Structural Causal Models

Also known as SCM

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8 papers in the last four weeks, up 60% on the four weeks before. 0.1% of all new papers.

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Latest papers 97

Jul 3, 2026cs.AI

Personalized Causal Recourse: A Human-In-The-Loop Approach

Algorithmic recourse addresses the challenge of providing tailored recommendations to users affected by unfavorable machine learning decisions, in potentially high-stakes scenarios. Traditional approaches to recourse often rely on the closest counterfactual explanations or assume a priori knowledge of a user's causal structure, resulting in interventions that overlook individual contexts and specific feature interactions. To overcome these limitations, we study a human-in-the-loop framework that iteratively approximates the user's structural causal model through interactive queries via Bayesian inference before producing recourse recommendations. This framework exploits humans' feedback to improve the identification of causal effects, allowing personalized recourse that is plausible, cost-effective, and aligned with the actual causal dependencies of each user. As a proof of concept, we evaluate this framework through simulated human responses. Our simulations across linear and non-linear causal models show promising results, though challenges remain in capturing complex, non-linear structures, emphasizing the importance of accurate approximations and robust noise distribution modeling.

Denise Tampieri, Giovanni De Toni, Paolo Giudici

The University of Edinburgh, Edinburgh, UK · ⋆Work conducted during the author’s MSc at the University of Trento, Trento, Italy. · Fondazione Bruno Kessler, Trento, Italy +1

Structural Causal Models Causal Structure Learning Human-in-the-Loop AI Algorithmic Recourse

Jun 23, 2026math.CT

Infinitesimal Causality

This paper introduces a categorical account of infinitesimal causality in Frobenius Markov categories equipped with tangent-bundle semantics. IDC captures the infinitesimal layer in which interventions act as tangent deformations of copy/discard structure. Two distinct Frobenius structures interact: (1) the categorical Frobenius algebra on classical variables encoding copying, comparing, and discarding; and (2) the geometric Frobenius integrability condition, namely involutive closure of the intervention distribution, distinct from the algebraic Frobenius structure. Categorical causal sufficiency is defined as the compatibility of these two notions. A key observation is that, for structural causal models, infinitesimal causality is most naturally formulated in the slice of deterministic mechanisms over exogenous variables, with visible stochastic kernels obtained only after pushforward. Interventions are tangent vectors that deform the Frobenius copy/discard operations; their Lie brackets measure whether this deformation preserves classical information-flow structure. Pearl's do-calculus is used as a guiding example of intervention identities: ignoring irrelevant interventions corresponds to counit invariance, action/observation exchange to coproduct compatibility with pushforward, and independence to involutive bracket closure of the visible intervention distribution.

Sridhar Mahadevan

Adobe Research and University of Massachusetts, Amherst

Structural Causal Models Causal Inference Causal Intervention

Jun 23, 2026cs.CV

RetiSEM: Generalising Causal Models for Fragmented Biomedical Data

Learning causal models from fragmented biomedical data is challenging because clinical, molecular, and imaging variables are often incomplete or not jointly observed. We propose RetiSEM, a domain-constrained structural equation modelling (SEM) framework for causal graph recovery and mediation analysis under limited multimodal resources. This proposed work organises variables into biologically informed blocks, applies forbidden-edge constraints, and decomposes pathway-level effects into TE, NDE, and NIE components. We evaluate RetiSEM across ten synthetic benchmark scenarios that vary in dimensionality, nonlinearity, causal depth, and pathway structure, together with a fragmented real-world setting that combines NHANES clinical variables with externally derived retinal representations. This approach achieves lower structural error and higher causal accuracy than unconstrained baselines across the synthetic benchmarks. In the real-data analysis, retinal variables behave mainly as downstream biomarker-like indicators, with smaller but detectable indirect effects. These findings support our strategy as an interpretable framework for testing structured causal hypotheses in limited-resource biomedical AI. The code and resources for this work are publicly available at: https://github.com/Inamullah-Colab/ReitSEM.

Inam Ullah, Imran Razzak, Shoaib Jameel

University of Southampton, Southampton, SO18 1PB, Hampshir, United Kingdom · Mohamed bin Zayed University of Artificial Intelligence, United Arab Emirates

Latent Variable Models Structural Causal Models Causal Mediation Analysis Causal Discovery Causal Inference

Jun 19, 2026cs.LG

Causal Variational Deep Embedding: A Family of Interventional Generators for Confounded Images

Deep generative models reproduce the observational distribution of their training data, inheriting any spurious associations it contains. A common source is an unobserved confounder that shapes both an attribute the user wants to control at sampling time and an attribute expected to vary in response. Existing causal generative approaches resolve the resulting ambiguity by imposing structural assumptions strong enough to single out one interventional distribution; in image domains, such assumptions are rarely warranted, and the data is generally consistent with a set of distinct causal mechanisms -- a feasible region of interventional distributions. We propose CauVaDE (Causal Variational Deep Embedding), built on a canonical augmented SCM in which the unobserved confounder collapses, without loss of generality, into a discrete latent cluster of bounded support while continuous variation is absorbed into independent noises. We prove that this canonical class is dense, in both observational and interventional Wasserstein distance, in the class of augmented SCMs compatible with a given causal diagram, and instantiate it as a mixture variational autoencoder whose cluster variable plays the role of the canonical confounder. An entropy regularizer with weight

γ

on the cluster posterior then traces a family of candidate causal effects that fit the observational data to comparable likelihood while spanning the feasible region. Experiments on image data benchmarks show that CauVaDE produces diverse interventional samples and improves FID against an unconfounded reference.

Jingyuan Chen, Kangrui Ruan, Junzhe Zhang

Department of EECS Syracuse University · AWS AI Lab

Variational Autoencoders Structural Causal Models Generative Modeling Causal Inference Controllable Image Generation

Jun 19, 2026cs.LG

A Causal DAG Prior for Synthetic Time-Series Classification Datasets

A Prior-data fitted Network learns the posterior predictive induced by its training prior; bringing this paradigm to multivariate time-series classification therefore calls for a synthetic generator that produces complete labelled datasets with temporal structure. We introduce a causal prior that synthesizes each dataset from a randomly sampled DAG over typed nodes across two modalities (tabular attributes and time series), natively producing multivariate, multi-class TSC datasets with cross-modal causal structure across channels, timesteps and labels, a regime not addressed by existing synthetic priors. To validate the prior, we finetune TabPFN v2.5 with minimal adaptations and evaluate on 75 UCR/UEA datasets within TabPFN's operating regime. Finetuning on our generator significantly outperforms both the unmodified upstream model and a tabular-only ablation of the same prior (Wilcoxon signed-rank

p=3.0\times 10^{-8}

on ROC-AUC), isolating the contribution of the cross-modal temporal structure.

Franco Martino O'Rourke, Ana Trisovic, Dimitris Bertsimas

Massachusetts Institute of Technology, Cambridge, MA, USA.

Structural Causal Models Multivariate Time Series Classification Time Series Classification Synthetic Data Generation Time Series Generation Prior-Data Fitted Networks

Jun 19, 2026cs.LG

A Framework for Directed Acyclic Hypergraph Learning

Continuous optimization methods for learning Directed Acyclic Graphs (DAGs) operate on weighted adjacency matrices and are therefore limited to pairwise causal relationships. We propose a framework for learning Directed Acyclic Hypergraphs (DAHGs) from observational data, capturing joint parental influences that pairwise models cannot represent. Our approach rests on three components: (i) a generalized linear structural equation model (SEM) with multiplicative interaction terms whose non-zero weights correspond one-to-one with directed hyperedges; (ii) a weighted adjacency tensor representation whose acyclicity is characterized via nilpotency under the tensor t-product; and (iii) a differentiable acyclicity constraint derived through the Fourier decomposition of the t-product, which reduces tensor nilpotency to slice-wise matrix nilpotency and enables least-squares learning via the augmented Lagrangian method.

Zhiyuan Dong, Carlos Mundo-Levano, Wei Qian +2

Institute for Financial Services Analytics, University of Delaware, Newark, DE 19716, USA · Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA · Department of Applied Economics AND Statistics, University of Delaware, Newark, DE 19716, USA +1

Structural Causal Models Causal Structure Learning Hypergraph Learning

Jun 19, 2026cs.LG

DCD-PFN: A Decoupling-Aware Foundation Model for Causal Discovery

Causal discovery is critical for understanding complex data-generating mechanisms, yet traditional algorithms often struggle with highly non-linear and noisy systems, or suffer from severe computational bottlenecks. Recent tabular foundation models based on Prior-Data Fitted Networks (PFNs) have demonstrated remarkable zero-shot inference capabilities, but their potential for explicit structural causal discovery remains underexplored. To bridge this gap, we propose DCD-PFN, a decoupling-aware foundation model for causal discovery. Instead of directly amortizing global graph reconstruction, DCD-PFN focuses on local causal discovery through a decoupling-based paradigm. Through pre-training on diverse synthetic Structural Causal Models (SCMs), the model learns sample-wise decoupling weights that enable Markov boundary (MB) identification. Furthermore, by leveraging parallelized local discovery, DCD-PFN efficiently reconstructs global causal graphs while remaining grounded in the theoretical foundations of decoupling-based causal discovery. Experiments demonstrate that our foundation model achieves robust zero-shot generalization.

Zhengkang Guan, Yikang Chen, Yi He +5

College of Computer Science and Technology Zhejiang University

Causal Foundation Models Structural Causal Models Causal Discovery Causal Structure Learning Prior-Data Fitted Networks

Jun 19, 2026stat.ML

Two Layers of Instability in Causal Estimation

There is a precise sense in which drawing causal inferences from observational data is hard, even when identifiability is assumed. In particular, Robins and Ritov (1997) and Robins et al. (2003) showed that causal effects can be discontinuous as a function of the data distribution: two arbitrarily close data distributions might correspond to different causal effects. This is a fact independent of the choice of estimator; however, not all estimators are equally unstable. Our contribution is to surface a second layer of instability that depends on the choice of estimator. We show that many standard point estimates can be read as point summaries of multimodal distributions over the space of structural causal models. As such, estimators can jump discontinuously in the data distribution. This defines a taxonomy of estimators that admits a decision-theoretic reading: stability depends on whether the implicit loss function an estimator optimizes is aligned with the causal effect itself. Specifically, inverse propensity weighted estimators and regression estimators are examples of discontinuous summaries, while explicit posterior means and medians are shown to be continuous.

Alexis Bellot

Research conducted independently. Preprint.

Causal Effect Estimation Structural Causal Models

Jun 18, 2026cs.AI

DeepSWIP: Quotient-WMC Counterfactuals for Neural Probabilistic Logic Programs

Neurosymbolic systems such as DeepProbLog combine neural perception with probabilistic logic, but standard inference is associational. Counterfactual reasoning additionally requires a causal semantics for interventions and evidence. We introduce DeepSWIP, a single-world counterfactual semantics for DeepProbLog programs. Using neural materialization, we reduce fixed-context neural predicates to ordinary ProbLog choices, apply Single World Intervention Programs (SWIPs), and compute counterfactuals by weighted model counting (WMC) over a single transformed program. Under finite grounding and unique-supported-model assumptions, DeepSWIP is exact relative to the learned materialized FCM. The standard quotient-WMC form of ProbLog conditionals identifies active neural probabilities and explains intervention cleaning, calibration sensitivity, and rare-evidence instability. Experiments on MPI3D confirm the transformation against a DeepTwin construction against 12,000 queries, as predicted and a 2.14

\times

inference speedup from avoiding the Twin's endogenous duplication. A SUMO HOV experiment shows that neural calibration degradation biases plug-in estimates, while a correctly scoped randomized-policy AIPW estimator removes most first-order bias for population mean and ATE estimands. Code is at https://github.com/saibib/deep_SWIP.

Saimun Habib, Vaishak Belle, Fengxiang He

University of Edinburgh

Probabilistic Logic Structural Causal Models Neuro-Symbolic Reasoning Probabilistic Programming Counterfactual Reasoning

Jun 17, 2026cs.LG

Unsupervised Causal Abstractions Discovery

Causal abstractions formalize when a high-level structural causal model (SCM) captures the interventional behavior of a lower-level SCM. Existing applications of this notion largely follow a hypothesis-testing paradigm: an expert proposes a candidate high-level model and then evaluates if the low-level system implements it. We study the complementary problem of learning a high-level model directly from low-level measurements. Our contributions leverage hypotheses from low-rank causal discovery, and can be summarized as follows: (1) we show that observations generated by a low-rank graph induce latents that form a causal abstraction, (2) we provide identifiability results about these latents, and (3) we propose a practical objective to learn this high-level SCM.

Théo Saulus, Simon Lacoste-Julien, Dhanya Sridhar

Mila - Quebec AI Institute · Université de Montréal · Canada CIFAR AI Chair

Structural Causal Models Causal Discovery Causal Abstraction Causal Identifiability

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, 2026stat.ML

Tensor-based second-order causal discovery

Causal discovery seeks to uncover the causal dependencies among variables. For this purpose, we propose an algorithm called Tensor-based Second-order Causal Discovery (TSCD). Its input is a tensor obtained from the covariance matrices of observational and interventional data. Assuming the causal dependencies follow a linear structural equation model on a directed acyclic graph (DAG), TSCD outputs the DAG and the functions on its edges, requiring only that the noise variables are uncorrelated. We also implement a version of the approach for nonlinear models. Our focus on second-order statistics (via the covariance matrices) is motivated by their statistical and computational efficiency relative to higher-order moments, their identifiability relative to first-order statistics, and that they work regardless of whether the variables are Gaussian. We show that TSCD has identifiable causal order and parameters from a number of interventions that is logarithmic in the number of variables. Experiments show that TSCD is robust to noise, competitive with existing methods, and scales to hundreds of variables.

Nathan Ouyang, Kexin Wang, Anna Seigal

Structural Causal Models Causal Discovery

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 14, 2026cs.LG

Bayesian Networks with Latent Time Embedding for Stage-Aware Causal Modeling of Alzheimer's Disease Progression

Alzheimer's disease (AD) progression is often described through the amyloid-tau-neurodegeneration, or AT(N), cascade. However, most longitudinal models represent this cascade either as a fixed sequence of biomarkers or as a black-box forecasting task. This makes it difficult to determine when biologically guided biomarker relationships influence future regional pathology. In this study, we introduce Bayesian Networks with Latent Time Embedding (BN-LTE), a Bayesian structural framework for stage-aware modeling of AD progression. BN-LTE estimates disease pseudotime from baseline biomarker profiles and constrains directed dependencies according to biologically plausible AT(N) ordering. Posterior spline-varying structural equations are then used to link initial multimodal measurements with future annualized regional tau-PET change. Across repeated subject-disjoint evaluations using ADNI data, BN-LTE shows strong spatial reconstruction of tau progression compared with the included forecasting baselines. Beyond spatial reconstruction, BN-LTE recovers posterior stage-varying AT(N)-constrained effects and identifies a mid-pseudotime window of amyloid sensitivity. This window is supported by model-implied g-formula contrasts, root-adjusted AIPW, mechanism-sensitive ablations, and robustness analyses across spline and prior specifications. Overall, these findings position BN-LTE as a Bayesian structural framework for forecasting tau progression while examining stage-dependent AT(N)-cascade mechanisms in observational longitudinal neuroimaging data. Our code is available at https://github.com/danleneurocom/BN-LTE.

Nguyen Linh Dan Le

Department of Biomedical Engineering The University of Melbourne, Melbourne, Australia

Causal Effect Estimation Structural Causal Models Bayesian Networks Neuroimaging Alzheimer's Disease Progression Prediction

Jun 14, 2026cs.LG

From Correlation to Causation in Lane Change Prediction for Automated Driving: A Causal Explanation Framework

Lane-change prediction is a central task in intelligent vehicles, where early maneuver anticipation can support safer decision-making. However, many existing approaches mainly learn statistical associations between observed driving variables and future maneuvers, while overlooking the causal dependencies among the input variables themselves. This limits interpretability, especially when physically related variables such as longitudinal gap, relative longitudinal velocity, and Time-To-Collision (TTC) are treated as independent flat inputs. This article presents a causal-inference-based framework for lane-change prediction and explanation. The proposed approach combines linguistic feature construction, expert-constrained causal discovery, deep structural causal modeling with Deep End-to-end Causal Inference (DECI), intervention-based effect analysis, refutation testing, and recursive causal-chain explanation. The objective is not only to predict the future maneuver, but also to identify candidate variables that directly contribute to the prediction, the upstream factors influencing them, and the causal chains through which these effects propagate. The framework achieves average F1-scores above 95% during the first three seconds before the lane-marking crossing event. Beyond prediction accuracy, the framework uses intervention-based effect analysis to distinguish influential from weakly influential variables under the learned causal structure. It further distinguishes candidate direct contributors from mediated effects and generates contrastive causal-chain explanations that clarify why the predicted maneuver is favored and why the alternative maneuvers are less supported. The main contribution is therefore a mechanism-aware lane-change prediction pipeline that moves beyond correlation-based classification toward more interpretable causal reasoning for maneuver prediction.

Mohamed Manzour, Aditya Kumar, Augusto Luis Ballardini +1

Computer Engineering Department, University of Alcalá, Madrid, Spain

Structural Causal Models Autonomous Driving Causal Explanation Vehicle Trajectory Prediction

Jun 12, 2026cs.AI

Relational Structural Causal Models

An artificial intelligence must have a model of its environment that is causal, supporting reasoning about interventions and counterfactuals, and also combinatorial, supporting generalization to unseen combinations of objects. In this work, we formally study when and how such a model can be learned. We develop relational structural causal models, extending structural causal models (Pearl 2009) to settings where objects and their relations vary. First, we show how answers to not only causal but also observational queries about unseen combinations of objects can not be identified without further assumptions. To enable such identification--including in the presence of unobserved confounding--we define relational causal graphs and derive symbolic identification criteria. Finally, we propose relational neural causal models, a provably correct approach that outperforms non-relational baselines on simulated traffic scenes with varying cars, signals, and pedestrians.

Adiba Ejaz, Elias Bareinboim

Causal AI Lab, Department of Computer Science, Columbia University, NY, USA.

Structural Causal Models Causal Identifiability Causal Inference

Jun 10, 2026cs.LG

How Useful is Causal Invariance for Domain Adaptation in Finite-Sample Settings?

Machine learning models often degrade when they are deployed on a target distribution that differs from the source distributions they were trained on. Recent work in causality-based domain generalization has shown how shared causal structure between domains can induce invariant predictors, e.g., models on a subset of features which have stable risk across structured domain shifts. However, the extent to which such population-level causal invariances can lead to gains in finite-sample settings remains underexplored. In particular, in practice we often have access to a few labeled target samples, a setting called supervised domain adaptation (sDA). In this paper, we explore when (full or partial) causal knowledge can provably improve supervised domain adaptation. As a first step, we study linear regression, where full or partial causal knowledge specifies a collection of invariant or possibly invariant feature subsets, each yielding a source-trained candidate predictor. We derive matching upper and lower bounds showing that finite-sample gains are governed by the target-risk margins separating the candidates, together with the finite-source estimation error. When these margins are sufficiently large relative to

n_Q

, an adaptive aggregation procedure can match the best candidate predictor while avoiding negative transfer relative to target-only learning. On the other hand, when the margins are too small, no algorithm can reliably exploit the candidate collection to obtain faster finite-sample rates. We further connect these margins to structural shift magnitude in linear SCMs and validate the theory on real-world causal benchmarks.

Julia Kostin, Kasra Jalaldoust, Elias Bareinboim +2

Department of Computer Science, ETH Zurich · Causal Artificial Intelligence Lab, Columbia University · Department of Statistics, Columbia University

Structural Causal Models Statistical Learning Theory

Jun 9, 2026cs.AI

WorldKernel: A World Model is the Coupling Kernel of Admissible Possible Worlds

A common assumption holds that enough observational and interventional data, given to a strong enough predictor, suffices. We report a failure mode that contradicts it. Across hundreds of structural causal models, on identified quantities a strong predictor and a Bayesian baseline both succeed, but on unidentified quantities (the couplings between counterfactual worlds) the predictor collapses to a point, on 28% of models to one no valid model can produce, while the truth is an admissible interval more data never narrows. The gap is structural: prediction cannot represent uncertainty over counterfactual couplings. We cast a world model as a single positive semidefinite coupling kernel K(T,T') over admissible worlds, whose diagonal is the ordinary posterior (what a predictor recovers) and whose off-diagonal is the cross-world coupling it cannot, which every counterfactual reads. The paper is the theory of that off-diagonal. It is real: two states with identical posteriors differ on a cross-world query, and the off-diagonal is the coupling that fixes counterfactuals. It can be bounded: positive semidefiniteness is partial-identifying information the marginals lack, and enforcing it bounds counterfactuals in polynomial time where the exact response-type program is intractable. Logical structure sharpens it: ontology axioms tighten the bound by up to a third, propagating to couplings they never touch. It can be acquired: targeted scars, constraints learned from encountered infeasibilities, close the gap several times faster than untargeted ones. Its full reconstruction is approximate counting of the admissible worlds, tractable below the Sly-Sun threshold and inapproximable above; we do not claim to beat the worst case.

Fabio Rovai

Structural Causal Models Causal World Models Causal Identifiability Causal Inference Counterfactual Reasoning Counterfactual Learning

Jun 8, 2026stat.ML

Estimate Collapsibility of Causal Effects in Completed Partial DAGs via Strong d-Convex Hulls

This paper proposes a collapsible method for estimating causal effects that maintains the estimator's consistency before and after marginalization over some variables in completed partially directed acyclic graphs (CPDAGs). We first introduce the estimate collapsibility for CPDAGs and characterize the minimal collapsible sets as strong d-convex hulls. An efficient algorithm is devised to obtain such sets in DAGs and is generalized to CPDAGs. Then, we combine the graph reduction procedure with the IDA framework. Finally, experiments and empirical analysis show the effectiveness of the collapsibility for causal estimations in CPDAGs. Code is available at https://github.com/Jamyang-D/strongly-convex.

Yuxin Deng, Yi Sun, Zhiming Li +1

College of Mathematics and System Science, Xinjiang University, Urumuqi, 830000, Xinjiang, China · Institute of Statistics and Data Science, Xinjiang University of Finance and Economics, Urumuqi, 830000, Xinjiang, China

Causal Effect Estimation Structural Causal Models

Jun 5, 2026cs.LG

Trio: Learning Time-Series Forecasting with Temporal-Spatial-Sample Attention and Structural Causal Priors

Multivariate time-series forecasting requires models to reason over temporal dynamics, cross-variable dependencies, and historical input-output correspondences. Recent Prior-Data Fitted Networks (PFNs) suggest that synthetic tasks can be useful for learning transferable inference behavior. However, directly transferring this paradigm to time-series forecasting remains difficult, since temporal order, dynamic lags, and recurring historical patterns are not naturally captured by ordinary tabular priors. Motivated by this observation, we propose Trio, a sample-aware time-series forecasting architecture based on Temporal-Spatial-Sample attention. Temporal attention captures within-window dynamics, spatial attention models inter-variable dependencies, and sample attention retrieves relevant historical lookback-future pairs to guide the current prediction. Rather than claiming a fully general PFN-style forecaster, our goal is to study how historical input-output examples can be explicitly organized and reused within a forecasting model. We further introduce a Time-Series Structural Causal Model (TS-SCM) generator to create structured synthetic forecasting tasks with dynamic lags, cross-variable interactions, noise, feedback, and distributional drift. Experiments on synthetic, industrial, and public benchmarks show that the proposed architecture improves forecasting performance. Exploratory zero-shot experiments further suggest that TS-SCM-generated tasks may provide useful structural priors, while fully general PFN-style time-series forecasting remains an open problem.

Tao Chen, Yexu Zhou, Zhi Gong +9

SUPCON Technology Co., Ltd. Hangzhou, China · Hangzhou Dianzi University, HangZhou, 310018, China · Xidian University, Xi’an 710071, Shaanxi, China.

Synthetic Data Pretraining Multivariate Time Series Forecasting Structural Causal Models Retrieval-Augmented Time Series Forecasting

Jun 4, 2026cs.LG

Causal Atlases from Entropic Inference: Bayesian Networks beyond Optimal DAGs

Data-driven causal relationship identification is pertinent to advancing understanding of complex systems both within and beyond science. Bayesian networks offer a probabilistic method for modelling generic causal relationships via directed acyclic graphs (DAGs). However, typical techniques for constructing Bayesian networks rely on optimization, which can be ill-suited for learning causal relationships because the underlying data may admit multiple chains of causation. More data-faithful representations of causal relationships would provide frameworks for constructing multiple causal maps that are consistent with the variability that is inherent in underlying data. Here, we show that entropy-based inference generates atlases of plausible causal relationships that are consistent with underlying data. On simulated noisy data of 2- and 20-node linear structural equation models, we sample a maximum-entropy ensemble of graphs that allow us to quantify the inherent structural ambiguity in underlying causal relationships. Our method shows that "optimized" DAGs can contain causal artifacts are not consistent across equivalently accurate topologies.

Hazhir Aliahmadi, Irina Babayan, Greg van Anders

Department of Physics, Engineering Physics and Astronomy, Queen’s University, Kingston ON, Canada

Structural Causal Models Bayesian Networks Causal Discovery

Jun 4, 2026stat.ML

EML-CD: Causal Mechanism Recovery via EML Symbolic Trees in Structure Learning

Neural network (NN)-based nonlinear causal discovery methods recover DAG structure but leave each causal mechanism as a black box. Waxman et al. argued that extracting causal mechanisms from NN weights is ill-posed. We propose EML-CD, a framework that integrates the EML operator (capable of composing elementary functions from a single binary operator) into causal structure learning, with interpretable mechanism recovery as the primary objective. EML-CD represents each edge mechanism as a gated EML binary tree and automatically discovers closed-form causal equations. Analytical Jacobians can be directly computed from the output equations, enabling quantitative understanding of causal effects. On real data (Sachs protein signaling, d=11), EML-CD achieves SHD=11.2 +/- 0.4 (5-seed mean; baselines are single deterministic runs), on par with PC/GES within seed variance and below CAM, while attaching closed-form equations to each detected edge (precision 0.756, recall 0.365). In a controlled bivariate test with known mechanisms, EML-CD recovers 10 of 11 elementary function families faithfully (held-out shape correlation >= 0.96; only high-frequency sine is partial). On a symbolic synthetic benchmark, EML-CD attains a substantially lower and more stable held-out mechanism f-MSE than a fixed SINDy dictionary (mean 3.67 vs. 7644, the latter inflated by catastrophic extrapolation on one seed), although its structure recovery (SHD 14.0) only matches the dictionary and stays below specialized optimizers; on the Causal Chambers light-tunnel subset, a depth-2 model improves F1 over linear OLS-BIC (0.444 vs. 0.273).

Sota Asanuma

SoftBank Corp.

Structural Causal Models Causal Structure Learning Causal Interpretability Symbolic Regression

Jun 4, 2026cs.LG

Causal Longitudinal Prior-Fitted Networks for Counterfactual Outcome Prediction

Longitudinal treatment decisions from multivariate time-series data require predicting potential outcomes under future treatment sequences in the presence of time-varying confounding, heterogeneous patient dynamics, and limited domain-specific data. Existing longitudinal causal estimators typically address this problem by training a new model for each cohort or simulator. We introduce Causal Longitudinal Prior-Fitted Networks (CausalLongPFN), a prior-fitted network for time-series causal inference in longitudinal treatment-response data and zero-shot in-context counterfactual outcome prediction. The model is pretrained entirely on synthetic episodes sampled from a broad prior over temporal structural causal models, exposing it to treatment-confounder feedback, latent heterogeneity, nonlinear state evolution, delayed effects, and cumulative treatment responses. At test time, CausalLongPFN remains frozen and is used zero-shot: it conditions on support trajectories, a query history, and a planned future treatment sequence, and returns a predictive distribution over future outcomes without gradient updates or propensity-model fitting. Multi-step predictions are obtained by recursively applying the one-step predictor under the specified treatment sequence. We evaluate the model on branchable cancer, HIV, and warfarin benchmarks with ground-truth counterfactual labels, and on factual-only rolling-origin prediction in MIMIC-III ICU trajectories. CausalLongPFN is competitive with domain-trained longitudinal baselines on counterfactual benchmarks and performs strongly on factual MIMIC-III prediction, suggesting that broad synthetic causal pretraining can provide a frozen, amortized alternative for zero-shot longitudinal treatment-response prediction when repeated domain-specific training is costly or impractical.

Amirhossein Zare, Amirhessam Zare, Herlock Rahimi +2

School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. · Department of Electrical and Computer Engineering, Yale University, New Haven, CT, USA. · School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran. +2

Structural Causal Models Counterfactual Prediction Prior-Data Fitted Networks Causal Inference Longitudinal EHR Modeling Counterfactual Learning

Jun 4, 2026cs.LG

Causal Modeling of Selection in Evolution

Understanding potential selection in data is crucial for causal discovery; we argue that "selection" in common narratives takes two forms, which we term static and evolutionary selection, respectively. Static selection refers to a one-shot filtering process where observed data consist of a subset of the population of interest, as in survey volunteer bias. Evolutionary selection, in contrast, operates through repeated rounds of differential fitness in reproduction, where observed data constitute the latest generation shaped by a historical trajectory, as in immune adaptation, antibiotic resistance, and social norm emergence. Existing methods largely conflate these two forms and rely on an identical graphical model of selection. We show that this model is valid for static settings but fails to characterize data under evolution, yielding false discovery results. To address this, we introduce a new model that specifically characterizes evolutionary selection, and develop a sound and complete procedure for identifying such models from data across one or multiple environments or generations. Experimental results validate the method's ability to uncover the relevant mechanisms underlying evolution from data.

Haoyue Dai, Zeyu Tang, Peter Spirtes +1

Carnegie Mellon University · Stanford University · Mohamed bin Zayed University of Artificial Intelligence

Structural Causal Models Causal Discovery Causal Structure Learning Data Selection Causal Identifiability

May 30, 2026cs.LG

On the Recoverability of Causal Relations from Bulk Gene Expression Data

Bulk gene expression profiling, which aggregates pooled RNA across cells within a biological sample, remains important in the single-cell era because it is typically less noisy, more sensitive, and more cost-effective than single-cell assays. Accordingly, a growing body of computational methods seeks to recover causal relations among genes from bulk expression data. However, aggregation is a lossy, non-invertible coarsening of the underlying cellular system, and it remains unclear whether and under what conditions causal relations are recoverable from aggregated bulk gene expression data. To answer this, we formalize recoverability under aggregation through two notions of consistency: functional-form consistency and conditional-independence consistency. We then derive necessary and sufficient conditions for recoverability, showing that these properties are preserved only under linear aggregations (e.g., sum/mean) coupled with affine structural equations. To assess the practical plausibility of these conditions, analyses of four bulk and four single-cell gene expression datasets further reveal that the estimated pairwise regulatory functions among genes deviate from linearity in both data types, providing limited empirical support for the linearity assumptions required for recoverability. Together, these results caution against recovering causal relations from aggregated bulk expression data without strong additional assumptions.

Gongxu Luo, Boyang Sun, Kun Zhang

Mohamed bin Zayed University of Artificial Intelligence · Carnegie Mellon University

Structural Causal Models Causal Discovery Causal Identifiability Gene Regulatory Network Inference

May 29, 2026cs.AI

Evaluating Bivariate Causal Statements Based on Mutual Compatibility

For many real-world systems, causal ground truth is difficult to obtain, making claims about causal effects hard to assess. We develop methods for evaluating collections of

\binom{n}{2}

bivariate causal statements over a set of

n

variables. In the setting of acyclic linear statements, any such collection can be extended to a unique multivariate causal model, but we argue that this induced model is implausible if it imposes substantial additional confounding to explain observed correlations. We introduce a compatibility score that quantifies this notion of plausibility, notably without relying on the faithfulness assumption. Additionally, we define an incompatibility score for purely graphical bivariate causal statements, based on global consistency constraints that are derived from acyclicity and faithfulness assumptions. We give theoretical and empirical evidence that both scores can successfully distinguish correct from incorrect causal statements in generic settings. Moreover, we demonstrate the practical applicability of our methods by analyzing causal claims made by large language models. Our work aims to provide a foundation for assessing the reliability of causal information derived from human experts or artificial intelligence in settings where alternative forms of validation are unavailable.

Erik Jahn, Dominik Janzing

1California Institute of Technology, USA · 2Amazon Research Tübingen, Germany

Structural Causal Models Causal Reasoning Causal Inference

May 29, 2026cs.AI

Formalizing and falsifying causal pathways of rare events

Building on recent formalizations of root cause analysis for rare events (``outliers'') in structural equation models, we propose a formal definition of a causal pathway and discuss its testable implications. We identify conditions under which these implications depend only on a causal abstraction defined by the pathway of rare events, rather than on the full causal graph of the underlying system. Accordingly, we introduce an abstraction of causal structure to pathways of rare events that bridges simple verbal causal explanations and detailed causal modeling.

Anahita Haghighat, Dominik Janzing

Independent · Amazon Research, Tübingen, Germany

Structural Causal Models Causal Abstraction Causal Inference Causal Explanation Root Cause Analysis

May 29, 2026cs.LG

TabCausal: Pretraining Across Causal Environments for Tabular Causal Discovery

Causal discovery aims to recover directed causal relations from observational and interventional data, providing a basis for mechanistic understanding and reliable decision-making. Causal discovery foundation models (CDFMs) seek to amortize this problem by mapping a dataset directly to a causal graph in a single forward pass, avoiding per-dataset testing, search, or optimization. However, existing CDFMs remain limited, often failing to consistently match strong classical methods, and we find that a key bottleneck is how causal pretraining tasks are constructed. Based on this observation, we propose TabCausal, a data-driven CDFM trained with broad causal pretraining over diverse graph priors, structural mechanisms, noise models, dimensions, sample sizes, and intervention regimes. A dynamic task construction strategy composes these causal environments into varied discovery tasks, enabling more transferable structural learning from observational and mixed-interventional data. On large-scale synthetic benchmarks, TabCausal achieves better macro-averaged performance than a diverse set of causal discovery baselines. To further bridge abstract synthetic generators and realistic causal reasoning scenarios, we introduce a protocol-guided and LLM-audited semantic causal environment benchmark, where domain-grounded SCMs generate interpretable observational and interventional datasets for out-of-distribution analysis. Across both synthetic and semantic environments, TabCausal demonstrates robust structure recovery, especially under interventional evidence, highlighting broad causal pretraining as a key ingredient for transferable amortized causal discovery.

Zi-Rong Li, Si-Yang Liu, Tian-Zuo Wang +1

Nanjing University

Causal Foundation Models Synthetic Data Pretraining Structural Causal Models Causal Discovery

May 28, 2026cs.AI

Certified Policy Optimisation for Nested Causal Bandits via PAC-Bayes Risk

Critical sequential decisions are rarely single-timescale: a strategic decision causally shapes the context in which every subsequent tactical choice is made; standard bandit and reinforcement-learning theory does not capture this causal coupling between timescales. We formalise the problem class as Nested Contextual Causal Bandits (NCCBs), a hierarchical SCM where each level's action sets the next level's context distribution, and propose Nested Causal Thompson Sampling (NCTS), which draws one mechanism-factorised belief per episode and acts recursively under it. Our main theoretical result is a causal PAC-Bayesian excess-risk bound that certifies any candidate deployment policy from historic data alone, off-policy and anytime, answering the deployment question: can we trust this agent here, and at what risk? Experiments on a hierarchical SCM show that, against a matched RFF-GP joint regression on the same function class, the factorised SCM-mechanism posterior transfers significantly better zero-shot under exogenous distribution shifts, the recursive meta-to-inner commit significantly dominates the joint-commit alternative in distribution, and the certificate significantly contracts as offline data accumulates. Combining these results, we establish progressive certified handover, a safe-deployment method: each timescale flips from a legacy controller to NCTS when gains can be certified, independently of the others.

Tim Woydt, Paul-David Zuercher

ProdAxon · Department of Computer Science Technical University Darmstadt · Institute for Manufacturing Department of Engineering University of Cambridge

PAC-Bayesian Generalization Bounds Multi-Armed Bandits Structural Causal Models Off-Policy Evaluation Contextual Bandits

May 28, 2026cs.LG

The Good, the Bad, and the Ugly of Markov Boundary for Tabular Prediction

Under standard graphical assumptions, the Markov boundary of a target variable is the smallest set of features that renders every other feature redundant. Once the boundary is observed, the target is conditionally independent of the rest of the table. This is a tempting object for tabular prediction, since it names exactly the columns a model should need. Yet modern regressors are still trained on the full feature set. We ask whether the Markov boundary is genuinely useful for prediction on SCM3K, a 3,450-task synthetic SCM benchmark with feature counts from 40 to 1000 and six SCM families, evaluated with six regressors. The answer is more nuanced than the theory suggests. Restricting a regressor to the oracle boundary often improves prediction substantially, and the improvement grows as the feature space becomes larger and sparser. But the natural pipeline of recovering the boundary with causal discovery and training on the recovered mask does not deliver. Existing estimators exhaust the compute budget before reaching the regime where the boundary helps most, and even where they run they rarely beat the full feature set. We trace this to three causes. Discovery optimizes structural recovery rather than prediction. False negatives and false positives carry sharply asymmetric predictive cost. The exact boundary is only one of many feature sets that beat all features. We then develop what these facts imply for prediction-aligned feature selection and for tabular models that learn to use causal structure.

Shu Wan, Abhinav Gorantla, Huan Liu +1

Arizona State University Tempe, United States

Structural Causal Models Causal Discovery Feature Selection Tabular Prediction