Daily Papers

Protein-molecule virtual screening is increasingly cast as a problem of representation learning in a shared embedding space. Existing methods rely on dense holistic alignment, entangling invariant binding determinants with nuisance correlations and limiting transfer to new targets. It has been noted that binding in protein-molecule systems involves sparse cross-modality interactions: binding is governed by a small contact interface and a few decisive local interactions (e.g., hydrogen bonds, hydrophobic contacts, and salt bridges) rather than the global structures of the protein and molecule. We hypothesize that uncovering and leveraging sparse interaction patterns is critical for generalization beyond the training data, as these patterns are reusable and expected to improve performance across different scenarios. In this paper, we aim to identify and leverage sparse interaction patterns, and verify our hypothesis. Since the training data contain only observed binding pairs, we formalize this prior via a V-structure causal model under Heckman-style selection, and establish three theoretical results: (i) the latent concepts of interacting proteins and molecules are not identifiable without appropriate sparsity constraints; (ii) these concepts and their sparse interactions are component-wise identifiable under structural sparsity conditions; and (iii) a low-rank relaxation of these conditions yields subspace identifiability of the concepts and interactions. Inspired by these principles, we propose CausalBind with three implementation variants. Extensive experiments on DUD-E and LIT-PCBA benchmarks show that all variants consistently outperform strong retrieval baselines, with the largest gains on LIT-PCBA early enrichment, and further generalize to target- and scaffold-level out-of-distribution splits. Code is available at https://github.com/lokali/CausalBind.

We introduce a new approach to functional causal modeling from observational data, called Causal Generative Neural Networks (CGNN). CGNN leverages the power of neural networks to learn a generative model of the joint distribution of the observed variables, by minimizing the Maximum Mean Discrepancy between generated and observed data. An approximate learning criterion is proposed to scale the computational cost of the approach to linear complexity in the number of observations. The performance of CGNN is studied throughout three experiments. Firstly, CGNN is applied to cause-effect inference, where the task is to identify the best causal hypothesis out of Xrightarrow Y and Yrightarrow X. Secondly, CGNN is applied to the problem of identifying v-structures and conditional independences. Thirdly, CGNN is applied to multivariate functional causal modeling: given a skeleton describing the direct dependences in a set of random variables X = [X_1, ldots, X_d], CGNN orients the edges in the skeleton to uncover the directed acyclic causal graph describing the causal structure of the random variables. On all three tasks, CGNN is extensively assessed on both artificial and real-world data, comparing favorably to the state-of-the-art. Finally, CGNN is extended to handle the case of confounders, where latent variables are involved in the overall causal model.

Grounding large language models (LLMs) in domain-specific tasks like post-hoc dash-cam driving video analysis is challenging due to their general-purpose training and lack of structured inductive biases. As vision is often the sole modality available for such analysis (i.e., no LiDAR, GPS, etc.), existing video-based vision-language models (V-VLMs) struggle with spatial reasoning, causal inference, and explainability of events in the input video. To this end, we introduce iFinder, a structured semantic grounding framework that decouples perception from reasoning by translating dash-cam videos into a hierarchical, interpretable data structure for LLMs. iFinder operates as a modular, training-free pipeline that employs pretrained vision models to extract critical cues -- object pose, lane positions, and object trajectories -- which are hierarchically organized into frame- and video-level structures. Combined with a three-block prompting strategy, it enables step-wise, grounded reasoning for the LLM to refine a peer V-VLM's outputs and provide accurate reasoning. Evaluations on four public dash-cam video benchmarks show that iFinder's proposed grounding with domain-specific cues, especially object orientation and global context, significantly outperforms end-to-end V-VLMs on four zero-shot driving benchmarks, with up to 39% gains in accident reasoning accuracy. By grounding LLMs with driving domain-specific representations, iFinder offers a zero-shot, interpretable, and reliable alternative to end-to-end V-VLMs for post-hoc driving video understanding.

Knowledge-grounded dialogue systems aim to generate informative, contextually relevant responses by conditioning on external knowledge sources. However, most existing approaches focus exclusively on English, lack explicit citation mechanisms for verifying factual claims, and offer limited transparency into model decision-making. We present XKD-Dial, a progressive four-stage training pipeline for explainable, knowledge-grounded dialogue generation in a bilingual (English-Hindi) setting, comprising: (1) multilingual adaptation, (2) English dialogue SFT with citation grounding, (3) bilingual dialogue SFT, and (4) GRPO alignment with citation-aware rewards. We evaluate six models spanning encoder-decoder (250M-3B) and decoder-only (1B-7B) architectures at every pipeline stage. Our key contributions are: (i) three post-hoc explainability analyses - cross-attention alignment, Integrated Gradients attribution, and occlusion-based causal grounding - applied systematically across the training trajectory to reveal how citation behaviour is learned, not only whether it is learned; (ii) citation-grounded SFT reduces hallucination to 0.0% for encoder-decoder models from Stage 2 onward; (iii) the progressive pipeline prevents catastrophic forgetting while improving Hindi capabilities; (iv) smaller models match larger models on English after SFT; and (v) GRPO provides marginal improvement over well-designed SFT for structured citation tasks. We evaluate across six automatic metrics (BLEU, ROUGE, BERTScore, FactScore, Citation-F1, and hallucination rate).

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

We present a general causal generative modelling framework for accurate estimation of high fidelity image counterfactuals with deep structural causal models. Estimation of interventional and counterfactual queries for high-dimensional structured variables, such as images, remains a challenging task. We leverage ideas from causal mediation analysis and advances in generative modelling to design new deep causal mechanisms for structured variables in causal models. Our experiments demonstrate that our proposed mechanisms are capable of accurate abduction and estimation of direct, indirect and total effects as measured by axiomatic soundness of counterfactuals.

Structural Causal Models (SCM) are a powerful framework for describing complicated dynamics across the natural sciences. A particularly elegant way of interpreting SCMs is do-Shapley, a game-theoretic method of quantifying the average effect of d variables across exponentially many interventions. Like Shapley values, computing do-Shapley values generally requires evaluating exponentially many terms. The foundation of our work is a reformulation of do-Shapley values in terms of the irreducible sets of the underlying SCM. Leveraging this insight, we can exactly compute do-Shapley values in time linear in the number of irreducible sets r, which itself can range from d to 2^d depending on the graph structure of the SCM. Since r is unknown a priori, we complement the exact algorithm with an estimator that, like general Shapley value estimators, can be run with any query budget. As the query budget approaches r, our estimators can produce more accurate estimates than prior methods by several orders of magnitude, and, when the budget reaches r, return the Shapley values up to machine precision. Beyond computational speed, we also reduce the identification burden: we prove that non-parametric identifiability of do-Shapley values requires only the identification of interventional effects for the d singleton coalitions, rather than all classes.

Causal discovery, the process of recovering underlying causal structures from observational data, is a fundamental pursuit across scientific disciplines. Over the past decades, numerous algorithms have been developed to tackle this challenge through workflows tailored to the specific causal mechanisms underlying each type of dataset, demonstrating effectiveness across a wide range of applications. However, as the volume and heterogeneity of real-world data continue to grow, this dataset-specific approach inevitably leads to a fragmented, test-driven paradigm that struggles to scale to the demands of modern scientific discovery. To address this, we formulate the Causal Discovery Foundation Model (CDFM) as a unified, general-purpose framework for zero-shot structural inference. To ensure reliable generalization across unknown domains, we first investigate the theoretical boundaries of causal identifiability, revealing the indispensable role of causal prior mechanisms in this process. Building on these insights, we formulate a principled variational framework that treats unknown causal mechanisms as latent variables and mathematically decomposes the intractable marginal likelihood into distinct, tractable learning modules. The variational decomposition provides a conceptual design principle for the architecture design of CDFM, while comprehensive causal knowledge guides the large-scale synthesis of our pretraining data. By pretraining on a massive, highly diverse space of synthetic structural causal models, CDFM successfully internalizes complex statistical asymmetries. Extensive experiments demonstrate that CDFM consistently outperforms traditional algorithms, driving a paradigm shift toward a general-purpose causal discovery foundation model.

Recent advances in artificial intelligence reveal the limits of purely predictive systems and call for a shift toward causal and collaborative reasoning. Drawing inspiration from the revolution of Grothendieck in mathematics, we introduce the relativity of causal knowledge, which posits structural causal models (SCMs) are inherently imperfect, subjective representations embedded within networks of relationships. By leveraging category theory, we arrange SCMs into a functor category and show that their observational and interventional probability measures naturally form convex structures. This result allows us to encode non-intervened SCMs with convex spaces of probability measures. Next, using sheaf theory, we construct the network sheaf and cosheaf of causal knowledge. These structures enable the transfer of causal knowledge across the network while incorporating interventional consistency and the perspective of the subjects, ultimately leading to the formal, mathematical definition of relative causal knowledge.

Causal discovery aims to uncover causal structures from data and is fundamental to scientific reasoning and intervention-based decision making. Its evaluation relies heavily on structural causal models (SCMs), which specify a causal graph together with the mechanisms that generate data, yet existing studies differ substantially in graph families, mechanisms, and evaluation protocols. The emergence of causal discovery foundation models (CDFMs) further complicates evaluation: performance may reflect not only causal discovery ability, but also overlap between pretraining environments and test SCMs, making results on fixed synthetic benchmarks difficult to interpret. We introduce CausalArena, a unified and evolvable benchmark for causal discovery under a common protocol. Synthetic SCMs supply controlled breadth over structures and mechanisms; semantic operational SCMs provide human-auditable, semantically grounded environments beyond standard synthetic generators; and formula-grounded SCMs test discovery under explicit scientific mechanisms. Public real-world datasets provide an additional external-validity check. Experiments across classical, neural, and pretrained methods reveal substantial ranking shifts across SCM families and protocols, showing that strong performance in one benchmark regime does not reliably transfer to others. These results highlight benchmark diversity and pretraining--evaluation overlap as central challenges for evaluating causal discovery in the foundation model era.

In-context learning for tabular data sets strong predictive standards in observational settings; it however primarily relies on correlational structure, which becomes unreliable under distribution shift or intervention. While established methods to discover causal structure exist, they are often focused on structure identifiability and decoupled from the predictive architectures that could benefit from them. To bridge these perspectives, we study how to simultaneously infer and enforce causal structure in the form of topological variable orderings into tabular prediction. Unlike standard architectures, our model TabOrder uses causal order-constrained attention, basing predictions only on features that precede a target under a learned causal order. Similar to causal discovery methods, TabOrder learns the optimal variable ordering in an unsupervised manner through a likelihood-based objective. We justify this choice under standard functional model classes and also study how sample missingness, a common challenge in tabular data, interacts with causal direction identification. Empirically, we confirm that TabOrder recovers accurate variable orderings while addressing prediction and imputation tasks, as well as gives insight into real-world biological data under intervention.

Counterfactual inference in Gaussian-process structural causal models (GP-SCMs) has been developed primarily for continuous endogenous variables, limiting applicability to causal graphs that contain discrete child nodes with continuous parents. We introduce a unified probabilistic framework for counterfactual inference with heterogeneous variable types by pairing GP predictors with explicit exogenous noise mechanisms. For discrete outcomes, we derive exact conditional noise-abduction procedures using a uniform threshold for binary variables, a Gumbel-max race for nominal categories, and a latent Gaussian cut-point model for ordinal ones. In each case, we propagate abducted noise through interventions while accounting for posterior uncertainty in the GP latent functions, and prove that the resulting mechanisms reproduce the fitted model's observational and interventional distributions. On synthetic SCMs with known ground-truth counterfactuals, we evaluate estimation accuracy, consistency, and robustness to coupling misspecification. A key finding is that applying a categorical coupling to ordinal data inflates counterfactual error roughly threefold even when observational fit remains comparable, and that this error does not diminish with more data. As the training set grows, the fitted structural equation converges to the truth while the counterfactual error flattens onto a floor. In the reverse direction, forcing a false order onto nominal data instead degrades the fitted equation itself. The choice of coupling must therefore be justified on structural grounds rather than read off the fit.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

A faithful and interpretable explanation of an AI model's behavior and internal structure is a high-level explanation that is human-intelligible but also consistent with the known, but often opaque low-level causal details of the model. We argue that the theory of causal abstraction provides the mathematical foundations for the desired kinds of model explanations. In causal abstraction analysis, we use interventions on model-internal states to rigorously assess whether an interpretable high-level causal model is a faithful description of an AI model. Our contributions in this area are: (1) We generalize causal abstraction to cyclic causal structures and typed high-level variables. (2) We show how multi-source interchange interventions can be used to conduct causal abstraction analyses. (3) We define a notion of approximate causal abstraction that allows us to assess the degree to which a high-level causal model is a causal abstraction of a lower-level one. (4) We prove constructive causal abstraction can be decomposed into three operations we refer to as marginalization, variable-merge, and value-merge. (5) We formalize the XAI methods of LIME, causal effect estimation, causal mediation analysis, iterated nullspace projection, and circuit-based explanations as special cases of causal abstraction analysis.

Most benchmarks for causal inference over time series are observational, small, or domain-specific, leaving interventional and counterfactual estimation under-served exactly where it matters most, such as in healthcare, policy evaluation, and climate science. We introduce DoTime, an open, scalable, and theoretically grounded generator of multivariate temporal structural causal models (TSCMs) with interventions, released as the dotime PyPI package together with four frozen evaluation suites. Beyond existing work, it adds capabilities absent from prior generators: continuous-time intervention windows, counterfactual sampling modes with a positivity guard, regime-switching SCMs as a strict generalization of interrupted time series, non-stationary dynamics by construction with switching SCM parameters, and deterministic ramp and sinusoidal intervention profiles that place trends and structural breaks inside the evaluation window. Moreover, it demonstrates the suitability of the generator as a prior for a causal foundation model reference implementation. The released suites span a training-scale snapshot of 100{,}000 trajectories and eight named identification structures, each with exact ground truth: paired interventional trajectories from the same SCM throughout, and shared-noise counterfactuals in the continuous-time suite. We ship reference baseline implementations with an evaluation harness, and pose a falsifiable claim: interventional training buys a measurable direction-accuracy advantage over an observational model of identical capacity. It is tested across three training seeds per arm. Under structure-matched evaluation on held-out episodes, the interventional prior-fitted network's (PFN) gap is positive in every structure, trajectory length, and seed tested.

Fair machine learning seeks to identify and mitigate biases in predictions against unfavorable populations characterized by demographic attributes, such as race and gender. Recently, a few works have extended fairness to graph data, such as social networks, but most of them neglect the causal relationships among data instances. This paper addresses the prevalent challenge in fairness-aware ML algorithms, which typically assume Independent and Identically Distributed (IID) data. We tackle the overlooked domain of non-IID, graph-based settings where data instances are interconnected, influencing the outcomes of fairness interventions. We base our research on the Network Structural Causal Model (NSCM) framework and posit two main assumptions: Decomposability and Graph Independence, which enable the computation of interventional distributions in non-IID settings using the do-calculus. Based on that, we develop the Message Passing Variational Autoencoder for Causal Inference (MPVA) to compute interventional distributions and facilitate causally fair node classification through estimated interventional distributions. Empirical evaluations on semi-synthetic and real-world datasets demonstrate that MPVA outperforms conventional methods by effectively approximating interventional distributions and mitigating bias. The implications of our findings underscore the potential of causality-based fairness in complex ML applications, setting the stage for further research into relaxing the initial assumptions to enhance model fairness.

Enhancing node-level Out-Of-Distribution (OOD) generalization on graphs remains a crucial area of research. In this paper, we develop a Structural Causal Model (SCM) to theoretically dissect the performance of two prominent invariant learning methods -- Invariant Risk Minimization (IRM) and Variance-Risk Extrapolation (VREx) -- in node-level OOD settings. Our analysis reveals a critical limitation: due to the lack of class-conditional invariance constraints, these methods may struggle to accurately identify the structure of the predictive invariant ego-graph and consequently rely on spurious features. To address this, we propose Cross-environment Intra-class Alignment (CIA), which explicitly eliminates spurious features by aligning cross-environment representations conditioned on the same class, bypassing the need for explicit knowledge of the causal pattern structure. To adapt CIA to node-level OOD scenarios where environment labels are hard to obtain, we further propose CIA-LRA (Localized Reweighting Alignment) that leverages the distribution of neighboring labels to selectively align node representations, effectively distinguishing and preserving invariant features while removing spurious ones, all without relying on environment labels. We theoretically prove CIA-LRA's effectiveness by deriving an OOD generalization error bound based on PAC-Bayesian analysis. Experiments on graph OOD benchmarks validate the superiority of CIA and CIA-LRA, marking a significant advancement in node-level OOD generalization. The codes are available at https://github.com/NOVAglow646/NeurIPS24-Invariant-Learning-on-Graphs.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

Causal structures for observational survival data provide crucial information regarding the relationships between covariates and time-to-event. We derive motivation from the information theoretic source coding argument, and show that incorporating the knowledge of the directed acyclic graph (DAG) can be beneficial if suitable source encoders are employed. As a possible source encoder in this context, we derive a variational inference based conditional variational autoencoder for causal structured survival prediction, which we refer to as DAGSurv. We illustrate the performance of DAGSurv on low and high-dimensional synthetic datasets, and real-world datasets such as METABRIC and GBSG. We demonstrate that the proposed method outperforms other survival analysis baselines such as Cox Proportional Hazards, DeepSurv and Deephit, which are oblivious to the underlying causal relationship between data entities.

Understanding and reasoning about the physical world is the foundation of intelligent behavior, yet state-of-the-art vision-language models (VLMs) still fail at causal physical reasoning, often producing plausible but incorrect answers. To address this gap, we introduce CausalPhys, a benchmark of over 3,000 carefully curated video- and image-based questions spanning four domains: Perception, Anticipation, Intervention, and Goal Orientation. Each question is paired with an expert-annotated causal graph capturing object-attribute-event dependencies, enabling interpretable and fine-grained evaluation of causal understanding. Building on this, we formulate a causal-graph-grounded metric that quantitatively measures how well a model's chain-of-thought reasoning aligns with the correct causal relations, moving beyond answer-only accuracy and enabling systematic diagnosis of VLMs' causal reasoning failures. Using this metric, we conduct a comprehensive analysis of leading VLMs, revealing systematic gaps in capturing causal dependencies and underscoring the need for causality-aware learning. To address these limitations, we further propose Causal Rationale-informed Fine-Tuning (CRFT), which explicitly aligns VLM reasoning with causal structures. Extensive experiments demonstrate that CRFT substantially enhances both reasoning accuracy and interpretability across multiple model backbones. By unifying dataset curation, causal evaluation, and causality-informed learning, CausalPhys establishes a strong foundation for advancing modern VLMs toward causally grounded physical reasoning.

Causal generative models provide a principled framework for answering observational, interventional, and counterfactual queries from observational data. However, many deep causal models rely on highly expressive architectures with opaque mechanisms, limiting auditability in high-stakes domains. We propose KaCGM, a causal generative model for mixed-type tabular data where each structural equation is parameterized by a Kolmogorov--Arnold Network (KAN). This decomposition enables direct inspection of learned causal mechanisms, including symbolic approximations and visualization of parent--child relationships, while preserving query-agnostic generative semantics. We introduce a validation pipeline based on distributional matching and independence diagnostics of inferred exogenous variables, allowing assessment using observational data alone. Experiments on synthetic and semi-synthetic benchmarks show competitive performance against state-of-the-art methods. A real-world cardiovascular case study further demonstrates the extraction of simplified structural equations and interpretable causal effects. These results suggest that expressive causal generative modeling and functional transparency can be achieved jointly, supporting trustworthy deployment in tabular decision-making settings. Code: https://github.com/aalmodovares/kacgm

Quantifying the causal influence of input features within neural networks has become a topic of increasing interest. Existing approaches typically assess direct, indirect, and total causal effects. This work treats NNs as structural causal models (SCMs) and extends our focus to include intrinsic causal contributions (ICC). We propose an identifiable generative post-hoc framework for quantifying ICC. We also draw a relationship between ICC and Sobol' indices. Our experiments on synthetic and real-world datasets demonstrate that ICC generates more intuitive and reliable explanations compared to existing global explanation techniques.

Faithful evaluation of language model capabilities is crucial for deriving actionable insights that can inform model development. However, rigorous causal evaluations in this domain face significant methodological challenges, including complex confounding effects and prohibitive computational costs associated with extensive retraining. To tackle these challenges, we propose a causal representation learning framework wherein observed benchmark performance is modeled as a linear transformation of a few latent capability factors. Crucially, these latent factors are identified as causally interrelated after appropriately controlling for the base model as a common confounder. Applying this approach to a comprehensive dataset encompassing over 1500 models evaluated across six benchmarks from the Open LLM Leaderboard, we identify a concise three-node linear causal structure that reliably explains the observed performance variations. Further interpretation of this causal structure provides substantial scientific insights beyond simple numerical rankings: specifically, we reveal a clear causal direction starting from general problem-solving capabilities, advancing through instruction-following proficiency, and culminating in mathematical reasoning ability. Our results underscore the essential role of carefully controlling base model variations during evaluation, a step critical to accurately uncovering the underlying causal relationships among latent model capabilities.

It is commonplace to encounter heterogeneous or nonstationary data, of which the underlying generating process changes across domains or over time. Such a distribution shift feature presents both challenges and opportunities for causal discovery. In this paper, we develop a framework for causal discovery from such data, called Constraint-based causal Discovery from heterogeneous/NOnstationary Data (CD-NOD), to find causal skeleton and directions and estimate the properties of mechanism changes. First, we propose an enhanced constraint-based procedure to detect variables whose local mechanisms change and recover the skeleton of the causal structure over observed variables. Second, we present a method to determine causal orientations by making use of independent changes in the data distribution implied by the underlying causal model, benefiting from information carried by changing distributions. After learning the causal structure, next, we investigate how to efficiently estimate the "driving force" of the nonstationarity of a causal mechanism. That is, we aim to extract from data a low-dimensional representation of changes. The proposed methods are nonparametric, with no hard restrictions on data distributions and causal mechanisms, and do not rely on window segmentation. Furthermore, we find that data heterogeneity benefits causal structure identification even with particular types of confounders. Finally, we show the connection between heterogeneity/nonstationarity and soft intervention in causal discovery. Experimental results on various synthetic and real-world data sets (task-fMRI and stock market data) are presented to demonstrate the efficacy of the proposed methods.

In disentangled representation learning, the goal is to achieve a compact representation that consists of all interpretable generative factors in the observational data. Learning disentangled representations for graphs becomes increasingly important as graph data rapidly grows. Existing approaches often rely on Variational Auto-Encoder (VAE) or its causal structure learning-based refinement, which suffer from sub-optimality in VAEs due to the independence factor assumption and unavailability of concept labels, respectively. In this paper, we propose an unsupervised solution, dubbed concept-free causal disentanglement, built on a theoretically provable tight upper bound approximating the optimal factor. This results in an SCM-like causal structure modeling that directly learns concept structures from data. Based on this idea, we propose Concept-free Causal VGAE (CCVGAE) by incorporating a novel causal disentanglement layer into Variational Graph Auto-Encoder. Furthermore, we prove concept consistency under our concept-free causal disentanglement framework, hence employing it to enhance the meta-learning framework, called concept-free causal Meta-Graph (CC-Meta-Graph). We conduct extensive experiments to demonstrate the superiority of the proposed models: CCVGAE and CC-Meta-Graph, reaching up to 29% and 11% absolute improvements over baselines in terms of AUC, respectively.

Causal Discovery plays a pivotal role in revealing relationships among observed variables, particularly in the temporal setup. While the majority of CD methods rely on synthetic data for evaluation, and recently for training, these fall short in accurately mirroring real-world scenarios; an effect even more evident in temporal data. Generation techniques depending on simplified assumptions on causal structure, effects and time, limit the quality and diversity of the simulated data. In this work, we introduce Temporal Causal-based Simulation (TCS), a robust framework for generating realistic time-series data and their associated temporal causal graphs. The approach is structured in three phases: estimating the true lagged causal structure of the data, approximating the functional dependencies between variables and learning the noise distribution of the corresponding causal model, each part of which can be explicitly tailored based on data assumptions and characteristics. Through an extensive evaluation process, we highlight that single detection methods for generated data discrimination prove inadequate, accentuating it as a multifaceted challenge. For this, we detail a Min-max optimization phase that draws on AutoML techniques. Our contributions include a flexible, model-agnostic pipeline for generating realistic temporal causal data, a thorough evaluation setup which enhances the validity of the generated datasets and insights into the challenges posed by realistic data generation. Through experiments involving not only real but also semi-synthetic and purely synthetic datasets, we demonstrate that while sampling realistic causal data remains a complex task, our method enriches the domain of generating sensible causal-based temporal data.

Answering counterfactual queries has many important applications such as knowledge discovery and explainability, but is challenging when causal variables are unobserved and we only see a projection onto an observation space, for instance, image pixels. One approach is to recover the latent Structural Causal Model (SCM), but this typically needs unrealistic assumptions, such as linearity of the causal mechanisms. Another approach is to use na\"ive ML approximations, such as generative models, to generate counterfactual samples; however, these lack guarantees of accuracy. In this work, we strive to strike a balance between practicality and theoretical guarantees by focusing on a specific type of causal query called domain counterfactuals, which hypothesizes what a sample would have looked like if it had been generated in a different domain (or environment). Concretely, by only assuming invertibility, sparse domain interventions and access to observational data from different domains, we aim to improve domain counterfactual estimation both theoretically and practically with less restrictive assumptions. We define domain counterfactually equivalent models and prove necessary and sufficient properties for equivalent models that provide a tight characterization of the domain counterfactual equivalence classes. Building upon this result, we prove that every equivalence class contains a model where all intervened variables are at the end when topologically sorted by the causal DAG. This surprising result suggests that a model design that only allows intervention in the last k latent variables may improve model estimation for counterfactuals. We then test this model design on extensive simulated and image-based experiments which show the sparse canonical model indeed improves counterfactual estimation over baseline non-sparse models.

Heterogeneity and comorbidity are two interwoven challenges associated with various healthcare problems that greatly hampered research on developing effective treatment and understanding of the underlying neurobiological mechanism. Very few studies have been conducted to investigate heterogeneous causal effects (HCEs) in graphical contexts due to the lack of statistical methods. To characterize this heterogeneity, we first conceptualize heterogeneous causal graphs (HCGs) by generalizing the causal graphical model with confounder-based interactions and multiple mediators. Such confounders with an interaction with the treatment are known as moderators. This allows us to flexibly produce HCGs given different moderators and explicitly characterize HCEs from the treatment or potential mediators on the outcome. We establish the theoretical forms of HCEs and derive their properties at the individual level in both linear and nonlinear models. An interactive structural learning is developed to estimate the complex HCGs and HCEs with confidence intervals provided. Our method is empirically justified by extensive simulations and its practical usefulness is illustrated by exploring causality among psychiatric disorders for trauma survivors.

Despite remarkable advances in the field, LLMs remain unreliable in distinguishing causation from correlation. Recent results from the Corr2Cause dataset benchmark reveal that state-of-the-art LLMs -- such as GPT-4 (F1 score: 29.08) -- only marginally outperform random baselines (Random Uniform, F1 score: 20.38), indicating limited capacity of generalization. To tackle this limitation, we propose a novel structured approach: rather than directly answering causal queries, we provide the model with the capability to structure its thinking by guiding the model to build a structured knowledge graph, systematically encoding the provided correlational premises, to answer the causal queries. This intermediate representation significantly enhances the model's causal capabilities. Experiments on the test subset of the Corr2Cause dataset benchmark with Qwen3-32B model (reasoning model) show substantial gains over standard direct prompting methods, improving F1 scores from 32.71 to 48.26 (over 47.5% relative increase), along with notable improvements in precision and recall. These results underscore the effectiveness of providing the model with the capability to structure its thinking and highlight its promising potential for broader generalization across diverse causal inference tasks.

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.

This paper proposes a Disentangled gEnerative cAusal Representation (DEAR) learning method under appropriate supervised information. Unlike existing disentanglement methods that enforce independence of the latent variables, we consider the general case where the underlying factors of interests can be causally related. We show that previous methods with independent priors fail to disentangle causally related factors even under supervision. Motivated by this finding, we propose a new disentangled learning method called DEAR that enables causal controllable generation and causal representation learning. The key ingredient of this new formulation is to use a structural causal model (SCM) as the prior distribution for a bidirectional generative model. The prior is then trained jointly with a generator and an encoder using a suitable GAN algorithm incorporated with supervised information on the ground-truth factors and their underlying causal structure. We provide theoretical justification on the identifiability and asymptotic convergence of the proposed method. We conduct extensive experiments on both synthesized and real data sets to demonstrate the effectiveness of DEAR in causal controllable generation, and the benefits of the learned representations for downstream tasks in terms of sample efficiency and distributional robustness.

Causal inference plays a vital role in diverse domains like epidemiology, healthcare, and economics. De-confounding and counterfactual prediction in observational data has emerged as a prominent concern in causal inference research. While existing models tackle observed confounders, the presence of unobserved confounders remains a significant challenge, distorting causal inference and impacting counterfactual outcome accuracy. To address this, we propose a novel variational learning model of unobserved confounders for counterfactual inference (VLUCI), which generates the posterior distribution of unobserved confounders. VLUCI relaxes the unconfoundedness assumption often overlooked by most causal inference methods. By disentangling observed and unobserved confounders, VLUCI constructs a doubly variational inference model to approximate the distribution of unobserved confounders, which are used for inferring more accurate counterfactual outcomes. Extensive experiments on synthetic and semi-synthetic datasets demonstrate VLUCI's superior performance in inferring unobserved confounders. It is compatible with state-of-the-art counterfactual inference models, significantly improving inference accuracy at both group and individual levels. Additionally, VLUCI provides confidence intervals for counterfactual outcomes, aiding decision-making in risk-sensitive domains. We further clarify the considerations when applying VLUCI to cases where unobserved confounders don't strictly conform to our model assumptions using the public IHDP dataset as an example, highlighting the practical advantages of VLUCI.

Recent work has shown promising results in causal discovery by leveraging interventional data with gradient-based methods, even when the intervened variables are unknown. However, previous work assumes that the correspondence between samples and interventions is known, which is often unrealistic. We envision a scenario with an extensive dataset sampled from multiple intervention distributions and one observation distribution, but where we do not know which distribution originated each sample and how the intervention affected the system, i.e., interventions are entirely latent. We propose a method based on neural networks and variational inference that addresses this scenario by framing it as learning a shared causal graph among an infinite mixture (under a Dirichlet process prior) of intervention structural causal models. Experiments with synthetic and real data show that our approach and its semi-supervised variant are able to discover causal relations in this challenging scenario.

Multimodal Large Language Models (MLLMs) have emerged as a central focus in both industry and academia, but often suffer from biases introduced by visual and language priors, which can lead to multimodal hallucination. These biases arise from the visual encoder and the Large Language Model (LLM) backbone, affecting the attention mechanism responsible for aligning multimodal inputs. Existing decoding-based mitigation methods focus on statistical correlations and overlook the causal relationships between attention mechanisms and model output, limiting their effectiveness in addressing these biases. To tackle this issue, we propose a causal inference framework termed CausalMM that applies structural causal modeling to MLLMs, treating modality priors as a confounder between attention mechanisms and output. Specifically, by employing backdoor adjustment and counterfactual reasoning at both the visual and language attention levels, our method mitigates the negative effects of modality priors and enhances the alignment of MLLM's inputs and outputs, with a maximum score improvement of 65.3% on 6 VLind-Bench indicators and 164 points on MME Benchmark compared to conventional methods. Extensive experiments validate the effectiveness of our approach while being a plug-and-play solution. Our code is available at: https://github.com/The-Martyr/CausalMM

Linear structural equation models are multivariate statistical models encoded by mixed graphs. In particular, the set of covariance matrices for distributions belonging to a linear structural equation model for a fixed mixed graph G=(V, D,B) is parameterized by a rational function with parameters for each vertex and edge in G. This rational parametrization naturally allows for the study of these models from an algebraic and combinatorial point of view. Indeed, this point of view has led to a collection of results in the literature, mainly focusing on questions related to identifiability and determining relationships between covariances (i.e., finding polynomials in the Gaussian vanishing ideal). So far, a large proportion of these results has focused on the case when D, the directed part of the mixed graph G, is acyclic. This is due to the fact that in the acyclic case, the parametrization becomes polynomial and there is a description of the entries of the covariance matrices in terms of a finite sum. We move beyond the acyclic case and give a closed form expression for the entries of the covariance matrices in terms of the one-connections in a graph obtained from D through some small operations. This closed form expression then allows us to show that if G is simple, then the parametrization map is generically finite-to-one. Finally, having a closed form expression for the covariance matrices allows for the development of an algorithm for systematically exploring possible polynomials in the Gaussian vanishing ideal.

Most existing causal discovery methods rely on the assumption of no latent confounders, limiting their applicability in solving real-life problems. In this paper, we introduce a novel, versatile framework for causal discovery that accommodates the presence of causally-related hidden variables almost everywhere in the causal network (for instance, they can be effects of observed variables), based on rank information of covariance matrix over observed variables. We start by investigating the efficacy of rank in comparison to conditional independence and, theoretically, establish necessary and sufficient conditions for the identifiability of certain latent structural patterns. Furthermore, we develop a Rank-based Latent Causal Discovery algorithm, RLCD, that can efficiently locate hidden variables, determine their cardinalities, and discover the entire causal structure over both measured and hidden ones. We also show that, under certain graphical conditions, RLCD correctly identifies the Markov Equivalence Class of the whole latent causal graph asymptotically. Experimental results on both synthetic and real-world personality data sets demonstrate the efficacy of the proposed approach in finite-sample cases.

Discovering causal structures with latent variables from observational data is a fundamental challenge in causal discovery. Existing methods often rely on constraint-based, iterative discrete searches, limiting their scalability to large numbers of variables. Moreover, these methods frequently assume linearity or invertibility, restricting their applicability to real-world scenarios. We present new theoretical results on the identifiability of nonlinear latent hierarchical causal models, relaxing previous assumptions in literature about the deterministic nature of latent variables and exogenous noise. Building on these insights, we develop a novel differentiable causal discovery algorithm that efficiently estimates the structure of such models. To the best of our knowledge, this is the first work to propose a differentiable causal discovery method for nonlinear latent hierarchical models. Our approach outperforms existing methods in both accuracy and scalability. We demonstrate its practical utility by learning interpretable hierarchical latent structures from high-dimensional image data and demonstrate its effectiveness on downstream tasks.

Causal inference, estimating causal effects from observational data, is a fundamental tool in many disciplines. Of particular importance across a variety of domains is the continuous treatment setting, where the variable of intervention has a continuous range. This setting is far less explored and represents a substantial shift from the binary treatment setting, with models needing to represent effects across a continuum of treatment values. In this paper, we present the first causal foundation model for the continuous treatment setting. Our model meta-learns the ability to predict causal effects across a wide variety of unseen tasks without additional training or fine-tuning. First, we design a novel prior over data-generating processes with continuous treatment variables in order to generate a rich causal training corpus. We then train a transformer to reconstruct individual treatment-response curves given only observational data, leveraging in-context learning to amortize expensive Bayesian posterior inference. Our model achieves state-of-the-art performance on individual treatment-response curve reconstruction tasks compared to causal models which are trained specifically for those tasks.

Latent or continuous chain-of-thought methods replace explicit textual rationales with a number of internal latent steps, but these intermediate computations are difficult to evaluate beyond correlation-based probes. In this paper, we view latent chain-of-thought as a manipulable causal process in representation space by modeling latent steps as variables in a structural causal model (SCM) and analyzing their effects through step-wise do-interventions. We study two representative paradigms (i.e., Coconut and CODI) on both mathematical and general reasoning tasks to investigate three key questions: (1) which steps are causally necessary for correctness and when answers become decidable early; (2) how does influence propagate across steps, and how does this structure compare to explicit CoT; and (3) do intermediate trajectories retain competing answer modes, and how does output-level commitment differ from representational commitment across steps. We find that latent-step budgets behave less like homogeneous extra depth and more like staged functionality with non-local routing, and we identify a persistent gap between early output bias and late representational commitment. These results motivate mode-conditional and stability-aware analyses -- and corresponding training/decoding objectives -- as more reliable tools for interpreting and improving latent reasoning systems. Code is available at https://github.com/J1mL1/causal-latent-cot.

We present a constraint-based algorithm for learning causal structures from observational time-series data, in the presence of latent confounders. We assume a discrete-time, stationary structural vector autoregressive process, with both temporal and contemporaneous causal relations. One may ask if temporal and contemporaneous relations should be treated differently. The presented algorithm gradually refines a causal graph by learning long-term temporal relations before short-term ones, where contemporaneous relations are learned last. This ordering of causal relations to be learnt leads to a reduction in the required number of statistical tests. We validate this reduction empirically and demonstrate that it leads to higher accuracy for synthetic data and more plausible causal graphs for real-world data compared to state-of-the-art algorithms.

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.

Discovering causal structures from data is a challenging inference problem of fundamental importance in all areas of science. The appealing properties of neural networks have recently led to a surge of interest in differentiable neural network-based methods for learning causal structures from data. So far, differentiable causal discovery has focused on static datasets of observational or fixed interventional origin. In this work, we introduce an active intervention targeting (AIT) method which enables a quick identification of the underlying causal structure of the data-generating process. Our method significantly reduces the required number of interactions compared with random intervention targeting and is applicable for both discrete and continuous optimization formulations of learning the underlying directed acyclic graph (DAG) from data. We examine the proposed method across multiple frameworks in a wide range of settings and demonstrate superior performance on multiple benchmarks from simulated to real-world data.

Research community has witnessed substantial growth in the detection of mental health issues and their associated reasons from analysis of social media. We introduce a new dataset for Causal Analysis of Mental health issues in Social media posts (CAMS). Our contributions for causal analysis are two-fold: causal interpretation and causal categorization. We introduce an annotation schema for this task of causal analysis. We demonstrate the efficacy of our schema on two different datasets: (i) crawling and annotating 3155 Reddit posts and (ii) re-annotating the publicly available SDCNL dataset of 1896 instances for interpretable causal analysis. We further combine these into the CAMS dataset and make this resource publicly available along with associated source code: https://github.com/drmuskangarg/CAMS. We present experimental results of models learned from CAMS dataset and demonstrate that a classic Logistic Regression model outperforms the next best (CNN-LSTM) model by 4.9\% accuracy.

Causal inference is a critical task across fields such as healthcare, economics, and the social sciences. While recent advances in machine learning, especially those based on the deep-learning architectures, have shown potential in estimating causal effects, existing approaches often fall short in handling complex causal structures and lack adaptability across various causal scenarios. In this paper, we present a novel transformer-based method for causal inference that overcomes these challenges. The core innovation of our model lies in its integration of causal Directed Acyclic Graphs (DAGs) directly into the attention mechanism, enabling it to accurately model the underlying causal structure. This allows for flexible estimation of both average treatment effects (ATE) and conditional average treatment effects (CATE). Extensive experiments on both synthetic and real-world datasets demonstrate that our approach surpasses existing methods in estimating causal effects across a wide range of scenarios. The flexibility and robustness of our model make it a valuable tool for researchers and practitioners tackling complex causal inference problems.

Large language models (LLMs) have shown remarkable ability in various language tasks, especially with their emergent in-context learning capability. Extending LLMs to incorporate visual inputs, large vision-language models (LVLMs) have shown impressive performance in tasks such as recognition and visual question answering (VQA). Despite increasing interest in the utility of LLMs in causal reasoning tasks such as causal discovery and counterfactual reasoning, there has been relatively little work showcasing the abilities of LVLMs on visual causal reasoning tasks. We take this opportunity to formally introduce a comprehensive causal reasoning benchmark for multi-modal in-context learning from LVLMs. Our CausalVLBench encompasses three representative tasks: causal structure inference, intervention target prediction, and counterfactual prediction. We evaluate the ability of state-of-the-art open-source LVLMs on our causal reasoning tasks across three causal representation learning datasets and demonstrate their fundamental strengths and weaknesses. We hope that our benchmark elucidates the drawbacks of existing vision-language models and motivates new directions and paradigms in improving the visual causal reasoning abilities of LVLMs.

Market generators using deep generative models have shown promise for synthetic financial data generation, but existing approaches lack causal reasoning capabilities essential for counterfactual analysis and risk assessment. We propose a Time-series Neural Causal Model VAE (TNCM-VAE) that combines variational autoencoders with structural causal models to generate counterfactual financial time series while preserving both temporal dependencies and causal relationships. Our approach enforces causal constraints through directed acyclic graphs in the decoder architecture and employs the causal Wasserstein distance for training. We validate our method on synthetic autoregressive models inspired by the Ornstein-Uhlenbeck process, demonstrating superior performance in counterfactual probability estimation with L1 distances as low as 0.03-0.10 compared to ground truth. The model enables financial stress testing, scenario analysis, and enhanced backtesting by generating plausible counterfactual market trajectories that respect underlying causal mechanisms.

Model-based methods have recently shown promising for offline reinforcement learning (RL), aiming to learn good policies from historical data without interacting with the environment. Previous model-based offline RL methods learn fully connected nets as world-models that map the states and actions to the next-step states. However, it is sensible that a world-model should adhere to the underlying causal effect such that it will support learning an effective policy generalizing well in unseen states. In this paper, We first provide theoretical results that causal world-models can outperform plain world-models for offline RL by incorporating the causal structure into the generalization error bound. We then propose a practical algorithm, oFfline mOdel-based reinforcement learning with CaUsal Structure (FOCUS), to illustrate the feasibility of learning and leveraging causal structure in offline RL. Experimental results on two benchmarks show that FOCUS reconstructs the underlying causal structure accurately and robustly. Consequently, it performs better than the plain model-based offline RL algorithms and other causal model-based RL algorithms.

Prior-data fitted networks (PFNs) have emerged as powerful foundation models for tabular causal inference, yet their extension to time series remains limited by the absence of synthetic data generators that provide interventional targets. Existing time series benchmarks generate observational data with ground-truth causal graphs but lack the interventional data required for training causal foundation models. To address this, we propose CausalTimePrior, a principled framework for generating synthetic temporal structural causal models (TSCMs) with paired observational and interventional time series. Our prior supports configurable causal graph structures, nonlinear autoregressive mechanisms, regime-switching dynamics, and multiple intervention types (hard, soft, time-varying). We demonstrate that PFNs trained on CausalTimePrior can perform in-context causal effect estimation on held-out TSCMs, establishing a pathway toward foundation models for time series causal inference.

Recommendation systems (RS) aim to provide personalized content, but they face a challenge in unbiased learning due to selection bias, where users only interact with items they prefer. This bias leads to a distorted representation of user preferences, which hinders the accuracy and fairness of recommendations. To address the issue, various methods such as error imputation based, inverse propensity scoring, and doubly robust techniques have been developed. Despite the progress, from the structural causal model perspective, previous debiasing methods in RS assume the independence of the exogenous variables. In this paper, we release this assumption and propose a learning algorithm based on likelihood maximization to learn a prediction model. We first discuss the correlation and difference between unmeasured confounding and our scenario, then we propose a unified method that effectively handles latent exogenous variables. Specifically, our method models the data generation process with latent exogenous variables under mild normality assumptions. We then develop a Monte Carlo algorithm to numerically estimate the likelihood function. Extensive experiments on synthetic datasets and three real-world datasets demonstrate the effectiveness of our proposed method. The code is at https://github.com/WallaceSUI/kdd25-background-variable.

Large Vision Language Models (LVLMs) show promise in medical applications, but their inability to faithfully ground responses in visual evidence raises serious concerns about clinical trustworthiness. While visual attribution methods are widely used to explain LVLM predictions, whether these explanations actually reflect the visual evidence underlying the model's decision is largely unverified, since ground-truth annotations for internal model reasoning are typically unavailable. We address this question for chest X-ray (CXR) reasoning by developing a causal evaluation framework that retains only CXR-VQA samples for which the expert-annotated region is verified, via counterfactual editing, to be causally responsible for the model's prediction. Using this framework across 11 attribution methods, six open-source LVLMs, and two output modes (direct answer and step-by-step reasoning), we find that existing attribution methods often fail to identify the evidence used by LVLMs. To address this failure, we propose MedFocus, a concept-based attribution method that localizes clinically meaningful anatomical regions via unbalanced optimal transport and measures their causal effect on model outputs through targeted interventions. MedFocus produces spatial, concept-level, and token-level attributions and substantially outperforms prior methods, taking a step toward more trustworthy attribution for medical LVLMs. Our data and code are available at https://github.com/gzxiong/medfocus/.

Causal representation learning (CRL) has garnered increasing interest from the causal inference and artificial intelligence communities due to its potential to disentangle complex data-generating mechanism into causally interpretable latent features by leveraging the heterogeneity of modern datasets. In this paper, we further contribute to the CRL literature, by focusing on the stylized linear structural causal model over latent features and assuming a linear mixing function that maps latent features to the observed data or measurements. Existing linear CRL methods often rely on stringent assumptions, such as access to single-node interventional data or restrictive distributional constraints on latent features and/or exogenous measurement noise. However, these prerequisites can be easy to violate in practice. In this work, we propose a novel linear CRL algorithm that, unlike existing methods, operates under weaker assumptions on environment heterogeneity and data-generating distributions while still recovering latent causal features up to an equivalence class. We further validate our new algorithm via synthetic experiments and an interpretability analysis of large language models, demonstrating both its superiority over competing methods in finite samples and its potential in integrating causality into understanding artificial intelligence. The source code is available at https://github.com/utulie/code_for_linear_crl_paper_creator.

Diffusion models (DMs) have achieved remarkable success in image and video generation. However, they still struggle with (1) physical alignment and (2) out-of-distribution (OOD) instruction following. We argue that these issues stem from the models' failure to learn causal directions and to disentangle causal factors for novel recombination. We introduce the Causal Scene Graph (CSG) and the Physical Alignment Probe (PAP) dataset to enable diagnostic interventions. This analysis yields three key insights. First, DMs struggle with multi-hop reasoning for elements not explicitly determined in the prompt. Second, the prompt embedding contains disentangled representations for texture and physics. Third, visual causal structure is disproportionately established during the initial, computationally limited denoising steps. Based on these findings, we introduce LINA (Learning INterventions Adaptively), a novel framework that learns to predict prompt-specific interventions, which employs (1) targeted guidance in the prompt and visual latent spaces, and (2) a reallocated, causality-aware denoising schedule. Our approach enforces both physical alignment and OOD instruction following in image and video DMs, achieving state-of-the-art performance on challenging causal generation tasks and the Winoground dataset. Our project page is at https://opencausalab.github.io/LINA.

Schema-guided reasoning pipelines ask LLMs to produce explicit intermediate structures -- rubrics, checklists, verification queries -- before committing to a final decision. But do these structures causally determine the output, or merely accompany it? We introduce a causal evaluation protocol that makes this directly measurable: by selecting tasks where a deterministic function maps intermediate structures to decisions, every controlled edit implies a unique correct output. Across eight models and three benchmarks, models appear self-consistent with their own intermediate structures but fail to update predictions after intervention in up to 60% of cases -- revealing that apparent faithfulness is fragile once the intermediate structure changes. When derivation of the final decision from the structure is delegated to an external tool, this fragility largely disappears; however, prompts which ask to prioritize the intermediate structure over the original input do not materially close the gap. Overall, intermediate structures in schema-guided pipelines function as influential context rather than stable causal mediators.

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.

True intelligence hinges on the ability to uncover and leverage hidden causal relations. Despite significant progress in AI and computer vision (CV), there remains a lack of benchmarks for assessing models' abilities to infer latent causality from complex visual data. In this paper, we introduce \textbf{Causal3D}, a novel and comprehensive benchmark that integrates structured data (tables) with corresponding visual representations (images) to evaluate causal reasoning. Designed within a systematic framework, Causal3D comprises 19 3D-scene datasets capturing diverse causal relations, views, and backgrounds, enabling evaluations across scenes of varying complexity. We assess multiple state-of-the-art methods, including classical causal discovery, causal representation learning, and large/vision-language models (LLMs/VLMs). Our experiments show that as causal structures grow more complex without prior knowledge, performance declines significantly, highlighting the challenges even advanced methods face in complex causal scenarios. Causal3D serves as a vital resource for advancing causal reasoning in CV and fostering trustworthy AI in critical domains.

Interpretability research on large language models (LLMs) has yielded important insights into model behaviour, yet recurring pitfalls persist: findings that do not generalise, and causal interpretations that outrun the evidence. Our position is that causal inference specifies what constitutes a valid mapping from model activations to invariant high-level structures, the data or assumptions needed to achieve it, and the inferences it can support. Specifically, Pearl's causal hierarchy clarifies what an interpretability study can justify. Observations establish associations between model behaviour and internal components. Interventions (e.g., ablations or activation patching) support claims how these edits affect a behavioural metric (e.g., average change in token probabilities) over a set of prompts. However, counterfactual claims -- i.e., asking what the model output would have been for the same prompt under an unobserved intervention -- remain largely unverifiable without controlled supervision. We show how causal representation learning (CRL) operationalises this hierarchy, specifying which variables are recoverable from activations and under what assumptions. Together, these motivate a diagnostic framework that helps practitioners select methods and evaluations matching claims to evidence such that findings generalise.

Dataset bias often leads deep learning models to exploit spurious correlations instead of task-relevant signals. We introduce the Standard Anti-Causal Model (SAM), a unifying causal framework that characterizes bias mechanisms and yields a conditional independence criterion for causal stability. Building on this theory, we propose DISCO_m and sDISCO, efficient and scalable estimators of conditional distance correlation that enable independence regularization in gradient-based models. Across six diverse datasets, our methods consistently outperform or are competitive in existing observed bias mitigation approaches, while requiring fewer hyperparameters and scaling seamlessly to multi-bias scenarios. This work bridges causal theory and practical deep learning, providing both a principled foundation and effective tools for robust prediction. Source Code: https://github.com/yakamoz5/DISCO.

Foundation models have brought changes to the landscape of machine learning, demonstrating sparks of human-level intelligence across a diverse array of tasks. However, a gap persists in complex tasks such as causal inference, primarily due to challenges associated with intricate reasoning steps and high numerical precision requirements. In this work, we take a first step towards building causally-aware foundation models for treatment effect estimations. We propose a novel, theoretically justified method called Causal Inference with Attention (CInA), which utilizes multiple unlabeled datasets to perform self-supervised causal learning, and subsequently enables zero-shot causal inference on unseen tasks with new data. This is based on our theoretical results that demonstrate the primal-dual connection between optimal covariate balancing and self-attention, facilitating zero-shot causal inference through the final layer of a trained transformer-type architecture. We demonstrate empirically that CInA effectively generalizes to out-of-distribution datasets and various real-world datasets, matching or even surpassing traditional per-dataset methodologies. These results provide compelling evidence that our method has the potential to serve as a stepping stone for the development of causal foundation models.

Causal graphs provide a high-level language for making mechanisms transparent. Recent work uses Large Language Models (LLMs) to recover causal graphs of external-world processes. Instead, in this paper, we use causal graphs to model LLM inference itself, providing stakeholders with a transparent view of how the model perceives and organizes high-level concepts to produce a prediction. We propose a four-phase method for constructing such graphs. Given a target LLM and a set of textual examples, our method discovers class-discriminative, human-interpretable concepts and maps each input to LLM-perceived concept states. We then introduce an MCMC-inspired counterfactual augmentation procedure that expands the sparse observational data through chains of counterfactuals. This enables stable causal discovery with σ-CG, yielding informative, interpretable graphs. We apply our method to three LLMs across disease diagnosis, sentiment analysis, and LLM-as-a-judge classification tasks. We evaluate the learned graphs for predictive fidelity and structural stability, and the MCMC-inspired augmentation for convergence and downstream utility. Our results show that the discovered causal graphs capture meaningful dependencies consistent with LLMs' reasoning. Together, this paper provides a foundation for concept-level explainability of LLMs.

Understanding the physical structure is essential for real-world applications such as embodied agents, interactive design, and long-horizon manipulation. Yet, prevailing Vision-Language Model (VLM) evaluations still center on structure-agnostic, single-turn setups (e.g., VQA), which fail to assess agents' ability to reason about how geometry, contact, and support relations jointly constrain what actions are possible in a dynamic environment. To address this gap, we introduce the Causal Hierarchy of Actions and Interactions (CHAIN) benchmark, an interactive 3D, physics-driven testbed designed to evaluate whether models can understand, plan, and execute structured action sequences grounded in physical constraints. CHAIN shifts evaluation from passive perception to active problem solving, spanning tasks such as interlocking mechanical puzzles and 3D stacking and packing. We conduct a comprehensive study of state-of-the-art VLMs and diffusion-based models under unified interactive settings. Our results show that top-performing models still struggle to internalize physical structure and causal constraints, often failing to produce reliable long-horizon plans and cannot robustly translate perceived structure into effective actions. The project is available at https://social-ai-studio.github.io/CHAIN/.

Causal discovery for both cross-sectional and temporal data has traditionally followed a dataset-specific paradigm, where a new model is fitted for each individual dataset. Such an approach limits the potential of multi-dataset pretraining. The concept of large causal models (LCMs) envisions a class of pre-trained neural architectures specifically designed for temporal causal discovery. Prior approaches are constrained to small variable counts, degrade with larger inputs, and rely heavily on synthetic data, limiting generalization. We propose a principled framework for LCMs, combining diverse synthetic generators with realistic time-series datasets, allowing learning at scale. Extensive experiments on synthetic, semi-synthetic and realistic benchmarks show that LCMs scale effectively to higher variable counts and deeper architectures while maintaining strong performance. Trained models achieve competitive or superior accuracy compared to classical and neural baselines, particularly in out-of-distribution settings, while enabling fast, single-pass inference. Results demonstrate LCMs as a promising foundation-model paradigm for temporal causal discovery. Experiments and model weights are available at https://github.com/kougioulis/LCM-paper/.

Recent advances in causal interpretability have extended from language models to vision-language models (VLMs), seeking to reveal their internal mechanisms through input interventions. While textual interventions often target semantics, visual interventions typically rely on coarse pixel-level perturbations, limiting semantic insights on multimodal integration. In this study, we introduce V-SEAM, a novel framework that combines Visual Semantic Editing and Attention Modulating for causal interpretation of VLMs. V-SEAM enables concept-level visual manipulations and identifies attention heads with positive or negative contributions to predictions across three semantic levels: objects, attributes, and relationships. We observe that positive heads are often shared within the same semantic level but vary across levels, while negative heads tend to generalize broadly. Finally, we introduce an automatic method to modulate key head embeddings, demonstrating enhanced performance for both LLaVA and InstructBLIP across three diverse VQA benchmarks. Our data and code are released at: https://github.com/petergit1/V-SEAM.

Despite the impressive performance of vision-language models (VLMs) on downstream tasks, their ability to understand and reason about causal relationships in visual inputs remains unclear. Robust causal reasoning is fundamental to solving complex high-level reasoning tasks, yet existing benchmarks often include a mixture of reasoning questions, and VLMs can frequently exploit object recognition and activity identification as shortcuts to arrive at the correct answers, making it challenging to truly assess their causal reasoning abilities. To bridge this gap, we introduce VQA-Causal and VCR-Causal, two new benchmarks specifically designed to isolate and rigorously evaluate VLMs' causal reasoning abilities. Our findings reveal that while VLMs excel in object and activity recognition, they perform poorly on causal reasoning tasks, often only marginally surpassing random guessing. Further analysis suggests that this limitation stems from a severe lack of causal expressions in widely used training datasets, where causal relationships are rarely explicitly conveyed. We additionally explore fine-tuning strategies with hard negative cases, showing that targeted fine-tuning can improve model's causal reasoning while maintaining generalization and downstream performance. Our study highlights a key gap in current VLMs and lays the groundwork for future work on causal understanding.

This research aims to study a self-supervised 3D clothing reconstruction method, which recovers the geometry shape and texture of human clothing from a single image. Compared with existing methods, we observe that three primary challenges remain: (1) 3D ground-truth meshes of clothing are usually inaccessible due to annotation difficulties and time costs; (2) Conventional template-based methods are limited to modeling non-rigid objects, e.g., handbags and dresses, which are common in fashion images; (3) The inherent ambiguity compromises the model training, such as the dilemma between a large shape with a remote camera or a small shape with a close camera. In an attempt to address the above limitations, we propose a causality-aware self-supervised learning method to adaptively reconstruct 3D non-rigid objects from 2D images without 3D annotations. In particular, to solve the inherent ambiguity among four implicit variables, i.e., camera position, shape, texture, and illumination, we introduce an explainable structural causal map (SCM) to build our model. The proposed model structure follows the spirit of the causal map, which explicitly considers the prior template in the camera estimation and shape prediction. When optimization, the causality intervention tool, i.e., two expectation-maximization loops, is deeply embedded in our algorithm to (1) disentangle four encoders and (2) facilitate the prior template. Extensive experiments on two 2D fashion benchmarks (ATR and Market-HQ) show that the proposed method could yield high-fidelity 3D reconstruction. Furthermore, we also verify the scalability of the proposed method on a fine-grained bird dataset, i.e., CUB. The code is available at https://github.com/layumi/ 3D-Magic-Mirror .

In view of the problem that each subchain in the chain-of-model (CoM) relies only on the information of the previous subchain and may lose long-range dependencies due to the causal mask blocking the global context flow between multi-level subchains, this work proposes a graph of causal evolution (GoCE). Its core principle is to map the implicit token representation into a differentiable and sparse causal adjacency matrix, then permeate causal constraints through each layer of calculation using causal-masked attention and causal-MoE. By combining intervention consistency loss test and self-evolution gate, the dynamic balance between causal structure learning and adaptive updating of transformer architecture is realized. The researcher built experimental environments in sandboxes built with Claude Sonnet 4, o4-mini-high, and DeepSeek R1 respectively with the transformer variant architecture introduced in GoCE. It is evaluated on publicly available datasets including CLUTRR, CLADDER, EX-FEVER, and CausalQA and compared with the baseline LLMs. The finding proves that GoCE strengthens the transformer's ability to capture long-range causal dependencies, while the ability to self-evolve is improved. It not only surpasses the design of CoM in terms of design principles, but also provides experience for future research on causal learning and continuous adaptive improvement.

We study causal logistic bandits with counterfactual fairness constraints. The causal structure is given through known factual and counterfactual feature maps that share an unknown logistic reward parameter, but the learner observes only factual rewards. Consequently, the directions determining counterfactual feasibility need not be identifiable from the available feedback. The closest prior analyses either omit a coverage condition or impose a comparatively strong one, and do not establish matching lower bounds. We first show that some coverage condition is necessary: without a coverage-type restriction, factually indistinguishable environments with different optimal fair actions force Ω(T) expected joint loss. Under a weaker full-rank condition on the factual covariance pooled across actions, we identify a target-specific information scale V_star that measures the difficulty of estimating rewards and counterfactual effects from factual feedback. We construct worst-case families satisfying this condition on which every policy incurs expected joint loss Ωleft(left[V_starmin{log K,d}right]^{1/3}T^{2/3}right). We also give an explore--then--exploit procedure tuned using V_star and an adaptive algorithm that does not require its value. Both algorithms achieve max{R_T,V_T}=Oleft(left[V_starmin{log K,d}right]^{1/3}T^{2/3}+κd/σ_0^2right), where R_T is regret relative to the best fair action and V_T denotes the cumulative stage-wise positive violations. Thus the upper and lower bounds match in their leading dependence on T, V_star, and min{log K,d}, up to logarithmic factors.

The discovery of causal relationships between random variables is an important yet challenging problem that has applications across many scientific domains. Differentiable causal discovery (DCD) methods are effective in uncovering causal relationships from observational data; however, these approaches often suffer from limited interpretability and face challenges in incorporating domain-specific prior knowledge. In contrast, Large Language Models (LLMs)-based causal discovery approaches have recently been shown capable of providing useful priors for causal discovery but struggle with formal causal reasoning. In this paper, we propose LLM-DCD, which uses an LLM to initialize the optimization of the maximum likelihood objective function of DCD approaches, thereby incorporating strong priors into the discovery method. To achieve this initialization, we design our objective function to depend on an explicitly defined adjacency matrix of the causal graph as its only variational parameter. Directly optimizing the explicitly defined adjacency matrix provides a more interpretable approach to causal discovery. Additionally, we demonstrate higher accuracy on key benchmarking datasets of our approach compared to state-of-the-art alternatives, and provide empirical evidence that the quality of the initialization directly impacts the quality of the final output of our DCD approach. LLM-DCD opens up new opportunities for traditional causal discovery methods like DCD to benefit from future improvements in the causal reasoning capabilities of LLMs.

Time Series Foundation Models (TSFMs) have shown significant impact through their model capacity, scalability, and zero-shot generalization. However, due to the heterogeneity of inter-variate dependencies and the backbone scalability on large-scale multivariate datasets, most TSFMs are typically pre-trained on univariate time series. This limitation renders them oblivious to crucial information from diverse covariates in real-world forecasting tasks. To further enhance the performance of TSFMs, we propose a general covariate-aware adaptation (CoRA) framework for TSFMs. It leverages pre-trained backbones of foundation models while effectively incorporating exogenous covariates from various modalities, including time series, language, and images, to improve the quality of predictions. Technically, CoRA maintains the equivalence of initialization and parameter consistency during adaptation. With preserved backbones of foundation models as frozen feature extractors, the outcome embeddings from foundation models are empirically demonstrated more informative than raw data. Further, CoRA employs a novel Granger Causality Embedding (GCE) to automatically evaluate covariates regarding their causal predictability with respect to the target variate. We incorporate these weighted embeddings with a zero-initialized condition-injection mechanism, avoiding catastrophic forgetting of pre-trained foundation models and gradually integrates exogenous information. Extensive experiments show that CoRA of TSFMs surpasses state-of-the-art covariate-aware deep forecasters with full or few-shot training samples, achieving 31.1% MSE reduction on covariate-aware forecasting. Compared to other adaptation methods, CoRA exhibits strong compatibility with various advanced TSFMs and extends the scope of covariates to other modalities, presenting a practical paradigm for the application of TSFMs.

Practitioners inferring causality from observational data usually rely on a single method and treat its output as causal truth. Recent tools select an optimal method for a dataset, and recent ensembles aggregate multiple causal-discovery algorithms into one graph, but little work pools evidence across different mathematical traditions, including non-causal ones. We present Multi-Method Causal Evidence Synthesis (MCES), a framework that ranks which candidate drivers in an observational system are most likely relevant to a set of outcomes, and with what strength of evidence. MCES runs eleven methods across eight mathematical traditions on observational panel data and pools their outputs into a Convergent Evidence Score (CES), a linear opinion pool. CES quantifies convergence of evidence across analytical lenses: the degree to which methods with different assumptions point to the same driver-outcome relationship. It does not claim causal identification in the interventionist sense; it supports hypothesis prioritization, not a transferable probability of causation. MCES first applies Structural-Behavioral Decomposition to remove definitional (algebraic) relationships, then runs all methods, normalizes outputs to [0,1], and pools them. We distinguish MCES from method selection, structural ensembles, prediction ensembles, and literature synthesis. Using synthetic data with embedded ground truth, the Sachs protein-signaling benchmark, six Bayesian-network structure benchmarks, and two further synthetic domains, we show MCES ranks true edges near the top (Precision@5 = 1.0, Precision@10 = 0.96 on the primary scenario), with a low empirical rate of null pairs reaching Moderate-or-higher convergence. Our central point is not that the pool beats every individual method, but that no single method is uniformly best across the evaluated scenarios, so MCES offers a method-agnostic default.

We study the problem of model selection in causal inference, specifically for the case of conditional average treatment effect (CATE) estimation under binary treatments. Unlike model selection in machine learning, there is no perfect analogue of cross-validation as we do not observe the counterfactual potential outcome for any data point. Towards this, there have been a variety of proxy metrics proposed in the literature, that depend on auxiliary nuisance models estimated from the observed data (propensity score model, outcome regression model). However, the effectiveness of these metrics has only been studied on synthetic datasets as we can access the counterfactual data for them. We conduct an extensive empirical analysis to judge the performance of these metrics introduced in the literature, and novel ones introduced in this work, where we utilize the latest advances in generative modeling to incorporate multiple realistic datasets. Our analysis suggests novel model selection strategies based on careful hyperparameter tuning of CATE estimators and causal ensembling.

Large language models (LLMs) increasingly act as integrated data-science agents, combining abstract reasoning with advanced tool use. Yet the relevant benchmark landscape largely divides into symbolic causal reasoning benchmarks without realistic data analysis or data analysis benchmarks without a principled causal data-generating structure. Furthermore, existing causal evaluation datasets are often restricted to curated examples from existing sources, with diversity coming from limited templatized variations rather than from systematic generation of novel synthetic causal structures. We introduce CausalDS, a benchmark for evaluating causal reasoning in agentic data-science workflows. Each benchmark instance is a scene consisting of a sampled structural causal model (SCM) with generated observational data and an accompanying synthetic natural-language story grounded in a realistic domain. We optionally ground the composition of the benchmark components in empirical distributions obtained from real-world datasets, thus retaining empirical structure while reducing the "causal parrot" risk through completely synthetic generation. From each scene, we then derive tasks spanning all three of Pearl's rungs, with typical data-science prediction tasks appearing as Rung 1. Most tasks include a data science coding component, where the model typically needs to use several tools to arrive at the final answer due to the frequent presence of imperfect observations, which are generated by an observation model. Additionally, recognizing when a question admits no warranted answer and abstaining is treated as a first-class scored outcome. The benchmark thus jointly evaluates symbolic causal reasoning, data science, uncertainty quantification, abstention, and tool use/coding.

Causal representation learning aims to unveil latent high-level causal representations from observed low-level data. One of its primary tasks is to provide reliable assurance of identifying these latent causal models, known as identifiability. A recent breakthrough explores identifiability by leveraging the change of causal influences among latent causal variables across multiple environments liu2022identifying. However, this progress rests on the assumption that the causal relationships among latent causal variables adhere strictly to linear Gaussian models. In this paper, we extend the scope of latent causal models to involve nonlinear causal relationships, represented by polynomial models, and general noise distributions conforming to the exponential family. Additionally, we investigate the necessity of imposing changes on all causal parameters and present partial identifiability results when part of them remains unchanged. Further, we propose a novel empirical estimation method, grounded in our theoretical finding, that enables learning consistent latent causal representations. Our experimental results, obtained from both synthetic and real-world data, validate our theoretical contributions concerning identifiability and consistency.

Root cause analysis (RCA) in complex systems is challenging due to error propagation across multiple variables, the need for structural causal knowledge, and the computational cost of inference at test time. We introduce PRIM (Prior-fitted Root cause Identification with Meta-learning), a causal meta-learning approach that frames RCA as a Bayesian inference task over a synthetic prior of causal models. By marginalising out structural uncertainty, PRIM implicitly identifies changes in the data-generating mechanism between baseline and anomalous periods. In doing so, PRIM infers distributional differences without explicit statistical testing, and implicitly learns causal structure without model fitting at test time. Following the simulation-based meta-learning paradigm of prior-fitted networks, PRIM uses a Model-Averaged Causal Estimation (MACE) transformer neural process that jointly attends over observational and anomalous samples and the causal structure of nodes, enabling zero-shot inference in 17,ms for systems with up to 100 variables. Across synthetic benchmarks and two realistic benchmark datasets, PetShop and CausRCA, PRIM is competitive with methods that are aware of the system's causal graphical structure a priori while outperforming graph-unaware methods on several tasks. Lightweight fine-tuning to specific domains and data dynamics improves performance further.

We study counterfactual identifiability in causal models with bijective generation mechanisms (BGM), a class that generalizes several widely-used causal models in the literature. We establish their counterfactual identifiability for three common causal structures with unobserved confounding, and propose a practical learning method that casts learning a BGM as structured generative modeling. Learned BGMs enable efficient counterfactual estimation and can be obtained using a variety of deep conditional generative models. We evaluate our techniques in a visual task and demonstrate its application in a real-world video streaming simulation task.

Recent attempts to combine large language models (LLMs) with causal discovery ask models to infer pairwise directions, propose graph structures, or inject language-model outputs as priors and constraints. These approaches promise faster analysis, but they also obscure whether a causal evidence is supported by data and assumptions or by textual associations, prompt artifacts and hallucinated mechanisms. We argue for a different role for agents in causal discovery. Agents should inspect data, retrieve context, explain method assumptions and clarify graph outputs, but they should not supply edges, orientations, priors, constraints or causal conclusions. We propose the principle that agents assist the workflow, while causal claims remain grounded in data, explicit assumptions, formal algorithms, diagnostics and user or domain-expert decisions. We instantiate this principle in causal-learn+, an online platform that coordinates data analysis, preprocessing, method recommendation, expert-knowledge incorporation, formal discovery and interpretation around the algorithmic ecosystem of causal-learn. A case study on Big Five personality data illustrates agent-assisted pipeline of causal discovery without turning language-model unreliability into causal evidence. The platform is available at causallearn.com.

Many social and environmental phenomena are associated with macroscopic changes in the built environment, captured by satellite imagery on a global scale and with daily temporal resolution. While widely used for prediction, these images and especially image sequences remain underutilized for causal inference, especially in the context of randomized controlled trials (RCTs), where causal identification is established by design. In this paper, we develop and compare a set of general tools for analyzing Conditional Average Treatment Effects (CATEs) from temporal satellite data that can be applied to any RCT where geographical identifiers are available. Through a simulation study, we analyze different modeling strategies for estimating CATE in sequences of satellite images. We find that image sequence representation models with more parameters generally yield a greater ability to detect heterogeneity. To explore the role of model and data choice in practice, we apply the approaches to two influential RCTs -- Banerjee et al. (2015), a poverty study in Cusco, Peru, and Bolsen et al. (2014), a water conservation experiment in Georgia, USA. We benchmark our image sequence models against image-only, tabular-only, and combined image-tabular data sources, summarizing practical implications for investigators in a multivariate analysis. Land cover classifications over satellite images facilitate interpretation of what image features drive heterogeneity. We also show robustness to data and model choice of satellite-based generalization of the RCT results to larger geographical areas outside the original. Overall, this paper shows how satellite sequence data can be incorporated into the analysis of RCTs, and provides evidence about the implications of data, model, and evaluation metric choice for causal analysis.

Vision-language models (VLMs) generate fluent causal explanations, but current evaluations cannot distinguish linguistic plausibility from faithful causal reasoning. We introduce a dual-probe methodology that isolates these properties. The Text-Only Probe measures linguistic quality. The Chain-Text Probe requires models to first generate explicit causal chains. The Abstraction Gap (AG) metric quantifies the normalized performance difference. Evaluating eight VLMs on CAGE (Causal Abstraction Gap Evaluation), a benchmark of 49,500 questions across 5,500 images spanning Pearl's causal hierarchy, we find seven models exhibit AG exceeding 0.50 with text scores of 6--8 but chain scores below 2.5. Fine-tuning on 45,000 chain-annotated examples fails to close the gap. However, one model achieves near-zero AG. The capability exists within current VLM architectures and depends on pretraining and architectural choices. CAGE provides a diagnostic tool for assessing faithful causal reasoning in VLMs.

Revealing hidden causal variables alongside the underlying causal mechanisms is essential to the development of science. Despite the progress in the past decades, existing practice in causal discovery (CD) heavily relies on high-quality measured variables, which are usually given by human experts. In fact, the lack of well-defined high-level variables behind unstructured data has been a longstanding roadblock to a broader real-world application of CD. This procedure can naturally benefit from an automated process that can suggest potential hidden variables in the system. Interestingly, Large language models (LLMs) are trained on massive observations of the world and have demonstrated great capability in processing unstructured data. To leverage the power of LLMs, we develop a new framework termed Causal representatiOn AssistanT (COAT) that incorporates the rich world knowledge of LLMs to propose useful measured variables for CD with respect to high-value target variables on their paired unstructured data. Instead of directly inferring causality with LLMs, COAT constructs feedback from intermediate CD results to LLMs to refine the proposed variables. Given the target variable and the paired unstructured data, we first develop COAT-MB that leverages the predictivity of the proposed variables to iteratively uncover the Markov Blanket of the target variable. Built upon COAT-MB, COAT-PAG further extends to uncover a more complete causal graph, i.e., Partial Ancestral Graph, by iterating over the target variables and actively seeking new high-level variables. Moreover, the reliable CD capabilities of COAT also extend the debiased causal inference to unstructured data by discovering an adjustment set. We establish theoretical guarantees for the CD results and verify their efficiency and reliability across realistic benchmarks and real-world case studies.

As video diffusion models (VDMs) advance toward world models, a key question arises: do they truly understand causality, or merely overfit to statistical temporal patterns? Existing benchmarks mostly rely on synthetic data, limiting real-world generalization due to the sim-to-real gap. We present YoCausal, a two-level benchmark inspired by the Violation of Expectation (VoE) paradigm from cognitive science. By temporally reversing real-world videos at zero cost as natural counterfactual samples, YoCausal establishes an arbitrarily extensible evaluation protocol. Level 1 introduces the Reverse Surprise Index (RSI), quantifying arrow-of-time perception via denoising loss. Level 2 introduces the Causality Cognition Index (CCI), which leverages a VLM to stratify datasets into causal and non-causal subsets, disentangling genuine causal reasoning from temporal bias. Evaluation of 13 state-of-the-art VDMs reveals that perceiving the arrow of time does not imply understanding causality, and a significant gap persists relative to human-level causal cognition.

Evaluation of counterfactual queries (e.g., "If A were true, would C have been true?") is important to fault diagnosis, planning, determination of liability, and policy analysis. We present a method of revaluating counterfactuals when the underlying causal model is represented by structural models - a nonlinear generalization of the simultaneous equations models commonly used in econometrics and social sciences. This new method provides a coherent means for evaluating policies involving the control of variables which, prior to enacting the policy were influenced by other variables in the system.

Accurately predicting conversion rate (CVR) is essential in various recommendation domains such as online advertising systems and e-commerce. These systems utilize user interaction logs, which consist of exposures, clicks, and conversions. CVR prediction models are typically trained solely based on clicked samples, as conversions can only be determined following clicks. However, the sparsity of clicked instances necessitates the collection of a substantial amount of logs for effective model training. Recent works address this issue by devising frameworks that leverage non-clicked samples. While these frameworks aim to reduce biases caused by the discrepancy between clicked and non-clicked samples, they often rely on heuristics. Against this background, we propose a method to counterfactually generate conversion labels for non-clicked samples by using causality as a guiding principle, attempting to answer the question, "Would the user have converted if he or she had clicked the recommended item?" Our approach is named the Entire Space Counterfactual Inference Multi-task Model (ESCIM). We initially train a structural causal model (SCM) of user sequential behaviors and conduct a hypothetical intervention (i.e., click) on non-clicked items to infer counterfactual CVRs. We then introduce several approaches to transform predicted counterfactual CVRs into binary counterfactual conversion labels for the non-clicked samples. Finally, the generated samples are incorporated into the training process. Extensive experiments on public datasets illustrate the superiority of the proposed algorithm. Online A/B testing further empirically validates the effectiveness of our proposed algorithm in real-world scenarios. In addition, we demonstrate the improved performance of the proposed method on latent conversion data, showcasing its robustness and superior generalization capabilities.

Human understanding of video dynamics is typically grounded in a structured mental representation of entities, actions, and temporal relations, rather than relying solely on immediate deductive reasoning. In contrast, existing Video-LLMs largely depend on unstructured video reasoning, where critical visual evidence is embedded in verbose textual descriptions and temporal causality is often weakly modeled. This leads to inefficient processes and fragile causal inference. To bridge this cognitive gap, we propose constructing a compact representation of salient events and their causal relationships, which we name Structured Event Facts, prior to the reasoning stage. This structured prior serves as an explicit constraint to promote concise and causally grounded reasoning, while also making intermediate evidence easier to verify. To effectively train models on such structured facts, we introduce CausalFact-60K and a four-stage training pipeline comprising facts alignment, format warm-start, thinking warm-start, and reinforcement learning-based post-training. During RL stage, we find that this framework introduces competing objectives, as structural completeness and causal fidelity must be balanced against reasoning length, making it difficult to optimize. We address this challenge by formulating the optimization as a Multi-Objective Reinforcement Learning (MORL) problem and explicitly optimizing toward the Pareto-Frontier to balance these trade-offs. As a result, we introduce Factum-4B, which yields more reliable reasoning and delivers stronger performance on challenging video understanding tasks requiring fine-grained temporal inference.

The traditional i.i.d.-based learning paradigm faces inherent challenges in addressing causal relationships, which has become increasingly evident with the rise of applications in causal representation learning. Our understanding of causality naturally requires a perspective as the creator rather than observer, as the ``what...if'' questions only hold within the possible world we conceive. The traditional perspective limits capturing dynamic causal outcomes and leads to compensatory efforts such as the reliance on hidden confounders. This paper lays the groundwork for the new perspective, which enables the relation-first modeling paradigm for causality. Also, it introduces the Relation-Indexed Representation Learning (RIRL) as a practical implementation, supported by experiments that validate its efficacy.

Causal inference is often focused on average effects, which can hide important aspects of the effect distributions. Here we consider the entire posterior effects distribution by estimating full counterfactual outcome distributions. We propose a methodology for inference on counterfactual distributions which builds upon the martingale posterior framework of Fong et al. (2023). This provides a highly flexible approach to estimating densities, distribution functions, and derived quantities such as quantiles, which coherently quantifies the epistemic uncertainty on any target estimand of interest. As the predictive recursions are based on an underlying nonparametric model (a Dirichlet process mixture model), our method naturally inherits robustness with respect to restrictive parametric assumptions. In addition, implementation of our method is typically very fast. This approach can be applied to marginal or conditional counterfactual distributions and is easily extended to an instrumental variables setup. Using the concept of almost conditionally identically distributed random variables, we prove convergence of the martingale posterior inference on the counterfactual outcome distributions for the causal models considered in the paper. We illustrate our approach on both simulated and real data. Using the latter, we investigate the effect of zinc lozenges on common cold duration, the impact of vitamin A supplementation on children's survival rates with one-sided non-compliance (analysed in Imbens and Rubin, 1997a) and the effect of job training (LaLonde, 1986).

Causal effect estimation from observational data is fundamental across various applications. However, selecting an appropriate estimator from dozens of specialized methods demands substantial manual effort and domain expertise. We present CausalPFN, a single transformer that amortizes this workflow: trained once on a large library of simulated data-generating processes that satisfy ignorability, it infers causal effects for new observational datasets out-of-the-box. CausalPFN combines ideas from Bayesian causal inference with the large-scale training protocol of prior-fitted networks (PFNs), learning to map raw observations directly to causal effects without any task-specific adjustment. Our approach achieves superior average performance on heterogeneous and average treatment effect estimation benchmarks (IHDP, Lalonde, ACIC). Moreover, it shows competitive performance for real-world policy making on uplift modeling tasks. CausalPFN provides calibrated uncertainty estimates to support reliable decision-making based on Bayesian principles. This ready-to-use model does not require any further training or tuning and takes a step toward automated causal inference (https://github.com/vdblm/CausalPFN).

We develop a data-driven information-theoretic framework for sharp partial identification of causal effects under unmeasured confounding. Existing approaches often rely on restrictive assumptions, such as bounded or discrete outcomes; require external inputs (for example, instrumental variables, proxies, or user-specified sensitivity parameters); necessitate full structural causal model specifications; or focus solely on population-level averages while neglecting covariate-conditional effects. We overcome all four limitations simultaneously by establishing novel information-theoretic, data-driven divergence bounds. Our key theoretical contribution shows that the f-divergence between the observational distribution P(Y | A = a, X = x) and the interventional distribution P(Y | do(A = a), X = x) is upper bounded by a function of the propensity score alone. This result enables sharp partial identification of conditional causal effects directly from observational data, without requiring external sensitivity parameters, auxiliary variables, full structural specifications, or outcome boundedness assumptions. For practical implementation, we develop a semiparametric estimator satisfying Neyman orthogonality (Chernozhukov et al., 2018), which ensures root-n consistent inference even when nuisance functions are estimated via flexible machine learning methods. Simulation studies and real-world data applications, implemented in the GitHub repository (https://github.com/yonghanjung/Information-Theretic-Bounds), demonstrate that our framework provides tight and valid causal bounds across a wide range of data-generating processes.

Causal thinking enables humans to understand not just what is seen, but why it happens. To replicate this capability in modern AI systems, we introduce the task of visual causal discovery. It requires models to infer cause-and-effect relations among visual entities across diverse scenarios instead of merely perceiving their presence. To this end, we first construct the Visual Causal Graph dataset (VCG-32K), a large-scale collection of over 32,000 images annotated with entity-level causal graphs, and further develop CauSight, a novel vision-language model to perform visual causal discovery through causally aware reasoning. Our training recipe integrates three components: (1) training data curation from VCG-32K, (2) Tree-of-Causal-Thought (ToCT) for synthesizing reasoning trajectories, and (3) reinforcement learning with a designed causal reward to refine the reasoning policy. Experiments show that CauSight outperforms GPT-4.1 on visual causal discovery, achieving over a threefold performance boost (21% absolute gain). Our code, model, and dataset are fully open-sourced at project page: https://github.com/OpenCausaLab/CauSight.

We report the presence of a simple neural mechanism that represents an input-output function as a vector within autoregressive transformer language models (LMs). Using causal mediation analysis on a diverse range of in-context-learning (ICL) tasks, we find that a small number attention heads transport a compact representation of the demonstrated task, which we call a function vector (FV). FVs are robust to changes in context, i.e., they trigger execution of the task on inputs such as zero-shot and natural text settings that do not resemble the ICL contexts from which they are collected. We test FVs across a range of tasks, models, and layers and find strong causal effects across settings in middle layers. We investigate the internal structure of FVs and find while that they often contain information that encodes the output space of the function, this information alone is not sufficient to reconstruct an FV. Finally, we test semantic vector composition in FVs, and find that to some extent they can be summed to create vectors that trigger new complex tasks. Taken together, our findings suggest that LLMs contain internal abstractions of general-purpose functions that can be invoked in a variety of contexts.

The technique of data augmentation (DA) is often used in machine learning for regularization purposes to better generalize under i.i.d. settings. In this work, we present a unifying framework with topics in causal inference to make a case for the use of DA beyond just the i.i.d. setting, but for generalization across interventions as well. Specifically, we argue that when the outcome generating mechanism is invariant to our choice of DA, then such augmentations can effectively be thought of as interventions on the treatment generating mechanism itself. This can potentially help to reduce bias in causal effect estimation arising from hidden confounders. In the presence of such unobserved confounding we typically make use of instrumental variables (IVs) -- sources of treatment randomization that are conditionally independent of the outcome. However, IVs may not be as readily available as DA for many applications, which is the main motivation behind this work. By appropriately regularizing IV based estimators, we introduce the concept of IV-like (IVL) regression for mitigating confounding bias and improving predictive performance across interventions even when certain IV properties are relaxed. Finally, we cast parameterized DA as an IVL regression problem and show that when used in composition can simulate a worst-case application of such DA, further improving performance on causal estimation and generalization tasks beyond what simple DA may offer. This is shown both theoretically for the population case and via simulation experiments for the finite sample case using a simple linear example. We also present real data experiments to support our case.

Understanding and manipulating the causal generation mechanisms in language models is essential for controlling their behavior. Previous work has primarily relied on techniques such as representation surgery -- e.g., model ablations or manipulation of linear subspaces tied to specific concepts -- to intervene on these models. To understand the impact of interventions precisely, it is useful to examine counterfactuals -- e.g., how a given sentence would have appeared had it been generated by the model following a specific intervention. We highlight that counterfactual reasoning is conceptually distinct from interventions, as articulated in Pearl's causal hierarchy. Based on this observation, we propose a framework for generating true string counterfactuals by reformulating language models as Generalized Structural-equation. Models using the Gumbel-max trick. This allows us to model the joint distribution over original strings and their counterfactuals resulting from the same instantiation of the sampling noise. We develop an algorithm based on hindsight Gumbel sampling that allows us to infer the latent noise variables and generate counterfactuals of observed strings. Our experiments demonstrate that the approach produces meaningful counterfactuals while at the same time showing that commonly used intervention techniques have considerable undesired side effects.

As Large Language Model (LLM) agents are increasingly tasked with high-stakes autonomous decision-making, the transparency of their reasoning processes has become a critical safety concern. While Chain-of-Thought (CoT) prompting allows agents to generate human-readable reasoning traces, it remains unclear whether these traces are faithful generative drivers of the model's output or merely post-hoc rationalizations. We introduce Project Ariadne, a novel XAI framework that utilizes Structural Causal Models (SCMs) and counterfactual logic to audit the causal integrity of agentic reasoning. Unlike existing interpretability methods that rely on surface-level textual similarity, Project Ariadne performs hard interventions (do-calculus) on intermediate reasoning nodes -- systematically inverting logic, negating premises, and reversing factual claims -- to measure the Causal Sensitivity (φ) of the terminal answer. Our empirical evaluation of state-of-the-art models reveals a persistent Faithfulness Gap. We define and detect a widespread failure mode termed Causal Decoupling, where agents exhibit a violation density (ρ) of up to 0.77 in factual and scientific domains. In these instances, agents arrive at identical conclusions despite contradictory internal logic, proving that their reasoning traces function as "Reasoning Theater" while decision-making is governed by latent parametric priors. Our findings suggest that current agentic architectures are inherently prone to unfaithful explanation, and we propose the Ariadne Score as a new benchmark for aligning stated logic with model action.

Vision-language models (VLMs) achieve strong multimodal performance, yet how computation is organized across populations of neurons remains poorly understood. In this work, we study VLMs through the lens of neural topology, representing each layer as a within-layer correlation graph derived from neuron-neuron co-activations. This view allows us to ask whether population-level structure is behaviorally meaningful, how it changes across modalities and depth, and whether it identifies causally influential internal components under intervention. We show that correlation topology carries recoverable behavioral signal; moreover, cross-modal structure progressively consolidates with depth around a compact set of recurrent hub neurons, whose targeted perturbation substantially alters model output. Neural topology thus emerges as a meaningful intermediate scale for VLM interpretability: richer than local attribution, more tractable than full circuit recovery, and empirically tied to multimodal behavior. Code is publicly available at https://github.com/he-h/vlm-graph-probing.

The "thinking-with-images" paradigm equips multimodal LLMs with active visual operations such as crop-and-zoom. However, models using these operations often achieve only marginal or negative gains over direct inference at substantially higher token cost. They may also repeatedly crop irrelevant regions and fail on questions that direct inference answers correctly. We ask whether the returned visual evidence causally affects the answer. To answer this question, we formulate visual tool-use as a causal graph that separates observation-mediated paths from action-induced shortcuts. We then audit it through interventions at the three levels: policy (comparing tool-use with direct inference), trajectory (corrupting all observations during rollout), and step (counterfactually replacing one individual observation under a fixed prefix). Our step-level estimand, Visual Evidence Gain, isolates the contribution of each returned observation. Across six representative models and five fine-grained perception benchmarks, we uncover policy miscalibration with two failure modes. In Calling Without Looking, returned observations have no causal effect on the answer. In Looking Without Planning, observations are informative but the call schedule is incoherent. A trajectory-level diagnostic decomposes the policy-level accuracy gain and shows that the gain is concentrated in a Calibrated minority. We term this discrepancy the illusion of visual tool-use: despite aggregate accuracy gains, visual tool-use is not causally effective across a broad range of rollouts. The code is available at https://github.com/OpenCausaLab/CauAudit.

Vision-language models must reconcile visual evidence with memorized world knowledge when the two conflict. How they resolve this conflict shapes the reliability of multimodal systems, yet prior work characterizes it behaviorally without a component-level causal account. We combine activation patching across three granularities (residual stream, attention heads, and MLP sublayers) with model-component ablation studies and mechanistic analysis. Across three VLM families, we find that visual grounding emerges by default, whereas prior grounding depends on a small set of causally necessary attention heads (2.5-4.8%) concentrated in the second half of the network. These heads enable answers from stored world knowledge (e.g., "red" for a strawberry) despite conflicting visual input. Ablating them flips predictions from knowledge-grounded to visually grounded answers in 68-96% of cases under prior-knowledge prompts, but changes only 0.8-7.5% of visually grounded predictions, establishing an asymmetric causal structure. The identified heads decompose into routing heads, which modulate information flow, and writing heads, which directly project answer tokens into the residual stream. This structure is consistent across model families and scales, revealing a sparse causal circuit underlying perception-knowledge conflict in VLMs.

Causal Representation Learning (CRL) aims to uncover the data-generating process and identify the underlying causal variables and relations, whose evaluation remains inherently challenging due to the requirement of known ground-truth causal variables and causal structure. Existing evaluations often rely on either simplistic synthetic datasets or downstream performance on real-world tasks, generally suffering a dilemma between realism and evaluative precision. In this paper, we introduce a new benchmark for CRL using high-fidelity simulated visual data that retains both realistic visual complexity and, more importantly, access to ground-truth causal generating processes. The dataset comprises around 200 thousand images and 3 million video frames across 24 sub-scenes in four domains: static image generation, dynamic physical simulations, robotic manipulations, and traffic situation analysis. These scenarios range from static to dynamic settings, simple to complex structures, and single to multi-agent interactions, offering a comprehensive testbed that hopefully bridges the gap between rigorous evaluation and real-world applicability. In addition, we provide flexible access to the underlying causal structures, allowing users to modify or configure them to align with the required assumptions in CRL, such as available domain labels, temporal dependencies, or intervention histories. Leveraging this benchmark, we evaluated representative CRL methods across diverse paradigms and offered empirical insights to assist practitioners and newcomers in choosing or extending appropriate CRL frameworks to properly address specific types of real problems that can benefit from the CRL perspective. Welcome to visit our: Project page:https://causal-verse.github.io/, Dataset:https://huggingface.co/CausalVerse.

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 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.

We develop a method for generating causal post-hoc explanations of black-box classifiers based on a learned low-dimensional representation of the data. The explanation is causal in the sense that changing learned latent factors produces a change in the classifier output statistics. To construct these explanations, we design a learning framework that leverages a generative model and information-theoretic measures of causal influence. Our objective function encourages both the generative model to faithfully represent the data distribution and the latent factors to have a large causal influence on the classifier output. Our method learns both global and local explanations, is compatible with any classifier that admits class probabilities and a gradient, and does not require labeled attributes or knowledge of causal structure. Using carefully controlled test cases, we provide intuition that illuminates the function of our objective. We then demonstrate the practical utility of our method on image recognition tasks.

Graph anomaly detection (GAD) has become an increasingly important task across various domains. With the rapid development of graph neural networks (GNNs), GAD methods have achieved significant performance improvements. However, fairness considerations in GAD remain largely underexplored. Indeed, GNN-based GAD models can inherit and amplify biases present in training data, potentially leading to unfair outcomes. While existing efforts have focused on developing fair GNNs, most approaches target node classification tasks, where models often rely on simple layer architectures rather than autoencoder-based structures, which are the most widely used architecturs for anomaly detection. To address fairness in autoencoder-based GAD models, we propose DisEntangled Counterfactual Adversarial Fair (DECAF)-GAD, a framework that alleviates bias while preserving GAD performance. Specifically, we introduce a structural causal model (SCM) to disentangle sensitive attributes from learned representations. Based on this causal framework, we formulate a specialized autoencoder architecture along with a fairness-guided loss function. Through extensive experiments on both synthetic and real-world datasets, we demonstrate that DECAF-GAD not only achieves competitive anomaly detection performance but also significantly enhances fairness metrics compared to baseline GAD methods. Our code is available at https://github.com/Tlhey/decaf_code.

Conventional supervised learning methods typically assume i.i.d samples and are found to be sensitive to out-of-distribution (OOD) data. We propose Generative Causal Representation Learning (GCRL) which leverages causality to facilitate knowledge transfer under distribution shifts. While we evaluate the effectiveness of our proposed method in human trajectory prediction models, GCRL can be applied to other domains as well. First, we propose a novel causal model that explains the generative factors in motion forecasting datasets using features that are common across all environments and with features that are specific to each environment. Selection variables are used to determine which parts of the model can be directly transferred to a new environment without fine-tuning. Second, we propose an end-to-end variational learning paradigm to learn the causal mechanisms that generate observations from features. GCRL is supported by strong theoretical results that imply identifiability of the causal model under certain assumptions. Experimental results on synthetic and real-world motion forecasting datasets show the robustness and effectiveness of our proposed method for knowledge transfer under zero-shot and low-shot settings by substantially outperforming the prior motion forecasting models on out-of-distribution prediction. Our code is available at https://github.com/sshirahmad/GCRL.

Heterogeneous tabular data poses unique challenges in generative modelling due to its fundamentally different underlying data structure compared to homogeneous modalities, such as images and text. Although previous research has sought to adapt the successes of generative modelling in homogeneous modalities to the tabular domain, defining an effective generator for tabular data remains an open problem. One major reason is that the evaluation criteria inherited from other modalities often fail to adequately assess whether tabular generative models effectively capture or utilise the unique structural information encoded in tabular data. In this paper, we carefully examine the limitations of the prevailing evaluation framework and introduce TabStruct, a novel evaluation benchmark that positions structural fidelity as a core evaluation dimension. Specifically, TabStruct evaluates the alignment of causal structures in real and synthetic data, providing a direct measure of how effectively tabular generative models learn the structure of tabular data. Through extensive experiments using generators from eight categories on seven datasets with expert-validated causal graphical structures, we show that structural fidelity offers a task-independent, domain-agnostic evaluation dimension. Our findings highlight the importance of tabular data structure and offer practical guidance for developing more effective and robust tabular generative models. Code is available at https://github.com/SilenceX12138/TabStruct.

Interpretability research now offers a variety of techniques for identifying abstract internal mechanisms in neural networks. Can such techniques be used to predict how models will behave on out-of-distribution examples? In this work, we provide a positive answer to this question. Through a diverse set of language modeling tasks--including symbol manipulation, knowledge retrieval, and instruction following--we show that the most robust features for correctness prediction are those that play a distinctive causal role in the model's behavior. Specifically, we propose two methods that leverage causal mechanisms to predict the correctness of model outputs: counterfactual simulation (checking whether key causal variables are realized) and value probing (using the values of those variables to make predictions). Both achieve high AUC-ROC in distribution and outperform methods that rely on causal-agnostic features in out-of-distribution settings, where predicting model behaviors is more crucial. Our work thus highlights a novel and significant application for internal causal analysis of language models.

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.

Out-of-distribution (OOD) prediction is often approached by restricting models to causal or invariant covariates, avoiding non-causal spurious associations that may be unstable across environments. Despite its theoretical appeal, this strategy frequently underperforms empirical risk minimization (ERM) in practice. We investigate the source of this gap and show that such failures naturally arise when only a subset of the true causes of the outcome is observed. In these settings, non-causal spurious covariates can serve as informative proxies for unobserved causes and substantially improve prediction, except under distribution shifts that break these proxy relationships. Consequently, the optimal set of predictive covariates is neither universal nor necessarily exhibits invariant relationships with the outcome across all environments, but instead depends on the specific type of shift encountered. Crucially, we observe that different covariate shifts induce distinct, observable signatures in the covariate distribution itself. Moreover, these signatures can be extracted from unlabeled data in the target OOD environment and used to assess when proxy covariates remain reliable and when they fail. Building on this observation, we propose an environment-adaptive covariate selection (EACS) algorithm that maps environment-level covariate summaries to environment-specific covariate sets, while allowing the incorporation of prior causal knowledge as constraints. Across simulations and applied datasets, EACS consistently outperforms static causal, invariant, and ERM-based predictors under diverse distribution shifts.

As foundation models (FMs) approach human-level fluency, distinguishing synthetic from organic content has become a key challenge for Trustworthy Web Intelligence. This paper presents JudgeGPT and RogueGPT, a dual-axis framework that decouples "authenticity" from "attribution" to investigate the mechanisms of human susceptibility. Analyzing 918 evaluations across five FMs (including GPT-4 and Llama-2), we employ Structural Causal Models (SCMs) as a principal framework for formulating testable causal hypotheses about detection accuracy. Contrary to partisan narratives, we find that political orientation shows a negligible association with detection performance (r=-0.10). Instead, "fake news familiarity" emerges as a candidate mediator (r=0.35), suggesting that exposure may function as adversarial training for human discriminators. We identify a "fluency trap" where GPT-4 outputs (HumanMachineScore: 0.20) bypass Source Monitoring mechanisms, rendering them indistinguishable from human text. These findings suggest that "pre-bunking" interventions should target cognitive source monitoring rather than demographic segmentation to ensure trustworthy information ecosystems.

Despite the progress of foundation models, knowledge-based reasoning remains a persistent challenge due to their limited capacity for knowledge recall and inference. Existing methods primarily focus on encouraging these models to plan and solve problems or extensively sample reasoning chains independently. However, these methods often overlook conceptual errors and inferential fallacies, inevitably leading to a series of notorious issues such as misleading conclusions, cognitive biases, and reduced decision quality. While explicit modeling of causality is argued to hold promise in addressing these issues, contemporary research efforts have thus far fallen short in achieving causality-based foundation models. Drawing inspiration from the orchestration of diverse specialized agents collaborating to tackle intricate tasks, we propose a framework named Causal-Consistency Chain-of-Thought (CaCo-CoT) that harnesses multi-agent collaboration to bolster the faithfulness and causality of foundation models, involving a set of reasoners and evaluators. These agents collaboratively work within a reasoning-and-consensus paradigm to improve faithfulness. The reasoners are tasked with generating reasoning chains for knowledge-intensive problems by mimicking human causal reasoning. Meanwhile, the evaluator scrutinizes the causal consistency of a reasoner's reasoning chain from a non-causal and a counterfactual perspective. Our framework demonstrates significant superiority over state-of-the-art methods through extensive and comprehensive evaluations across text-based and multi-modal knowledge reasoning tasks (e.g., science question answering and commonsense reasoning).

We study experiment design for unique identification of the causal graph of a simple SCM, where the graph may contain cycles. The presence of cycles in the structure introduces major challenges for experiment design as, unlike acyclic graphs, learning the skeleton of causal graphs with cycles may not be possible from merely the observational distribution. Furthermore, intervening on a variable in such graphs does not necessarily lead to orienting all the edges incident to it. In this paper, we propose an experiment design approach that can learn both cyclic and acyclic graphs and hence, unifies the task of experiment design for both types of graphs. We provide a lower bound on the number of experiments required to guarantee the unique identification of the causal graph in the worst case, showing that the proposed approach is order-optimal in terms of the number of experiments up to an additive logarithmic term. Moreover, we extend our result to the setting where the size of each experiment is bounded by a constant. For this case, we show that our approach is optimal in terms of the size of the largest experiment required for uniquely identifying the causal graph in the worst case.

Large language models (LLMs) are increasingly deployed in high-stakes domains, where rare but severe failures can result in irreversible harm. However, prevailing evaluation benchmarks often reduce complex social risk to mean-centered scalar scores, thereby obscuring distributional structure, cross-dimensional interactions, and worst-case behavior. This paper introduces Social Harm Analysis via Risk Profiles (SHARP), a framework for multidimensional, distribution-aware evaluation of social harm. SHARP models harm as a multivariate random variable and integrates explicit decomposition into bias, fairness, ethics, and epistemic reliability with a union-of-failures aggregation reparameterized as additive cumulative log-risk. The framework further employs risk-sensitive distributional statistics, with Conditional Value at Risk (CVaR95) as a primary metric, to characterize worst-case model behavior. Application of SHARP to eleven frontier LLMs, evaluated on a fixed corpus of n=901 socially sensitive prompts, reveals that models with similar average risk can exhibit more than twofold differences in tail exposure and volatility. Across models, dimension-wise marginal tail behavior varies systematically across harm dimensions, with bias exhibiting the strongest tail severities, epistemic and fairness risks occupying intermediate regimes, and ethical misalignment consistently lower; together, these patterns reveal heterogeneous, model-dependent failure structures that scalar benchmarks conflate. These findings indicate that responsible evaluation and governance of LLMs require moving beyond scalar averages toward multidimensional, tail-sensitive risk profiling.

Causal discovery from observational tabular data remains fundamentally challenging, primarily due to the heterogeneity of underlying causal mechanisms and the high-dimensional combinatorial search space of Directed Acyclic Graphs (DAGs). In this paper, we propose DAG-FM, a novel foundation model architecture that amortizes causal discovery. Unlike direct matrix prediction, DAG-FM decomposes the causal discovery process into two auto-regressive stages using two specialized Transformer-based sub-modules: a leaf-node predictor and a parent-node predictor. To effectively model complex row-column interactions, we adopt a robust tabular interaction block to output feature-wise representations. Crucially, to handle diverse and unknown Functional Causal Model (FCM) assumptions in real-world scenarios, we introduce Mixture-of-Leaf-Experts (MoLE), allowing the model to dynamically route and adapt to identifiable mechanism families. Through an iterative inference algorithm, DAG-FM seamlessly extracts causal orderings and constructs valid DAGs. Extensive experiments demonstrate that DAG-FM achieves state-of-the-art performance on both synthetic benchmarks and complex real-world datasets, significantly outperforming traditional classical algorithms and recent foundation models in both accuracy and scalability.

We address causal reasoning in multivariate time series data generated by stochastic processes. Existing approaches are largely restricted to static settings, ignoring the continuity and emission of variations across time. In contrast, we propose a learning paradigm that directly establishes causation between events in the course of time. We present two key lemmas to compute causal contributions and frame them as reinforcement learning problems. Our approach offers formal and computational tools for uncovering and quantifying causal relationships in diffusion processes, subsuming various important settings such as discrete-time Markov decision processes. Finally, in fairly intricate experiments and through sheer learning, our framework reveals and quantifies causal links, which otherwise seem inexplicable.

In this paper, we propose REASON, a novel framework that enables the automatic discovery of both intra-level (i.e., within-network) and inter-level (i.e., across-network) causal relationships for root cause localization. REASON consists of Topological Causal Discovery and Individual Causal Discovery. The Topological Causal Discovery component aims to model the fault propagation in order to trace back to the root causes. To achieve this, we propose novel hierarchical graph neural networks to construct interdependent causal networks by modeling both intra-level and inter-level non-linear causal relations. Based on the learned interdependent causal networks, we then leverage random walks with restarts to model the network propagation of a system fault. The Individual Causal Discovery component focuses on capturing abrupt change patterns of a single system entity. This component examines the temporal patterns of each entity's metric data (i.e., time series), and estimates its likelihood of being a root cause based on the Extreme Value theory. Combining the topological and individual causal scores, the top K system entities are identified as root causes. Extensive experiments on three real-world datasets with case studies demonstrate the effectiveness and superiority of the proposed framework.

Existing 3D scene generation methods often struggle to model the complex logical dependencies and physical constraints between objects, limiting their ability to adapt to dynamic and realistic environments. We propose CausalStruct, a novel framework that embeds causal reasoning into 3D scene generation. Utilizing large language models (LLMs), We construct causal graphs where nodes represent objects and attributes, while edges encode causal dependencies and physical constraints. CausalStruct iteratively refines the scene layout by enforcing causal order to determine the placement order of objects and applies causal intervention to adjust the spatial configuration according to physics-driven constraints, ensuring consistency with textual descriptions and real-world dynamics. The refined scene causal graph informs subsequent optimization steps, employing a Proportional-Integral-Derivative(PID) controller to iteratively tune object scales and positions. Our method uses text or images to guide object placement and layout in 3D scenes, with 3D Gaussian Splatting and Score Distillation Sampling improving shape accuracy and rendering stability. Extensive experiments show that CausalStruct generates 3D scenes with enhanced logical coherence, realistic spatial interactions, and robust adaptability.

Researchers are usually interested in examining the impact of covariates when separating heterogeneous samples into latent classes that are more homogeneous. The majority of theoretical and empirical studies with such aims have focused on identifying covariates as predictors of class membership in the structural equation modeling framework. In other words, the covariates only indirectly affect the sample heterogeneity. However, the covariates' influence on between-individual differences can also be direct. This article presents a mixture model that investigates covariates to explain within-cluster and between-cluster heterogeneity simultaneously, known as a mixture-of-experts (MoE) model. This study aims to extend the MoE framework to investigate heterogeneity in nonlinear trajectories: to identify latent classes, covariates as predictors to clusters, and covariates that explain within-cluster differences in change patterns over time. Our simulation studies demonstrate that the proposed model generally estimates the parameters unbiasedly, precisely and exhibits appropriate empirical coverage for a nominal 95% confidence interval. This study also proposes implementing structural equation model forests to shrink the covariate space of the proposed mixture model. We illustrate how to select covariates and construct the proposed model with longitudinal mathematics achievement data. Additionally, we demonstrate that the proposed mixture model can be further extended in the structural equation modeling framework by allowing the covariates that have direct effects to be time-varying.

Humans can look at a static scene and instantly predict what happens next -- will moving this object cause a collision? We call this ability Causal Spatial Reasoning. However, current multimodal large language models (MLLMs) cannot do this, as they remain largely restricted to static spatial perception, struggling to answer "what-if" questions in a 3D scene. We introduce CausalSpatial, a diagnostic benchmark evaluating whether models can anticipate consequences of object motions across four tasks: Collision, Compatibility, Occlusion, and Trajectory. Results expose a severe gap: humans score 84% while GPT-5 achieves only 54%. Why do MLLMs fail? Our analysis uncovers a fundamental deficiency: models over-rely on textual chain-of-thought reasoning that drifts from visual evidence, producing fluent but spatially ungrounded hallucinations. To address this, we propose the Causal Object World model (COW), a framework that externalizes the simulation process by generating videos of hypothetical dynamics. With explicit visual cues of causality, COW enables models to ground their reasoning in physical reality rather than linguistic priors. We make the dataset and code publicly available here: https://github.com/CausalSpatial/CausalSpatial

Multimodal Large Language Models (MLLMs) have demonstrated remarkable potential in video understanding, yet their reliance on retrospective summarization and text-centric priors often limits their ability to bridge unobserved causal transitions when applied to Video Event Prediction (VEP). To address this, we propose VepAgent, an agentic framework that integrates causal-transition reasoning with tool-augmented reinforcement learning (RL) for robust VEP. Unlike prior methods that passively project future trajectories from historical dependencies, our approach explicitly models the logical progression from terminal observed states to future events. Specifically, we first construct futurebench-4K, a high-quality chain-of-thought dataset for supervised fine-tuning (SFT) that effectively bridges the causal-logic gap by structuring the deduction of unobserved intermediate states. Subsequently, we develop a diagnostic tool library integrating state tracking, frame retrieval, and region magnification, enabling the agent to dynamically augment reasoning with external tools to recover missing spatio-temporal evidence and resolve visual ambiguities during inference. Moreover, we propose a composite reward mechanism that jointly optimizes prediction accuracy, causal coherence, and reliable prior, compelling the agent to rely on genuine visual grounding rather than superficial textual similarities. Extensive evaluations on FutureBench and NEPBench datasets demonstrate that our method achieves state-of-the-art performance, significantly outperforming larger MLLMs and validating the empirical effectiveness of our agentic, future-oriented reasoning paradigm.

In this paper, the causal bandit problem is investigated, in which the objective is to select an optimal sequence of interventions on nodes in a causal graph. It is assumed that the graph is governed by linear structural equations; it is further assumed that both the causal topology and the distribution of interventions are unknown. By exploiting the causal relationships between the nodes whose signals contribute to the reward, interventions are optimized. First, based on the difference between the two types of graph identification errors (false positives and negatives), a causal graph learning method is proposed, which strongly reduces sample complexity relative to the prior art by learning sub-graphs. Under the assumption of Gaussian exogenous inputs and minimum-mean squared error weight estimation, a new uncertainty bound tailored to the causal bandit problem is derived. This uncertainty bound drives an upper confidence bound based intervention selection to optimize the reward. To cope with non-stationary bandits, a sub-graph change detection mechanism is proposed, with high sample efficiency. Numerical results compare the new methodology to existing schemes and show a substantial performance improvement in both stationary and non-stationary settings. Compared to existing approaches, the proposed scheme takes 67% fewer samples to learn the causal structure and achieves an average reward gain of 85%.

Counterfactual reasoning requires models to reason beyond the observed world and explain how altered conditions propagate through downstream consequences. Existing benchmarks largely target bounded settings with fixed variables or single gold outcomes, overlooking open-domain scenarios requiring causal-process evaluation. To this end, we present WhatIfBench, a diagnostic benchmark for open-domain, open-form, long-horizon counterfactual causal reasoning, containing 220 what-if questions across STEM, HSS, and Hybrid scenarios. To evaluate free-form responses, we further propose PRISM, which first converts each natural-language explanation into a Response-Derived Semantic Causal Graph of events, states, and mechanisms. On top of this graph, PRISM then jointly applies a Process Metric assessing graph-level causal validity and a Rubric Metric assessing answer-level explanatory adequacy. Evaluating six frontier LLMs with this framework, we find that WhatIfBench remains far from saturated: even the strongest model reaches only a 64.62% final score. Further analysis reveals persistent causal gaps, premise drift, and topology fragmentation, suggesting that fluent counterfactual narratives often mask fragile causal processes. The benchmark, code, and evaluation scripts are available at https://github.com/zju-gt/WhatIfBench{WhatIfBench}.

Understanding narratives requires reasoning about the cause-and-effect relationships between events mentioned in the text. While existing foundation models yield impressive results in many NLP tasks requiring reasoning, it is unclear whether they understand the complexity of the underlying network of causal relationships of events in narratives. In this work, we present CRAB, a new Causal Reasoning Assessment Benchmark designed to evaluate causal understanding of events in real-world narratives. CRAB contains fine-grained, contextual causality annotations for ~2.7K pairs of real-world events that describe various newsworthy event timelines (e.g., the acquisition of Twitter by Elon Musk). Using CRAB, we measure the performance of several large language models, demonstrating that most systems achieve poor performance on the task. Motivated by classical causal principles, we also analyze the causal structures of groups of events in CRAB, and find that models perform worse on causal reasoning when events are derived from complex causal structures compared to simple linear causal chains. We make our dataset and code available to the research community.

An introduction to the emerging fusion of machine learning and causal inference. The book presents ideas from classical structural equation models (SEMs) and their modern AI equivalent, directed acyclical graphs (DAGs) and structural causal models (SCMs), and covers Double/Debiased Machine Learning methods to do inference in such models using modern predictive tools.

Large language models (LLMs) exhibit logically inconsistent hallucinations that appear coherent yet violate reasoning principles, with recent research suggesting an inverse relationship between causal reasoning capabilities and such hallucinations. However, existing reasoning approaches in LLMs, such as Chain-of-Thought (CoT) and its graph-based variants, operate at the linguistic token level rather than modeling the underlying causal relationships between variables, lacking the ability to represent conditional independencies or satisfy causal identification assumptions. To bridge this gap, we introduce causal-DAG construction and reasoning (CDCR-SFT), a supervised fine-tuning framework that trains LLMs to explicitly construct variable-level directed acyclic graph (DAG) and then perform reasoning over it. Moreover, we present a dataset comprising 25,368 samples (CausalDR), where each sample includes an input question, explicit causal DAG, graph-based reasoning trace, and validated answer. Experiments on four LLMs across eight tasks show that CDCR-SFT improves the causal reasoning capability with the state-of-the-art 95.33% accuracy on CLADDER (surpassing human performance of 94.8% for the first time) and reduces the hallucination on HaluEval with 10% improvements. It demonstrates that explicit causal structure modeling in LLMs can effectively mitigate logical inconsistencies in LLM outputs. Code is available at https://github.com/MrLYG/CDCR-SFT.