal generative modeling is essential for developing reliable and transparent AI systems capable of counterfactual reasoning. While existing approaches focus on integrating causal constraints during the training of generative models, they often lack a unified framework to leverage the zero-shot reasoning capabilities of pretrained foundation models. We introduce FM-CGM, a modular framework for end-to-end visual causal reasoning using pretrained foundation models. FM-CGM formalizes the causal pipeline through three core components: a concept extractor, a concept manipulator, and a counterfactual generator. By leveraging a large reasoning model for causal inference and a text-to-image diffusion model for generation, our approach enables zero-shot causal discovery, intervention, and counterfactual generation. We then develop Causal Semantic Guidance (CSG), a cross-attention-based mechanism that ensures semantic interventions propagate to descendant concepts while preserving invariant regions. We empirically show that our approach can identify plausible causal structures and is suitable for faithful counterfactual image generation.

Aneesh Komanduri, Xintao Wu

University of Arkansas Fayetteville, Arkansas, USA

Causal Counterfactual Generation Image Generation Causal Discovery Generative Modeling Causal Inference

May 21, 2026stat.ME

Causal Discovery in Structural VAR Models Under Equal Noise Variance

Causal discovery from multivariate time series is challenging when causal effects may occur both across time and within the same sampling interval. This issue is especially important in applications such as neuroscience, where the sampling rate may be coarse relative to the underlying dynamics and contemporaneous effects need not form an acyclic graph. We study causal discovery in linear Gaussian structural VAR models under an equal noise variance assumption, meaning that the structural noise terms have a common variance. Unlike the DAG-based cross-sectional equal noise variance setting, the time-series setting considered here does not generally yield point identification of a unique causal graph. Instead, multiple structural VAR parameterizations can induce the same stationary observed process law. We introduce a notion of observational equivalence tailored to this setting and show that the corresponding equivalence class is characterized by orthogonal transformations of the structural equations together with a global positive scale. This characterization leads to an equivalence-aware model discrepancy, the observational alignment discrepancy, which compares structural models modulo transformations that preserve the observed law. Building on this theory, we propose ENVAR, a sparsity-based procedure that searches over the induced observational equivalence class for a sparse normalized structural representative. We evaluate the proposed methodology on synthetic structural VAR data and on an fMRI dataset.

SeyedSina Seyedi HasanAbadi, Fahimeh Arab, Erfan Nozari +1

Bourns College of Engineering, University of California, Riverside · University of California, San Francisco · Department of Mathematics and Statistics, Boston University

Time-Series Causal Discovery Causal Discovery Causal Identifiability Autoregressive Modeling

May 20, 2026stat.ML

Local Covariate Selection for Average Causal Effect Estimation without Pretreatment and Causal Sufficiency Assumptions

We study the problem of selecting covariates for unbiased estimation of the total causal effect.Existing approaches typically rely on global causal structure learning over all variables, or on strong assumptions such as causal sufficiency - where observed variables share no latent confounders - or the pretreatment assumption, which limits covariates to those unaffected by the treatment or outcome. These requirements are often unrealistic in practice, and global learning becomes computationally prohibitive in high-dimensional settings.To address these challenges, we propose a novel local learning method for covariate selection in nonparametric causal effect estimation that avoids both the pretreatment and causal sufficiency assumptions. We first characterize a local boundary that contains at least one valid adjustment set whenever one exists for identifying the causal effect, and then develop local identification procedures to efficiently search within this boundary.We prove that the proposed method is sound and complete. Experiments on multiple synthetic datasets and two real-world datasets show that our approach achieves accurate causal effect estimation while substantially improving computational efficiency.

Zeyu Liu, Zheng Li, Feng Xie +3

Department of Applied Statistics, Beijing Technology and Business University, Beijing, China · Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China · College of Computer Science and Artificial Intelligence, Fudan University, Shanghai, China +2

Causal Effect Estimation Causal Discovery Causal Identifiability Causal Inference

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 19, 2026stat.ML

A Unified Framework for Structure-Aware Clustering and Heterogeneous Causal Graph Learning

In complex multivariate systems, interactions among variables are defined by dependency structures, often encoded as directed acyclic graphs (

\text{DAGs}

). However, dependency structures can vary across subjects, and ignoring this structural heterogeneity introduces bias and obscures subpopulation-specific dependencies. To address this, we propose Directed Acyclic Graph-based Dependency Clustering via Alternating Direction Method of Multipliers (DAG-DC-ADMM), a unified framework built upon Structural Equation Modeling (SEM) that jointly learns cluster assignments and cluster-specific dependency structures. We encode acyclicity via a smooth constraint and integrate a groupwise truncated Lasso fusion penalty (gTLP) to cluster subjects based on their structural similarity. This yields a nonconvex optimization problem that incorporates sparsity, acyclicity, and structural consensus constraints. We address the nonconvexity by using the augmented Lagrangian method and solve it with an adapted version of the Alternating Direction Method of Multipliers (ADMM) for difference-of-convex programs. For certain graph structures, such as upper triangular adjacency matrices, our algorithm is guaranteed to converge to a Karush-Kuhn-Tucker (KKT) point. Experiments demonstrate that our method recovers cluster-specific causal dependency structures with a high true positive rate and a low false discovery rate. This capability enables the robust discovery of heterogeneous dependencies across subjects where the subpopulation label is unknown.

Honglin Du, Muxuan Liang, Xiang Zhong

Department of Industrial and Systems Engineering, University of Florida, Gainesville, FL 32611, USA · Department of Biostatistics, MD Anderson Cancer Center, Houston, TX 77030, USA

Structural Causal Models Clustering Causal Discovery Causal Structure Learning Alternating Direction Method of Multipliers

May 17, 2026cs.LG

TriOpt: A Scalable Algorithm for Linear Causal Discovery

Learning causal relations from observational data is challenging because the graph search space grows super-exponentially with the number of variables. Ordering-based methods reduce this space by first identifying the topological ordering, whereas continuous optimization methods explore most likely regions of the space by casting DAG learning as a differentiable objective with an acyclicity constraint. Despite their conceptual appeal, both paradigms face significant scalability limitations in high-dimensional settings, restricting their practical applicability. In this work, we introduce a new formulation for linear causal discovery that tightly integrates these two paradigms to achieve substantial gains in scalability without sacrificing accuracy. Our approach, TriOpt, decomposes the problem into two efficient stages. First, it recovers the topological ordering by exploiting the Sherman-Morrison rank-1 downdate together with the additive structure of linear kernels, enabling fast and scalable ordering estimation. Second, given this ordering, we reformulate structure learning as a convex continuous optimization problem that entirely avoids the need for enforcing costly acyclicity constraints. We theoretically show that, under the true ordering, TriOpt exactly recovers the underlying linear DAG. Empirically, across synthetic, semi-synthetic, and real-world datasets, TriOpt achieves orders-of-magnitude speedups over state-of-the-art linear causal discovery methods in high-dimensional regimes, while maintaining comparable or superior accuracy.

Rafat Ashraf Joy, Elena Zheleva

University of Illinois Chicago

Structural Causal Models Causal Discovery Causal Structure Learning

May 15, 2026cs.LG

SCOUT: Cyclic Causal Discovery Under Soft Interventions with Unknown Targets

Learning causal relationships between variables from data is a fundamental research area with many applications across disciplines. Most existing causal discovery algorithms rely on the assumptions that (i) the underlying system is acyclic, (ii) the exogenous noise variables are Gaussian, and (iii) the intervention targets for the data-generating experiments are known. While these assumptions simplify the analysis, they are violated in real-life systems. Most existing methods that address these issues either assume the underlying model is linear or are constrained to operate in limited interventional settings. To that end, we propose SCOUT, a novel causal discovery framework for learning nonlinear cyclic causal relationships from soft interventional data with unknown targets. Our approach maximizes the data log-likelihood to recover the graph structure, using two normalizing-flow architectures: contractive residual flows and neural spline flows. Through experiments on synthetic and real-world data, we show that SCOUT outperforms state-of-the-art methods in both causal graph recovery and unknown target recovery across various interventional and noise settings.

Alpar Turkoglu, Muralikrishnna G. Sethuraman, Faramarz Fekri

School of Electrical and Computer Engineering, Georgia Institute of Technology.

Causal Discovery Causal Intervention

May 14, 2026cs.LG

PACER: Acyclic Causal Discovery from Large-Scale Interventional Data

Inferring the structure of directed acyclic graphs (DAGs) from data is a central challenge in causal discovery, particularly in modern high-dimensional settings where large-scale interventional data are increasingly available. While interventional data can improve identifiability, existing methods remain limited by soft acyclicity constraints, leading to optimization over invalid cyclic graphs, numerical instability, and reduced scalability. We introduce PACER (Perturbation-driven Acyclic Causal Edge Recovery), a scalable framework for causal discovery that guarantees acyclicity by construction. PACER parameterizes a distribution over DAGs through a joint model of variable permutations and edge probabilities, enabling direct optimization over valid causal structures without surrogate penalties. The framework supports a unified likelihood-based treatment of observational and interventional data, flexible conditional density models, and the incorporation of structural prior knowledge. For linear-Gaussian mechanisms, we derive closed-form expressions for the expected interventional log-likelihood and its gradients, yielding substantial computational gains. Empirically, PACER matches or exceeds state-of-the-art methods on protein signaling and large-scale genetic perturbation benchmarks, while scaling efficiently to networks with thousands of variables and achieving up to two orders of magnitude speedups over penalty-based differentiable approaches. These results demonstrate that exact and scalable causal discovery from high-dimensional perturbation data is achievable through principled search space design.

Ramon Viñas Torné, Sílvia Fàbregas Salazar, Soyon Park +4

Swiss Federal Technology Institute of Lausanne (EPFL), Switzerland · ETH Zurich, Zurich, Switzerland · Cornell University, USA

Causal Discovery Causal Structure Learning

May 13, 2026stat.ML

Causal Learning with the Invariance Principle

Causal discovery, the problem of inferring the direction of causality, is generally ill-posed. We use the language of structural causal models (SCM) to show that assuming that the causal relations are acyclic and invariant across multiple environments (e.g., the way minimum wage affects employment rate is stable across different geographical regions), \textit{only} two auxiliary environments are sufficient to infer the causal graph for arbitrary nonlinear mechanisms. Moreover, we demonstrate that this implies identifiability of the SCM functional mechanisms: as a corollary, we show that \textit{two} auxiliary environments are sufficient to guarantee correct counterfactual inference. We empirically support our theoretical results on synthetic data.

Francesco Montagna, Francesco Locatello

Institute of Science and Technology Austria

Structural Causal Models Causal Discovery Causal Identifiability Causal Inference

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 11, 2026stat.ML

Coarsening Linear Non-Gaussian Causal Models with Cycles

Recent work on causal abstraction, in particular graphical approaches focusing on causal structure between clusters of variables, aims to summarize a high-dimensional causal structure in terms of a low-dimensional one. Existing methods for learning such summaries from data assume that both the high- and low-dimensional structures are acyclic, which is helpful for causal effect identification and reasoning but excludes many high-dimensional models and thus limits applicability. We show that in the linear non-Gaussian (LiNG) setting, the high-dimensional acyclicity assumption can be relaxed while still allowing recovery of a low-dimensional causal directed acyclic graph (DAG). We further connect identifiability of this low-dimensional DAG to existing results: LiNG models with cycles are observationally identifiable only up to an equivalence class whose members differ by reversals of directed cycles; our low-dimensional DAG, which is invariant across all members of a given equivalence class, thus forms a natural representative of the class. While existing approaches for learning this observational equivalence class over high-dimensional variables have exponential time complexity, our low-dimensional summary is learned in worst-case cubic time and comes with explicit bounds on the sample complexity. We provide open source code and experiments on synthetic data to corroborate our theoretical results.

Francisco Madaleno, Francisco C Pereira, Alex Markham

Department of Technology, Management and Economics, Technical University of Denmark · Department of Mathematical Sciences,11 University of Copenhagen

Structural Causal Models Causal Discovery Causal Structure Learning Causal Abstraction Causal Identifiability

May 11, 2026cs.LG

Intervention-Based Time Series Causal Discovery via Simulator-Generated Interventional Distributions

We propose SVAR-FM (Structural VAR with Flow Matching), a framework for time series causal discovery that treats a physics-based simulator as a mechanical realization of Pearl's do operator. Clamping a variable inside the simulator physically severs confounding paths, producing interventional data by construction. Conditional Flow Matching then learns the nonlinear interventional conditionals. Theoretically, we prove that the full structural VAR becomes identifiable under a coverage condition on the simulator-clampable variables, and derive an end-to-end error bound that decomposes into Monte Carlo, simulator fidelity, and Flow Matching terms. A sign-flip corollary predicts that when simulator accuracy falls below a threshold, the estimated causal effect reverses sign. Empirically, a benchmark across four scientific domains confirms that SVAR-FM recovers the correct causal sign where observational methods produce sign-reversed estimates due to confounding. A case study in ultrafast laser physics verifies the sign-flip prediction by physically varying the accuracy level of a first-principles quantum solver: the low-accuracy setting reverses the causal sign, while the high-accuracy setting recovers the correct direction (R-squared = 0.983, zero bias).

Tsuyoshi Okita

Kyushu Institute of Technology

Time-Series Causal Discovery Causal Discovery Causal Identifiability

May 10, 2026cs.CL

Perception Without Engagement: Dissecting the Causal Discovery Deficit in LMMs

Although Large Multimodal Models (LMMs) have achieved strong performance on general video understanding, their susceptibility to textual prior shortcuts during causal discovery has been recognized as a critical deficit. The underlying mechanisms of this phenomenon remain incompletely understood, as existing benchmarks only measure response accuracy without revealing the sources and extent of the deficit. We introduce ProCauEval, a perturbation-based evaluation protocol that shifts from outcome assessment to mechanism diagnosis, probing causal discovery through five controlled configurations that systematically manipulate visual and textual modalities to decompose their respective contributions to model behavior and dissect the failure modes. Evaluating 17 mainstream LMMs, we find that models faithfully perceive video content yet systematically underexploit it during causal reasoning. We further observe that stronger post-training amplifies rather than mitigates textual prior reliance, and that higher baseline performance correlates with greater fragility under perturbation. To address these, we propose Anti-Distillation Policy Optimization (ADPO), a reinforcement learning framework built on negative teacher alignment, which augments GRPO by explicitly pushing the policy away from a prior-only counterfactual teacher induced by visual corruption. Specifically, ADPO maximizes the divergence between the policy distributions conditioned on the original and visually corrupted inputs, thereby forcing the model to ground its reasoning in visual evidence rather than textual shortcuts. Extensive experiments show that ADPO improves visual engagement without sacrificing fundamental comprehension, thus offering a preliminary step toward reliable causal discovery.

Jiafeng Liang, Zhihao Zhu, Zihan Zhang +7

Harbin Institute of Technology · Harvard University · Peking University +2

Causal Discovery Multimodal Large Language Models Causal Reasoning in Videos Multimodal Model Evaluation RL for VLMs Multimodal Learning

May 9, 2026cs.LG

Prediction Bottlenecks Don't Discover Causal Structure (But Here's What They Actually Do)

A Mamba state-space model trained only for next-step prediction appears to recover Granger-causal structure through a simple readout

S = |W_{out} W_{in}|

, with early experiments suggesting the phenomenon generalized across architectures and benefited from interventional data at

p < 10^{-5}

. We package the protocol used to test that claim -- standardized synthetic generators (VAR/Lorenz/CauseMe-style), three intervention semantics (

do(X=c)

, soft-noise, random-forcing), edge-provenance cards on three real datasets, and size-matched control arms -- as a reusable falsification benchmark, and walk the claim through it in five stages. The method-level claim does not survive: (i) a plain linear bottleneck does as well or better; (ii) tuned Lasso beats the bottleneck on synthetic CauseMe-style benchmarks, and on Lorenz-96 (the only real benchmark with unambiguous ground truth) classical PCMCI and Granger lead a tight cluster in which the bottleneck trails; (iii) the headline intervention advantage is roughly 60% a sample-size confound, and the residual disappears under standard

do(X=c)

interventions, surviving only under a non-standard random-forcing scheme; (iv) even that residual reproduces, with a larger effect, in classical bivariate Granger -- the effect is method-agnostic. What survives is a narrow characterization result; the benchmark is the lasting artifact, and each stage above is one of its control arms.

Ankit Hemant Lade, Sai Krishna Jasti, Indar Kumar +1

Time-Series Causal Discovery Causal Discovery

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

May 8, 2026cs.LG

PerCaM-Health: Personalized Dynamic Causal Graphs for Healthcare Reasoning

Personalized healthcare decisions require reasoning about how physiological and behavioral variables influence an individual patient over time. Existing temporal causal discovery methods are poorly matched to this setting: cohort-level models provide stable but non-personalized structures, while per-patient discovery is unreliable because individual trajectories are short, noisy, irregular, and non-stationary. This creates a fundamental gap between population-level causal modeling and the patient-specific, time-varying mechanisms needed for intervention reasoning. We introduce PerCaM-Health, a framework for learning personalized dynamic causal graphs from longitudinal health data. The framework learns a knowledge-guided population temporal graph, then conservatively adapts and evolves it using patient-specific temporal evidence and rolling-window updates, producing interpretable and auditable graph sequences. By coupling these graphs with temporal structural equations, the framework enables patient-level counterfactual queries, such as estimating short-horizon outcome changes under hypothetical behavioral interventions. Experiments on a semi-synthetic dynamic health benchmark show that PerCaM-Health improves graph recovery, dynamic edge tracking, and intervention direction accuracy compared to cohort-level, per-patient, and non-personalized temporal baselines. These results demonstrate that jointly modeling personalization and temporal evolution yields more reliable causal structure and intervention reasoning.

Elahe Khatibi, Ziyu Wang, Saba A. Farahani +4

University of California, Irvine · Washington University in St. Louis

Structural Causal Models Healthcare Time-Series Causal Discovery Causal Discovery Causal Structure Learning Clinical Reasoning+1

May 8, 2026cs.LG

Arrow: A Foundation Model for Causal Discovery

We introduce Arrow, a foundation model for zero-shot causal discovery on observational tabular data. Arrow factorizes a directed acyclic graph into an undirected skeleton and a topological order, guaranteeing acyclicity by construction. Given a new dataset, it uses a transformer-based architecture to contextualize variables within and across observations, then predicts skeleton edge probabilities and node order scores that together define a graph. Arrow is trained in a supervised fashion on synthetic datasets with ground-truth graphs, using an end-to-end differentiable directed edge composite likelihood induced by the skeleton-order factorization. The training distribution spans diverse graph families, functional forms, noise models, and dataset shapes. Across in- and out-of-distribution synthetic, semi-synthetic, and real datasets, Arrow matches or outperforms existing causal discovery methods at substantially lower inference cost than competitive alternatives. Our results demonstrate that large-scale pretraining on diverse synthetic data can yield zero-shot causal discovery models that are fast, accurate, and reusable on new datasets.

Ryan Thompson, He Zhao, Daniel M. Steinberg +1

University of Technology Sydney · CSIRO’s Data61

Causal Foundation Models Tabular Foundation Models Causal Discovery

May 7, 2026stat.ME

A Topological Sorting Criterion for Random Causal Directed Acyclic Graphs

Random directed acyclic graphs (DAGs) based on imposing an order on Erdős-Rényi and scale free random graphs are widely used for evaluating causal discovery algorithms. We show that in such DAGs, the set of nodes reachable via open paths, termed relatives, increases monotonically along the causal order. We assess the prevalence of this pattern numerically, and demonstrate that it can be exploited for causal order recovery via sorting by the estimated number of relatives. We note that many simulations in the literature feature settings where this yields an excellent proxy for the causal order, and show that a strict increase of relatives along the causal order leads to a singular Markov equivalence class. We propose sampling time-series DAGs as a possible alternative and discuss implications for causal discovery algorithms and their evaluation on synthetic data.

Alexander G. Reisach, Antoine Chambaz, Gilles Blanchard +1

Laboratoire de Mathématiques d’Orsay Université Paris-Saclay 91400 Orsay, France · CNRS, MAP5 Université Paris Cité F-75006 Paris, France · Department of Mathematical Sciences and Pioneer Centre for Artificial Intelligence, University of Copenhagen, Denmark

Causal Discovery Causal Identifiability

May 7, 2026stat.ML

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

Gaussian process (GP) marginal likelihood scores and kernel conditional independence tests are theoretically appealing for nonlinear causal discovery but computationally prohibitive at scale. We present three complementary RFF-based methods forming a practical toolkit for score-based, constraint-based, and hybrid causal discovery. The Fourier Feature Marginal Likelihood (FFML) score approximates the exact GP marginal likelihood by replacing the

n x n

kernel Gram matrix with a finite-dimensional feature representation, reducing cost to

O(nm^2 + m^3)

while retaining the probabilistic interpretation and automatic complexity penalty of the exact score. FFML extends to mixed (continuous and discrete) parent sets via a product-kernel construction, with a Kronecker path for small discrete parent sets and a Hadamard-product path otherwise. The Tetrad Random Fourier Feature (TRFF) score is a complementary BIC-style alternative using penalized Student-t regression with random Fourier features. TRFF offers robustness to heavy-tailed noise and faster runtime than FFML. Empirically, TRFF and FFML exhibit a complementary precision-recall profile: TRFF achieves higher precision while FFML achieves better recall and lower SHD overall. The Fourier Feature Conditional Independence (FFCI) test is a fast nonparametric CI test for mixed data, using ridge residualization in feature space and a Frobenius-norm cross-covariance statistic approximated as a weighted sum of chi-squared variables. Empirically, BOSS+FFML achieves the lowest SHD on nonlinear data, while BOSS+TRFF offers the highest precision. When run through PC-Max, FFCI and RCIT exhibit complementary precision-recall profiles: RCIT is more precise while FFCI achieves better recall and substantially lower SHD, at approximately twice the runtime.

Joseph D. Ramsey

Department of Philosophy Carnegie Mellon University Pittsburgh, PA 15213

Fourier Feature Embeddings Causal Discovery Random Feature Methods Causal Inference Conditional Independence Testing

May 7, 2026stat.ML

Relaxed Sparsest-Permutation Formulation for Causal Discovery at Scale

Despite the growing availability of large datasets, causal structure learning remains computationally prohibitive at scale. We revisit sparsest-permutation learning for linear structural equation models and show that exact Cholesky factorization is unnecessary for structure recovery. This observation motivates a support-level relaxation that searches for sparse triangular factors over a precision-support screening graph. The relaxed formulation can be efficiently evaluated via masked zero-fill incomplete Cholesky factorization, enabling scalable comparison of candidate orderings. At the population level, we establish soundness for Markov equivalence class (MEC) recovery under no-cancellation and sparsest Markov representation assumptions, as well as robustness to ordering misspecification. Motivated by these guarantees, we introduce SCOPE, a sparse-Cholesky pipeline that provides a scalable implementation of the relaxed formulation. Experiments on synthetic and real datasets demonstrate that SCOPE matches the MEC recovery accuracy of substantially slower baselines, while achieving significantly reduced runtime and scaling to 10k variables.

Sunmin Oh, Sang-Yun Oh, Gunwoong Park

Department of Statistics, Seoul National University, South Korea · Department of Statistics and Applied Probability, University of California Santa Barbara, CA, USA · Scientific Data Division, Lawrence Berkeley National Laboratory, CA, USA +2

Structural Causal Models Causal Discovery Causal Structure Learning

May 6, 2026cs.RO

Creative Robot Tool Use by Counterfactual Reasoning

We propose a causal reasoning framework for creative robot tool use where a suitable tool for a task is correctly identified for use beyond its primary objectives. The proposed framework first discovers the causal relationships between the tool and the task by conducting simulated experiments in a dynamics model. We decouple the causal discovery problem into two complementary components: VLM-based feature suggestion and counterfactual tool generation via targeted geometric and physical feature perturbations. Then, novel objects are classified based on identified causal features, and the tool use skill is transferred via keypoint matching conditioned on the identified causal features. By reconstructing the task in a dynamics model, our approach grounds tool use in the physics of the problem. We illustrate our approach in reaching a distant object with different sticks, scooping candies from a bowl using diverse items, and using different boxes or crates as stepping platforms to retrieve an object from a high shelf. Our baseline comparisons show that identifying causal features and grounding them in physical tool properties leads to more reliable tool selection and stronger skill keypoint transfer.

M. Tuluhan Akbulut, Varun Satheesh, Ahmed Jaafar +5

Brown University, Providence, RI, USA

Causal Discovery Robotic Tool Use Tool Selection Counterfactual Reasoning

May 6, 2026cs.LG

Order-based Rehearsal Learning

When a machine learning (ML) model forecasts an undesired event, one often seeks a decision to avoid it, known as the avoiding undesired future (AUF) problem. Many rehearsal learning methods have been proposed for AUF, but they rely on an underlying graph structure; learning such a graph from observational data is challenging and can incur substantial estimation error. In this work, we demonstrate that the order structure can be sufficient for AUF decision-making, and propose the first order-based rehearsal learning method. Although an order is less informative than a graph, it can be sufficient to identify the influence of decisions from observational data, suggesting that learning the entire graph is not always necessary. To learn the order, we develop an information-theoretic method that imposes no restrictions on the form of structural functions or the type of noise distributions. For AUF decision-making, we construct an order-based sampler to approximate the influence of decisions and, combined with a surrogate objective for maximizing the post-decision success probability, reduce the AUF task to a differentiable optimization problem. Experiments show that our order learning method outperforms existing methods, and that our AUF approach not only surpasses methods relying on learned graphs or learned orders, but also matches or even exceeds oracle baselines that are given the true graph.

Yu-Xuan Tao, Tian-Zuo Wang, Zhi-Hua Zhou

National Key Laboratory for Novel Software Technology, Nanjing University, China · School of Artifcial Intelligence, Nanjing University, China

Causal Discovery Causal Structure Learning

May 6, 2026cs.LG

When Does Gene Regulatory Network Inference Break? A Controlled Diagnostic Study of Causal and Correlational Methods on Single-Cell Data

Despite theoretical advantages, causal methods for Gene Regulatory Network (GRN) inference from single-cell RNA-seq data consistently fail to match or outperform correlation-based baselines in many realistic benchmarks, a persistent puzzle which casts doubt on the value of causality for this task. We argue that existing benchmarks are insufficiently controlled to answer this question because they evaluate on real or semi-real data where multiple pathologies co-occur, confounding failure modes, and obscuring the specific conditions under which different inference methods excel or fail. To address this gap, we introduce a controlled diagnostic framework that isolates seven biologically motivated pathologies (dropout, latent confounders, cell-type mixing, feedback loops, network density, sample size, and pseudotime drift) and measure how six representative methods spanning three inference paradigms degrade as each pathology intensifies. Across 6,120 controlled experiments, we find that causal methods genuinely dominate in clean and structurally favorable regimes, but specific pathologies (notably dropout and latent confounders) selectively neutralize their advantages. We further introduce an error-type decomposition that reveals methods with similar aggregate accuracy commit qualitatively different errors. To probe whether single-pathology effects persist when multiple stressors co-occur, we perform an interaction sweep over the three most impactful pathologies and find that their joint effects are sub-additive, while also exposing density-conditional cross-overs invisible to single-dial analysis. Our findings offer a nuanced understanding of when and why different methods succeed or fail for GRN inference, providing actionable insights for method development and practical guidance for practitioners.

Miguel Fernandez-de-Retana, Ruben Sanchez-Corcuera, Unai Zulaika +2

Faculty of Engineering University of Deusto Bilbao, Spain

Causal Discovery Gene Regulatory Network Inference Spurious Correlation Robustness Genomics Single-Cell RNA Sequencing

May 6, 2026stat.ME

PAIR-CI: Calibrated Conditional Independence Testing for Causal Discovery with Incomplete Data

The standard constraint-based paradigm for causal discovery with incomplete data -- impute first, test second -- is frequently miscalibrated: any consistent conditional independence (CI) test rejects a true null with probability approaching 1 when imputation error induces spurious conditional dependence. We introduce PAIR-CI, a nonparametric CI test that restores calibration by integrating multiple imputation directly into the inferential procedure via a paired permutation design. PAIR-CI compares cross-validated models that include and exclude the candidate variable while receiving the same imputed conditioning set, forcing imputation error to cancel in their loss difference rather than contaminate the test statistic. A provably consistent variance estimator jointly accounts for uncertainty arising from cross-validation and multiple imputation -- to our knowledge, the first formal unification of these two inferential frameworks. In simulations, existing imputation-based CI tests exhibit false positive rates of 28--45% when data are missing not at random (MNAR), whereas PAIR-CI averages below the nominal 5% level across data-generating processes and missingness mechanisms. These gains are largest in nonlinear settings and grow with causal graph size: when integrated into the PC algorithm, PAIR-CI reduces structural Hamming distance by 8% on 10-variable nonlinear graphs, 15% on 30-variable equivalents, and up to 44% on the 56-variable HAILFINDER network, with stable performance in all settings.

Thomas S. Robinson, Ranjit Lall

Department of Methodology London School of Economics and Political Science London, UK · Department of Politics and International Relations University of OxfordMay Oxford, UK

Incomplete Data Imputation Causal Discovery Causal Inference Conditional Independence Testing

May 6, 2026stat.ME

Causal discovery under mean independence and linearity

Causal discovery methods such as LiNGAM identify causal structure from observational data by assuming mutually independent disturbances. This assumption is fragile: shared volatility, common scale effects, or other forms of dependence can cause the methods to recover the wrong causal order, even with infinite data. We introduce the Linear Mean-Independent Acyclic Model (LiMIAM), which replaces full independence with weaker one-sided mean-independence restrictions on the disturbances. Under finite-order consequences of these restrictions, source nodes are generically identifiable, and hence a compatible causal order can be recovered recursively. Our proof is constructive and leads to DirectLiMIAM, a sequential residual-based algorithm for causal discovery under dependent noise. In simulations with mean-independent but dependent disturbances, DirectLiMIAM outperforms LiNGAM methods. A large-scale empirical application to the oil market highlights the implausibility of the independence assumption and the ability of DirectLiMIAM to recover a realistic causal ordering, from policy to production and from prices to inflation.

Geert Mesters, Alvaro Ribot, Anna Seigal +1

Structural Causal Models Causal Discovery Causal Identifiability

May 5, 2026stat.ML

Partial Effective Information Decomposition for Synergistic Causality

Causality is a central topic in scientific inquiry, yet for complex systems, the identification and analysis of synergistic causation remain a challenging and fundamental problem. In the context of causal relations among multivariate variables, a decomposition framework grounded in interventionist causation is still lacking. To address this gap, this paper proposes Partial Effective Information Decomposition (PEID), a framework that decomposes the influence of multiple source variables on a target variable under maximum-entropy interventions into unique and synergistic information, thereby providing a unified and computable characterization of synergistic causal relations. Theoretically, in the three-variable case, the proposed framework is compatible with the major axioms of Partial Information Decomposition (PID). Empirically, under maximum-entropy interventions, correlations among input variables are removed, causing redundancy to vanish and thereby enabling PEID to compute synergistic relations. Furthermore, based on this framework, it is possible to define causal graphs containing hyperedges as well as downward causation, thus offering a unified toolkit for analyzing cross-scale and multivariate causal mechanisms in complex systems. Finally, applying the framework to a machine-learning-based air quality forecasting task on KnowAir-V2, we demonstrate that PEID can extract interpretable inter-station causal structures from a learned dynamical model. These results suggest that PEID provides a general interventionist information-theoretic tool for analyzing multivariate and synergistic causal mechanisms in complex systems.

Mingzhe Yang, Shuo Wang, Jiang Zhang

School of Systems Science Beijing Normal University

Causal Discovery Causal Intervention