Causal

Large language models are rapidly becoming infrastructural components in high-stakes institutional settings, including public administration, legal reasoning, and healthcare, where opacity is not merely inconvenient but institutionally and legally untenable. Existing approaches to explainability are predominantly post-hoc, offering unstable, non-contestable accounts that have no formal relationship to the reasoning process that produced the output. We argue that the problem is not the absence of explanation but the absence of structured reasoning in the first place. This paper makes the case for a fundamentally different architecture, which we call the Glassbox Framework, in which Bayesian networks serve as transparent, ante-hoc mediation layers for generative models. Bayesian networks encode domain knowledge, causal assumptions, and probabilistic dependencies before inference occurs, enabling auditable reasoning traces, uncertainty quantification, and contestable outputs. We characterise the architecture of this framework and ground it in a benefit eligibility scenario, identifying the foundational challenges spanning semantic alignment, dynamic model construction, probabilistic grounding, and human governance that must be solved to realise it at scale. By shifting from post-hoc explanation to ante-hoc probabilistic mediation, this work outlines a principled path toward AI systems that are not only powerful but fundamentally accountable.

Transfer learning addresses the challenge of transfering knowledge from one domain to another. Traditional transfer learning focuses on adapting models trained on a source domain (with a lot of observations) to improve performance on a target domain (with few observations). In this work we consider the case of a model shift and we focus on the transfer learning applied to a causal forest namely HTERF. This causal forest aims to estimate the Conditional Average Treatment Effect (CATE). The approach considered is the offset method presented by Wang (2016) adapted to a causal context. This method relies on the use of intermediate models in order to estimate the offset between source and target distributions. Our main result is a bound on the CATE error of HTERF on target depending on the error of the intermediate models. Simulation studies show the good performances of this approach in different settings on simulations and on a real-world dataset.

A central goal of mechanistic interpretability is to identify which internal components causally drive a language model's behavior. Because these importance estimates serve as the evidence for identifying circuits, systematic errors can lead to the misidentification of the underlying mechanisms. While activation patching provides a gold-standard causal metric, its computational cost is prohibitive at scale. Practitioners instead rely on attribution patching, a gradient-based, first-order approximation whose reliability remains poorly understood. In this work, we characterize the source of this unreliability, demonstrating that the dominant error stems from the non-linearities in the downstream network rather than local curvature at the patched component. This insight yields three practical tools: (i) a reliability score to detect untrustworthy estimates, (ii) error bounds quantifying potential attribution mis-specifications, and (iii) a Hessian-vector-product (HVP) correction that eliminates the leading-order error with only one additional backward pass. In evaluations across five model families (124M-9B parameters) and both random-token and naturalistic (name-swap) perturbations, HVP is the only second-order correction feasible at larger scale, where standard baselines like Integrated Gradients become computationally prohibitive. In comparative experiments, a multi-step HVP variant matches or exceeds the accuracy of Integrated Gradients at significantly lower compute, outperforming prior second-order baselines. These improvements lead to higher-fidelity circuit recovery on standard benchmarks and support a Screen-Flag-Fix workflow that targets computational effort only toward the components flagged as unreliable.

Modern image-analysis pipelines often convert images into structured semantic variables, such as facial attributes, object concepts, and scene descriptors. Learning directed dependencies among these variables can produce interpretable visual semantic graphs, but continuous directed acyclic graph learning is limited by the cost of enforcing acyclicity. We present polyDAG, a polynomial acyclicity framework for efficient continuous causal discovery in visual semantic graphs. polyDAG replaces the matrix-exponential acyclicity constraint with a finite polynomial trace constraint and proves that the new constraint is zero exactly for acyclic graphs. We further derive a geometric-series implementation that avoids the explicit summation loop while preserving the same acyclicity condition. Experiments on synthetic Erdos-Renyi graphs and CelebA facial visual attributes show that polyDAG improves efficiency and structure recovery. Averaged over the revised synthetic protocol with d in {100, 200, 500}, polyDAG reduces mean structural Hamming distance from 318.4 to 285.4 and improves mean F1 score from 0.725 to 0.756. At 100 nodes, the geometric variant runs in 3.44 seconds compared with 5.16 seconds for the exponential baseline, corresponding to a 33.4 percent speedup. Code and data are publicly available at https://github.com/wenhaoz-fengcai/polyDAG.

Causal mediation analysis decomposes a treatment effect into indirect pathways through mediators and direct pathways not operating through them. Modern biomedical studies often involve high-dimensional covariates and mediators that are noisy proxies for lower-dimensional latent biological processes. Existing methods typically rely on sparsity, linear factor models, or ignore the connection among variables in the learned representations, which can be restrictive when measurements are nonlinear and covariate and mediator factors are structurally dependent. We propose MediEncoder, a representation-learning framework for nonlinear high-dimensional mediation analysis. MediEncoder jointly learns low-dimensional covariate and mediator representations using a coupled encoder-decoder architecture with a cross-factor network that links treatment and covariate representations to mediator representations. The learned features are then used in a cross-fitted efficient influence function-based estimator of natural direct and indirect effects. The resulting estimator is multiply robust and asymptotically normal under suitable regularity conditions. Simulations show that MediEncoder improves estimation accuracy over competing dimension-reduction approaches, and an application to Alzheimer's Disease Neuroimaging Initiative data illustrates its utility in high-dimensional biomedical causal mediation analysis.

A long-standing finding in the causal learning literature is that adults struggle to identify conjunctive causal rules, where an effect requires the simultaneous presence of multiple causes, while performing better in disjunctive settings. However, most demonstrations of this conjunctive handicap'' rely on passive observation paradigms with limited evidence, where learners have no control over evidence generation. This paper asks whether this bias persists when adults are granted agency through active exploration. Using a modified blicket detector'' task, adult participants freely intervened to identify causal objects under conjunctive or disjunctive rule structures. We show that active exploration substantially improves adults' conjunctive causal reasoning, although conjunctive rules still require more tests to infer than disjunctive rules. We further compare human performance to a range of large language models in the same setting. While some state-of-the-art models approach human-level performance on hypothesis inference accuracy, they often exhibit less efficient exploration strategies and similar conjunctive-disjunctive performance gaps.

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

Causal representation learning aims to infer the high-level latent causal concepts that give rise to observed low-level measurements. This is particularly relevant for heterogeneous data from different environments or domains since distribution shifts often arise through sparse, localized changes in some of the underlying causal mechanisms, while other parts of the generative process remain unchanged. Whereas identifiability of causal representations has been studied extensively, practical uncertainty-aware methods and real-world use cases remain less explored. In this work, we propose a Bayesian approach to learning causal representations from multi-environment data, focusing on the case of discrete causal concepts and unknown multi-node soft interventions. To this end, we translate causal assumptions and interpretability desiderata into suitable priors and parametric choices within a hierarchical model. We then devise an inference scheme based on sequential Monte Carlo sampling to approximate the resulting multimodal posterior. We showcase our approach through case studies on social survey data, where latent causal concepts correspond to cultural values or political opinions, measurements to survey responses, and environments to different countries or states. Our model infers meaningful high-level concepts and plausible causal relations among them, demonstrating its utility for learning causal representations of complex real-world data.

Advances in computational modeling, neuroimaging, and artificial intelligence are revolutionizing the modeling of neurological disorders for improved diagnostics, prognosis, and treatment planning. Mechanistic models provide valuable scientific insight into the disorders, but in practice they are often simplified with assumptions or computationally expensive and slow to solve. However, while purely data driven approaches provide speed and scalability, they require large, high quality data to train and generally suffer from interpretability and generalization issues. This perspective paper presents a structured overview of hybrid modeling strategies, which combine deep learning models with physics based solvers, and are categorized into parallel, series, and parallel-series architectures. Three main approaches that have been emphasized are residual modeling for missing or incomplete physics, Neural Ordinary Differential Equations (NODEs) for continuous time dynamics approximation, and solver in the loop that accelerates traditional solvers with neural approximations. These hybrid models integrate the governing differential equation based formulations and deep learning to characterize the evolution of neurological disorders, and promise advanced personalized neurological modeling. In addition, the study explores and proposes different hybrid configurations to improve diagnosis accuracy, predict disease progression, and inform treatment strategies across a range of neurological disorders. These capabilities outperform standalone mechanistic or purely data driven approaches, making hybrid modeling a powerful tool, especially in applications involving modeling the progression and treatment responses in neurological conditions such as brain tumors, Alzheimer's disease, and stroke.

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

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

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

Foundation models mark a profound paradigm shift in time series modeling, with task-specific models being superseded by general-purpose zero-shot models. Yet, current approaches primarily focus on forecasting, while real-world time series are often irregularly and partially observed, requiring models that can jointly forecast, impute missing values, and handle degraded sampling conditions. To address these challenges, we introduce TS-ICL, a novel probabilistic In-Context Learning encoder--regressor Transformer that unifies forecasting and imputation. TS-ICL formulates time series tasks as timestamp-aligned regression and naturally incorporates covariates by training on synthetic dependency structures generated from a novel causal data prior. Empirically, TS-ICL achieves a new state-of-the-art in imputation, while remaining competitive with leading forecasting foundation models across both univariate and covariate-aware benchmarks. It shows particularly strong performance in forecasting with partially observed look-back windows.

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

Deep learning has enabled significant advances in time-series causal inference, yet progress remains constrained by the lack of realistic benchmarks with observable counterfactual outcomes. Existing datasets either rely on real-world observations without ground-truth counterfactuals or on simplified simulations that fail to capture complex causal dynamics. To address this gap, we develop a large-scale benchmark for counterfactual prediction in epidemic time series under dynamic interventions. Unlike existing benchmarks, it supports static and time-varying treatments, as well as both single-policy and multi-policy intervention settings, enabling evaluation of causal inference methods across a broad range of causal inference scenarios. Leveraging a calibrated agent-based model grounded in real-world demographic, mobility, epidemiological, and policy data, we generate realistic counterfactual trajectories across more than 150 U.S. counties. Using this benchmark, we evaluate widely used and state-of-the-art causal inference methods, revealing substantial performance differences and highlighting the challenges of realistic time-series causal reasoning.

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

Root-Cause Analysis (RCA) seeks to identify the variables responsible for abnormal system behavior in complex domains such as manufacturing, cloud computing, and healthcare. Existing approaches face a critical bottleneck: graph-based causal methods can identify intervention targets but typically require a known or accurately estimated causal graph, while graph-free statistical methods either localize marginal anomalies rather than structural causes, or rely on restrictive assumptions about graph structure or functional form. We propose StableRCA, a local mechanism-level RCA framework that avoids global graph discovery by estimating local Markov boundaries and detecting conditional distribution shifts within them. Leveraging the Independent Causal Mechanism principle, we show that intervention targets can be identified with probability converging exponentially in sample size under faithful Markov boundary recovery and non-degenerate mechanism shifts. Experiments on synthetic benchmarks and five real-world datasets demonstrate that StableRCA is robust to graph misspecification, effective under multiple intervention targets, scalable to large systems, and reliable across diverse application domains. Code is available at: https://anonymous.4open.science/r/StableRCA-E362

How does a system that merely predicts the world come to distinguish its own causal influence from everything else? We trace this transition in a minimal 192-dimensional GRU through 40 controlled experiments arranged as a developmental sequence, adding components one at a time and tracking whether the system can distinguish self-caused from world-caused changes. The developmental path reveals four conditions that must be satisfied in strict order: (1) persistent state forming stable attractors, (2) a causal action loop linking output to input, (3) proprioceptive feedback that makes implicit causal knowledge explicit, and (4) asynchronous awakening - perceptual learning must consolidate before action learning begins. We propose agency gain (A = Err_world - Err_self), the predictive advantage of knowing one's own action, as a metric to track this process. The self-aware predictor consistently outperforms the self-blind predictor across periodic (sinusoidal) and chaotic (Lorenz) environments, and the metric survives ablation of all auxiliary components. Only forward-sampled action selection produces meaningful agency gain; two gradient-based alternatives degenerate. Equally significant are 12 falsified hypotheses mapping where development stalls: predictive coding alone does not produce self-represent

As urban environments continue to evolve rapidly, accurately modeling the dynamic behaviour of Points of Interest is essential for supporting data-driven urban planning and commercial decision-making. While recent advancements in spatio-temporal graph learning have improved POI forecasting, most methods rely on proximity-based graphs and correlation-driven modeling, which overlook the functional dependencies between POIs and fail to capture the causal effects of urban interventions. In this paper, we introduce a novel research problem -- cold-start POI check-in forecasting, which aims to predict the future check-in pattern of a newly introduced POI, by modeling its temporal evolution and functional interactions with nearby POIs in a structured urban spatial context. To address these challenges, we propose CausalPOI, a spatio-temporal graph-based causal representation learning framework. CausalPOI leverages Spatio-Temporal Functional Interaction Graph to model semantic and spatial relationships between POIs, and constructs structurally aligned treatment and control graphs to simulate factual and counterfactual scenarios. Extensive experiments on real-world SafeGraph datasets demonstrate that CausalPOI significantly outperforms state-of-the-art baselines across the board, validating its effectiveness in spatio-temporal forecasting, semantic interaction modeling, and causal effect estimation, providing a more interpretable and actionable foundation for urban intervention analysis. Source code is available at Github.

Textual event records, such as alarm logs, have become an increasingly common data source in engineering and manufacturing systems. Beyond identifying correlations or recurring patterns, engineers are often interested in understanding which types of events causally trigger or influence other events during system operation. Textual event descriptions may contain semantic clues about such causal relationships, and recent large language models (LLMs) provide a promising tool for extracting these signals. However, relying solely on LLM-encoded textual information is insufficient for accurate causal discovery, since semantic patterns do not directly reveal causal mechanisms and may confuse causation with correlation or frequent sequential patterns. To address these challenges, we propose \textbf{LMT}, a Bayesian causal discovery framework for engineering event data that jointly leverages textual descriptions and timestamps. Specifically, LMT first uses LLMs to extract semantic causal signals from event descriptions and constructs a prior distribution over causal graphs among event types or event clusters. It then incorporates temporal evidence through a Poisson-process-based likelihood, allowing the LLM-informed prior to be refined by timestamp-based statistical evidence. By integrating the textual and temporal information, LMT produces a causal graph that is both interpretable and data-supported. Simulation studies show that the proposed framework is effective across different settings and is especially advantageous in small-sample alarm-event scenarios.

We consider multi-environment prediction problems. We assume the environments change the distribution of a latent variable, while the mechanisms generating observed covariates and targets remain stable conditional on that variable. For example, hospitals or clinical cohorts may differ in the prevalence of latent patient states, even though the relationships between those states, physiological measurements, and outcomes remain unchanged. Given a dataset from multiple environments, we formulate a Bayesian model for such problems and derive the corresponding variational objective. We show that this objective decomposes into per-environment terms and an additional cross-environment balancing term induced by the model's structure. We use an empirical Bayes method to set the prior and incorporate it into the objective. Based on this objective, we develop an amortized variational algorithm for posterior approximation, and use the resulting learned latent variables to form predictions in new environments.We study our approach through simulations and real-world studies of astronomical source identification, microbiome-based disease detection, and ICU sepsis prediction. Across these settings, our method outperforms previous approaches for prediction in new environments.

Controlled experiments are the backbone of machine learning research, but at the scale of modern foundation models, they have become prohibitively expensive. Instead, the community increasingly relies on research strategies that approximate the ideal experiment at a fraction of the cost: proxy experiments and scaling laws, observational studies with publicly available models, and single-run designs that leverage variation within individual training runs. In this work, we argue that there is no free lunch when approximating large-scale experiments on a compute budget. Specifically, savings in compute come at the cost of validity threats -- hidden and sometimes untestable assumptions that, when violated, can invalidate research claims. To help navigate such threats, we propose an evaluation framework that casts foundation model research as a causal inference problem. Within this framework, we evaluate different research strategies through four types of validity adapted from the empirical social sciences -- statistical, internal, external, and construct validity. We find that each strategy comes with a characteristic validity profile: proxy experiments trade external and construct validity for statistical and internal validity; observational studies face confounding and effect heterogeneity; and single-run designs are strained by interference between treated units. This analysis reveals several validity threats that have received insufficient attention in the literature. Overall, our evaluation framework provides researchers with a practical toolkit for scrutinizing validity threats in foundation model research~designs.

CARE-link is an open-source, web-based clinical support platform designed to improve the management of gestational diabetes by linking clinicians and patients through an LLM-mediated workflow. The system aggregates patient-generated data outside the hospital, summarizes relevant clinical information, and delivers context-aware decision support to clinicians. For patients, CARE-link provides clear explanations of management plans and delivers timely lifestyle guidance through a WhatsApp interface. The integrated dual-facing design aims to promote continuous monitoring, support individualized care, and reduce the burden of in-clinic follow-ups. Built with a modular architecture, the platform can be adapted to other chronic conditions requiring longitudinal tracking and behavioral support. CARE-link has the potential to enhance clinical oversight, promote patient compliance, and strengthen continuity of care particularly in resource-constrained settings.

Large language models reach 50 to 70% accuracy on causal reasoning benchmarks such as CLadder, but it is unclear whether this reflects structural reasoning or lexical pattern matching. We introduce Caliper, a controlled perturbation that replaces semantic variable names with placeholder tokens while preserving the causal graph and probabilistic specification of each question. Across nine instruction-tuned LLMs from 3.8B to 671B and three causal reasoning benchmarks, lexical anonymization yields robust accuracy drops of +7.6, +27.0, and +11.1 pp on a local 3.8B-14B set, rising to +29.6 and +18.0 pp on CRASS and e-CARE across nine frontier models spanning the 2024-2026 generations. Of 40 engaged model-by-benchmark cells, 39 show a positive gap, and the gap collapses by 17x on CLadder's pseudoword subset. Structured scaffolding and few-shot in-context learning each narrow the gap, but mainly by lowering P0 accuracy on smaller models rather than recovering P1. Current instruction-tuned LLMs, evaluated zero-shot, show little evidence of structural causal reasoning once lexical anchors are removed.

Causal modeling of physical temporal phenomena must handle interventions that act along trajectories, nonstationary induced laws, path-dependent effects, and feedback mediated by dynamics, all challenging in standard causal models. We introduce Hamiltonian Causal Models (HCMs), a trajectory-level framework in which observed variables interact with local environments and interventions act as controls of Hamiltonian mechanisms. HCMs separate immutable equations of motion from intervenable mechanisms and define causal effects as discrepancies between interventional path laws. A key motivation for HCMs is their natural interface with non-equilibrium thermodynamics. Entropy production quantifies the irreversibility of a process and is a central causal observable: it is estimable from data and witnesses causal effects along the system's evolution that are invisible to endpoint and cumulative versions of the standard average treatment effect. As in physics, cause and effect are not primitives of the relation between two random variables but arise from the non-invertibility of the thermodynamic arrow. With this, our paper reconciles the language of statistical causal models and non-stationary thermodynamics, offering new tools to describe causality in a wide range of physical systems.

Many current agentic systems and LLM pipelines correct mistakes by optimizing outcome reward. This addresses only the what of failure: when an outcome diverges from prediction, the why and when of the mismatch are not systematically logged, reviewed, or corrected, so the same error can recur episode after episode. We argue that this is a structural problem, not merely a model-capacity one. We propose long-horizon temporal regret as a first-class objective alongside outcome regret and epistemic regret over the working causal model. Temporal regret captures when failure persists: how long a miscalibrated causal model is tolerated before correction. Epistemic regret captures why failure persists: residual uncertainty or error in the working causal model. Together, the three regrets give a falsifiable account of what, why, and when a long-lived agent can fail. Modeling the agent as a stream of E episodes, we prove three conditional results under explicit causal-probing, persistence, and detectability assumptions. First, under observationally equivalent confounding, outcome-only learning cannot distinguish causal from spurious structure without an intervention channel, so temporal miscalibration can persist linearly even after outcome regret is driven to zero. Second, with a persistent causal log and budgeted probes, total probe complexity is logarithmic in the episode horizon, inducing O(log E) temporal regret. Third, under K detectable change-points, the rate extends to O(K log E). We instantiate Trivium and pre-register five falsifiable predictions. On CausalBench-Seq, Trivium follows the predicted logarithmic envelope while outcome-only baselines grow linearly. A pilot real-LLM stream provides preliminary external-validity evidence across one full E = 500 run and three E = 100 frontier-model pilots. Self-learning here means revising an external causal model, not retraining LLM weights.

Multi-view cardiac magnetic resonance (CMR) imaging provides complementary anatomical information and is widely used for noninvasive disease assessment. Recent transformer-based models have demonstrated strong representation learning capabilities for CMR analysis; however, they typically learn unified latent embeddings that entangle view-specific anatomical variations with disease-related features. Such entanglement biases classifiers toward structural attributes rather than view-invariant pathological patterns. This issue is exacerbated in low-data regimes, particularly for underrepresented cardiac conditions, where limited samples increase the susceptibility to shortcut learning and view-dependent decision boundaries. To address this, we propose a Motion-Guided View--Disease Disentanglement framework MoViD built upon a ViT-MAE backbone. The model explicitly factorizes latent representations into view-specific and disease-discriminative components using dual-branch supervised contrastive objectives and a gradient-reversal adversarial constraint that minimizes disease leakage into the view embedding. Additionally, an annotation-free temporal motion feature, derived from inter-frame difference maps, is introduced to localize the beating heart region and suppress background artifacts. A focal reweighting mechanism is incorporated into the contrastive loss to mitigate class imbalance. We evaluate the framework on a private clinical venous thrombosis dataset and two public benchmarks (M&Ms, M&Ms2). Across disease classification and cardiac segmentation tasks, our approach consistently outperforms standard transformer baselines and demonstrates competitive performance against large-scale pretrained foundation models, validating the efficacy of structural disentanglement in medical image analysis.

Online reviews provide valuable insights into the perceived quality of facets of a product or service. While aspect-based sentiment analysis has focused on extracting these facets from reviews, there is less work understanding the impact of each aspect on overall perception. This is particularly challenging given correlations among aspects, making it difficult to isolate the effects of each. This paper introduces a methodology based on recent advances in text-based causal analysis, specifically CausalBERT, to disentangle the effect of each factor on overall review ratings. We enhance CausalBERT with three key improvements: temperature scaling for better calibrated treatment assignment estimates; hyperparameter optimization to reduce confound overadjustment; and interpretability methods to characterize discovered confounds. In this work, we treat the textual mentions in reviews as proxies for real-world attributes. We validate our approach on real and semi-synthetic data from over 600K reviews of U.S. K-12 schools. We find that the proposed enhancements result in more reliable estimates, and that perception of school administration and performance on benchmarks are significant drivers of overall school ratings.

Advertising platforms use randomized lift tests to measure incrementality, but privacy-preserving reporting systems degrade the observed signal through match-rate loss, linkability loss, attribution-window loss, aggregation-threshold suppression, randomized reporting noise, and segment-heterogeneous signal loss. This paper formulates privacy-constrained advertising measurement as a robust causal decision problem under the mentioned signal losses. Given a randomized experiment and an ambiguity set for privacy-induced degradation, the framework projects the observation-compatible fiber of clean/unfiltered experimental worlds onto the incrementality functional and returns certified, rejected, and unresolved decisions. The main result gives a sharp decision frontier. Reports outside the frontier support uniformly valid certification or rejection, whereas reports inside it contain too little information for any method to uniformly distinguish above-threshold incrementality from non-incrementality. Supporting results give finite-sample certification, sample-complexity guarantees, a minimax lower bound showing that signal loss reduces effective information, and a reporting-granularity tradeoff. On 2.0M Criteo Uplift rows and the 64K-row Hillstrom email experiment, clean conversion lift is positive in both datasets, with lifts 0.00112 and 0.00495, respectively. Population certification survives mild degradation in Criteo and severe degradation in Hillstrom, while all considered finite-sample stress settings in both datasets remain unresolved after simultaneous uncertainty and reporting noise are included. Overall, the research contributes a decision-theoretic layer for privacy-aware incrementality measurement whose output is the strongest causal-claim justified by degraded ads signals.

Activation patching can identify a mixture-of-experts (MoE) block whose clean output restores a corrupted factual prediction. However, because the block output combines contributions from multiple routed experts, block-level rescue does not establish whether the recovery localizes to an individual expert or depends on the routed expert set. We study this question on single-token COUNTERFACT contrasts by corrupting subject-token embeddings, restoring clean block outputs, and then restoring clean-minus-noised expert updates under fixed routing. In Qwen3-30B-A3B-Base, a discovery sweep selects layer 44, and held-out analysis identifies L44E069 as a recurrent routed contributor with positive specificity over same-layer active experts. Its effect is fact-matched and improves true-token probability and rank, which explains part of the layer rescue. In Mixtral-8x7B-v0.1, the selected recurrent singleton is not specific; matched-size controls instead show specificity of the clean-routed top-2 set. These findings show that successful MoE-block restoration does not necessarily imply localization to a single expert.

The do-calculus defines a general system of inference for interventional queries, allowing causal quantities to be transformed through successive applications of its rules. This process induces a rich space of equivalent interventional expressions, but combining and ordering these rules remains challenging. In this work, we introduce derivation graphs, which represent how do-calculus rules are applied and combined, and characterize the full space of observational and interventional probabilities which are equivalent under the do-calculus. The structure of these graphs yields a simple procedure that uses at most four applications of do-calculus rules. Finally, we show how applying identification algorithms to equivalent causal queries produces multiple valid estimands for the same causal quantity, eventually yielding more efficient estimators.

Causal discovery from observational data remains challenging due to the fundamental limitations of purely statistical methods, such as statistical distinguishability within equivalence classes and sensitivity to finite sample sizes. While large language models (LLMs) offer a promising source of domain knowledge to complement statistical inference, existing LLM-augmented methods are vulnerable to LLM errors and incur high token costs. Moreover, reliance on a single data-centric algorithm can make results sensitive to algorithm-specific biases. To address these limitations, we propose CauTion, a framework that reliably integrates LLM domain knowledge into an ensemble of statistical causal discovery algorithms through consensus filtering and LLM reliability estimation. CauTion proceeds in three stages. First, an algorithm ensemble utilizes a consensus voting to resolve up to 96% of edges on which algorithms agree, achieving near-perfect accuracy on the filtered consensus edges. Second, a trust-calibrated arbitration mechanism estimates the relative reliability of the LLM and the algorithms via an annotation-free trust calibration procedure, which is then utilized to govern a trust-weighted voting process that restricts LLM arbitration exclusively to edges with unreliable algorithmic evidence. Third, a cycle repair step is applied to guarantee the final causal graph is validly acyclic. Experiments on six datasets demonstrate that CauTion consistently outperforms both data-centric and LLM-augmented baselines, with larger gains on larger graphs and strong robustness to LLM errors. Code is available at https://github.com/OpenCausaLab/CauTion.

Probabilistic models are typically trained using task-agnostic objectives like log-loss, which can lead to significant errors in downstream estimation. This disconnect is especially critical in Inverse Probability Weighting (IPW) for causal inference, where propensity score errors near $0$ and $1$ often lead to high bias and variance. We propose a principled framework for deriving task-specific strictly proper scoring rules by matching the local curvature of the downstream error metric. We apply this to the Average Treatment Effect (ATE) estimation, deriving a closed-form loss and its corresponding canonical probability mapping that can be readily integrated with any model like a neural network or a gradient boosting algorithm. Extensive evaluations on causal inference benchmarks demonstrate that our tailored objective consistently outperforms standard likelihood-based and covariate-balancing approaches.

In nature, events that affect some individuals or groups but not others constitute an implicit intervention and are known as natural experiments. For example, the COVID-19 pandemic was an intervention by the coronavirus on the sub-population infected with COVID. We ask, do natural experiments occur in existing real-world datasets? If yes, how should we treat them? To detect natural experiments in data, we use causal discovery to recover the underlying causal graph and perform feature selection based on causal links. If downstream performance improves by treating the data as interventional rather than observational, we argue that this suggests the dataset contains natural experiments. We first validate this hypothesis by simulating datasets with and without natural experiments using synthetic graphs. We then perform a systematic empirical evaluation on a large suite of real-world datasets. Our results indicate that real-world datasets do contain natural experiments and we can take advantage of those natural experiments to improve model performance using causal inference. Our work represents the initial foray into this area, offering a preliminary exploration within a limited scope.

Causal discovery with instantaneous effects in multivariate time series is challenging, as the instantaneous structure must be acyclic. Prior methods enforce this by either separating instantaneous and lagged estimation into multi-stage pipelines or imposing algebraic acyclicity constraints via complex augmented Lagrangian optimization, both of which incur high computational cost. In this work, we propose a different approach: we learn a differentiable permutation of variables using the Gumbel--Sinkhorn operator and triangularize the instantaneous coefficient matrix of a Structural Vector Autoregressive (SVAR) model in the learned order. This converts acyclicity from a hard constraint into a parameterization and keeps it valid throughout optimization. In doing so, our method enables unified, continuous optimization with gradient-based learning, leading to improved efficiency in time--series causal discovery. Across three real-world benchmarks, our method achieves the best overall performance compared with 12 baselines in both discovery accuracy and efficiency. On the large-scale benchmark, it further demonstrates strong scalability, achieving more than a 6x speedup over competing methods.

Large language models (LLMs) have shown growing potential for Cognitive Behavioral Therapy (CBT) counseling. However, most existing approaches still formulate counseling as a local response generation problem, focusing on empathetic replies within short, text-only, or single-session interactions. We argue that this formulation fundamentally mismatches the nature of real psychotherapy. In clinical CBT, therapy is a longitudinal process in which therapists continuously infer, update, and intervene on evolving therapeutic states across sessions. Realistic CBT further involves multimodal inference and delayed cross-session intervention effects, requiring models to capture longitudinal therapeutic state evolution under partial observability. We propose DMT-CBT, a framework for Dynamic Modeling of evolving Therapeutic states in CBT counseling. DMT-CBT maintains structured therapeutic states across sessions while incorporating multimodal behavioral grounding and tool-augmented intervention to support adaptive therapeutic reasoning. Based on this framework, we construct DMTCorpus, a synthetic multi-session multimodal CBT counseling dataset featuring evolving therapeutic states, image-grounded client behaviors, and cross-session intervention continuity. Experimental results show that DMT-CBT improves counseling fidelity and therapeutic alliance, produces more favorable longitudinal affective trajectories, and preserves therapeutic states more faithfully than post-hoc extraction approaches.

A core goal of computational social science is to discover interpretable differences in how language varies across outcomes of interest, such as political affiliation or instructional quality. Recent LLM-based hypothesis generation methods describe such differences in natural language, but select for globally discriminative patterns without accounting for covariates that shape the data based on researchers' domain knowledge. When covariates are ignored, selected patterns can reflect confounds rather than differences of substantive interest. We introduce conditional hypothesis generation, a framework that incorporates researcher-specified covariates to steer hypothesis discovery toward differences that hold within relevant subgroups. Two challenges arise: the target subgroup may be underrepresented (stratum imbalance), and the direction of a difference may reverse across subgroups (sign reversal). We propose two econometrics-inspired methods: one introduces feature--covariate interactions to detect sign reversals, and the other applies within-stratum demeaning and inverse-frequency reweighting to equalize underrepresented strata. Synthetic experiments show each method outperforms global baselines in its targeted setting, and expert evaluation on two real-world datasets confirms that covariate-aware generation surfaces more useful hypotheses within relevant subgroups.

Temporal systems often exhibit non-stationary behaviour, such as seasonal climate variation or glucose fluctuations in patients with type-1 diabetes. One way to model non-stationarity is through discrete latent regimes, i.e., stationary segments of time. Such systems induce a Markov Switching Model (MSM), a class of Hidden Markov Models with autoregressive dependencies among latent regimes and observed variables. Identifying latent regimes is challenging in the presence of frequent regime switches and nonlinear and non-Gaussian dynamics, particularly when there are instantaneous effects between the variables, e.g., due to slow rates of measurements. In this work, we establish the identifiability of both latent regimes and regime-dependent causal structures under temporal regime dependencies, nonlinear lagged and instantaneous effects, and independent noise from the exponential family. Our identifiability theory subsumes non-temporal mixtures of causal models. Furthermore, we introduce FlowMSM, a regime detection framework that can be paired with any stationary causal discovery method to recover regime-dependent causal structures. Experiments on synthetic benchmarks and a financial economics dataset demonstrate the effectiveness of our approach to detect latent regimes and discover causal structures from non-stationary time series.

Multi-task learning (MTL) aims to construct a joint model for multiple tasks by sharing a common representation across domains. To achieve this goal, existing optimization-centric methods either balance task gradients or modify the shared architecture. However, as these approaches remain agnostic to the content of the shared representation, they fail to disentangle task-relevant structure from spurious context, leading to negative transfer and poor generalization. To overcome this limitation, we propose Causal Orthogonal Representations for Multi-Task Learning (CORE-MTL), a causally motivated representation-centric framework that encourages a structured semantic-residual factorization of the shared representation, concentrating task-relevant structure in the semantic stream while relegating nuisance variation to the residual stream. We instantiate this framework in the visual domain by leveraging physical priors for structured scenes and statistical constraints for attributes. Theoretically, our method enjoys a tighter out-of-distribution generalization bound than optimization-centric methods and reduces task gradient interference without explicit gradient projection or reweighting. Empirically, CORE-MTL consistently outperforms existing methods on visual multi-task benchmarks in both in-distribution and out-of-distribution settings. Code is publicly available at https://github.com/Hope-Rita/CORE-MTL.

This paper proposes a method of creating synthetic data (SD) that will have two important advantages for the user compared to other methods currently available. The first is transparency; unlike other methods, the person in receipt of the SD will know which of the relationships between variables in the original data will be approximately maintained in the SD. The second is a guarantee that the SD is derived from information that has already been judged to be free of disclosure risk. This is achieved by first defining and calculating the margins where relationships between variables will be maintained in the SD. Each margin will then be subject to statistical disclosure control (SDC) to the standards defined by the data custodian, e.g. top-coding and bottom-coding, combination of small categories and/or modifying small counts. Further adjustment of the curated margins is advised by coarsening all counts in the table to multiples of the disclosure limit. These adjusted margins are used to create SD by the Iterative Proportional Fitting (IPF) algorithm. The practical steps involved in creating such SD are illustrated using data from the 1901 Census of Scotland.

Current benchmarks for embodied vision-language planning often favor linguistic next-token prediction over physically grounded next-state reasoning. This rewards models that mimic statistical language priors rather than track causal dependencies, reducing physical planning to shallow sequence modeling. We argue that reliable physical autonomy requires a shift from linguistically grounded token prediction toward physically grounded causal reasoning. To this end, we introduce Causal-Plan-Bench, a high-fidelity diagnostic suite curated through multi-stage verification to evaluate embodied planning across four causal dimensions. We also construct Causal-Plan-1M, a million-scale corpus of explicit reasoning traces produced by a four-stage annotation pipeline over egocentric videos. Extensive evaluation shows that leading models still struggle to demonstrate genuine physical agency, with Gemini 3 Pro reaching only 38.18 on our benchmark. In contrast, our training recipe enables Causal Planner, built on Qwen3-VL-8B, to internalize physical logic for more accurate next-state estimation. The model achieves strong in-domain performance and cross-benchmark generalization, and reveals a Causal Scaling Law: scaling causal training data to one million instances yields a 36.3% relative gain, from 33.22 to 45.28. Overall, our work provides a concrete step toward turning agents from superficial token predictors into physically grounded causal reasoners.

In graphical causal model, causal discovery aims to construct a causal graph based on numerical data and domain knowledge in plain text. However, the evaluation of causal discovery methods remains a challenge in the area as the progress of domain researches often makes benchmark causal graphs contain mis-aligned knowledge. This problem especially affects the evaluation of large language model (LLM) based causal discovery methods as they are sensitive to the new discoveries in the literature. This work is the first to systematically study the quality of benchmark causal graphs. Specifically, we design a pipeline that automatically retrieves relevant research papers from scientific databases, and prompts LLMs to check the consistency between the benchmark causal graphs and domain research papers. We evaluate 11 popular real-world benchmarks, for which our pipeline in total proceeds 38,081 domain papers. Our results show that popular benchmarks vary significantly in their consistency with domain research, with clear implications for causal discovery research.

Real-world regression often exhibits shortcuts: attributes that are spuriously correlated with continuous targets in training, yet unreliable under deployment shifts; regressing targets using such shortcuts may fail catastrophically at test time. Existing studies on spurious correlations focus primarily on classification, where labels are categorical and groups are naturally defined. However, many real-world tasks require continuous prediction, where hard label boundaries or discrete group-label pairs do not exist. We define Deep Spurious Regression (DSR) as learning from regression data with attribute-label confounding, addressing continuous spurious correlations, and generalizing to all attribute-label combinations at test time. Motivated by the intrinsic difference between classification and regression shortcuts, we propose to exploit the similarity among spurious attributes in both label and feature spaces, thereby accounting for nearby targets and related groups while calibrating both label and learned feature distributions across attributes. Extensive experiments on common real-world DSR datasets that span computer vision, environmental sensing, and large language model (LLM) regression verify the superior performance of our strategies. Our work fills the gap in benchmarks and techniques for studying spurious correlations in continuous prediction.

Estimating the causal effect of time-varying treatments on survival outcomes in large observational studies is computationally demanding, particularly when outcomes are rare. While g-formula-based methods such as the iterative conditional expectation (ICE) estimator provide a principled framework for longitudinal causal inference, they become computationally expensive, especially when bootstrap-based variance estimation is required. In addition, outcome rarity at each time point induces severe class imbalance, leading to instability and convergence issues in logistic regression and related models. To address these challenges, we propose a principled subsampling and reweighting strategy for longitudinal survival data that can be applied to a range of existing causal effect estimators in this setting, including the ICE estimator. The proposed method substantially reduces computational burden while preserving consistency and improving estimation stability in rare-outcome settings. We evaluate the method through simulations and validate it using a large-scale EHR cohort study on social and behavioral determinants of health (SBDH) and suicide risk, demonstrating its effectiveness for modeling rare outcomes in longitudinal data.

Bayesian optimization is a popular way to optimize expensive systems, where every experiment, simulation, or intervention costs time or money. In its standard form, it treats the variables we control as plain inputs to a black box and cannot tell apart mere correlation from a real cause and effect. Causal Bayesian optimization closes part of this gap by using a known causal graph together with observational data to decide which variables are worth intervening on. Existing methods, however, learn the effect of each possible intervention almost in isolation, even though in a causal system these effects usually share the same underlying mechanisms. We propose graph-coupled causal Bayesian optimization, which ties the different intervention effects together through the uncertainty we have about a small set of shared causal parameters. The result is a causal kernel that lets evidence collected from one intervention improve our estimate of related interventions. For identifiable linear Gaussian causal models, we show that this kernel has low rank, bounded by the number of shared parameters rather than by the size of the intervention menu. This in turn yields an information-gain bound that grows only logarithmically in the optimization horizon, and a regret bound that cleanly separates three sources of error: optimization, causal estimation, and the choice of which intervention sets to consider. We also describe nonlinear and adaptive extensions. Across theory-aligned Gaussian systems, shared-mechanism stress tests, and standard causal optimization benchmarks, the method keeps the benefits of causal Bayesian optimization while transferring information across related interventions, with the clearest gains when direct interventions on the target's parents are unavailable and sparse interventional data must be reused across a large family of candidate interventions.

Latent reasoning enables Large Language Models (LLMs) to perform multi-step inference within continuous hidden states, offering efficiency gains over explicit Chain-of-Thought (CoT). However, the opacity of these continuous thought vectors hinders their reliability and controllability. This paper bridges the gap between mechanistic interpretability and actionable control. We first present a systematic analysis using structural, causal, and geometric probes, revealing that latent vectors encode compressed, faithful representations of reasoning steps, with early vectors acting as critical causal hubs. Building on this, we operationalize these interpretability insights into a suite of training-free, decode-time interventions that refine the latent reasoning process by imposing the identified geometric and semantic priors. Extensive experiments across multiple model scales and diverse task domains demonstrate that our approaches consistently improve reasoning accuracy. Our interpretability-guided interventions consistently unlock latent capabilities and improve reasoning accuracy without any parameter updates.

Many interventions alter the structure of an outcome distribution rather than its mean: they can split a population into disconnected regimes, create loops or holes, generate branches, or reorganize an outcome cloud while leaving the average response nearly unchanged. In such settings, mean-based causal estimands such as the average treatment effect may miss important structural effects. We introduce topological-geometrical causal metrics based on summaries of interventional outcome laws, including density-superlevel Betti summaries, Euler signatures, and persistent-homology summaries. These metrics quantify structural differences between treated and untreated outcome laws beyond averages. We also study the assumptions needed for causal interpretation. We introduce topological ignorability, a topological analogue of conditional ignorability that requires invariance of the chosen structural feature rather than the full counterfactual distribution. When the chosen summary is injective, this condition coincides with weak ignorability; for noninjective summaries, it can identify the structural feature of interest without identifying the full interventional law. We define a covariate-standardized topological-geometrical causal effect and develop practical estimators. We validate the framework in two hidden-confounding benchmarks: a fully synthetic exact benchmark and a real-covariate semi-synthetic benchmark using Wisconsin breast-cancer covariates. In both, weak ignorability fails and balancing observed covariates nearly eliminates standardized mean differences, yet the coordinate-mean average treatment effect remains biased. By contrast, selected finite density-superlevel Betti and Euler contrasts remain stable across oracle, observational, and weighted analyses.

Dynamic medical treatment requires deciding treatment intensity and intervention timing, while patient states evolve continuously and adverse events may occur between clinical interactions. Most existing treatment learning methods assume fixed schedules or enforce safety only at discrete decision points. We propose Interaction-Limited Safe Continuous-Time Reinforcement Learning, a framework that jointly optimizes treatment administration and clinical interaction timing under trajectory-level safety constraints. Our key idea is to reformulate the continuous time treatment problem as an option-based semi-Markov decision process, where each option specifies a continuous-time treatment policy and its duration. We develop a safety-tightening mechanism showing that suitably constructed constraints at interaction times guarantee safety over the full continuous-time trajectory with high probability. We further establish finite-sample guarantees for policy learning from logged treatment trajectories and introduce a practical data-driven conservative surrogate. Experiments show that the proposed adaptive interaction-timing mechanism improves both safety and treatment effectiveness over equidistant interaction schemes across different safe policy optimization methods.

Medical treatment recommendation poses several challenges to reinforcement learning (RL): patient physiology evolves in continuous time, measurements and interventions are performed at irregular intervals, and treatment effects vary substantially across individuals. Existing RL formulations and simulated environments, however, are based on discrete-time MDPs with fixed decision intervals. Thus, it remains difficult to evaluate whether RL methods can handle time-interval-dependent disease progression, personalized treatment response, and safety between consecutive measurement points. To address this gap, we introduce MedGym, a benchmark environment for dynamic treatment recommendation. MedGym models longitudinal patient evolution in a continuous-time framework and constructs a configurable medical RL benchmark from clinical data by using Physics-Informed Neural Networks. The resulting benchmark enables direct comparison between discrete-time and continuous-time methods under irregular treatment timing and patient-specific dynamics. Furthermore, MedGym supports evaluation from clinically important perspectives, such as personalization and trajectory-level safety. By providing a standardized and configurable benchmark for continuous-time dynamic treatment, MedGym enables more realistic and informative evaluation of medical RL methods.

In this work, we propose a prototype machine-to-machine (M2M) knowledge-guided Large Language Model (LLM) framework for automated radiotherapy treatment planning. In the proposed paradigm, Treatment Planning Parameter (TPP) distribution knowledge discovered by a Deep Reinforcement Learning (DRL) agent is transferred to an LLM agent through in-context learning, enabling autonomous iterative planning without human intervention. While standard LLM-based planning often lacks physical intuition and struggles with convergence, the integration of DRL-derived guidance constrains the agent to a physically valid parameter space. Experimental evaluations are performed across three diverse planning scenarios: basic prostate cases, complex prostate configurations with increased organ-at-risk (OAR) constraints, and liver cases. The evaluation results demonstrate that the guided LLM agent consistently achieves optimal planning scores while significantly reducing the number of iterations compared to unguided planning. Analysis of the final TPP configurations reveals that the agent successfully learns a hierarchical priority of objectives, effectively restoring a logical "cause-and-effect" relationship between parameter tuning and dosimetric outcomes. Crucially, this prototype framework exhibits robust generalizability, maintaining high planning quality regardless of specific patient anatomy, treatment site, or initial plan quality. By bridging the specialized optimization of DRL with the adaptive reasoning of LLMs, this M2M framework establishes a scalable foundation towards generalizable autonomous treatment planning, ultimately benefiting clinical practice in realistic environments.

The treatment of ischemic stroke using mechanical thrombectomy involves difficult decisions under intense time constraints. Numerical physics simulations can in theory inform operators to make better decisions regarding treatment approaches and device selection, but are too slow to do so in practice. In this thesis, we investigate if current machine learning based surrogates can accurately emulate these simulations in a step-by-step manner while making them significantly faster. To do this we train three surrogate models on two simulations that involve a simplified aspiration procedure, with varying levels of geometric complexity. Our results show that two of our models accurately predict singular simulation steps and provide substantial speedups, especially when combined with specific data augmentations. However, the models showed a lack of stability when emulating simulations with complex geometries over longer time periods. Overall, this work provides a foundation for future studies to develop stable methods that scale to realistic numerical physics simulations of mechanical thrombectomy.

Metamodels for discrete-event simulations approximate the behavior of simulation models without running expensive simulations. Prior work introduced modular dynamic Bayesian networks (MDBNs) -- a class of metamodels that can estimate a range of probabilistic and causal queries (PCQs) using a single, trained model -- but the method was limited to Markovian systems. In this paper, we initiate an extension of MDBNs to non-Markovian queues by approximating non-exponential distributions using phase-type distributions. This approach raises novel challenges, including balancing metamodeling accuracy and tractability when choosing the number of phases, efficiently learning metamodel parameters, and choosing the sampling interval that is used to approximate a continuous-time simulation by a discrete-time MDBN. We provide preliminary solutions to these challenges, yielding the first causal metamodeling technique for non-Markovian systems. Experiments on a G/M/1 queue demonstrate that the MDBN can produce accurate answers to PCQs with orders-of-magnitude speedup of inference times relative to direct simulation.

We introduce causal density functions: Radon-Nikodym derivatives that compare interventional laws to observational laws and therefore act as local density ratios for causal effects. Whereas many causal-strength measures compare whole distributions after graph surgery, causal density functions provide a pointwise change-of-measure object that can be estimated, calibrated, and used to score directed influence. The basic identity $$\mathbb{E}_{\mathrm{do}}[f(Y)] = \mathbb{E}_{\mathrm{obs}}\!\left[f(Y)ρ(X,Y)\right]$$ makes causal density directly testable: if the estimated density ratio is correct, observational expectations reweighted by $ρ$ reproduce interventional expectations. We derive practical estimators for do-curves and directed edge scores, relate the construction to Radon-Nikodym/Kan semantics for conditioning and intervention, and evaluate the resulting estimators on synthetic and real perturbation benchmarks.

Large Language Models (LLMs) aligned via outcome-based Reinforcement Learning (RL) frequently exhibit a critical failure mode: they achieve high performance on in-distribution benchmarks while demonstrating brittle reasoning capabilities on out-of-distribution (OOD) tasks. We term this phenomenon Reward-Induced Manifold Collapse. We establish a theoretical framework bridging Structural Causal Models (SCM) and the Information Bottleneck (IB) principle to explain this paradox. We define reasoning as a high-complexity causal process and shortcut learning as the exploitation of low-complexity spurious correlations. Under the implicit inductive bias of Stochastic Gradient Descent (SGD), models optimized for outcome rewards are biased toward shortcut solutions whenever the training distribution allows for a ``Markovian Screening'' of the true causal mechanism. We derive a new generalization bound based on Semantic Coverage Measure ($η$) rather than sample size, showing why data scaling on homogeneous distributions may fail to correct reasoning flaws. We also show that Process Reward Models (PRMs) function as Topological Filters, enforcing step-wise mutual information constraints that render the low-complexity shortcut manifold inadmissible. These results provide a mathematical grounding for the role of process supervision beyond simple credit assignment.

Network faults propagate layer by layer along topology and protocol dependencies, yet operations systems typically observe only symptomatic alerts at the tail end of propagation chains, where distinct root-cause faults may produce highly similar end-point symptoms. Existing approaches, whether rule-based, machine learning (ML)-based, or large language model (LLM)-based, fundamentally map the alert set to a diagnosis in a single pass and are structurally incapable of resolving this end-point ambiguity. This paper proposes PropLLM, which is the first to integrate the hop-by-hop scene reconstruction paradigm with the generative reasoning capabilities of LLMs. Starting from end-point alerts, PropLLM traces back hop-by-hop along the propagation path, retrieving verifiable factual evidence from a dual-layer knowledge graph (KG) at each hop, while the proposed Temporal Causal Propagation Attention (TCPA) mechanism encodes known topological causal priors directly into the attention computation to guide the model along the correct causal direction, ultimately localizing the root cause and determining the fault type through a fully evidenced causal chain. On a real-world Wi-Fi multimodal fault dataset, PropLLM improves fault type diagnosis accuracy by 3.9% and root cause localization accuracy by 4.7% over the strongest baseline, while reducing the hallucination rate by 50.8%. Supplementary experiments on the TeleLogs 5G dataset further demonstrate the effectiveness of the proposed method across different network scenarios.

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

In many modern machine learning pipelines, abundant pretrained representations serve as noisy proxy covariates, while task-specific labels remain scarce. We study semi-supervised regression in this setting, and propose a simple two stage estimator that learns kernel eigenfeatures from all proxy covariates and fits a ridge predictor on labeled data. We derive finite sample bounds showing that fast labeled sample rates are recovered when proxy perturbation is controlled and unlabeled proxy covariates are sufficiently abundant. We also show that distribution regression is a direct special case, with analogous guarantees when the finite bag size is large enough. Experiments show consistent gains over supervised and semi-supervised baselines, especially in low label regimes.

For many real-world systems, causal ground truth is difficult to obtain, making claims about causal effects hard to assess. We develop methods for evaluating collections of $\binom{n}{2}$ bivariate causal statements over a set of $n$ variables. In the setting of acyclic linear statements, any such collection can be extended to a unique multivariate causal model, but we argue that this induced model is implausible if it imposes substantial additional confounding to explain observed correlations. We introduce a compatibility score that quantifies this notion of plausibility, notably without relying on the faithfulness assumption. Additionally, we define an incompatibility score for purely graphical bivariate causal statements, based on global consistency constraints that are derived from acyclicity and faithfulness assumptions. We give theoretical and empirical evidence that both scores can successfully distinguish correct from incorrect causal statements in generic settings. Moreover, we demonstrate the practical applicability of our methods by analyzing causal claims made by large language models. Our work aims to provide a foundation for assessing the reliability of causal information derived from human experts or artificial intelligence in settings where alternative forms of validation are unavailable.

Multimodal models in oncology can produce accurate predictions, but accurate prediction does not reveal whether the model has learned biology that is shared across modalities, biology confined to one modality, or spurious correlations that reflect confounders rather than genuine biology. We introduce DECAT, a model-agnostic post-hoc evaluation framework that classifies multimodal representations into four diagnostic scenarios for a given task and modality, using five null-referenced metrics and a rule-based decision procedure. The framework operates on learned representations, requires no knowledge of which specific confounder is present, and returns indeterminate when the evidence is insufficient. We validate DECAT on synthetic data across four multimodal model classes (over 2,500 trained representations) and on real data from 8,979 TCGA patients, evaluating both multimodal embeddings and five pretrained pathology foundation models. Entangled models (e.g., CLIP) achieve near-perfect shared biology detection but falsely claim shared biology in the majority of cases where it is absent on real foundation model embeddings. This false claim rate increases with confound strength so that larger cohorts and stronger representations produce more confident but still incorrect diagnoses. Applied to both multimodal TCGA embeddings and five pathology foundation models without paired RNA, DECAT detects confounding invisible to AUROC without requiring the confounder labels, as confirmed by post-hoc stratification.

We present a regression-adjustment framework designed for the estimation of longitudinal treatment effects in randomized experiments under static regimes. While regression-adjustment methods are useful for variance reduction in randomized experiments by using pre-treatment covariates, they usually focus only on average effects, from which we cannot obtain valuable insights into when the effects appear and how long they continue. To address this issue, we consider intermediate outcomes and evolving post-treatment covariates over time, and we represent such dynamic trajectories using transition kernels. Furthermore, we establish the asymptotic normality and the semiparametric efficiency bound for our estimator, enabling more powerful statistical inference. Simulation studies and empirical analysis using A/B test data from a streaming platform in Japan show the practical advantages of our method.