Causal Reasoning

Counterfactual inference approaches for sequential decision-making typically assume deterministic causal models, where all randomness stems from latent variables. However, Markov Decision Processes (MDPs) are inherently stochastic. We address this by formalising counterfactual policy optimisation under probabilistic nondeterministic causal models, which properly separates latent confounding from irreducible stochasticity, and here propose a first practical optimisation problem for identifying robust counterfactual policies under a sensitivity analysis framework. We validate our approach on a sepsis treatment simulator, where diabetes status acts as a hidden global confounder.

Traffic police gestures are safety-critical perception cues for autonomous driving. A deployable recognizer must infer commands causally from continuous full-frame video, remain stable around transitional arm motion, and avoid over-trusting corrupted pose measurements. This study presents RSC-GestureNet, a reliability-aware selective causal recognizer, for Chinese traffic police gestures. The model treats pose confidence as a first-class signal: unreliable joints are down weighted during graph reasoning, temporal evidence is aggregated causally, and calibrated predictions are selectively emitted through a reliability-aware inference rule. We further introduce CTPGesture-C, a reproducible feature-level corruption benchmark with seven pose/RGB degradation families, and an RGB-level diagnostic in which corrupted frames are reprocessed by MediaPipe before recognition. On the complete official CTPGesture v1 split (134,424 labeled frames and 33,451 causal windows), RSC-GestureNet achieves 93.33+-0.24% accuracy, 91.71+-0.27% macro-F1, 91.69+-0.29% online macro-F1, 98.80+-0.07% Early@10, 0.153+-0.013 s TTC, and the best robust macro-F1 among evaluated methods. Under the same split and causal protocol, it exceeds reproduced traffic-specific MD-GCN and HLP-GCN baselines by 3.23-4.11 macro-F1 points and 2.15-3.07 online-F1 points. These results, together with calibration, selective-risk, statistical, adaptive-branching, and image-level re-extraction analyses, indicate that explicit pose-reliability modeling improves early, stable, and robust traffic-command recognition.

Large Language Models (LLMs) perform strongly in English medical tasks but degrade substantially in Arabic, a gap widely attributed to limited training data. We systematically investigate this assumption via tuned lens probing and causal activation patching, and find that Arabic medical knowledge is present in intermediate model representations but fails to surface at the output. This mechanistic insight motivates a targeted adaptation strategy: rather than fine-tuning the full network, we propose Targeted Low-Rank Adaptation (TLoRA), restricted to the layer window where cross-lingual representations diverge, upstream of the output layers where the failure manifests. We evaluate TLoRA on multiple-choice medical QA, where our approach outperforms full-network LoRA, zero-shot, and few-shot baselines. We further evaluate it on short-answer generation and multi-turn clinical dialogue, where it performs competitively without the need for task-specific finetuning. We additionally introduce AraClinicDialog, a clinician-constructed Arabic medical dialogue benchmark in MSA with validated variants across four Arabic dialects. Together, these contributions demonstrate that mechanistic diagnosis can serve as a practical guide for targeted adaptation in underrepresented-language medical LLMs.

Environmental time-series causal discovery requires expert decisions about method choice, conditional-independence tests, lag horizons, sample-size adequacy, multiple-testing control, and evidence interpretation. Applied inconsistently across datasets, these choices yield graphs that cannot be compared, reproduced, or audited. We present AutoCause, an open-source Python workflow that records each decision, derives defaults from an extended causal-audit module, and admits domain-informed overrides. The workflow wraps four established causal-discovery methods from three families, adds non-causal reference models, and grades links by method-count support. On 145 datasets from DGP-Atlas, TimeGraph, and a topology-derived CausalRivers reference, the methods recover complementary parts of the reference graphs. Majority-supported links are more precise than single-method links on the synthetic benchmarks but not against river topology. AutoCause converts inconsistent expert practice into an auditable, repeatable analysis; causal interpretation remains with the analyst. Available at https://github.com/marcoruizrueda/autocause.

Computer-use agents often fail on transient GUI events because they produce the correct action only after the relevant window has already closed. We identify the main cause as expensive autoregressive decoding on the decision-time critical path. We propose Adaptive Anticipatory Policy Trees (AAPT), which eliminates this delay without modifying the underlying model. During idle screen periods, the same frozen multimodal model constructs a bounded conditional policy tree with observable guards, pre-authorized actions, and branch-specific deadlines. The tree is sized to cover the model's own decoding latency. When an event occurs, a lightweight observer matches change-gated frames to a prepared branch and immediately executes the corresponding action without generating new text. In paired trials with pre-registered endpoints and exact McNemar tests, AAPT improves the success rate from 0.50 to 0.79 within a contested decision window ($p=1.8\times10^{-3}$), while producing no incorrect actions. Both open-loop and predict-and-replan baselines achieve zero success because they still decode during execution. A preparation-time sweep shows that the gain emerges where the latency-based tree-sizing rule predicts, and ablations reveal three key requirements: fast observer decoding, valid tree planning, and accurate branch routing. A pre-registered oracle probe rejects our initial hypothesis and instead points to branch routing as the causal bottleneck. We further reproduce the effect on an independent general-purpose multimodal model over 126 paired trials ($p=4.9\times10^{-13}$). On an external benchmark, AAPT matches the overall performance of a reactive baseline, although the two methods exhibit complementary strengths. Together, these results suggest that AAPT performs best when candidate actions can be enumerated in advance, whereas reactive execution remains stronger when they cannot.

Causal discovery in multivariate time series data is challenging due to complex interactions, high dimensionality, and nonlinear dependencies among variables. Existing methods often struggle to capture these complexities, resulting in inaccurate causal structures. To address this issue, we propose a novel framework that leverages self-attention mechanisms within the transformer architecture for causal discovery. Our approach introduces a novel inverted causal self-attention mechanism (CSAM) that emphasizes latent and indirect causal relationships by inverting tokens and inducing sparsity in attention scores, focusing on significant causal interactions and reducing spurious correlations. Additionally, we develop a global causal algorithm to identify global causal links, providing a holistic metric for causal influence, along with a causal verification module to ensure robustness in the identified causal relationships, enhancing the reliability of our framework. Experiments on both linear and nonlinear datasets, along with ablation studies and sensitivity analyses, show that our framework outperforms existing methods, demonstrating its potential for causal discovery in complex multivariate time series.

Identical language-model answers can arise from hidden states that support different future computations, so current-answer probes do not establish a reusable internal interface. We introduce forked futures: future operations are sampled only after a prefix state has formed, and states are compared through the response distributions induced by those operations. This yields an empirical causal quotient over hidden states without requiring researcher-specified latent labels. Shared, Local, Mixture, and Distributed interfaces then compete under prequential causal description length subject to future-signature fidelity and matched capacity constraints. In the two detailed model evaluations, Shared has the lowest held-out description length, with gains of 0.216 nats on Qwen2.5-1.5B and 0.294 nats on Llama-3-8B, while maintaining tightly clustered mean future-signature distortion; a five-backbone sweep preserves the positive direction of Sharedness Gain. The figure-aligned transplantation analysis gives Shared the strongest joint target-correctness, locality, copy-preservation, and composite profile, and API-aligned paths mediate 0.749 of the target effect versus 0.150 for matched null paths. In the blind four-class model-organism test, 14/16 architectures are recovered, with one observed non-Shared to Shared error among 12 non-Shared organisms. These results support an economical reusable causal interface within the tested operation banks, while keeping the claim explicitly conditional on the candidate architectures, interventions, and held-out futures.

Key-value (KV) cache management through compression and eviction strategies has emerged as an important research direction in recent years. Computational demands of large language models (LLMs) and their multi-modal variants during output generation can be partially alleviated by caching previous key and value calculations needed by subsequent scaled dot-product attention operations. However, this leads to another problem: the size of the resulting KV cache grows linearly with context length and quickly consumes all available GPU memory when either the prompt or the generated output are long. KV cache management periodically prunes entries from the cache thereby reducing its memory footprint while attempting to retain sufficient information for accurate generation. A by-product is faster inference speed. We propose a simple yet effective KV eviction scheme motivated by the insight that past tokens which can be well-predicted from more recent tokens are redundant and their associated keys and values can be removed from the cache. To score entries for eviction we run the model on the tokens in their original order, reusing the key and value representations already stored in the KV cache, and applying a counter-causal attention mask so that each position attends only to its future context. This is in-distribution, tied directly to the actual cache contents, and requires no additional training. To further reduce cost, we additionally propose a fast single-layer approximation that restricts the counter-causal pass to the last transformer layer, achieving a significant speedup per refresh cycle at marginal accuracy cost. We evaluate our strategy on various open-source LLMs and benchmark datasets showing competitive or improved performance over other state-of-the-art methods. Reference code is available at https://github.com/metacognitionai/counter_causal.

The same diagnostic result can support or challenge one causal claim yet fail to address another when the claims concern different populations, outcomes, estimands, pathways, or identifying assumptions. When the evidence and target vary together, a correct answer may reflect favorable or adverse wording, lexical overlap, or a familiar diagnostic pattern rather than matching the evidence to the causal question. We introduce paired prompts that repeat the same diagnostic evidence verbatim while changing the causal target. Each prompt is labeled Favors, Challenges, Unresolved, or Wrong Target according to how the evidence bears on the causal question. A pair is recovered only when both prompts are classified correctly. Using linear readouts trained on a separate development set, we analyze the final-token hidden state from the penultimate transformer block of Qwen2.5-7B-Instruct, Qwen3-8B, and Llama-3.1-8B-Instruct. On the 49-pair primary benchmark spanning nine diagnostic families, balanced accuracy ranges from 0.654 to 0.659 and 18-21 pairs are recovered. Two independent human reviewers assigned the same label to 95 of the 98 prompts (96.9%). Across checkpoints, balanced accuracy and complete-pair recovery exceed permutation nulls that preserve development scenario groups. In Qwen2.5, full-prompt balanced accuracy exceeds both restricted inputs, with paired-bootstrap intervals for both differences above zero. Readouts trained without development examples from the evaluated diagnostic family recover 21 pairs, including at least one in each of the nine families. The hidden-state readout exceeds a linear classifier on answer-option logits and text baselines in balanced accuracy and recovered pairs. These results show that the hidden state contains linearly decodable information about whether diagnostic evidence favors, challenges, or fails to address the causal target.

Transformer adaptation is typically distributed across model depth, even when the intended change is narrow. We investigate how adaptation site shapes what a model learns, how well that learning generalizes, and how selectively it is applied. We introduce a controlled benchmark spanning five objectives (lexical binding, factual association, behavioral policy learning, causal mapping, and procedural reasoning) and define each objective's "adaptation geometry" as its profile of acquisition, transfer, and boundedness under full-stack and early-, middle-, or late-layer LoRA. The objectives exhibit distinct geometries. Lexical binding favors early-layer adaptation for acquisition and boundedness but requires broader updates for transfer; factual association favors later layers among localized adapters; behavioral learning separates late-layer action acquisition from middle-layer policy gating; and causal and procedural transfer benefit most from middle- or full-stack adaptation. These patterns largely persist under parameter-matched controls, and most corresponding directional contrasts replicate across five model families. These findings establish adaptation site as a key design variable for controlling what models learn, generalize, and leave unchanged.

Given a model that is already trained, which features does it rely on causally versus spuriously? Existing methods require access to the training procedure and cannot answer this post-hoc. We introduce the \textbf{Normalised Sensitivity Ratio~(NSR)}, a post-hoc, model-agnostic diagnostic for this question under a structured-shift regime: environments differ primarily in the mean of spurious features while the causal mechanism and causal marginals remain stable, as in multi-site clinical data or multi-batch genomics. Within this regime, causal features induce constant model sensitivity across environments while spurious features track shift. NSR formalises this as the squared coefficient of variation of per-environment sensitivity. Under a linear structural causal model (SCM) with $K\ge3$ non-degenerate environments, NSR achieves exact identification (Theorem~1). We fully characterise failure: weak shifts ($O(\varepsilon^4)$ collapse), degenerate geometry, and proxy attenuation ($O((1-α)^4)$), giving practitioners quantitative criteria for assessing whether the regime holds. Finite-sample rates are $O_p(n^{-1})$ under the null and $O_p(n^{-1/2})$ under the alternative. Experiments confirm all theoretical predictions on synthetic data (area under the ROC curve [AUROC] $= 1.000$ under conditions satisfying the regime), show consistent rankings across five model families (Kendall $τ\ge0.529$), and recover six of eight causal features on bike-sharing data (Precision@7 $= 0.75$) without modifying any trained model.

Consider a model trained at a single hospital to predict patient recovery, where the measured feature $X$ bundles the patient's true health signal ($C$) with a systematic artefact from that hospital's equipment ($S$). Within that hospital, the artefact correlates with outcomes through unmeasured confounders such as patient demographics; an in-context learner rationally routes predictions through $S$, not $C$, and fails silently when deployed at a new hospital with different equipment. We formalise this as \emph{spurious routing in composite representations}: when a feature $X = [C;\,αS;\,η]$ encodes a causal signal $C$ and a spurious signal $S$ in distinct subspaces, the ICL cannot determine which drives predictions. We prove that under ridge ICL, a linear in-context learner, this routing is unavoidable regardless of context size; TabPFN, a state-of-the-art pretrained tabular ICL model, shows qualitatively consistent behaviour empirically. We derive a closed-form characterisation, $\mathrm{CSR} \propto ρ_S/ρ_C$, confirmed at $r = 0.997$ for linear ICL and $r = 0.979$ for TabPFN. Contrary to intuition, larger context sharpens commitment to the dominant in-context signal, amplifying spurious routing by up to $1.74\times$; in the high-spurious corner, more expressive models show greater vulnerability empirically ($+2.22$ CSR gap at high entanglement). We introduce two lightweight mitigations: environment-stratified context construction and S-swap augmentation, that require only weak environment labels and no knowledge of the causal partition. S-swap reduces spurious routing by $74\%$ for linear ICL and $98.8\%$ for TabPFN, with TabPFN's causal sensitivity increasing $8.4\times$ simultaneously: the model does not become agnostic, it reroutes through the causal signal.

Trajectory data collected in real-world settings is frequently incomplete due to sensor failure, communication loss, or occlusion. We address the task of \emph{trajectory inpainting}: reconstructing contiguous missing segments from observed context. We propose a Temporal Convolutional Network (TCN) with symmetric dilation that relaxes the standard causality constraint, allowing each time step to draw on both past and future observations, a property that is essential for inpainting, but absent from forecasting-oriented architectures. The model is trained with a composite loss that combines weighted mean squared error, boundary--continuity penalties, and a smoothness regularizer. Trained on a synthetic dataset of $1,000$ (train), $200$ (validation), and $300$ (test) two-dimensional trajectories with randomly placed 20% masked segments, the model achieves good R$^{2}$, MSE and MAE metrics.

We describe Causal-TS, an open-source Python library for causal discovery in high-dimensional and nonstationary multivariate time series. Causal-TS provides four specialized algorithms-CDNOTS, CDNOTS+, CEDAR, and GRACE-along with wrappers for GES, Granger, LASSO-VAR, and LGES, all sharing a unified conditional independence (CI) test layer with GPU acceleration via PyTorch. A regime discovery pipeline detects structural breaks via pluggable changepoint detectors and runs discovery per regime with regime-specific parameters. A command-line interface, synthetic data generators, and optional DoWhy integration provide an end-to-end pipeline from raw time series to causal effect estimates. The library is pip-installable, tested on Python 3.10--3.12, and available at https://github.com/bloomberg/causal-ts.

Effective flood risk management relies on accurate forecasting, yet the "black box" nature of stateof-the-art Deep Learning models creates a barrier to trust and accountability in high-stakes public safety decisions. While existing Explainable AI (XAI) methods offer local attributions, they fail to provide the verifiable, operationally meaningful causal narratives required by disaster response authorities. To address this societal challenge, we propose Context-Aware Concept Distillation (CACD), a framework developed in collaboration with domain experts to distill opaque LSTMs into interpretable, hydrology-aware surrogate models. We introduce an unsupervised pipeline to discover a "Hydrological Language" and a Residual Hypernetwork that dynamically modulates these concepts based on static basin characteristics. Evaluated on 5,203 basins globally, our model achieves high fidelity (Median NSE 0.70), significantly outperforming black-box baselines (e.g., Multi Layer Perceptrons) on unseen future data. By demonstrating that human-interpretable concepts are sufficient to reconstruct flood dynamics, this work balances AI accuracy with the transparency required for responsible environmental decision-making.

Pearl's structural causal model (SCM) framework, built on directed acyclic graphs (DAGs) and the do-calculus, is the dominant formal language for causal reasoning. Yet it carries two structural restrictions: every relationship must be pre-specified as a directed causal edge, and feedback cycles are forbidden. This paper examines two classes of phenomena that strain these restrictions. First, symmetric physical and economic constraints, the ideal gas law being the canonical case, carry no intrinsic causal direction. Direction emerges only under intervention, and which variable is solved for must be specified as part of the intervention. We formalize such constraints as causal zeros within an Extended Causal Model by adding an activation operator, subject to local solvability and graph-admissibility conditions. Second, for the class of finite-propagation state-space systems considered here, we treat apparent instantaneous cycles as artifacts of suppressed time and ground both causal zeros and feedback in Causal Differential Equations (CDEs). In these, the transient regime is a time-unrolled acyclic causal process, and causal zeros arise as the defining functions of attracting equilibrium manifolds; periodic and chaotic attractors define further regimes of the same dynamics, treated through attractor-relative intervention. We give the extended do-calculus, identifiability conditions, counterfactual semantics, and open problems.

Automating theoretical research requires generating candidate results and evaluating them reliably. Models keep getting better at the first, while the second remains hard. A common approach asks one large language model (LLM) to review what another produced, yet such reviewers are empirically unreliable: they may accept fabricated papers and catch the fabrication at close to chance rates~\citep{badscientist2025}. We present \textsc{CausalSmith}, a framework for automated theoretical research in causal inference built on the Lean proof assistant, where a proof is checked by a program rather than read by a referee. \textsc{CausalSmith} rests on \textsc{Causalean}, a foundational Lean library for causal inference holding 8,179 machine-checked definitions and theorems, developed with language-model assistance under human design and review. Around it, we build a self-improving agentic pipeline that selects research topics, proposes results, formalizes statements, constructs proofs, and presents the resulting artifacts for human inspection. Moreover, the pipeline pairs Lean verification with a statement audit that compares each formal theorem against the informal claim behind it. We evaluate the system using artifacts produced by completed autonomous research runs. The source code, formal library, and run records are available at https://github.com/Jiyuan-Tan/CausalSmith.

We study information bottlenecks in modern deep-learning architectures -- RNNs, softmax transformers, linear-attention transformers and state-space models -- through the lens of the indexing primitive. In this primitive, the input consists of $n$ bits and one integer $i$ from $1$ to $n$ called the index, and the output equals the value of the $i$-th bit. We introduce causal complexity for masked architectures. We show that architectures with low causal complexity cannot solve the indexing primitive in any constant number of layers when the index appears at the end of the input. In particular, this limitation applies to low-parameter RNNs, SSMs and masked linear-attention transformers. In contrast, small softmax transformers can solve it in one layer, while non-masked linear-attention transformers can solve it in 2, which separates them from their masked counterparts. In turn, when the index appears at the beginning, we show that small RNNs are capable of solving this task in 1 layer, while all the other architectures require 2. All our impossibility results are unconditional and apply even to models that employ infinite-precision real arithmetic. Moreover, experiments for up to $n=64$ qualitatively align with our theory: configurations with low-parameter theoretical solutions learn the indexing task easily, while configurations that do not admit such theoretical solutions struggle to learn as the sequence length grows.

Constructing causal directed acyclic graphs (DAGs) is a core step in biomedical causal analysis, yet it remains a largely manual process. Analysts must connect study variables to prior literature, evaluate uncertain causal claims, and preserve sufficient provenance for expert review. We present EviDAG, a browser-based system for authoring causal DAGs as auditable, evidence-linked artifacts from biomedical literature. Given free-text descriptions of study concepts, EviDAG creates a reproducible literature snapshot, uses an LLM-based reasoning module to generate structured pairwise causal judgments, links literature-supported judgments to verbatim evidence excerpts, and assembles the judgments into a constraint-checked graph. Each proposed edge includes confidence estimates, provenance, and a reviewable rationale. The interface supports study specification, progress monitoring, evidence review, graph comparison, adjustment-set computation, and export. In evaluations against both compact benchmark DAGs and reference DAGs derived from published literature, EviDAG achieves high edge recall on the literature-based cohort while retaining verifiable evidence trails absent from LLM-only baselines. EviDAG thus reduces the burden of causal DAG curation while making the resulting assumptions auditable, supporting the design, analysis, and interpretation of biomedical studies.

Predictive machine learning (ML) models are increasingly used to aid human decision-makers across various high-risk domains such as healthcare and criminal justice. There is a growing recognition of the need to evaluate the causal impact of deploying these systems on downstream outcomes, such as patient survival or crime recidivism. Randomized control trials (RCTs) can provide high-quality evidence on the impact of a deployed model, but they run into a challenge: it is often infeasible to run repeated trials when models are updated or retrained to improve predictive performance. In this work, we present a partial-identification approach to using prior RCT data to construct bounds on the causal effect of a new model. The core innovation in our approach is to leverage assumptions relating fine-grained predictive accuracy to downstream outcomes. We do so via two monotonicity assumptions: first, on individual-level `counterfactual correctness' (all else being equal, a correct prediction leads to non-inferior outcomes); and second, on the relation between subgroup predictive performance and outcomes, interpretable as an assumption regarding trust in model outputs. We demonstrate our method with a simulation study, illustrating how incorporating this information can lead to more informative bounds compared to prior work.

Bridge infrastructure deteriorates gradually, yet its root causes---salt intrusion, freezing, fatigue cracking, and others---remain invisible to the naked eye. Expert diagnosis relies on tacit knowledge built over years of practice. We address the challenge of automating this latent causal reasoning by proposing a Damage Cause Encoder that classifies 10-class damage causes from visible damage descriptions $S_i$ for use in autonomous bridge diagnostic agents. Our approach chains three components: (i)Knowledge Triple Extraction---a large language model extracts causal triples of the form (damage $\xrightarrow{\mathtt{caused\_by}}$ cause) from 15--35 diagnostic PDF manuals and indexes them in a FAISS vector store; (ii)Retrieval-Augmented Context---at training and inference time, relevant causal triples $\mathcal{C}_i$ are retrieved and concatenated with $S_i$, converting implicit domain knowledge into explicit Encoder context; (iii)Systematic Fine-tuning Comparison---we conduct a rigorous comparison of LoRA, QLoRA, and QA-LoRA on a fixed Golden Testset (116 stratified samples), demonstrating that QLoRA achieves the optimal trade-off: identical test accuracy (87.07%) to full-precision LoRA, 11% faster inference, 72% lower GPU memory, and superior generalization across diverse unseen inputs. A controlled Golden Testset---stratified, deduplicated, and difficulty-tagged---is introduced as a reusable benchmark contribution. QLoRA further outperforms LoRA by 13 percentage points on a 100-sample diverse evaluation spanning all 10 damage cause classes.These findings enable memory-efficient, high-accuracy diagnostic agents on consumer-grade hardware for edge deployment.

Motivated by challenging modelling issues in the life sciences, we investigate the relationship between logic programming semantics and the eventual states of causal processes compatible with those logic programs. More precisely, we show that while stable models of positive logic programs correspond to the eventual states of processes commencing from a neutral state and continuing undisturbed indefinitely, supported models describe the eventual states reachable from arbitrary starting points. This also contributes to the discussion of the appropriate semantics for logic programming as a causal rule language, adding a temporal perspective to recent interpretations of the stable and supported model semantics from an explanatory viewpoint of causality.

Pearl famously argues that causal knowledge enables the prediction of intervention effects. By contrast, purely descriptive knowledge supports only conclusions drawn from observations. His theory of causality, however, is developed exclusively within Bayesian networks and causal models. Consequently, it is largely restricted to acyclic causal relationships, and transferring its ideas to other formalisms risks misinterpretation or inconsistency. This paper brings Pearl's approach to causality into probabilistic logic programming (PLP). To this end, such programs are aligned with philosophical foundations established in prior work that do not rely on temporal notions; that is, all relevant events are assumed to occur simultaneously. A formal causal semantics for these programs, together with a notion of intervention and an implementation, is proposed. It is shown that this semantics coincides with the P-log semantics for stratified ProbLog programs, while the two may differ in the non-stratified case and for other PLP formalisms.

While automated research systems promise to accelerate empirical analysis, they are prone to silent failures: instances in which analysis code executes successfully yet relies on invalid causal assumptions. We present the Artificial Intelligence (AI)-based Epidemiology Research Assistant (ARA), a framework that makes these failures visible by explicitly encoding causal design principles, study-specific assumptions, and methodological constraints. ARA integrates protocol construction, synthetic data generation, and adversarial validation into a unified pipeline. The framework translates natural language research questions into structured causal protocols and executable analysis code by first constructing a protocol and then generating synthetic datasets using Structural Causal Models (SCMs) with known ground-truth effects. This synthetic-data step can also support pipeline development when access to confidential data, such as medical data, is restricted. The generated analysis is then evaluated under controlled violations of identification assumptions. We evaluate ARA on the Automated Causal Reasoning Benchmark, assessing recovery of identification strategies, causal quantities, treatment and outcome variables, and consistency between generated code and approved protocol. Protocol construction and adversarial validation did not consistently improve numerical agreement with benchmark estimates compared with standard LLM-based generation. However, they changed the failure mode: instead of silently returning causal estimates, ARA often surfaced protocol concerns, diagnostic failures, incomplete inference, or downgraded non-causal interpretations. These findings suggest that validity-first automated science systems should be evaluated not only by answer accuracy, but also by whether they indicate when causal claims are unwarranted.

We propose CEDAR (Causal Edge Discovery for Autoregressive Processes), a constraint-based method for lagged causal edge discovery in sparse autoregressive time series. CEDAR screens candidate cross-variable lags using AR(1)-residualized, U-centered distance correlation, then applies two targeted conditional-independence tests per significant cross-variable lag candidate and accepts at most one lag per ordered pair. A stable MCI pruning step removes indirect edges, and optional deterministic C-nodes adjust for specified trend-like nonstationarity. In sparse regimes where few lags survive screening, CEDAR requires $O(d^2)$ CI tests after screening while retaining edge-level interpretability. CEDAR is most effective when data are scarce and variables exhibit lag-1 self-dynamics; methods with richer conditioning sets become preferable as $T$ grows or when higher-order autoregressive or simultaneous multi-lag effects are common.

Large language models (LLMs) are known to be sensitive to prompt and input formulations. However, existing studies have focused on lexical realization and largely ignored constructional choice. This paper studies whether linguistic construction can systematically shift LLM decisions and where these shifts can be causally localized inside the model. We use political stance judgment as a meaning-sensitive case study and extend an English political statements dataset, resulting in six controlled linguistic rewrite types that preserve or invert the meaning of a statement. Experiments on four open-weight models show that stance instability affect both meaning-preserving and meaning-inversing rewrites. Because output shifts reveal that rewrites affect stance, but not where in the model, we apply activation patching, where activations from the original statement are substituted into the forward pass for the rewritten statement and measure which components recover the original stance distribution. The results show that mid-to-late decoder layers, especially block outputs at the final prompt position, provide the strongest restoration signal.

LLM-based game agents often perform poorly on more complex tasks. This work examines whether these failures are linked to limited spatial reasoning and evaluates whether causal prompt augmentation and multi-step planning can improve win-rates while managing response latency. Using the open-source Qwen3 model family, we conduct experiments across varying model scales, reasoning modes, and planning horizons. We further introduce a focused GVGAI benchmark consisting of three custom games with five difficulty levels to isolate spatial navigation. The evaluation follows two paradigms: an initial ``positioning experiment'' to test an agent's ability to find its exact coordinates, and a study of game-play success. Our results show that while larger models with an enabled thinking mode identify their positions more accurately, overall performance in coordinate matching remains limited for smaller models. Win rates decrease as game levels and layout complexity increase, validating the benchmark's difficulty scaling. Integrating causal context into the prompts tends to improve the agents' success rates, particularly for bigger models. While enabling thinking mode and longer planning horizons significantly improve performance, multi-step planning further reduces mean per-step response times, offering a practical trade-off between reasoning depth and execution speed.

Discovering the direct causes and effects of a target variable from observational data is a fundamental problem in causal discovery, with broad applications in domains such as gene regulatory analysis and biomedical research. Existing causal discovery methods either learn a global causal structure, which incurs substantial computational cost, or assume the absence of latent variables and selection bias, assumptions that are often violated in real-world settings. Motivated by these challenges, we study local causal structure learning in the presence of latent variables and selection bias. Specifically, we first characterize a local region that enables target-specific causal discovery without recovering the entire global structure. We then establish a theoretical bridge between causal information learned from the observed distribution induced on this local region and the corresponding information in the global causal structure. Building on these foundations, we propose LoCaLS, a local causal structure learning algorithm that is sound and complete under standard assumptions and identifies the same direct causes and effects of a target variable as those identifiable by global causal discovery methods, while allowing for latent variables and selection bias. Extensive experiments on random and real-world structures demonstrate that the proposed method consistently achieves higher structural accuracy than existing local methods while requiring substantially less computational effort than state-of-the-art global methods. Furthermore, applications to two real-world gene expression datasets reveal biologically plausible target-specific causal structures, demonstrating its practical applicability in large-scale biological data analysis.

Genomic language models achieve strong performance across regulatory-genomics tasks, yet what these models internally represent remains opaque, and the field lacks a principled procedure for verifying that an apparent concept'' inside a model is real rather than an artifact of sequence composition. We introduce a framework that combines sparse dictionary learning with causal intervention to extract, validate, and causally test interpretable features in genomic foundation models. Training top-$k$ sparse autoencoders on the hidden activations of two architecturally distinct models, Nucleotide Transformer ($6$-mer tokenization) and DNABERT-2 (byte-pair encoding), we recover thousands of monosemantic features that map to transcription-factor (TF) sequence motifs. We show that the naive validation of such features against position weight matrices is severely confounded by GC composition and repetitive elements, producing hundreds of spurious TF features'', and we develop a composition-matched, binding-resolved protocol that removes these confounds. Critically, we move beyond correlation: by ablating individual dictionary directions during the model's forward pass and measuring the induced shift in the model's own predictive distribution, we establish that specific features are \emph{causally} used to represent cell-type-specific TF binding, not merely motif presence. Across three transcription factors (CTCF, GATA1, REST) and both architectures, causally validated binding features emerge reproducibly ($7$--$14$ of $15$ tested features per condition), while two classes of negative control, scrambled binding labels and randomly selected features, yield no detectable signal. The framework is purely computational, uses only public data, and provides a reusable standard for interpretability claims in genomic deep learning.

Power grids, markets, and interacting populations, settle into feedback driven equilibria observed through unknown sensors. Our Equilibrium Causal Game (ECG) joins a game to its cyclic causal model, hidden inputs, sensor map, and rules for interventions and equilibrium selection; interventions edit declared objects and recompute equilibrium. Under stated conditions, ECG-separation is sound but incomplete in our examples. Back-door/half-trek routes identify observed queries. Yet for an untouched rotationally symmetric Gaussian block, second moments determine only a source-frame rotation, across which distinct-variable effects generically change. Unknown sensing creates a separate ambiguity. In passive stable linear models without self-effects, unknown wiring and full-rank unknown sensing leave $B$ completely unidentified for $d\ge2$. Under LiNG, non-Gaussianity removes the source rotation; mechanism interventions separate sensing from interactions. With unknown support, invariant sensing, aligned responses, and well-posed single-target interventions identify $(H,B)$ up to declared equivalence. Of $d$ targets, $d-1$ suffice exactly when the sole untargeted node directly parents all others; otherwise $d$ are needed. Acquisition probes are excluded; known wiring gives no universal count. With nonlinear sensing, isotropic Gaussian source blocks admit hidden twists within and across blocks in labelled environments preserving required radial laws. Conversely, under stated positivity, informative one-block changes, rank, and irreducibility conditions, the finest independent source-block representation is identified within the stated alternative class up to block permutation and blockwise coordinate changes, but not downstream mechanisms or the sensor/interaction split. Together, these results show which causal conclusions equilibrium data support and which require targeted experiments.

This paper develops temporal-causal unity (TCU), a framework connecting a process-philosophical thesis -- time is the ordered unfolding of causal change -- to an operational model of cognitive and social dynamics. The framework deliberately separates three claims: an interpretive thesis about becoming, a measurable causal-progress coordinate, and a stochastic network model. Causal progress is defined by $τ(t)=\int_0^tλ(s\mid\mathcal H_s)\,{\rm d}s$, where the nonnegative event intensity $λ$ must be specified independently of the outcome. Agents carry an orientation phase and an activation amplitude; weighted interaction, heterogeneous drift, external input, anchoring, and diffusion govern their evolution in $τ$. First- and second-harmonic order parameters separate consensus from bipolar polarization. For the all-to-all noisy Kuramoto special case with Lorentzian drift width $Δ$, synchronization begins at the conditional threshold $K_c = 2(Δ+ D)$, not at a universal constant. Reproducible numerical illustrations illustrate (not empirically demonstrate) this threshold, causal-clock curve collapse, and the consensus-polarization distinction. Six historical episodes are treated as scope probes rather than validation data. The paper derives falsifiable hypotheses and an out-of-sample protocol for comparing causal-progress and chronological-time models. TCU is therefore offered as a disciplined bridge between process ontology and complex-systems modeling, not as a replacement for spacetime physics or as an empirically established identity between time and causation.

Discourse relations provide document structure, critical to language understanding and enabling language model performance and ethicality. In this work, we investigate how instruction-tuned Transformer models (LLaMA and Mistral) encode discourse relations in English, with a particular focus on the contrasting relations of causation and antithesis. Framing the task as a next-token prediction task and applying a suite of interpretability techniques to test model internals, our findings show that certain early layers make predictive decisions at mid-sequence tokens, while some mid-level layers finalize their decisions closer to the last token. Most of the remaining layers primarily propagate earlier decisions rather than actively influencing them. Additionally, we observe that some layers exhibit a preference for one answer over alternatives, suggesting asymmetric representation of discourse-based reasoning.\footnote{Our code is available at https://github.com/abhidipbhattacharyya/causation_vs_antithesis}

We develop an adjoint-sensitivity framework for positional influence in causal residual Transformers and separate unconditional analytic results from conditional boundary-shape conclusions. The principal unconditional theorem is the residual-to-depth-flow estimate for layer controls converging in $L^1$, complemented by a finite-token-to-Volterra attention estimate that explicitly controls the first cells near the causal endpoint. We define a normalized adjoint-energy influence density and derive its exact evolution along full-batch gradient flow. The adjoint admits an exact generator-term decomposition into residual transmission, nonlocal Volterra, and local channels, including all covariance cross terms. Causal masking can amplify early-position sensitivity and residual identity paths can transmit a right-localized terminal bias, but neither mechanism alone forces a U-shaped profile. We therefore state boundary advantages under independently checkable energy, correlation, and local-channel bounds; these conditions are sufficient rather than necessary. Finite-token influence balancing, positional reweighting, and task-aligned observability are presented as diagnostics or regularizers with explicit differentiation requirements, computational costs, and limitations. Controlled simulations illustrate that each intervention controls its designated surrogate, while observability balance or outer-loop reweighting need not monotonically reduce the influence-based Lost-in-the-Middle diagnostic.

Imitation learning enables learning a policy in an unknown environment with a latent reward signal using expert demonstrations, but it struggles when the imitator's and expert's observations are mismatched and unobserved confounders are present in expert demonstrations. By identifying appropriate adjustment sets via the sequential $π$-backdoor criterion, causal imitation learning (CIL) provides a framework for approximating the expert's policy from confounded data. However, existing CIL methods, Causal Behavioral Cloning (Causal BC) and Causal Generative Adversarial Imitation Learning (Causal GAIL), are designed for short-horizon, low-dimensional settings. When applied to continuous control tasks with long horizons and high-dimensional state-action spaces, these methods exhibit poor performance: Causal BC suffers from compounding errors, Causal GAIL is unstable and sample-inefficient, and sequential $π$-backdoor adjustment becomes impractical. We introduce Causal Soft Q Imitation Learning (SQIL) and Causal Inverse soft-Q Learning (IQ-Learn), two off-policy causal imitation learning algorithms that combine the causal adjustment framework with state-of-the-art inverse reinforcement learning objectives. Both algorithms operate on causally-adjusted state representations produced by an efficient approximation of the sequential $π$-backdoor criterion, exploiting the causal structure of continuous control environments to reduce the full-horizon adjustment to a fixed-size sliding window. We evaluate all methods in a suite of confounded environments and find that Causal SQIL and Causal IQ-Learn substantially outperform prior CIL algorithms on long-horizon tasks, sometimes surpassing the expert, whereas all causally unaware imitation methods fail to learn meaningful behavior.

The Credit Assignment Problem (CAP) is fundamental to developing efficient and explainable Reinforcement Learning (RL) agents. Existing frameworks, whether relying on temporal contiguity or hindsight-conditioned reward reweighting, frequently fail to attribute properly between an agent's policy (skill) and environmental stochasticity (luck). A principled approach to CAP must isolate the true causal drivers of observed outcomes from spurious correlations and environmental randomness. We introduce Counterfactual Shapley Credit Assignment, a novel framework grounded in causal theory that attributes credit and blame via the Counterfactual Shapley Value ($φ$-value). By redistributing environmental rewards, $φ$-values enhance temporal credit assignment across three critical dimensions: sparse causality, high stochasticity, and delayed rewards, all while preserving the optimal policy. We derive a consistent estimator that computes $φ$-values efficiently, enabling a new class of policy gradient methods, $φ$-PPO, combined with Prioritized Trajectory Replay (PTR). Empirical results demonstrate that $φ$-values align precisely to the ground truth causes of task rewards with superior sample efficiency in challenging environments where prior state-of-the-art methods fail to converge.

Safe adaptive control is online adaptation under a safety guarantee on the learning trajectory itself. The controller may use any causal, history-dependent rule and act differently across environments as data arrive. Only its safety guarantee is uniform: the same rule must satisfy it under every initially plausible model. Performance is measured against a safe oracle that knows the realized model. Many finite-time analyses assume persistent excitation of the uniformly safe closed loop, so the data distinguish every pair of models requiring different control decisions. Under that assumption, feasibility is already settled; only the rate remains. We ask instead: Do the safety constraints permit such an informative experiment at all? While an alternative remains plausible, the controller must preserve a safe continuation under it. We call the first action that forecloses such a continuation commitment. Chance safety allows commitment only on an event rare under the alternative, and the evidence must arrive beforehand: the observation generated by the committing action is too late. We define precommitment information as the KL divergence between learner-visible laws stopped before commitment. Our main result is a causal reduction. The commitment rule determines (1) the probability that safety permits commitment under the alternative, (2) the target-side cost of remaining noncommittal, (3) and the information available when the decision is made. Bounded precommitment information therefore leaves a fixed fraction of the oracle gap unavoidable. If the gap is Ω(T), every uniformly safe policy has linear regret. We establish the obstruction in a constrained linear system with quadratic regulation cost. We also prove recovery in special cases and derive semidefinite upper certificates for deterministic linear-Gaussian systems.

This paper proposes a causal independence principle for value -- the value Causal Markov Condition (v-CMC) -- and develops the conceptual and mathematical foundations of a "causal value theory" linking causality and utility. After motivating a local formulation of the v-CMC, we introduce a probability-value duality that translates standard causal-inference results into the value setting. In particular, we formulate local, global, and decomposition versions of the v-CMC and prove their equivalence. We also define v-separation and show that it is sound and complete for conditional value independence. Furthermore, we derive a Bellman-type recursion as a special case of the v-CMC, thereby generalizing standard Bellman recursion from linear chains to causal DAGs. Finally, we show how the v-CMC supports modular transfer and updating of utility information across causal contexts and develop algorithms for causally structured utility elicitation and canonical influence-diagram construction.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Biological systems exhibit a hierarchical structure, characterised by directed flow from upstream regulators to downstream effects. Although this ordering provides a natural scaffold for causal inference, most causal discovery and GRN methods either ignore the tiered organisation or condition on all upstream variables, which becomes infeasible for high-dimensional omics data. We present ASCEND (Ancestral Scalable Causal discovEry via iNherited Descent), a constraint-based framework that leverages known two-tiered structure to enable genome-scale causal discovery. ASCEND introduces a divide-and-conquer strategy that maintains dynamically updated ancestral conditioning sets for each downstream variable, dramatically reducing the number of conditional independence tests required, and achieves polynomial-time complexity where traditional approaches face exponential blow-up. Through extensive simulations and real biological data, we demonstrate that ASCEND accurately recovers ancestral relationships, scales properly and much faster, and outperforms existing gene regulatory network inference methods in both causal precision and computational efficiency. The algorithm's ability to resolve directionality makes it particularly suited for integrating multi-omic data where upstream regulators (e.g., SNPs, methylation sites) and downstream responses (e.g., gene expression) are measured jointly.

Building AI Scientist agents with Large Language Models (LLMs) has recently attracted growing attention. Since scientific discovery fundamentally relies on uncovering causal relationships from observations, the capability of causal thinking, i.e., distinguishing causation from correlation and recognizing hidden biases, is essential to LLM agents. Although a number of benchmarks exist for AI Scientists, none explicitly incorporate challenges from selection bias, measurement error, and hidden confounders that widely exist in real-world scientific discovery. To this end, we present CausalGame, a benchmark that evaluates the causal thinking capabilities of LLM agents through interactive games. CausalGame asks LLM agents to actively design experimental protocols, collect observation data, and derive a final solution with an explanation report. To emulate realistic scientific discovery challenges, we design 14 scenarios that incorporate selection bias, measurement error, and hidden confounders. Across 30 LLM agents, none demonstrates reliable causal thinking: the best model reaches only 68.0% survival against analytical optima of 78-85%, and merely 5-7% of sessions receive credits on the causal-reasoning rubrics. CausalGame provides a scalable and controlled testbed for evaluating the causal thinking of AI Scientist agents.

Causal discovery with nonlinear mechanisms and latent confounders remains challenging. Existing methods often rely on either linear assumptions or causal sufficiency, limiting their applicability. We propose an MDL-based causal discovery framework that explicitly accounts for latent confounders while allowing flexible nonlinear mechanisms by minimizing the luckiness normalized maximum likelihood (LNML) code-length. The causal relationship between each variable pair is determined by selecting the shortest code-length of the causal model, and we introduce the notion of $Δ$-pseudo-collinearity to identify dependencies induced by latent confounders. Based on these ideas, we develop a greedy algorithm, termed Pseudo-Collinearity Guided Causal Discovery (PCG-CD). Experiments on synthetic and real-world datasets demonstrate that the proposed method accurately recovers directed causal relationships and effectively detects latent confounders.

In-context learning (ICL) has emerged as a central capability of pretrained language models, yet its theoretical analysis has focused primarily on causal language models trained by left-to-right autoregressive prediction, such as GPT-style models. Masked language models instead recover masked tokens from bidirectional context, and their role in ICL remains less understood. We develop a statistical learning framework that represents the context examples by their empirical measure and models prediction as a function of the context and the query. This formulation places autoregressive and masked pretraining objectives within a common excess-risk analysis. Under Wasserstein-type regularity conditions, we relate pretraining with T tasks and N samples per task to k-shot excess risk at inference, obtaining same-order upper bounds for masked and autoregressive objectives. We also study task-distribution shift, where pretraining tasks are sampled from P and inference tasks from Q; the resulting bound contains an additional term controlled by the lifted Wasserstein distance between P and Q. The bounds further imply an order-optimal allocation under a fixed pretraining data budget and refined rates under intrinsic low-dimensional structure. Experiments on controlled function-learning tasks show that the Masked Pair Encoder (MPE) can achieve performance comparable to GPT-2-style causal Transformers, suggesting that ICL behavior is not specific to causal language models.

Background: Growing individual case safety report (ICSR) volumes have intensified demand for scalable automated causality assessment. Large Language Models (LLMs) show promise, yet performance on clinically demanding tasks remains suboptimal and inference-time hyperparameter optimization has not been investigated. Objective: To develop a Gaussian Process (GP)-compatible optimization objective and investigate whether temperature optimization improves LLM-expert agreement on Naranjo causality assessment of FAERS ICSRs. Methods: Expert causality assessments were performed on 723 stratified FAERS cases. OpenAI's GPT-5.2 was evaluated using chain-of-thought (CoT) prompting. Four composite metrics were developed: Weighted Cosine Similarity (WCS), Information-Weighted Agreement Score (IWAS), Entropy-Weighted Agreement and Cosine Similarity Score (EWACS), and Consensus-Weighted Cosine Similarity (CWCS) and Bayesian optimization using a GP surrogate with Probability of Improvement (PoI) acquisition was applied across temperature [0, 2]. Results: GPT-5.2 outperformed prior biomedical LLMs at baseline (T = 0), achieving 74.1% agreement on question 5 and 65.4% on question 10 of Naranjo algorithm. Entropy analysis identified these as the sole informative optimization targets. Temperature showed no systematic population-level effect (\b{eta} = 0.002, p = 0.959). EWACS-guided Bayesian optimization improved causality classification agreement from 45.0% to 72.0% (+27 pp), with the largest gain in Doubtful cases (+42.9 pp). Conclusion: EWACS was identified as the optimal GP-compatible metric. The absence of a universal temperature optimum indicates LLM performance is driven primarily by ICSR content, yet case-specific temperature selection produced meaningful improvements, supporting temperature optimization for LLM-assisted pharmacovigilance.