Causal

Topos causal models recast causal inference inside a topos: a causal world is a presheaf, an intervention is a sub-model named by a characteristic map into the subobject classifier $\Om$, and reasoning is Kripke-Joyal forcing in an intuitionistic internal language. We give the first axiom-free machine-checked account of this 1-topos core, in Cubical Agda over a previously verified probability monad and do-calculus; the framework is otherwise developed on paper, with central claims stated rather than proved. Three of our results go beyond faithful transcription. We exhibit a contextuality obstruction the programme does not treat: pairwise-consistent local causal data with no global model, detected by a degree-one holonomy class. We delimit the claim that interventions are modelled by the subobject classifier: an intervention and an observation name the same subobject, so $\Om$ fixes the target of a do-operation but not the operation itself, which is surgery on the kernels --- where, on a confounder, the interventional and observational laws differ. And we settle the modal unit --- inflationarity is derivable from $j\top = \top$ and naturality, not a fourth axiom. We also machine-check the classifier of sieves with its classification theorem, the pullback collating local mechanisms, and the Kripke-Joyal forcing clauses. The development assumes no axioms and typechecks under Agda's \texttt{--safe} flag, with the ordered field discharged at $\mathbb{Q}$; type-level sheafification and a directed do-calculus are future work.

Predictive models deployed at scale influence future data, a phenomenon called performativity. And there is always one way to cope: Train the model on new data, deploy it again, and repeat. This process, called retraining or repeated risk minimization, creates a feedback loop between model and data that real-world learning systems can't avoid. Results on performative prediction shed light on this dynamic: If the model's influence on the data is small, retraining reaches a fixed point. What remains open is why fixed points should naturally exist, and what governs retraining when the model's influence is strong. In this work we develop a new perspective on retraining -- the stable signal principle -- that addresses these questions. We start from the assumption that the prediction target has at least some small model-independent component, a stable signal, such as the intrinsic quality of an item. We prove that when a nonzero stable signal exists, repeated risk minimization, suitably regularized, converges geometrically to the direction of this stable signal. This is true even if the model's influence on the target is arbitrarily large relative to the stable signal. Regularization emerges naturally as a force to control performativity, rather than to promote generalization, revealing a new facet of an old concept. We extend the analysis to a broad family of affine retraining operators under arbitrary model-induced feature changes, heterogeneous time-varying effects, and nonlinear responses. The stable signal perspective also applies to data feedback loops in language modeling, providing new explanations for the stability of language model training from model-generated data.

This article explores the application of covariate balance diagnostics for detecting the presence of hidden confounding/model miss-specification in studies applying offline reinforcement learning (RL) to deriving optimal treatment recommendations. The results demonstrate that, either there is a high risk of bias within existing offline RL studies for treatment recommendations or, existing covariate balance metrics are not sufficient to assess such studies. Regardless, existing offline RL studies cannot be concluded as being statistically robust. The conclusions propose future research directions for obtaining more methodologically robust applications of offline RL to treatment recommendation problems.

We study causal inference under outcome interference for sequential, observational settings. Specifically, we consider settings where the binary outcomes over N units are Markovian across T time steps. At each time step, the outcomes of N units have dependencies captured through an Ising model; each outcome is also impacted through an external field capturing the effects of its treatment as well as latent confounders. Similar to panel data literature, these latent confounders are modeled to have a low-rank factor structure. Our data is a single sample from this high-dimensional distribution. To estimate causal quantities of interest, we provide a computationally efficient method based on Maximum Pseudo-Likelihood Estimation (MPLE) for learning the model parameters. Under mild assumptions, we establish non-asymptotic consistency for parameter estimation and show this translates to faithful estimation of causal quantities of interest after sampling from the learned model. We demonstrate the efficacy of the method through synthetic experiments as well as a real-world case-study investigating causal effects of vaccine rates on COVID-19 death rates within US counties nationwide.

Safe physical AI for robot actions are required not only likely to succeed but tested to be safe before execution. In practice, however, formal testing of motion parameters is computationally expensive, and the cost scales poorly with the dimensionality of the action space. When a proposed action is rejected by a tester, the naive response is to resample blindly until a passing candidate is found. This is wasteful, uninformative, and offers no convergence. We argue that rejection should instead trigger causal diagnosis: a principled identification of which action parameter caused the failure and what corrective value maximises the probability of passing testing under the interventional probability distribution. We propose a closed-loop framework that couples a Joint Probability Tree (JPT) with a Causal Circuit derived from a Marginal-Deterministic Variable Tree, enabling exact polytime computation without retraining, or additional data collection. The framework validates tractability of all interventional queries before the robot begins operating, and out-of-support candidates are detected and excluded from correction automatically. We perform experiments in a ROS2 simulation environment, and the framework demonstrates complementary roles across quality of distribution: under a high-quality JPT, the Causal Circuit reduces failed attempts by 10.3% and under a degraded JPT, it reduces total failed attempts by 37%. Every rejected plan produces a structured, interpretable causal report naming the primary cause variable, its observed value, and the recommended corrective region, supporting operator oversight and autonomous recovery without a separately trained failure model.

Autonomous driving vision-language models (VLMs) struggle in roadwork zones, where familiar visual cues such as lane markings and permanent signs are altered or absent, and temporary devices such as cones and barriers redefine the drivable corridor. VLMs can detect these objects, but without explicit guidance they anchor their reasoning on familiar elements from pre-training and fail to connect work-zone observations to correct planning decisions. We propose WorkDrive, a framework that constructs perception-grounded causal reasoning for work zones and aligns it with trajectory prediction. An automated multitask perception pipeline extracts structured scene facts and injects them into a Chain-of-Causation (CoC) annotation pipeline, redirecting the annotator's attention to domain-specific elements. The resulting reasoning labels are used for supervised fine-tuning, followed by reinforcement learning with a single reward: consistency between lateral meta-actions and the predicted trajectory. On ROADWork, the largest public work-zone dataset, the proposed roadwork CoC reduces trajectory average displacement error (ADE) by 9.0%, and consistency-based GRPO yields a further 3.0%, achieving progressive improvement over the trajectory-only baseline. Code and data will be publicly released.

Deep learning models for prostate MRI-based cancer grading may encode clinical covariates that either reflect useful disease-related signal or non-generalising shortcut information, but their role is usually assumed. We propose a causal-reasoning framework for probing covariate dependence in MRI-based International Society of Urological Pathology (ISUP) Grade Group prediction. Rather than treating mpMRI as a direct cause of grade, we model MRI appearance and ISUP grade as observations of latent tumour pathology, and test whether candidate clinical variables act as nuisance correlates, disease-related proxies, or irrelevant covariates in the learned representation. We implement this using an adversarial framework that suppresses the decodability of individual clinical covariate at a time while preserving MRI-based grade prediction. The approach is developed and evaluated on 2,903 prostate MRI examinations, with external validation on 576 patients. We report a set of interesting and previously under-explored imaging-to-clinical-variable interactions in the context of deep learning generalisation. For examples, in binary ISUP Grade Group $\geq2$ classification, suppressing age, BMI, and alcohol use improved AUC by 1.23%, 0.84%, and 1.42%, respectively (all p < 0.05), suggesting reduced non-generalising covariate information; In contrast, suppressing PSA and prostate volume degraded AUC by 1.91% and 7.61% (all p < 0.001), indicating that these variables carried task-relevant signal. These findings show that adversarial covariate suppression can provide a practical representation-level analysis for distinguishing potentially harmful dependence from informative signal in prostate MRI grading models.

Abductive reasoning operates in two directions. The synthetic mode builds explanations from available hypotheses; the analytic mode, conversely, identifies the latent factors whose interaction accounts for a complex observed state. This paper develops the analytic mode as a non-greedy, risk-sensitive discipline of commitment, in which candidate factors coexist and interact, resolving into committed conclusions only when explicit governance conditions are met. The formal core is the $κ$-$τ$ apparatus: $κ$ encodes the epistemic interaction among hypotheses, and $τ$ sets a commitment threshold calibrated to the decision's stakes. The central contribution is the causal cluster, a structured object recording which latent factors participate in a decomposition, with what weights and interaction structure, together with a two-level architecture (intra-cluster $κ^*$, inter-cluster $κ^{**}$) that guards against causal misattribution. Demonstrated in epidemiological crisis decomposition and adversarial cyber threat analysis, the framework's contribution to human-AI reasoning is the legibility of suspended decomposition as a shared coordination object, providing structural resistance to premature convergence. In practice, the decision-maker is handed not a single imposed answer but the competing explanatory scenarios, weighted by plausibility and paired with the evidence that would resolve between them, so that sound action is possible even before the ambiguity is resolved.

Online controlled experiments are the gold standard for hypothesis testing in online platforms. Notwithstanding their ubiquity, they are notoriously expensive to run, and issues of variance hamper statistical power in assessing treatment effects. While standard variance reduction techniques leverage model-based control variates to reduce outcome noise, they remain agnostic to potential structural relationships between competing policies. In this work, we identify a critical inefficiency in the standard A/B-testing protocol: when a treatment and control policy agree on an action, the resulting outcome contributes noise but no signal regarding the treatment effect -- unnecessarily inflating confidence intervals. We propose a novel experimental protocol that exploits this policy overlap to accelerate experimentation. The key insight is to frame the randomised treatment assignment mechanism as a meta-policy, and leverage $Δ$-Off-Policy Estimation methods to obtain unbiased estimates for average treatment effects. We prove analytically that our approach recovers standard A/B-testing practices in the general case, but that its variance scales with the divergence between policies rather than raw outcome variance. Hence, we dominate the standard Difference-in-Means estimator whenever policies have common support, and the improvement is strict whenever the overlap region contributes non-zero residual variance. Empirical results corroborate these theoretical insights -- holding promise for significant impact on the real-world evaluation of recommender systems, information retrieval pipelines, and large language model interfaces.

This study investigated the public acceptance of Society of Automotive Engineers Level 3 conditionally automated cars, which can self-drive under certain specified conditions but require the human driver to remain ready to resume control when requested. Previous Unified Theory of Acceptance and Use of Technology 2 (UTAUT2)-based research has focused mainly on European samples, and so it is still unclear whether the same factors shape acceptance across broader world regions. This knowledge gap was addressed using the L3Pilot Global User Acceptance Survey. From an original dataset of 18,631 respondents, the final analytic sample comprised 18,603 respondents from 17 countries across Africa, Asia, Europe, North America, and South America. The data were analyzed using a UTAUT2-based structural equation model to examine how performance expectancy, effort expectancy, social influence, facilitating conditions, and hedonic motivation shape the intention to use Level 3 cars. The model showed strong explanatory power. Across the analytic sample, the intention to use Level 3 cars was driven mainly by performance expectancy, social influence, and hedonic motivation. Effort expectancy and facilitating conditions also contributed, but they played smaller direct roles. Age, gender, and previous experience with advanced driver assistance systems were statistically significant, but comparatively weak predictors. Overall, the findings suggest that the acceptance of Level 3 automated cars depends less on demographic characteristics or ease-of-use concerns and more on whether people see the technology as useful, socially supported, and enjoyable to use.

The interconnected nature of global financial systems makes them vulnerable to systemic risks, where the failure of a few institutions can trigger catastrophic cascading defaults. Traditional risk models often fail to capture the complex, non-linear dynamics of these networks. While Graph Neural Networks (GNNs) have shown promise in modeling relational data, they primarily learn correlative patterns and function as black boxes, offering little insight into the causal mechanisms of shock propagation. This limitation is critical for regulators who require explainable models to perform stress tests and devise effective interventions. We introduce CausalGraphX, a novel framework that integrates GNNs with counterfactual reasoning to provide explainable assessments of systemic risk. CausalGraphX employs a Graph Attention mechanism to learn representations of institutional vulnerability and uses an adversarial regularization technique to ensure these representations capture causal drivers rather than spurious correlations. Furthermore, we propose an optimization-based approach to generate counterfactual explanations, answering questions such as, "What minimum capital injection would have prevented Bank A's default under a specific stress scenario?" We validate CausalGraphX on large-scale synthetic financial networks. Our results demonstrate that CausalGraphX significantly outperforms traditional and deep learning baselines in predicting cascading defaults while providing sparse, plausible, and actionable counterfactual explanations.

Policy learning methods are increasingly used to inform treatment allocation under budget constraints. Most proposed methods assume complete treatment data, yet applications frequently suffer from missingness that can bias estimates and lead to suboptimal policies. We address this gap by extending efficient estimators for average treatment effect (ATE) estimation to policy value and conditional average treatment effect (CATE) estimation under missing at random (MAR) and missing completely conditionally at random (MCCAR) treatment data. Through asymptotic efficiency analysis, we prove that the MAR estimator, which leverages partially-observed units, is both valid and more efficient than the MCCAR estimator when MCCAR assumptions hold. This result provides formal justification for preferring MAR-based estimation in policy learning under both missing data settings. Our comprehensive experiments using synthetic and semi-synthetic datasets confirm that correctly specifying the missingness mechanism is crucial: misspecified estimators remain biased regardless of sample size, while our estimators achieve near-oracle performance when assumptions are satisfied. Our work provides practitioners with theoretically grounded, empirically validated tools for robust policy learning in the presence of missing treatment data.

Longitudinal tumor measurements, dropout information, and genetic covariates provide complementary information about treatment response, but integrating these data sources within a single population modeling framework remains challenging. We extend the empirical Bayes variational autoencoder (EB-VAE) framework to joint longitudinal and time-to-event modeling and evaluate it on tumor growth data. The framework represents inter-individual variability using latent individual effects regularized by a covariate-conditioned empirical Bayes prior, while a decoder maps these latent effects to tumor-volume trajectories. To account for informative dropout, the decoder was augmented with a hazard model, yielding joint predictions of tumor growth and time to dropout. We further compared fully neural and hybrid semi-mechanistic decoder formulations and incorporated genomic covariates through a genetics-conditioned prior adaptation. The hybrid decoder recovered treatment-effect parameters broadly consistent with previously reported nonlinear mixed-effects estimates, while achieving prior predictive performance comparable to the neural decoder. The joint model reproduced both tumor-volume distributions and dropout patterns in held-out individuals, and genetic conditioning improved individual-level prior predictions in both cutaneous melanoma and breast cancer experiments. Stability selection identified several biologically plausible genetic indicators, including alterations in BRAF, NRAS, NF1, and MDM2. These results demonstrate that EB-VAE provides a flexible probabilistic framework for combining neural dynamics, mechanistic structure, time-to-event modeling, and high-dimensional covariates in pharmacometric applications.

We formalize verification in causal graphical models: deciding whether a given observational formula identifies a target interventional distribution. This opens a problem complementary to identification, asking not whether any identifying formula exists, but whether the given formula is identifying. We show that even sound and complete solutions to identification do not solve verification. We propose a falsifier as a first practical route forward, prove that it induces an almost-surely correct verifier for regular exponential-family models, and use the resulting verifier to develop the gateway test, which finds all sets admissible for use in a front-door formula.

Brain tumor progression exhibits spatially heterogeneous growth, patient-specific treatment response, and complex interactions with surrounding anatomy, making accurate long-term prediction challenging. We propose an AI-augmented adaptive digital twin (DT) framework for brain tumor evolution prediction and treatment scheduling. The framework integrates an interpretable reaction--diffusion (RD) model, a 3D residual learning module for model-form correction, patient-specific DT updating during recursive rollout, and model predictive control (MPC) for constrained chemotherapy and radiotherapy scheduling. Experiments on 387 synthetic tumor trajectories with 120-step evolution show that the baseline RD model captures tumor location and overall temporal behavior but underestimates heterogeneous tumor burden during long-horizon prediction. Hybrid RD--residual modeling reduces masked voxel-wise mean squared error by 84.3% and increases Dice overlap by 43.5% relative to the RD baseline under dense simulated observations. Online DT updating further reduces mean squared error by 45.9% and improves Dice overlap by 9.6% compared with the non-updated hybrid model. In MPC-based scheduling simulations, the updated DT controller reduces final tumor burden by 22.4% relative to a fixed treatment schedule under the terminal-burden objective. Together, these results demonstrate a unified framework for patient-specific initialization, mechanistic modeling, adaptive learning, and constrained treatment optimization. Although validated using patient-data-informed synthetic trajectories rather than clinical longitudinal data, the proposed framework establishes a foundation for future translation to real-world adaptive treatment planning.

Systematic comparisons between current situations and structurally similar past events in the historical, i.e., historical analogies, is among the most powerful tools for foresight analysis. In this work, we present a new task called Analogical Deep Research (ADR) to Large Language Model (LLM) agents and construct the first ADR benchmark ADR-bench to study whether LLM agents are able to find and leverage historical analogies when doing foresight analysis. Our investigation reveals a key obstacle: LLM agents are poor at finding analogies because they match on surface features rather than underlying mechanisms. We argue that ADR is inherently a causal question as it requires understanding why the event occurred. Based on our theoretical analysis, we propose two principles required for ADR, including the mechanism alignment and cross-analogy confirmation. Built upon our theoretical results, we propose a new agentic framework called Causal Analogical Researcher (CANA) that guides LLMs to find and integrate historical analogies. CANA incorporates a simple yet effective structural decomposition representation, and integrates structural feedback for reflective improvements of historical analogy identification and integration. We show that CANA brings up to 10% improvements in historical analogy generation, and surpasses the state-of-the-art deep research agents in the ADR-bench. Case studies with the ongoing events confirm the effectiveness of CANA in leveraging historical analogies.

Identifying root causes in production microservice failures requires reasoning over large-scale, multimodal telemetry spanning metrics, logs, and traces, a problem that has proved resistant to both classical and LLM-based approaches. The OpenRCA dataset exemplifies these challenges: it is large-scale, multimodal, and lacks detailed domain knowledge, and yields consistently low accuracy across all existing methods. We show that classical causal discovery methods and existing LLM-based multi-agent systems fail to reliably identify root causes on this benchmark, and present a Structured Multi-Agent RCA pipeline that substantially outperforms existing LLM-based and classical baselines, supporting both domain-knowledge and knowledge-free operating modes. To diagnose where failures originate, we introduce a reverse reasoning agent that, given the correct answer, identifies which signals in the extracted anomalies support it and determines whether Stage~1 had access to those signals, classifying each failure as Reasoning Gap (evidence present but unused) or Data Ambiguity (evidence genuinely absent). This analysis reveals that the required evidence is present in the vast majority of failures: the bottleneck is not data access but the agent's ability to reason over it correctly. We further introduce an automated rule mining pipeline that systematically extracts discrimination rules from reverse reasoning reports, reducing reliance on manual knowledge curation. Across all configurations, model reasoning capability and domain knowledge are the primary constraints: stronger models embed more domain expertise, and explicit knowledge injection partially compensates for this gap. Reasoning performance remains practically bounded even when evidence extraction is perfect: scaffold engineering and better data pipelines alone cannot close this gap; progress requires improvements at the model level.

Quantifying directional influence between node populations is a fundamental problem in graph-based modeling, particularly in spatial biological systems where cell-cell interactions shape functional outcomes. Existing approaches based on attention, attribution, or correlation capture associations but do not provide a principled framework for evaluating directional effects under controlled perturbations. We introduce a framework for structured counterfactual interventions in graph-based models to estimate directional influence between node types. Our approach trains a Neighbor Influence Model (NIM) to predict node states from local neighborhoods and applies constrained interventions that modify neighborhood composition while preserving key spatial and structural properties. We define the Counterfactual Directionality Score (CDS), which measures the change in predicted node state induced by targeted perturbations, and provide a theoretical interpretation of CDS as a finite-difference measure of local intervention sensitivity. To obtain valid uncertainty estimates, we introduce a core-level bootstrap procedure that accounts for dependencies within spatial samples. Experiments on synthetic spatial graphs with known directional structure show that CDS recovers directional influence, remains well calibrated under null conditions, and is robust to confounding signals, while preliminary results on spatial transcriptomics data reveal biologically plausible and consistent interactions across tissue cores.

Positive-Unlabeled (PU) learning aims to achieve high-accuracy binary classification with limited labeled positive examples and numerous unlabeled ones. Existing cost-sensitive-based methods often rely on strong assumptions that examples with an observed positive label were selected entirely at random. In fact, the uneven distribution of labels is prevalent in real-world PU problems, indicating that most actual positive and unlabeled data are subject to selection bias. Building on the SAR-PU propensity-weighted framework of Bekker et al., we study a PU learning enhancement (PUe) framework using normalized propensity scores and normalized inverse probability weighting (NIPW). PUe's main contributions are a normalized inverse-probability-weighted PU risk formulation; additional theoretical analyses of normalized sample-weight error and common PU estimators under biased labeling; regularized deep propensity-score estimation; integration with modern cost-sensitive PU methods; and support for selectively labeled negative classes. Experiments on MNIST, CIFAR-10, and ADNI demonstrate improvements over several PU baselines under non-uniform label distributions.

Aligned language models routinely misreport under non-evidential incentive pressure: they agree with a confident user or overstate certainty even when their internal belief is unchanged. We cast this as a failure of internal incentive-compatibility (IC) and present a method for learning and certifying counterfactual report mediators that hold a model's reports to a causal contract: invariant to forbidden influences (pressure, prestige, restyling) and responsive to licensed ones (genuine evidence). These two demands, resist and update, pull in opposite directions. We study them on a Bayesian-witness benchmark with known posteriors, in which the same user disagreement is licensed evidence or forbidden pressure purely by stated source reliability. We (i) causally identify, by interchange interventions rather than probe accuracy, low-rank report coordinates for answer, confidence, and caveat that are near-orthogonal and independently controllable, and (ii) introduce a training-free counterfactual report-coordinate (CRC) clamp that references the model's own report under a counterfactually incentive-neutralized context. On the witness benchmark the two-pass clamp attains resist and update of 1.00 jointly (Wilson 95% CI [0.99,1.00]), a causal certificate under a constructible reference, not a deployed solution. Global decoding and steering show a single-parameter tradeoff; output-level fine-tuning matches both objectives only when both are enumerated; resist-only training loses evidence-responsiveness. The deployable single-pass compilation is lossy (0.73/0.97). The mechanism and clamp reproduce across three model families and transfer to a natural sycophancy benchmark (SycophancyEval). Our contribution is the interface and certification method: activation-level counterfactual incentive-invariance as a structural primitive for internal IC.

Music recordings and live streams are often affected by noise, reverberation, spectral imbalances, or artifacts that degrade listening quality. While speech enhancement has matured into a well-defined research area, music enhancement is less established because musical signals combine overlapping sources, wide bandwidths, strong dynamics, and intentional production effects. We study real-time music enhancement under strict causal and low-latency constraints. We formulate the task around recovery of the intended produced mix from acoustic and production-oriented degradations, adapt compact causal networks to music, and compare speech-derived real-time baselines, an external music-denoising model, an offline restoration reference, and a music-specific MusicFilterNet-MS variant. On the tested hardware, all causal models run faster than real time, but improvements depend strongly on the dataset, degradation type, and metric family; under several objective criteria, indiscriminate enhancement can worsen the degraded input. The main contribution is therefore a benchmark and an analysis rather than a universal best model: real-time music enhancement is feasible, but robust improvement requires degradation-aware modeling, stereo-aware processing, identity-preserving correction, and evaluation beyond a single objective score.

Circular data, representing angles or directions, are frequently encountered in computer vision, biology, geology, and meteorology. Traditional regression targets the conditional mean, which is often geometrically misleading for circular responses under multimodal, skewed, or asymmetric data structures. To address these limitations, a lightweight deep generative framework, namely ANGLE, is introduced for non-parametric distributional regression on the circle. The full conditional distribution of an angular response, given Euclidean and circular covariates, is learned through a generative map optimized via a generalized circular energy score (GCES) loss. Desirable theoretical properties, including the strict propriety of the loss and the rotational equivariance of the estimators, are established. Furthermore, both pre- and post-additive noise models are accommodated. A unified toolbox is provided for advancing previously underexplored challenges in circular statistics: extrapolation, sufficient dimension reduction, and conditional distribution equality testing. The framework's efficacy is demonstrated through extensive simulations and real-world applications. Specifically, the proposal is utilized for object pose estimation from imagery and wind direction prediction, which are integral to surveillance, autonomous vehicles, and energy systems, respectively. Superior predictive performance and robust uncertainty quantification of the proposed method in these tasks are revealed.

This paper addresses Carl Hempel's longstanding problem of statistical ambiguity in inductive-statistical inference, in which contradictory predictions are derived from statistical laws. To avoid such predictions, Carl Hempel proposed the Requirement of Maximal Specificity (RMS) for the statistical laws used in the inference. An analysis of the RMS refinements made by Wesley Salmon, Alberto Coffa, and James Fetzer led to the following definition of maximally specific statistical laws: "the lawlike premises of an adequate explanation must specify all and only those properties whose presence or absence made a difference to the occurrence of its explanandum-phenomenon." However, there was no proof of a solution to the statistical ambiguity problem based on this definition. We use Nancy Cartwright's definition of causes that raise probabilities across background contexts, and then introduce the concept of Causal Rules. Then we define a special semantic probabilistic inference procedure that incrementally refines these causal rules by incorporating all statistically relevant information. This procedure yields Maximally Specific Causal Relationships (MSCRs), for which we prove (Theorem 1) that predictions derived from them are consistent. This resolves the statistical ambiguity problem. The semantic probabilistic inference procedure provides a probabilistic causal learning system, which may be used in such new areas as Causal AI and Causal Machine Learning. They fundamentally explore causal inference as a tool for understanding cause-and-effect relationships within complex systems. Properties similar to RMS remain under discussion. Several notions related to RMS are considered: invariant feature learning, invariant causal prediction, and spurious association.

Generative modeling of longitudinal Electronic Health Records is increasingly important for privacy-preserving research, yet standard autoregressive models tend to underrepresent the co-occurrence structure of tail events (i.e., diseases, symptoms), reducing the fidelity and faithfulness of generated data for rare subpopulations. To this end, we propose AdaPCLA framework, which enables generative models to adaptively fit and generate EHR data through a data distribution-aware training strategy; this is achieved by internalizing data knowledge parameters by simulated annealing training. It also supports training-free adaptation to a diverse clinical population for generation through zero-shot distribution control. Moreover, our theoretical analysis characterizes rare-code logit updates through the label-wise empirical NTK and derives a prior-internalization bound for how annealing speed and NTK conditioning affect retained prior signals. Experiments on real-world data show that AdaPCLA achieves consistent gains in tail plausibility, downstream utility, and zero-shot control; in particular, it improves TailPairSeen over HALO by 114.2% on MIMIC-III and 65.1% on MIMIC-IV, outperforms GPT-style generation by 3.5% F1 for zero-shot cross-population adaptation.

How can an agent build a structured map of its world from nothing but an ongoing sequence of raw sensory input and its own movements, especially when natural variation means exact sensory patterns rarely repeat? The Clone-Structured Causal Graph algorithm (CSCG), a normative hippocampus model, shows how an interpretable map can be learned from aliased observations. However, CSCG requires a predefined discrete alphabet, and its expectation-maximization formulation is not easily combined with existing neural network modules, preventing the end-to-end processing of raw image sequences. We remove this barrier by reformulating CSCG as a single, fully differentiable module, gradCSCG, and coupling it to a learned vector-quantized variational autoencoder (VQ-VAE) perceptual front-end. A soft emission forward pass allows the map-learning objective to flow back into perception, while a set of loss-balancing mechanisms mitigates module collapse during joint training. We demonstrate, first, that gradient training reproduces CSCG's results on original symbolic grid worlds by recovering room topology from heavily aliased observations. Second, we show that map recovery remains robust on MNIST image sequences, where each visit to a location yields a newly sampled image of its assigned digit. Across four heavily aliased environments, the end-to-end pipeline successfully uncovers the underlying adjacency graph with high edge precision and recall, directly from visual input. This work provides a proof of principle that CSCG can serve as a composable building block in a deep learning architecture.

Causal inference using front door intervention and multi-instance learning (MIL) has advanced the analysis of Whole Slide Images (WSI) in digital pathology. These methods adjust feature distributions of subtle evidence sub-images to correctly associate them with WSI-level diagnoses. We propose and prove 2 hypotheses for evaluating such methods: 1) Causal inference MIL introduces an independent classification channel that effectively completes WSI classification; 2) Greater difference between features extracted by the new and baseline channels increases effectiveness in eliminating false correlations. This hypothesis describes the core of causal inference MILs: overlaying parallel, independent channels to eliminate false associations between WSI-level diagnostic and non-diagnostic evidence sub-images by increasing deep feature diversity. Based on these hypotheses, we evaluated several causal inference MILs on breast cancer and non-small cell lung cancer datasets. This hypothesis provides a new theoretical perspective for applying causal inference to WSI analysis.

We study linear regression when the regressor is latent and observed only through multiple noisy measurements, each a smooth but possibly nonlinear function of the latent variable. The problem is acute in the measurement of occupational exposure to artificial intelligence, where competing scores yield downstream estimates that differ by a factor of eleven. A regression on any single measurement recovers a source-specific coefficient rather than the structural one. We fix the latent scale by requiring the consensus measurement function to be linear and bound the remaining curvature heterogeneity across sources relative to slope. Under this bound, the structural coefficient lies in a closed-form interval centered at a symmetric cross-source estimator. The interval is invariant to unknown source loadings, and its half-width is second order in the curvature bound and sharp to the same order. With at least four measurements, the bound is estimable from the joint distribution of the sources through a split-instrument auxiliary regression, and Imbens-Manski confidence intervals with the Stoye critical value attain uniform coverage over the curvature class, including at the point-identified boundary. The application matches six exposure measures to an American Community Survey panel of 8.88 million person-year observations for 2015 to 2024. The post-2022 employment coefficient changes sign between the language-model measures and the Webb patent-text measure, and an ex ante factor-analytic rule separates the Webb measure as a distinct construct. The five retained sources yield a loading-invariant consensus coefficient of -0.239, with a partial-identification half-width of 1.23 percent of the point estimate, or 1.88 percent at the one-sided 95 percent upper bound on the curvature. We read the application as measurement reconciliation rather than as a causal estimate of AI displacement.

True causal relationships are rarely known, and inferring causal graphs from data is hard. A fundamental challenge is how to assess whether a given causal graph is good in the absence of a ground truth. We propose falsifying candidate causal graphs based on whether they can explain the propagation of an outlier event. Our approach leverages a key principle: weak outliers rarely cause strong ones. While this principle has previously been used in root cause analysis to identify root causes without prior knowledge of the graph, we turn it on its head and use it to falsify candidate causal graphs whose implied outlier propagation is inconsistent with the data. To this end, we present the first statistical tests for the hypothesis that a candidate graph is the true causal graph, and show they have false positive control, power guarantees against incorrect causal graphs, and can operate with a single outlier sample.

Causal discovery algorithms learn a network that describes the causal dependencies among random variables. A common workflow involves first utilizing conditional independence properties on observational data to determine partially directed causal relationships, then applying interventions to orient the unknown causal directions. A critical assumption for the first step is faithfulness: a requirement that causally linked variables exhibit statistical dependence. Many natural systems include buffering and stabilizing pathways that cancel out to achieve systemic robustness. This cancellation of pathways violates faithfulness, leading causal discovery algorithms to incorrectly remove causal dependencies. In this paper, we argue that hard interventions contain information about the presence/absence of causal linkage that is overlooked in the first stage of structure discovery. We show that a mild assumption -- called intervention-immediacy faithfulness -- that allows cancellations, is sufficient to nonparametrically identify causal structures with hard interventions. These results position interventions as the primary carriers of information about causal structure, which should take precedence over conditional independence testing. To flip the paradigm, we also specify equivalence classes when the identification criteria are not met due to limitations in the scope of interventions.

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 \textbf{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.

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 large language models (LLMs) and vision-language models (VLMs) have enabled increasingly capable digital agents for computer use. However, real-world tasks are often long-horizon and involve evolving contexts containing accumulated observations, intermediate edits, failed attempts, and partially completed executions. Existing agents typically operate over raw interaction history, making task progress difficult to interpret, verify, and recover, which ultimately limits reliable long-horizon execution. In this paper, we argue that addressing this challenge requires explicitly structuring both the agent's state and workflow around a unified causal representation of task progress. We present \textbf{StructAgent}, a state-centered framework that introduces a unified state for maintaining compact, verifiable task progress and a structured workflow that regulates progress through verifier-backed state transitions. Building on this design, StructAgent further enables explicit progress checkpointing, evidence-driven task completion, targeted failure recovery, and tool-supported execution, while ensuring that all progress updates remain grounded in verification. Extensive experiments demonstrate that StructAgent consistently improves a wide range of LLM and VLM backbones on long-horizon computer-use tasks. On OSWorld-Verified, it improves Qwen3.5-9B from 27.0% to 46.9% success rate and Qwen3.5-27B from 31.6% to 62.2%, while achieving a new open-source state of the art of 78.9% with MiniMax-M3. Moreover, the same framework generalizes beyond desktop environments to Minecraft, demonstrating the generality of our design.

Dual-source trolleybuses alternate between overhead catenary supply and on-board battery operation, creating energy-use patterns driven by route attributes, high-frequency trajectories, and hourly weather. Existing models struggle to represent these heterogeneous inputs and rarely explain the causal drivers of consumption. This paper proposes a time-aware tabular deep learning framework for inter-stop energy management. Periodic time encoding is integrated into a parameter-efficient batch-ensemble backbone to jointly learn static and sequential features, while Bayesian optimization with tree-structured density estimation tunes hyperparameters. To move beyond prediction, a three-layer causal explanation pipeline combines feature attribution for marginal effects, a linear non-Gaussian acyclic model for causal direction discovery, and a meta-learner for net average treatment effects. Experiments on the Zurich trolleybus dataset enriched with meteorological records achieve a MAPE of 6.52% and R of 0.982, outperforming ten statistical, tree-ensemble, and deep learning baselines. Ablation results show that periodic time encoding contributes most to the accuracy gain. Causal analysis identifies regenerative braking ratio and average speed as the strongest energy-saving factors, while coasting distance is the main driver of excess consumption. The findings offer actionable thresholds for vehicle technology, driving behavior, capacity allocation, and catenary network planning.

Physics-Informed Neural Networks (PINNs) provide a meshless approach for solving partial differential equations (PDEs), but suffer severe degradation in stiff and shock-dominated problems, where small PDE residuals can correspond to globally inaccurate solutions. We show these failures are multi-causal, arising from the concurrent interplay of (i) spectral bias against sharp features, (ii) imbalanced multi-term optimization and loss-weight collapse, (iii) violation of temporal causality, and (iv) under-resolved collocation. We present SPARC-Net, a unified architecture and training framework that jointly addresses all four pathologies. SPARC-Net leverages an adaptive multi-scale spectral encoder with a learnable spectral gate, a gated residual backbone, adaptive activations, and a hard-constraint output ansatz that exactly enforces initial and boundary conditions, structurally eliminating loss-weight collapse. Training employs stabilized gradient-norm loss balancing, floored causality-respecting residual weighting, and residual-based adaptive collocation (RAD). Validated against exact analytic and high-order spectral reference solutions across four canonical benchmarks -- viscous Burgers', Allen-Cahn, convection (beta=30), and reaction -- SPARC-Net yields substantial improvements over vanilla PINNs: relative L2 error drops from 1.47e-1 to 1.14e-1 on Burgers' (22% reduction), 9.93e-1 to 5.78e-2 on Allen-Cahn (94% reduction), and 9.82e-1 to 3.54e-3 on reaction (100% reduction). A characteristic-coordinate encoder for hyperbolic transport further reduces convection error from 5.14e-1 to 9.88e-5 (100% reduction). We report five-seed mean +/- standard deviation errors, Wilcoxon significance tests, full ablation studies, hyperparameter sensitivities, an extension to the 2D heat equation, and comparisons against parameter-matched baselines.

The test suites used as RLVR rewards for code have natural false positives: per-task, persistent, asymmetric errors that accept the same wrong programs every time they appear, unlike the symmetric or resampled noise assumed by existing noise-robustness analyses. We run a preregistered two-arm causal contrast on a deployed suite: GRPO on identical MBPP tasks, seeds, and compute, rewarded by the original MBPP tests (leaky) versus the MBPP+ extra tests (hardened). Two further families replicate the design under a preregistration frozen before their data existed. [C] The average held-out effect is bounded: non-inferior under a preregistered 1.5-pt margin (gap 0.20 pt, one-sided 95% upper bound 0.75 pt). [C] Rewarded false-positive mass tracks a cheap static leakiness audit computed before training (Spearman 0.80), and the registered train-side test puts the leak-stratum FP share +43.8 pt above clean tasks. [E] Auditing every rewarded FP under signed, human-adjudicated rules finds a large residual of verified genuinely wrong code: 47.57% record-weighted; both replication families reproduce a large share. The reward paid for real bugs, not merely suite artifacts. [E] Mechanism evidence is consistent with selection of pre-existing error modes rather than learned exploitation: FP incidence does not grow within our horizon, and untrained base models already produce the same wrong outputs under the leaky filter. We then turn the same instrument on the frontier judges themselves: on their own false positives they self-assess only weakly, a same-author test is unresolved, and even the highest-scoring reader we probe stays far below its score on a weaker policy's errors -- two subjects on MBPP, licensing nothing about frontier models in general. A cheap static audit locates exposure before training; hardening the reward removes the measurement inflation, though here it buys little capability.

Identifying heterogeneous treatment effects under unobserved confounding is central in observational causal inference. In proxy models with a discrete latent confounder, prior Synthetic Potential Outcomes (SPO) [Mazaheri-Squires-Uhler '25] recover the mixture of treatment effects through recursively constructed scalar moments. We show that this sequence is one projection of a more fundamental object. Under the same population factorization assumptions, there is an exact compressed observable operator: after projecting onto the shared proxy signal subspace, the difference of two treatment-arm quotient operators is similar to the diagonal matrix of latent treatment effects. Its eigenvalues are the latent effects; its lifted left eigenvectors, after anchor normalization, recover the target-proxy feature matrix and then the latent mixture proportions. Every scalar SPO moment is a bilinear functional of a power of this operator. The resulting estimator handles overcomplete proxy systems, replaces high-order scalar inversion with finite-dimensional spectral analysis, and admits high-probability first-order perturbation bounds for treatment effects, feature rows, and simplex-projected mixture weights.

We propose a two-stage estimator for structural mediation parameters that combines deep representation learning with G-estimation under the "no essential heterogeneity" (NEH) assumption. We call the method UNIT. In the first stage,TARNet estimates the heterogeneous effect of a randomized treatment on a mediator by learning a shared covariate representation across treatment arms.The resulting conditional average treatment effect (CATE) estimate provides a plug-in approximation to the heterogeneity-dependent component of the weight function entering the G-estimating equation of Zheng and Zhou (2015), which identifies the structural parameters even in the presence of unmeasured mediator-outcome confounding. We show that more accurate first-stage representation learning can yield a more informative plug-in weight and thereby improve the precision of the structural parameter estimator. In simulations with non-Gaussian covariates and nonlinear mediator effects, TARNet weights reduce the Stage-2 standard error of the mediation coefficient by a factor of $1.45$ to $1.51$ (median across replications, $n \ge 2000$) relative to the classical approach, at no cost to bias or coverage.

Expert background knowledge is often available in practical applications of causal discovery. Such constraints on the true causal graph can help causal discovery in terms of identifiability of causal effects and accuracy of the learned structure, but also in reducing the space of candidate causal graphs. As causal discovery can become computationally expensive for large number of variables, it is crucial to utilize background knowledge effectively during the causal discovery process. However, most current methods only use background knowledge in a postprocessing step after causal discovery to refine the learned graph. In this work, we develop a framework for utilizing background knowledge during the causal discovery process, focusing especially on scalable causal discovery methods that recover only a subset of the whole graph. We implement our framework for multiple algorithms and empirically show that utilizing background knowledge can both reduce computational requirements and increase the quality of the learned structures.

Cross-model comparisons read divergence in value dispositions as evidence that language models hold individuated values. Under single-draw measurement this conflates two quantities: a difference in central tendency (a genuine value difference) and a difference in response determinism (how sharply a model commits to a forced choice). We introduce a separation protocol -- no-rule value dilemmas with counterbalanced, repeated forced-choice measurement and a determinism index -- and a determinism-corrected decomposition that splits an apparent cross-model distance into a direction-flip component (genuine disagreement) and a same-side-more-extreme component we label determinism. Across nine models, determinism varies substantially (0.66-0.95 among engaging models); whether it is a per-model trait or tracks provider and scale is a question our method makes measurable but our sample leaves open. Correcting for determinism shrinks apparent individuation, while a few cross-family disagreements survive a strict test. We then isolate a second confound: the access harness serving each model. Re-collecting the same models through raw provider APIs, we find the deployment client shifts a model's value profile substantially and client-specifically: one subscription CLI moves a profile by 0.31, flips four of eighteen items, and inflates the flagship's apparent softness (0.34 via CLI vs 0.66 via raw API), whereas another provider's client is clean, confounding provider family with access client. The harness is a value-shaping layer: a base model that refuses one-in-ten forced choices is made compliant by an agent system prompt, established causally in a white-box control. An audit ranking models by single-draw value distance thus ranks a determinism-inflated quantity, confounded further by the client used. We contribute the decomposition and identify the deployment harness as a distinct value confound.

Many real-world processes can be represented as compositions of functions along a directed acyclic graph (DAG). In causal modelling, these correspond to the underlying mechanisms; in engineering, to multiple fidelity levels; and in gene-regulatory networks, to transcription factors. These functions are partially observed across the DAG, with noisy and heterogeneously sampled measurements, posing significant challenges for reconstruction, uncertainty propagation, and inference. To tackle these challenges, we place priors over functions and naturally arrive at Deep Gaussian Processes over DAGs. We theoretically study their prior-collapse behaviour, and the effect of graph topology and intermediate observations on the preservation of information. We obtain almost-sure lower bounds on the asymptotic frequency of depths at which the distinction between inputs is preserved, identify broad kernel classes for which these hold, and prove an observation by \cite{dunlop2018} on the role of input connections. We offer a structured variational approximation that retains graph dependencies, preserves compositional uncertainty, and captures the explaining-away behaviour of colliders. Finally, we empirically validate our theoretical results and our methodology, and model a latent-collider DAG, a protein signalling network, and a multi-fidelity heavy-ion collision emulation task, attaining state-of-the-art performance while recovering low-fidelity contributions and yielding interpretability of the simulator hierarchy.

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

Flexible machine-learning methods can be sensitive to hidden confounding: they may learn associations induced by unobserved confounders rather than stable signals. Spectral deconfounding mitigates this problem by shrinking high-variance directions of the covariate matrix that, under dense confounding, carry latent confounder information. Existing work has largely focused on linear models. We develop a nonlinear spectral deconfounding framework for gradient boosting. Our approach replaces the ordinary squared-error loss by a spectral loss, which alters the boosting dynamics by slowing down learning in confounding-aligned directions. We show that deconfounding is not achieved by the spectral loss alone, but by the interaction between spectral shrinkage and regularization, especially in terms of early stopping. Moreover, we provide a mixed-model interpretation that connects LAVA-type shrinkage to random-effects adjustment and yields an empirical-Bayes procedure for tuning the spectral loss. We also extend the method to general likelihoods and nonlinear confounding using Laplace approximations and kernel random effects. Across synthetic and real-world experiments, spectrally deconfounded boosting improves estimation of the target function under hidden confounding and is substantially more scalable than existing nonlinear spectral deconfounding baselines.

Causal discovery from unstructured data is a challenging yet underexplored task in high-expertise domains such as healthcare, finance, and education. Existing methods typically leverage the general knowledge of large language models (LLMs) to identify causal factors from unstructured data and annotate them into structured data for causal graph construction. However, they remain limited by two key challenges (CHs): (CH1) insufficient identification of latent factors, which are implicit in the data yet essential for causal discovery, due to the lack of domain-specific knowledge; and (CH2) unreliable factor annotation, caused by the lack of domain-grounded reasoning, which propagates errors to the resulting causal graphs. To address these challenges, we introduce a novel Domain Knowledge-enhanced Causal Discovery framework (DKCD) for causal discovery from unstructured data in high-expertise domains with three interconnected components: (1) Knowledge Mining: It retrieves relevant domain knowledge based on observable factors to support subsequent causal reasoning. (2) Knowledge-guided Causal Reasoning: Reasoning with relevant knowledge, it discovers latent causal factors to address CH1 and generates key causal clues for more accurate data annotation to address CH2. (3) Causal Structure Discovery: It constructs the final causal graphs based on a more complete factor set and accurate annotations. Experiments on two domain-specific datasets show that DKCD significantly improves both causal factor identification and causal graph construction.

Hepatocellular carcinoma (HCC) is a common malignancy and a leading cause of cancer-related mortality. Current guidelines and staging systems provide coarse categories, but often miss within-stage heterogeneity and the clinical context in electronic medical records (EMRs). We present HCC-STAR (Hepatocellular Carcinoma Staging, Treatment And pRognosis), a clinically aligned large language model that reads routine EMR narratives and jointly outputs risk score-based staging, ranked guideline-consistent treatments with evidence-based rationales, and individualized survival estimates. We curated about 30,000 HCC cases from SEER and expanded them into EMR-style narrative training data using a clinician-validated, prompt-based augmentation workflow. On this corpus, we developed a knowledge-aligned reasoning framework optimized with a step-verifiable composite reward, moving beyond text-level memorization of clinical guidelines. In a multi-center cohort of 6,668 patients from 12 hospitals in China, HCC-STAR achieved state-of-the-art performance in treatment recommendation and risk stratification compared with clinical guidelines and competitive models, including GPT-5 and Gemini-2.5 Pro. Hypothetical overall-survival analysis showed a median survival of 51 months under adherence to HCC-STAR recommendations, compared with 29 and 32 months under BCLC and CNLC. In clinician-centric evaluations, blinded hepatobiliary specialists rated HCC-STAR's reasoning and evidence-based justifications as trustworthy. The model surpassed resident and attending physicians in treatment accuracy and helped physicians make more accurate decisions faster when used as an assistant. These findings support HCC-STAR as a reliable and verifiable decision-support system for risk stratification and precision therapy in HCC.

The operational integrity of complex industrial systems relies on precise anomaly detection and diagnosis. The vast majority of existing methods narrowly focus on capturing temporal similarities of representations, often overlooking the disruption of internal causal relationships, which characterizes system failures and latent anomalies. In this paper, we propose a novel framework (CAAD) that reframes anomaly detection as the continuous verification of Granger causality consistency through exogenous variables. Specifically, the CAAD framework models exogenous time-series variables as residuals, identifying anomalies as significant deviations caused by external interventions. The proposed framework leverages multi-scale alignment to internalize system dynamics and utilizes a gradient-based matrix to monitor internal causal relationship breakdowns. By quantifying causal deviations of both dynamic evolution and relational topology, the CAAD is able to capture subtle causal shifts to achieve precise anomaly detection. Extensive experiments on real-world industrial datasets demonstrate that the CAAD achieves high-precision anomaly detection, outperforming most state-of-the-art baselines.

Mechanistic interpretability often evaluates explanations by intervening on a model: swapping hidden states, patching activations, ablating components, or comparing a compressed model to the original one. These experiments are usually summarized by a point estimate, even though the evaluation may be monitored while it runs or adapted toward suspected failures. This makes it hard to tell whether a reported fidelity or patching effect is a stable causal claim or a consequence of finite sampling and evaluation choices. We introduce Certified Interventional Fidelity (CIF), a statistical layer for interventional interpretability evaluations. CIF first writes the quantity being reported as a causal estimand: an expectation of a bounded score over a stated input distribution and a stated intervention distribution. It then provides confidence intervals and anytime-valid confidence sequences for this estimand, including under adaptive intervention sampling via bounded mixture importance weighting. We instantiate CIF with Hoeffding-style sequences and variance-adaptive betting sequences, the latter reducing certification cost by 10-30x in our experiments. On MNIST abstractions and GPT-2 Small IOI circuits, CIF certifies high-fidelity claims, shows when apparent method differences are not statistically supported, and makes sensitivity to the intervention distribution explicit.

Quantifying variability in a target population relative to a reference population is central to many scientific and clinical problems (e.g., diseased vs. healthy). Yet, without paired data and in the presence of heterogeneous target variation, existing methods struggle to separate multiple modes of target-specific variation. We propose \textit{CASL-VAE}, a deep contrastive latent variable model that learns structured latent generative factors from unpaired data. CASL-VAE factorizes variation into continuous common latent factors shared across populations and hierarchical salient latent factors that model target-specific heterogeneity as discrete subtypes and continuous within-subtype variation. Using variational inference, we show how approximate joint likelihood optimization over reference and target domains can be performed using unpaired data, providing a principled basis for paired-sample generation and cross-domain analysis. We validate CASL-VAE on semi-synthetic neuroimaging data, demonstrating improved subtype recovery and paired-sample generation compared to baseline clustering and generative models. We also validate its ability to reveal biologically plausible heterogeneity in Alzheimer's disease.

Workload-based differentially private (DP) synthetic data methods privately measure aggregate queries and post-process the noisy answers into synthetic records. Generic workloads can achieve strong distributional fidelity, but causal estimands such as the average treatment effect (ATE) depend on treatment-arm balance and outcome moments that generic marginals need not preserve. We propose causal workloads: DP query sets designed around the orthogonal moments used by doubly robust causal estimators. The released workload can be used directly by stable moment-map estimators or reconstructed by maximum-entropy calibration into reusable synthetic data; our theory decomposes ATE error into sampling, privacy, workload-approximation, Monte Carlo, and calibration terms. We also introduce Causal-AIM, an adaptive workload selector, and a noise-aware multiple-imputation (NA+MI) procedure for confidence intervals from DP synthetic data. Because the workload is released once, the same DP synthetic table can support ATE, ATT, and subgroup analyses without additional privacy spending. Empirically, causal workloads are most useful at strict privacy budgets and for calibrated uncertainty, while generic workloads often retain an advantage for point RMSE as privacy relaxes. The broader lesson is a tradeoff: distributional fidelity can help point accuracy, but valid causal inference requires preserving causal moments and propagating DP noise rather than treating synthetic rows as real.

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.

Coding agents now author entire pull requests, and practitioners sharply disagree about what this does to code review: whether it becomes the bottleneck, whether human review is still necessary, and whether it quietly erodes the understanding that it once built. Repository-mining studies measure surface trends but seldom explain the mechanisms beneath them, and the trends themselves prove unstable. A motivating observational analysis of public GITHUB activity finds that agent-authored pull requests are reviewed less often, merged several times faster, and discussed less than human-authored ones, yet the direction of these trends flips under different but equally defensible analysis choices, so the traces establish what is changing without explaining why. To recover the mechanisms, we synthesize practitioner discourse at scale into an explanatory theory: we collect 38,709 grey-literature documents (engineering blogs and Reddit threads), filter to those substantively about code review, and code a stratified random sample of 3,100 with an LLM-assisted pipeline, from which we build a causal model of 26 constructs and 67 relationships (64 directed, 3 contested). Its organizing claim is that review is the control point through which a coding agent's effect on software is decided, and that AI does not fix the sign of that effect: the team sets it, through the expertise its humans bring and how it structures the review process. The theory makes the competing positions explicit and turns "AI is changing code review" into falsifiable propositions with named constructs and moderators. As a secondary contribution, we offer the underlying LLM-assisted, grey-literature theory-building method as a scalable template for software-engineering research, with a public implementation.

Parameterized quantum circuits (PQCs) are increasingly used as policies and value functions in quantum reinforcement learning, yet it remains unclear when and why quantum policies generalize. We give a PAC-Bayesian account in which generalization is governed not by the raw number of circuit parameters, but by the effective dimension of the Fisher geometry induced by the circuit. This quantity is inflated by entanglement, making entangling connectivity an independent axis of complexity.In controlled experiments that fix the number of trainable rotations and vary only entanglement, we find that circuits with larger Fisher effective dimension exhibit larger train-test gaps, while parameter count is a weak predictor. The resulting bound acts primarily as a ranking certificate: it correctly orders circuits with identical parameter count, which parameter-counting bounds cannot do. We validate this mechanism across supervised classification, quantum contextual bandits, and value-function generalization, where entangled circuits consistently generalize worse than non-entangled circuits of equal parameter count, with gaps shrinking as sample size increases.Our strongest evidence comes from low-variance decision models, including single-observable classifiers, value heads, and one-step policies. In end-to-end multi-step policy learning, entanglement effects remain statistically significant but high return variance leaves the full ordering only partially resolved. Partial-correlation analysis shows that Fisher effective dimension screens off entangling pattern, and controls for training accuracy, readout, and optimizer rule out major optimization confounders. The effect also persists on an IBM Heron quantum processor under real noise. Overall, our results reframe quantum policy design around an entanglement--generalization trade-off rather than expressivity alone.

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

Training data for machine learning is routinely collected by a selection process the model never sees: loans are observed only when granted, outcomes only when a test was ordered. The standard fixes -- importance weighting, covariate-shift correction, MAR imputation -- assume selection is ignorable given observables. Econometrics solved the harder case in 1979: Heckman's two-equation model jointly fits a probit selection equation and an outcome equation linked through correlated errors, and the inverse-Mills-ratio term corrects for selection on unobservables, where importance weighting is structurally helpless. We instantiate this for deep epistemic uncertainty: a deep outcome network, a linear selection head, and a joint bivariate-normal likelihood over all units, ensembled for predictive variance. In a controlled generator where sampling probability depends on an unobservable correlated (rho up to 0.9) with the outcome noise, deep ensembles, MC dropout, and GP baselines are overconfident exactly where data was avoided: coverage of nominal-90% intervals falls to 64.4% at rho=0.9, and importance weighting with oracle propensities does not fix it (43.1%) -- reweighting corrects the covariate distribution, not the conditional bias E[y|x,selected] != E[y|x]. The Heckman correction restores coverage (88.9%) when the selection equation has an instrument -- a variable affecting selection but not the outcome -- and degrades measurably without one (40.3%); we chart this honesty curve rather than hide it. On real tabular data with induced MNAR selection, the corrected intervals are the best-calibrated (lowest region-ECE) non-oracle method in selected-against regions; baselines matching its raw coverage do so only by over-widening everywhere. Our estimators reproduce classic Stata output to seven digits. We state which identification regime a practitioner is in, and release the code.

Tool-augmented large language models extend their capabilities beyond parametric knowledge through external tools, but tend to invoke them unnecessarily. We investigate whether tool-use decisions have any stable internal representation that can be extracted and manipulated, a question that is non-trivial given that tools exist entirely in context at inference time and have no direct encoding in model weights. We show that steering vectors extracted from heading-anchors positions exert bidirectional causal control over tool-invocation behavior across five open-source models and three domains, suppressing unnecessary tool use most effectively in domains where parametric reasoning suffices. However, geometric analysis reveals that this causal effectiveness does not correspond to clean linear structure: tool-invocation steps exhibit diffuse, bimodal alignment with the suppression vector rather than the consistent negative alignment a linear encoding account would predict, and different tool types recruit largely distinct internal signatures with low cross-tool feature overlap. We hypothesize these geometric properties are indicative of the non-parametric nature of tools, and distinguish tool-use steering vectors from those extracted for parametrically grounded concepts. The relationship between this geometric irregularity and the observed causal effectiveness remains an open question.

Interpretable explanation methods in Artificial Intelligence aim to uncover the underlying causes and their effects, enabling a deeper understanding of why a system behaves in a certain way under different inputs. Unlike traditional explainability methods, which mainly highlight correlations between input and output variables, causal explanation focuses on interventional questions. By doing so, it provides more robust insights, helping users understand automated decisions, especially in high-risk domains. Recovering an explicit directed causal structure, however, is often impractical in large-scale, hybrid cyber-physical systems with feedback loops and partial observability. This paper introduces a novel framework inspired by statistical mechanics that instead models variable dependencies through an undirected, energy-based representation of cyber-physical IoT systems. Our approach enables rigorous dependency-aware attribution by analysing how variations in the energy landscape reflect the influence of individual components, without recovering a directed causal graph. It also supports reasoning about perturbation effects across hybrid interactions, providing reliable explanations of abnormal behaviours. We empirically examined our framework through simulations on an industrial IoT testbed with hybrid continuous and discrete variables, demonstrating higher attribution accuracy, improved robustness and better scalability than state-of-the-art graph-based approaches. While the attributions are not intended to fully recover the system's generative dynamics, they provide valuable, dependency-aware explanations supporting both human interpretation and downstream predictive and diagnostic tasks. Although demonstrated in industrial IoT security, our framework also applies to other high-dimensional cyber-physical and socio-technical systems requiring principled, structural explanations.

Personalized incentive allocation is vital for e-commerce, where uplift modeling is the standard for estimating Individual Treatment Effects (ITE). However, traditional models often fail in complex multi-seller environments with violations of the Stable Unit Treatment Value Assumption (SUTVA). We identify two critical challenges: Seller-level Cannibalization, where incentives shift expenditure between shops without growing the platform, and Incentive-level Cannibalization, where organic conversions or alternative rewards introduce significant noise into incrementality estimation. In this paper, we propose CanniUplift, a unified framework to mitigate these dual-source cannibalization effects. Specifically, we design Platform-level Global Alignment (PGA) to capture cross-shop substitution through global GMV consistency constraints. To tackle incentive-driven noise, we introduce Redemption-based Decomposition Denoising (RDD), which uses redemption behavior to decompose treated outcomes and reduce attribution noise within an entire-space framework. Furthermore, a Treat-Attention mechanism is designed to model intricate interactions between users' historical behaviors and current treatment options. Extensive experiments on both synthetic and large-scale industrial datasets demonstrate that CanniUplift significantly outperforms state-of-the-art baselines. Ablation studies confirm that the integration of PGA and RDD consistently improves wAUUC and wQINI. Successfully deployed online, our framework achieved a 4.08% relative increase in platform-wide incremental GMV (Delta GMV) over the production baseline and improved ROI in online A/B tests, proving effective in driving global platform growth.

Scientists often seek to draw causal inferences from structured data that is not independently and identically distributed, such as spatial data, network data, or molecular data. We develop geometric causal models (GCMs), a framework for causal inference from dependent data that exploits underlying symmetries of the data generating process. For example, in spatial data, we consider processes that are symmetric under translations, or in graph data, symmetric under permutations of the nodes. We show how symmetries, formalized with group theory, can enable causal identification and estimation. We deploy ergodic theory for amenable groups to establish identification, and combine geometric deep learning with scalable Bayesian inference for estimation. We recover i.i.d. causal models and do-calculus when the data is a sequence and the symmetry is permutation equivariance, and find novel types of causal models when we use alternate structures and symmetries. As an example, we construct a causal model that satisfies the symmetries of DNA. This GCM enables new estimators for the effects of genetic variation, combining deep functional genomics models to describe outcomes and DNA language models to describe propensities. We illustrate on semisynthetic data.

Scalable Bayesian inference for generalized linear mixed models (GLMMs) provides uncertainty-aware analysis of correlated longitudinal data, but existing scalable approaches largely assume low-dimensional tabular predictors and do not directly accommodate high-dimensional modalities such as images and text. We address this limitation by learning one or more modality-specific neural encoders jointly with a GLMM objective, then performing variance-corrected stochasticgradient MCMC for the GLMM parameters conditional on the learned representation. This conditional-Bayes design combines supervised representation learning with posterior uncertainty quantification for population-level effects, subjectspecific heterogeneity, and modality-level random slopes. The resulting model preserves interpretable fixed and random effects for structured covariates and learned modalities while scaling gracefully to large longitudinal datasets. In simulation studies, our method recovers posterior means and variance estimates from full-data MCMC benchmarks after covariance correction. We further evaluate uncertainty through parameter-level interval coverage in simulations and predictive calibration on held-out data. Applications to glaucoma progression and adolescent mental health demonstrate that the framework allows nuanced assessment of the relative importance of each modality on both individual and population levels without sacrificing predictive performance.

We study how correctness is assembled inside aligned language models, not only whether the final answer is right. Using layer-wise difference-in-differences (DiD) trajectories over polarity-controlled minimal pairs, we identify the wrong-dip: in mid layers (25-90% depth), internal preference transiently commits to the incorrect answer and is rescued only by late-layer correction. We verify this causally with patchscope-style activation transplantation across 17 models, three families, and 64x scale (0.5B-32B). Four findings follow. (1) Alignment amplification of the causal wrong-dip is recipe-specific and emergent: it emerges at 3B in Qwen2.5, remains high, and peaks at 32B (paired t up to 9.7), reverses in Llama-3-8B (t=-2.31), and sits between for Mistral-7B. (2) The dip predicts real compression failures: high-dip items are 3-7x more likely to flip under late-layer low-rank compression, block dropping, or structured pruning, while quantization flips are dip-blind, a double dissociation confirmed by late-layer ablation. (3) The dip is trainable: a LoRA fine-tune with a mid-layer wrong-margin penalty matches output-only SFT accuracy while cutting the causal dip by 67-70% and improving compression robustness; output-only SFT worsens the causal dip by up to 2.8x at perfect surface accuracy. (4) With controlled readouts, the phenomenon survives natural-language I/O: dip stratification of structural-damage failures is significant on naturalistic vignettes, and free-form fragility separates into a dip-auditable late-rescue layer and a dip-blind interface layer. Together, output-level correctness can hide a late-rescue process that governs compression risk, post-training quality, and evaluation distortion.

Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and unstable, whereas knowledge-graph methods provide mechanistic context yet remain static and fail to capture drug-induced transcriptomic perturbation dynamics. We propose PREDIKTOR, a patient-centered multi-view framework that aligns a personalized network view with a transferable transcriptomic perturbation view to predict clinical drug response. For each patient, we construct an individualized gene regulatory network from tumor expression using DysRegNet and augment it with drug-target links from DrugBank; a graph neural encoder yields a drug-centric, mechanistically grounded embedding. In parallel, a frozen condition-specific gene-gene attention model pretrained on LINCS L1000 generates a simulated post-perturbation transcriptomic profile for the same patient-drug pair. We align the two views in a shared latent space via a CLIP-style contrastive objective with drug-context hard negatives, then concatenate the representations for end-to-end response classification. On TCGA, PREDIKTOR consistently outperforms state-of-the-art baselines under patient-, drug-, and tissue-split evaluations, and transfers zero-shot to the I-SPY2 trial, improving AUROC by 5.6% over competing methods. The aligned embeddings yield stable gene and pathway attributions that recover known mechanisms, supporting actionable and interpretable precision oncology.