Identifying latent variables and their induced causal structure is fundamental in various scientific fields. Existing approaches often rely on restrictive structural assumptions (e.g., purity) and may become invalid when these assumptions are violated. We introduce Conditional Independent Component Analysis (CICA), a new tool that extracts components that are conditionally independent given latent variables. Under mild conditions, CICA can be optimized using a tractable proxy such as rank-deficiency constraints. Building on CICA, we establish an identifiability theory for linear non-Gaussian acyclic models with latent variables: solving CICA and then applying an appropriate row permutation to the sparsest CICA solution enables recovery of the causal structure. Accordingly, we propose an estimation method based on the identifiability theory and substantiate the algorithm with experiments on both synthetic and real-world datasets.

Compositional generalization -- the ability to understand and generate novel combinations of learned concepts -- enables models to extend their capabilities beyond limited experiences. While effective, the data structures and principles that enable this crucial capability remain poorly understood. We propose that compositional generalization fundamentally requires decomposing high-level concepts into basic, low-level concepts that can be recombined across similar contexts, similar to how humans draw analogies between concepts. For example, someone who has never seen a peacock eating rice can envision this scene by relating it to their previous observations of a chicken eating rice.In this work, we formalize these intuitive processes using principles of causal modularity and minimal changes. We introduce a hierarchical data-generating process that naturally encodes different levels of concepts and their interaction mechanisms. Theoretically, we demonstrate that this approach enables compositional generalization supporting complex relations between composed concepts, advancing beyond prior work that assumes simpler interactions like additive effects. Critically, we also prove that this latent hierarchical structure is provably recoverable (identifiable) from observable data like text-image pairs, a necessary step for learning such a generative process. To validate our theory, we apply insights from our theoretical framework and achieve significant improvements on benchmark datasets.

Abstract In many empirical studies, it may not be available to observe the accurate data. For instance, [1] indicated that over 75% of the variance in fat intake data from the Epidemiologic Study Cohort in NHANES-I stems from measurement error. This chapter focuses on continuous treatment data measured with classical error, where researchers only observe the sum of the treatment and a random error, rather than the actual treatment received.

Recently, it has received growing attention in building AI Scientist agents with Large Language Models (LLMs). Since scientific discovery fundamentally relies on uncovering causal relationships from observations, the capability of causal thinking that distinguish causation from correlation and hidden biases, is essential to LLM agents. Despite a number of existing benchmarks for AI scientists, none of them are designed with the consideration of hidden biases and confounders, that widely exist in real-world scientific discovery. To this end, we present CausalGame, a benchmark that evaluates the causal thinking capabilities of LLM agents through interactive games. More specifically, we ask LLM agents to actively design experimental protocols, collect observation data and derive a final solution with an explanation report. To emulate realistic scientific discovery challenges, we design 14 game settings with the incorporation of selection bias, noisy measurements, and hidden confounders. The results with 16 frontier LLM agents show that they consistently fail to reason about and recover the underlying causal relationships required to solve the games. CausalGame provides a rigorous measurement of capabilities essential to AI Scientist agents.

Due to their inherent complexity, reasoning tasks have long been regarded as rigorous benchmarks for assessing the capabilities of machine learning models, especially large language models (LLMs). Although humans can solve these tasks with ease, existing models, even after extensive pre-training and post-training at scale, still fail to perform reasoning reliably. In this paper, we revisit reasoning tasks from a causal perspective, seeking to understand their behavior in latent space and to offer insights for addressing their challenges. Specifically, we cast reasoning tasks as a selection mechanism, in which high-level logical concepts function as selection operators on the given observations, such as, identifying the correct answer in a math problem or filling the appropriate entry in Sudoku. We emphasize two key properties of this formulation that shed light on the difficulty of reasoning tasks. First, the latent space exceeds the observation space in complexity, even when the correct answer is fully determined by the observed input. Second, the latent variables, corresponding to logical thought, are densely structured and exhibit strong dependencies. Building on this formulation, we introduce a framework, called SR$^2$, that incorporates the estimated latent variables as feedback into the selection mechanism, thereby facilitating the learning of dense dependencies among latent representations. The framework consists of three key modules: reflective representation learning, dependency self-refinement, and periodic intermediate alignment. Experimentally, we show that our approach yields significant gains in reasoning accuracy, for example, attaining over 10% improvement in performance with 8$\times$ fewer parameters on the Sudoku and Maze tasks over the recent advances.

Causal effect estimation is a fundamental task in many scientific fields. Selecting appropriate covariates for adjustment is crucial for obtaining unbiased causal effects. However, most existing methods either rely on learning the global causal structure, assume the absence of latent variables, or impose the pretreatment assumption-restricts covariates to those unaffected by the treatment or outcome. These assumptions are often unrealistic in real-world scenarios, and global structure learning can be computationally intensive and inefficient. To address these challenges, we first characterize the local existence boundary of adjustment sets for causal effect estimation. Based on this characterization, we develop a novel local learning method for covariate selection in nonparametric causal effect estimation. This method accommodates the presence of latent variables and eliminates the need for the pretreatment assumption. We prove that the proposed method is both sound and complete under standard assumptions. Its effectiveness is validated through extensive experiments on both synthetic and real-world datasets.

Out-of-distribution (OOD) data lead to degradation of the generalization performance of graph neural networks (GNNs) in the node classification task. These data arise from distribution shifts in the structure or features of graphs between the training and test data. Recent studies have focused on the use of environment labels to mitigate this degradation from such shifts. However, whether using real or virtual ones, these approaches suffer from inherent inaccuracies, which introduce spurious correlations that mislead GNNs to rely on shift-variant superficial patterns rather than genuine causal relationship. To address this issue, we apply the frontdoor criterion from causal theory to intervene on the input graph. This criterion uses the ego-graph and node representations to achieve the inference of causal effects without any environment labels. Specifically, we propose a causal intervention framework with topology augmentation to achieve OOD generalization of GNNs. Based on a node-level invariance assumption, the framework constructs a causal graph and fuses multi-scale representations from GCN and GAT encoders. Moreover, a generator is designed to learn invariant ego-graph representation at the node-level. Three loss functions are derived via this criterion, which are aligned to realize the purpose of deconfounding. Extensive experiments conducted on five benchmark node classification datasets demonstrate that CITA outperforms state-of-the-art baselines, achieving robust generalization under three types of distribution shifts and a substantial reduction in running time compared with virtual label-basedmethods. Our codes are available at https://anonymous.4open.science/r/CITA-B526.

Instrumental variable (IV) methods are powerful for causal effect estimation with unmeasured confounding, but in practice researchers often face a set of candidate IVs whose validity is difficult to determine from observational data. This paper studies the problem of testing the validity of IV sets under Causal Additive Models with Non-Constant Effects (CAM-NCE). To address this problem, we propose a testable condition, termed the Cross Auxiliary-based independence Test (CAT) condition, for assessing IV set validity from observational data. We show that, under the completeness condition, if the CAT condition is violated, the corresponding set cannot be a valid IV set. Furthermore, under a cross distributional non-degeneracy condition, we establish that the CAT condition becomes both necessary and sufficient for characterizing valid IV sets under CAM-NCE. We then extend the CAT condition to settings with covariates and develop a practical finite-sample algorithm for testing the validity of candidate IV sets. Extensive experiments on synthetic data and three real-world datasets demonstrate the effectiveness and practical utility of the proposed method.

End-to-end automation of realistic healthcare operations stresses three capabilities underrepresented in current benchmarks: policy density, decisions must be grounded in a large library of medical, insurance, and operational rules; Multi-role composition: a single task requires the agent to play multiple roles with handoffs; and multilateral interaction: intermediate workflow steps are multi-turn dialogs, such as peer-to-peer review and patient outreach. We introduce χ-Bench, a benchmark of long-horizon healthcare workflows across three domains: provider prior authorization, payer utilization management, and care management. Each task hands the agent a clinical case in a high-fidelity simulator of 20 healthcare apps exposed via 87 MCP tools, which it must drive to a terminal status through tool calls and writing the role's artifacts, guided by a 1,290+ document managed-care operations handbook skill. Across 30 agent harness/models configurations, the best agent resolves only 28.0

Given only observational data $X = g(Z)$, where both the latent variables $Z$ and the generating process $g$ are unknown, recovering $Z$ is ill-posed without additional assumptions. Existing methods often assume linearity or rely on auxiliary supervision and functional constraints. However, such assumptions are rarely verifiable in practice, and most theoretical guarantees break down under even mild violations, leaving uncertainty about how to reliably understand the hidden world. To make identifiability *actionable* in the real-world scenarios, we take a complementary view: in the general settings where full identifiability is unattainable, *what can still be recovered with guarantees*, and *what biases could be universally adopted*? We introduce the problem of *diverse dictionary learning* to formalize this view. Specifically, we show that intersections, complements, and symmetric differences of latent variables linked to arbitrary observations, along with the latent-to-observed dependency structure, are still identifiable up to appropriate indeterminacies even without strong assumptions. These set-theoretic results can be composed using set algebra to construct structured and essential views of the hidden world, such as *genus-differentia* definitions. When sufficient structural diversity is present, they further imply full identifiability of all latent variables. Notably, all identifiability benefits follow from a simple inductive bias during estimation that can be readily integrated into most models. We validate the theory and demonstrate the benefits of the bias on both synthetic and real-world data.

We propose nonparametric identification and semiparametric estimation of joint potential outcome distributions in the presence of confounding. First, in settings with observed confounding, we derive tighter, covariate-informed bounds on the joint distribution by leveraging conditional copulas. To overcome the non-differentiability of bounding min/max operators, we establish the asymptotic properties for both a direct estimator with polynomial margin condition and a smooth approximation with log-sum-exp operator, facilitating valid inference for individual-level effects under the canonical rank-preserving assumption. Second, we tackle the challenge of unmeasured confounding by introducing a causal representation learning framework. By utilizing instrumental variables, we prove the nonparametric identifiability of the latent confounding subspace under injectivity and completeness conditions. We develop a “triple machine learning" estimator that employs cross-fitting scheme to sequentially handle the learned representation, nuisance parameters, and target functional. We characterize the asymptotic distribution with variance inflation induced by representation learning error, and provide conditions for semiparametric efficiency. We also propose a practical VAE-based algorithm for confounding representation learning. Simulations and real-world analysis validate the effectiveness of proposed methods. By bridging classical semiparametric theory with modern representation learning, this work provides a robust statistical foundation for distributional and counterfactual inference in complex causal systems.

Large language model test-time training (TTT) is often evaluated through local proxy metrics: models are updated on recent tokens, retrieved context, target-domain data, or verifiable task attempts, and then judged by perplexity, future-token loss, long-context performance, or reward. These metrics are well matched to claims about stream adaptation, domain adaptation, context compression, and reward-backed test-time improvement. They are weaker evidence, however, for a capability that TTT results are increasingly used to motivate: deployed assistant memory, personalization, or sparse post-deployment learning, which instead requires behavioral evidence such as later recall, paraphrase robustness, retention, locality, conflict handling, and use in downstream actions after the original support context is removed. We introduce a behavioral evaluation framework that calibrates TTT memory claims to the evidence that supports them. It has two components: a claim-calibrated evidence ladder that separates stream/domain adaptation, bridge internalization, and deployment-time behavioral learning; and an evaluation protocol with matched explicit-memory baselines and mutually exclusive failure categories. We validate the framework by auditing recent TTT and memory-adjacent work and by instantiating it as a controlled diagnostic in which, in a sparse nonce-fact setting, one-step LoRA updates lower support and answer loss across three Qwen3 model scales while generated free-form recall stays at zero, exposing a measurable gap between proxy improvement and deployment behavior. The framework gives authors and evaluators a concrete standard for aligning TTT memory claims with the evidence actually reported.

Causal discovery plays a pivotal role in scientific inquiry and subsequent applications in prediction or decision-making. While many methods have been proposed, many of them rely on independence tests. However, these tests are difficult to implement and computationally intensive. In this article, we aim to propose a direct and computationally efficient method to determine the causal relationship between two observed variables in the linear non-Gaussian case. Building on the insight that cumulants provide information about the shape of a probability distribution, we show that interestingly, the (in)dependence between two observed variables can be directly inferred from the difference in the product of certain joint cumulants of these variables. This concept is named the cause difference criterion. Based on this criterion, we introduce two practical methods, high-order cumulant (HC) and HC-linear non-Gaussian acyclic model (LiNGAM), for causal discovery in the high-dimensional case. Theoretical analyses ensure the identifiability of the proposed criteria and methods. Experimental results indicate that our methods outperform most existing methods.

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

Federated causal discovery aims to uncover causal relationships while protecting data privacy, with significant real-world applications. Existing methods focus on horizontal federated settings where clients share the same variables but have different samples. However, in practice, clients may have different variables, leading to spurious causal relationships. To address this issue, we comprehensively consider causal structure learning methods under both horizontal and vertical federated settings. Interestingly, we find that, higher-order cumulants rely solely on the joint distribution of the relevant variables and are useful to solve the above problem in the linear non-Gaussian case. This motivates us to provide the identification theories for determining the causal order over observed variables, leveraging the difference in the product of the (cross) cumulants of the specific variables. Based on these theories, we develop a method for learning causal order in the horizontal and vertical federated scenarios. Specifically, we first obtain local (cross) cumulant matrices of observed variables from all participating clients to construct a global cumulant matrix. This global cumulant matrix is then used for recursive source variable identification, ultimately yielding a causal strength matrix of the union of variables from all clients. Our algorithm demonstrates superior performance in experiments on both synthetic and real-world data.

Causal representation learning (CRL) and traditional representation learning have largely developed along different trajectories. Traditional representation learning has been driven mainly by applications and empirical objectives, whereas CRL has focused more on theoretical questions, particularly identifiability. This difference in emphasis has created a gap between the two fields in terminology, problem formulation, and evaluation, limiting communication and sometimes leading to disconnected or redundant efforts. In this paper, we argue that these two fields should be brought into dialogue rather than treated as separate paradigms. To this end, we introduce a unified formulation in which the representation learning is characterized by two components: a task component, which specifies what information the learned representation is required to preserve, and a constraint component, which specifies what structure is imposed on the latent space. Under this formulation, the benefits run in both directions. CRL provides theoretical tools for understanding when structured latent constraints are useful or necessary, while traditional representation learning offers practical insights on task design and objective choice that can improve the development of CRL methods. To illustrate this interaction, we experimentally study how different task components affect the behavior of CRL methods under different structured constraints. Results on CausalVerse show that the effectiveness of causal constraints depends strongly on the tasks with which they are paired.

Despite the impressive results achieved by multimodal large language models (MLLMs), their training typically relies on jointly curated multimodal data, requiring substantial human effort to construct multi-way aligned datasets and thereby limiting scalability across domains. In this work, we explore training MLLMs by only leveraging multiple paired modalities as a surrogate for the full joint multimodal distribution. Specifically, we first provide a theoretical analysis of the conditions under which the representations are identifiable with only observing pairwise modalities. Building on this analysis, we propose a representation learning framework for aligning latent representations across modalities using only pairwise data. The framework consists of two stages: latent representation alignment and cross-modal recomposition. Specifically, in the first stage, we learn the shared latent space across modalities by both self-modal reconstruction and pair-wise contrastive learning. We also incorporate an inductive bias in the contrastive learning process by partially aligning and minimal latent specification. In stage two, we integrate the encoder of newly introduced modalities with the decoders of the pre-trained modalities to facilitate cross-modal transfer and generation. We evaluate our method by newly adding 3D point clouds and tactile modalities into pre-trained MLLMs with three modality pairs and show that, by learning an aligned latent representation space, our model achieves strong cross-modal performance.

Large language model (LLM) agents are increasingly capable of automating components of machine learning development, yet existing biomedical benchmarks mainly focus on question answering, reasoning, and tool usage, or evaluate only narrow aspects of biomedical ML coding. We present BioXArena, a biomedical machine learning benchmark designed to evaluate whether agents can generate task-specific model training pipelines for heterogeneous and multi-modal biomedical datasets. BioXArena contains 76 end-to-end tasks across 9 domains, including sequence modeling, single-cell analysis, structural biology, network biology, chemical biology, perturbation dynamics, phenotype-disease modeling, biomedical imaging, and text-integrated learning. Each task is curated from primary biomedical sources into a unified evaluation framework with hidden labels, held-out graders, and biology-aware metrics normalized to a 0 to 1 scale. Agents are required to write executable code, train predictive models, and generate submissions for private test samples. Most tasks involve multiple input modalities, including tabular data, images, natural language, molecular sequences, omics matrices, and protein structures. We evaluate 11 agent configurations in a standardized 2-hour single-GPU environment. MLEvolve with Gemini-3.1-Pro achieves the highest average score of 0.666, followed by GPT-5.4 with 0.636, while no single agent consistently dominates across all domains. We additionally perform extensive ablation studies, robustness evaluations, scaling analyses, cost analyses, and failure-mode investigations to better understand how model backbones, agent scaffolds, inference budgets, and biomedical domains influence BioML coding performance. We will publicly release all benchmark tasks, graders, execution runners, leaderboard results, and agent trajectories.

Causal representation learning for time series has developed strong identifiability results in discrete-time latent causal models, but identifiability in continuous-time latent stochastic differential equation (SDE) models remains largely open. We address this gap using environment-induced shifts in diffusion covariance. We study additive-noise latent SDEs observed through an unknown nonlinear diffeomorphism, with shared drift but environment-specific diffusion covariance. We show that two diagonal diffusion regimes with pairwise distinct coordinate-wise variance ratios identify the latent coordinates up to permutation and scaling, without any sparsity assumption on the drift. We first prove this result for linear Ornstein–Uhlenbeck systems and then extend it to general additive-noise latent SDEs. Under mild smoothness, the instantaneous drift-Jacobian causal graph is identifiable up to the same permutation. We propose a two-stage estimator for latent disentanglement and optional graph recovery; experiments on synthetic systems confirm the predicted identifiability boundary, and an application to Hardanger Bridge monitoring data illustrates the approach on real sensor trajectories.