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01.
arXiv (CS.LG) 2026-06-15

A Statistical and Machine Learning Framework for Operational Threshold Detection and Deployable Dispatch Controller Development in Hydrogen Multi-Energy Systems

arXiv:2606.14601v1 Announce Type: new Abstract: This study presents a statistical and machine learning framework for characterizing a hydrogen-based multi-energy system (H-MES) using one year of high-resolution operational data. Statistical analysis revealed a binary operation driven by renewable surplus, with solar irradiance explaining 45.7% of rank-based variance in hydrogen production, a large effect by conventional standards. Only high-irradiance periods triggered meaningful electrolyzer engagement, while electricity demand exerted a weaker inverse suppression effect ($\epsilon^2 = 0.126$). Multiple regression confirmed electrolyzer power as the dominant linear predictor, with a synergistic solar-wind interaction. Notably, Random Forest analysis ranked wind output first in predictive importance despite its weak bivariate correlation (r = 0.167), revealing non-linear dynamics invisible to parametric methods. A sequence model exploited strong 24-hour autocorrelation (r = 0.845) for operational forecasting, while a reinforcement learning agent optimized hydrogen revenue dispatch. The core contribution is demonstrating that statistical and machine learning approaches are complementary for H-MES modeling and control.

02.
arXiv (CS.AI) 2026-06-11

GPO: Learning from Critical Steps to Improve LLM Reasoning

arXiv:2509.16456v3 Announce Type: replace Abstract: Large language models (LLMs) are increasingly used in various domains, showing impressive potential on different tasks. Recently, reasoning LLMs have been proposed to improve the reasoning or thinking capabilities of LLMs to solve complex problems. Despite the promising results of reasoning LLMs, enhancing the multi-step reasoning capabilities of LLMs still remains a significant challenge. While existing optimization methods have advanced the LLM reasoning capabilities, they often treat reasoning trajectories as a whole, without considering the underlying critical steps within the trajectory. In this paper, we introduce Guided Pivotal Optimization (GPO), a novel fine-tuning strategy that dives into the reasoning process to enable more effective improvements. GPO first identifies the `critical step' within a reasoning trajectory - a point that the model must carefully proceed to succeed at the problem. We locate the critical step by estimating the advantage function. GPO then resets the policy to the critical step, samples the new rollout and prioritizes the learning process on those rollouts. This focus allows the model to learn more effectively from pivotal moments within the reasoning process to improve the reasoning performance. We demonstrate that GPO is a general strategy that can be integrated with various optimization methods to improve reasoning performance. Besides theoretical analysis, our experiments across challenging reasoning benchmarks show that GPO can consistently and significantly enhance the performance of existing optimization methods, showcasing its effectiveness and generalizability in improving LLM reasoning by concentrating on pivotal moments within the generation process.

03.
arXiv (CS.CL) 2026-06-19

Beyond Uniform Forgetting: A Study of Sequential Direct Preference Optimization Across Preference Settings

Aligning language models with human preferences often requires optimising multiple behavioural objectives. A practical approach is to apply these objectives sequentially using preference optimisation methods such as Direct Preference Optimisation (DPO), but it remains unclear whether later training uniformly degrades preferences learned earlier or whether the effect depends on the relationship between objectives. We study sequential DPO across four preference settings covering distributional conflict, multi-attribute interaction, strong safety signal, and compatible response-quality objectives. Using Llama-3.1-8B-Instruct with LoRA adapters, we evaluate all objectives after every stage with a fixed base-model reference. We find that sequential DPO does not produce a single forgetting pattern; preference change ranges from partial degradation to stability, pair-level redistribution, or positive transfer depending on objective relationship, signal strength, and training order. Pair-level analysis using length-normalised policy margins shows that aggregate metrics can mask heterogeneous changes across preference pairs, whereas quartile decomposition reveals that high-confidence pairs can either degrade or improve depending on the setting. Mechanistic diagnostics show that Stage~2 gradients and adapter updates are near-orthogonal to the previous objective across all settings, providing little evidence that direct gradient opposition is the primary driver. These findings suggest that future sequential alignment pipelines should account for objective compatibility and signal strength, rather than assuming that later objectives affect earlier preferences uniformly.

04.
arXiv (CS.CL) 2026-06-15

Every Eval Ever: A Unifying Schema and Community Repository for AI Evaluation Results

AI evaluations are widely used for testing and understanding progress. However, the diverse evaluators bring with them inconsistencies that challenge analysis and comparison. First, results are saved in incompatible formats, scattered across leaderboards, papers, blog posts, evaluation harness logs, and custom repositories. Second, results are created by different evaluation frameworks, which produce divergent scores for nominally identical evaluations and record metadata inconsistently, hindering comparison, cross-community evaluation science, cost reduction, and reuse. We introduce Every Eval Ever, the first shared schema and community-crowdsourced repository for AI evaluation results. The schema standardizes how evaluations are represented in a unified, single JSON document. It is source-agnostic by design, ingesting results from evaluation harnesses and papers alike, and optionally stores per-instance outputs for fine-grained analysis. We contribute: (i) a community-governed metadata schema with a companion instance-level schema, the first standardization effort of its kind; (ii) automatic converters from popular formats, evaluation harnesses, and leaderboards to the unified schema; and (iii) a crowdsourced community database hosted on Hugging Face, currently spanning to date 22,235 models, 2,273 unique benchmarks, and 31 evaluation formats.

05.
arXiv (CS.CV) 2026-06-11

DroneShield-AI: A Multi-Modal Sensor Fusion Framework for Real-Time Autonomous Drone Threat Detection, Behavioral Intent Classification, and Swarm Intelligence in Contested Airspace

Unmanned Aerial Vehicle (UAV) threats have emerged as a defining security challenge of the 21st century. This paper presents DroneShield-AI, a unified open framework integrating six processing layers: RF signal classification, acoustic motor-signature detection, YOLOv8-based visual detection, evidence-weighted sensor fusion, a Behavioral Intent Classification Engine (BICE), and a Graph Neural Network Swarm Intelligence Module (GNN-SIM). BICE introduces the first systematic six-class threat taxonomy for drone flight patterns, enabling predictive operator alerts with a 30-second advance-warning horizon. GNN-SIM is the first open framework for adversarial multi-drone formation analysis using Graph Attention Networks. Evaluated on three publicly available real-world datasets, the fused pipeline achieves 96.1% detection accuracy, 3.2% false alarm rate, AUC-ROC: 0.981, and 142ms end-to-end latency on commodity CPU-class hardware at approximately $500-$780 USD total system cost. All code, model weights, and simulation datasets are publicly released at submission.

06.
arXiv (CS.LG) 2026-06-15

On Rate-Optimal Partitioning Classification from Observable and from Privatised Data

arXiv:2312.14889v4 Announce Type: replace-cross Abstract: In this paper we revisit the classical method of partitioning classification and prove novel convergence rates under relaxed conditions, both for observable (non-privatised) and for privatised data. We consider the problem of classification in a $d$ dimensional Euclidean space. Previous results on the partitioning classifier worked with the strong density assumption (SDA), which is restrictive, as we demonstrate through simple examples. Here, we study the problem under much milder assumptions. We presuppose that the distribution of the inputs is a mixture of an absolutely continuous and a discrete distribution, such that the absolutely continuous component is concentrated on a $d_a$ dimensional subspace. In addition to the standard Lipschitz and margin conditions, a novel characteristic of the absolutely continuous component is introduced, by which the convergence rate of the classification error probability is computed, both for the binary and for the multi-class cases. This bound can reach the minimax optimal convergence rate achievable using SDA, but under much milder distributional assumptions. Interestingly, this convergence rate depends only on the intrinsic dimension of the continuous inputs, $d_a$, and not on $d$. Under privacy constraints, the data cannot be directly observed, and the constructed classifiers are functions of the randomised outcome of a suitable local differential privacy mechanism. In this paper we add Laplace distributed noises to the discretisations of all possible locations of the feature vector and to its label. Again, tight upper bounds on the convergence rate of the classification error probability can be derived, without using SDA, such that this rate depends on $2d_a$.

07.
PLOS Medicine 2026-05-20

Brain morphology in Anorexia Nervosa and its subtypes: A multi-cohort study of individual participant data

by Fabio Bernardoni, Dominic Arold, Luis Schoppik, Klaas Bahnsen, Ruiyang Ge, Clara Moreau, Lasse Bang, Federico D’Agata, Giovanni Abbate-Daga, Christian K. Tamnes, Iain Campbell, Owen O’Daly, Ulrike Schmidt, Guido Frank, Stefanie Horndasch, Andreas Hess, Arnd Dörfler, Hans-Christoph Friederich, Joe Simon, Angela Favaro, Luca Lavagnino, Christina E. Wierenga, Amanda Bischoff-Grethe, Amy E. Miles, Allan Kaplan, Aristotle Voineskos, Paul A. M. Smeets, Annemarie A. van Elburg, Unna Danner, Sophia I. Thomopoulos, Laura Berner, Neda Jahanshad, Sophia Frangou, Joseph A. King, Paul Thompson, Stefan Ehrlich Background In a recent coordinated meta-analysis of neuroimaging data, we reported gray matter (GM) alterations in acutely underweight patients with anorexia nervosa (AN). Here, we extend these findings by examining individual variation in brain structure within AN, individual-level differentiation between AN and healthy controls (HC), and differences between AN subtypes, with potential relevance for understanding clinical heterogeneity. Methods and findings We analyzed individual-level data from 11 international sites in the ENIGMA Eating Disorders Working Group, including 570 female participants with AN and 739 HC. We examined cortical thickness, cortical surface area and subcortical volumes in AN versus HC using three complementary approaches: (i) group-level differences in a mega-analysis correcting for age effects, (ii) frequencies of extreme deviations (infra-/supranormal; z  1.96) based on normative reference models by the CentileBrain Initiative, and (iii) individual-level classification performance using machine learning. The same analytic framework was applied to compare AN restricting versus binge-eating/purging subtype, additionally correcting for BMI effects.Mega-analyses reinforced previous meta-analytic findings of pronounced and widespread GM deficits in AN compared to HC. Normative modelling revealed that the frequency of infranormal z-scores (23/68 cortical thickness, 13/14 subcortical volume metrics) and supranormal z-scores (35/68 cortical thickness, 17/68 cortical surface area metrics) was significantly higher in AN than expected based on reference data. Individuals with AN could be reliably differentiated from HC using machine-learning classifiers (ROC–AUC = 0.75–0.81). In contrast, neither group-level differences nor frequency of extreme z-scores differed between AN subtypes, and individuals with different subtypes could not be reliably differentiated from each other. Importantly, the observational design cannot distinguish neurobiological differences related to AN from the effects of starvation or low BMI in the AN versus HC analyses. The lack of differences between subtypes does not exclude brain structural differences between AN subtypes that might be detectable with other modalities or analytic approaches. Conclusion Using a mega-analytic approach, we confirm widespread GM deficits in AN, show that these alterations are (in some patients) extreme, and demonstrate that they enable robust classification with superior performance compared to most MRI-based psychiatric classification studies. The absence of differences between AN subtypes may reflect shared neurobiology, though other imaging modalities may reveal distinctions beyond brain structure.

08.
arXiv (CS.AI) 2026-06-12

Who Pays the Price? Stakeholder-Centric Prompt Injection Benchmarking for Real-world Web Agents

arXiv:2606.13385v1 Announce Type: cross Abstract: Web agents driven by large language models (LLMs) are increasingly deployed in real-world environments, where they operate over untrusted web content and execute actions with direct consequences. This makes them vulnerable to prompt-injection attacks, in which seemingly benign content embeds adversarial instructions that manipulate agent behaviour. Existing security benchmarks adopt an attack-centric perspective, focusing on the technical feasibility of injections while overlooking the nuanced distribution of resulting harms. In practice, however, prompt-injection risk is victim-dependent: a single exploit can produce asymmetric consequences for different stakeholders, and the same attack pattern may exhibit substantially different effectiveness depending on whom it targets. To capture these properties, we introduce \sysname, a stakeholder-centric benchmark to systematically categorize and attribute harm in real-world web agent systems. It distinguishes between affected entities (e.g., user, seller, platform), decomposes the attacks into concrete objectives, and evaluates each case with complementary outcome- and process-level metrics. Our results reveal substantial and heterogeneous vulnerabilities: not a single attack objective is reliably resisted by current agents, and failures distribute across qualitatively distinct modes ranging from stealthy parasitism (attack succeeds without disrupting the user's delegated task) to misaligned disruption (task disrupted without attack success) and compounded failure (both adversarial objective and task integrity simultaneously violated). These patterns are missed by conventional evaluation, highlighting the need for stakeholder-aware assessment of LLM-based agents in real-world deployments. Benchmark is available at https://github.com/StakeBench/SBC.

09.
arXiv (CS.LG) 2026-06-12

A Stabilized Path-Space Approach to Diffusion-Based Posterior Sampling

arXiv:2606.12710v1 Announce Type: new Abstract: Diffusion models provide expressive data-driven priors for Bayesian inverse problems, but many diffusion posterior samplers rely on heuristic guidance approximations that can fail for nonlinear operators and multimodal posteriors. In this work, we develop a stabilized path-space framework for diffusion-based posterior sampling. Starting from a base diffusion process whose terminal marginal represents the prior, we define a likelihood-weighted target measure on trajectories and cast posterior sampling as learning a controlled stochastic process whose path measure matches this target. This formulation connects diffusion posterior sampling to stochastic optimal control while preserving the Bayesian structure needed for uncertainty quantification. We introduce a time reparameterization that makes the path-space control problem well posed by removing the bias induced by the unknown initial value function, without auxiliary training. We then learn the control via a trust-region path-space optimization method with log-variance objectives. The path-space perspective also unifies our learned control approach with existing guidance-based samplers, quantifies the sampling error induced by approximate controls, and yields importance sampling corrections for asymptotically exact posterior expectations. We evaluate the proposed framework on a suite of benchmark inverse problems with analytically characterized or high-quality reference posteriors, enabling principled assessment of sampling accuracy and uncertainty quantification. These experiments provide insight into the behavior of diffusion-based posterior samplers and demonstrate improved accuracy and robustness over leading approaches.

10.
arXiv (CS.LG) 2026-06-18

Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scale

arXiv:2605.07022v3 Announce Type: replace Abstract: Manually curated biomedical repositories – spanning bioactivity, genomics, and chemistry – are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage. We show that PubMed itself can be autonomously and cost-effectively turned into structured datasets that are larger, more nuanced, and more accurate than the curated databases they replace. We present three coupled contributions: (1) an LLM-based entity-tagging pipeline, grounded in nine biomedical ontologies, that tags 4.5B entities across 19 categories in a 22.5M-paper, 2.5T-token PubMed corpus; (2) hybrid sparse-dense retrieval supporting entity-filtered semantic queries over the tagged corpus; and (3) Starling, a multi-agent deep research system that, given only a natural-language task description, designs precision- and recall-targeted retrieval filters, induces an extraction schema, and emits structured records with nuance-rich fields and supporting passages. Across six tasks – blood-brain barrier permeability, oral bioavailability, acute toxicity (LD50), gene-disease associations, protein subcellular localization, and chemical reactions – Starling produces ~6.3M records (91K-3M per task); several are, to our knowledge, the largest public datasets for their property. Frontier-model rejection of our extractions is 0.6-7.7% across tasks, far below error rates we measure on widely used curated counterparts (e.g., 16.5% on BBB_Martins, 7.3% on Bioavailability_Ma). Beyond scale and accuracy, the supporting passages carry nuance tabular databases discard – e.g., oral bioavailability may depend on fed vs. fasted state. Together, the corpus, retrieval, and agent establish a foundation for AI-driven therapeutic design. Code and datasets: https://github.com/starling-labs/starling.

11.
arXiv (CS.LG) 2026-06-16

Convex Approximation of Two-Layer ReLU Networks for Hidden State Differential Privacy

arXiv:2407.04884v4 Announce Type: replace Abstract: The hidden state threat model of differential privacy (DP) assumes that the adversary has access only to the final trained machine learning (ML) model, without seeing intermediate states during training. However, the current privacy analyses under this model are restricted to convex optimization problems, reducing their applicability to multi-layer neural networks, which are essential in modern deep learning applications. Notably, the most successful applications of the hidden state privacy analyses in classification tasks have only been for logistic regression models. We demonstrate that it is possible to privately train convex problems with privacy-utility trade-offs comparable to those of 2-layer ReLU networks trained with DP stochastic gradient descent (DP-SGD). This is achieved through a stochastic approximation of a dual formulation of the ReLU minimization problem, resulting in a strongly convex problem. This enables the use of existing hidden state privacy analyses and provides accurate privacy bounds also for the noisy cyclic mini-batch gradient descent (NoisyCGD) method with fixed disjoint mini-batches. Empirical results on benchmark classification tasks demonstrate that NoisyCGD can achieve privacy-utility trade-offs on par with DP-SGD applied to 2-layer ReLU networks.

12.
arXiv (CS.LG) 2026-06-19

Multi-Granular Attention-Driven Reinforcement Learning Framework for Web Intelligent Enhancement Systems

arXiv:2606.19690v1 Announce Type: new Abstract: From the past few years, web intelligent enhancement systems increasingly rely on heterogeneous and dynamic web data to deliver personalized, context-aware services. However, traditional machine learning, deep learning, and reinforcement learning models often struggle with semantic understanding, adaptability, and scalability in continuously evolving web environments. In this research, a Multi-Granular Attention-based Reinforcement Web Intelligent Enhancement System (MGAR-WIES) is proposed to address the challenges by integrating semantic graph modeling, attention mechanisms, and adaptive reinforcement learning. Initially, heterogeneous web data comprising structured, semi-structured and unstructured sources are collected and preprocessed for generating unified feature representations. These representations are transformed into a dynamic semantic graph, where entities and their relationships are modeled by using graph embeddings enhanced by attention mechanisms for capturing both local relevance and global contextual dependencies. Subsequently, an adaptive multi-agent reinforcement learning strategy leverages the attention-aware semantic states to optimize personalized web actions like content recommendation, navigation optimization, and service adaptation. Finally, the continuous online feedback is further integrated to update graph representations and learning policies in real time by ensuring sustained adaptability and performance. The proposed MGAR-WIES acheived better results in terms of accuracy (80%) when compared with existing approaches.

13.
Nature Medicine 2026-06-16

<b>Engineered heart muscle passes early clinical milestone</b>

Engineered heart muscle allografts derived from induced pluripotent stem cells show promising early outcomes in patients with treatment-refractory advanced heart failure with reduced left ventricular ejection fraction, in support of further clinical investigation. Engineered heart muscle allografts derived from induced pluripotent stem cells show promising early outcomes in patients with treatment-refractory advanced heart failure with reduced left ventricular ejection fraction, in support of further clinical investigation.

15.
medRxiv (Medicine) 2026-06-11

Allostatic Load in Endometrial Cancer Disparities

Background: Endometrial cancer incidence and mortality are increasing, particularly among Black women and for aggressive subtypes. Allostatic load (AL), a composite measure of physiologic dysregulation across metabolic, cardiovascular, and immune systems, varies by racial category and tumor subtype in other cancers. Endometrial cancer is strongly associated with obesity, and it is unknown whether AL scores maintain sufficient heterogeneity to evaluate differences across subgroups or with clinical outcomes. Objective: To describe the performance of AL scoring in endometrial cancer patients and examine associations with tumor characteristics (grade/histology) and survival outcomes. Methods: We evaluated AL among 398 participants newly diagnosed with endometrial cancer. AL score was calculated by assigning 1 point for each ''high-risk'' value (by clinical reference range or distribution-based) for 15 biologic variables for vital signs, anthropometrics, blood-based biomarkers, and medical comorbidities. Results: Distribution-based thresholds for variables were used to preserve heterogeneity in this obesity-dominant context. Overall, 68.7% of Black women had high AL compared to White (56.7%), Hispanic (56.7%), and other race (32.3%) women. Decision tree analyses revealed grade-dependent associations between AL and survival. For women with low-grade tumors, higher AL was associated with poorer overall survival. For high-grade tumors, intermediate AL ([&ge;]4,

16.
arXiv (CS.AI) 2026-06-12

Rarity-Gated Context Conditioning for Offline Imitation Learning-Based Maritime Anomaly Detection

arXiv:2606.13311v1 Announce Type: cross Abstract: Contextual anomaly detection aims to identify abnormal behavior conditional on context variables, but practical deployments often face highly imbalanced context distributions where rare regimes can be critical information. Under such frequency bias, context-conditioned models can produce unstable decisions and excessive false alarms in rare contexts. We propose Rarity-Gated Feature-wise Linear Modulation (RGFiLM), a rarity-aware conditioning module that combines feature-wise modulation (i.e., context-conditioned scaling and shifting of hidden features) with a gate controlled by a data-driven rarity score. The rarity score is estimated from the empirical distribution of context variables and regulates how strongly context modulates intermediate representations: the gate becomes more decisive under rare contexts while remaining conservative under frequent contexts. We evaluate RGFiLM on maritime trajectory anomaly detection using AIS motion sequences with ERA5 environmental context in an environment-sensitive detour scenario. When instantiated in a sequential anomaly scoring pipeline, RGFiLM achieves the best mean F1–False Positive Rate (FPR) trade-off among the compared context-agnostic and context-conditioned methods. These results suggest that explicitly accounting for context rarity is an effective approach for reducing false alarms in context-sensitive anomaly detection.

17.
arXiv (CS.AI) 2026-06-16

A Causal Model of Theory of Mind in Conflict for Artificial Intelligence

arXiv:2606.16944v1 Announce Type: new Abstract: Theory of mind (ToM), the capacity to ascribe mental states to others and use those ascriptions for prediction and inference, is widely assumed to be essential for effective human-machine integration. Existing AI-ToM models address how to mentalize, but leave the question of when largely unaddressed. The central question is: under what situational and agent-level conditions is ToM engagement causally warranted in conflict? This paper presents a structural causal model formalized as a directed acyclic graph (DAG), treating ToM as a mechanism activated by situational and agent-level conditions rather than as an always-on capacity. The model specifies four exogenous variables capturing situational and agent-level conditions, five endogenous mediators, and a mechanistic ToM node producing engagement states through three distinct causal pathways: a tractability pathway, a reasoning-depth pathway, and an enabling-cause pathway. The primary outcome is epistemic accuracy, which decouples social reasoning from behavioral policy and generalizes across social phenomena beyond conflict. The framework gives AI systems a principled, resource-rational decision procedure for mentalizing, with implications for efficiency, trust, and the development of robust artificial social intelligence. Simulation validation, empirical human-machine teaming studies, and ethical considerations arising from conflict-optimized mentalizing are discussed.

18.
arXiv (CS.AI) 2026-06-11

Sustainability assessment using multimodal AI agents

arXiv:2507.17012v2 Announce Type: replace Abstract: Reducing the rapidly growing environmental impact of the computing industry requires assessing the emissions of electronics at scale. However, a traditional life cycle assessment (LCA) of an electronic device, which maps materials and processes to environmental impacts, often requires proprietary or unavailable data. Here, we reimagine conventional sustainability assessment by introducing a multimodal multi-agent AI system that emulates the collaborative process between LCA professionals and stakeholders (such as product managers and engineers) to automatically estimate the carbon footprint of electronic devices. The agents iteratively construct a complete life-cycle inventory by leveraging a structured data abstraction and software tools that mine information from the public internet, including repair communities and government regulatory databases. This reduces data gaps and data collection from weeks or months of expert time to under one minute. The system can calculate carbon footprint within 19% of expert LCAs with zero proprietary data (typical of the variation between human LCAs). We also show that by encoding domain-specific knowledge, environmental impact estimation can be reframed as a data-driven prediction task, in which both unknown products and emission factors are represented as weighted combinations of similar ones with known emissions.

19.
bioRxiv (Bioinfo) 2026-06-16

DMcloud: Macromolecular Structure Modeling Using Local Structure Fitting for Medium to Low Resolution cryo-EM maps

Cryogenic electron microscopy (cryo-EM) has become an essential experimental approach in structural biology for determining macromolecular structures. When the resolution of a cryo-EM map is worse than approximately 5[A], fitting known or predicted molecular models into the map becomes a common strategy for interpretation. However, accurately fitting biomolecular models into cryo-EM maps, particularly for large macromolecular complexes, remains challenging when the input structure models contain errors or are in a conformation different from that represented in the map. Here, we present DMcloud, a method for local structure fitting of proteins and nucleic acids in cryo-EM maps. Instead of forcing an entire input model into the map, DMcloud divides input structures into local regions, identifies regions that are supported by the density, removes unsupported regions, and assembles the retained regions into a final model. We benchmarked DMcloud on 176 cryo-EM maps, including intermediate and high-resolution maps that include proteins, DNAs, or RNAs. For EM maps in the 5.0-10.0 [A] and 2.5-5.0 [A] resolution ranges, DMcloud achieved average sequence modeling coverage of 0.49 and 0.70, respectively. For DNA/RNA maps, DMcloud achieved an average sequence coverage of 0.75. Across all datasets, DMcloud consistently outperformed existing methods in model accuracy, map-model correlation, and modeling coverage.

20.
arXiv (CS.AI) 2026-06-17

FoundCause: Causal Discovery with Latent Confounders from Observational Data

arXiv:2606.17516v1 Announce Type: cross Abstract: Causal discovery from observational data remains challenging due to the need to recover directed structure and latent confounding without interventions. We propose FoundCause, an amortized causal discovery model trained entirely on synthetic data that maps datasets directly to causal graphs in a single forward pass. By learning from large collections of simulated structural causal models, FoundCause captures transferable statistical patterns that generalize beyond individual datasets. The architecture incorporates several key inductive biases for causal discovery. It uses a permutation-invariant transformer encoder with alternating attention over samples and variables to jointly model cross-variable dependence and per-variable distributions. Pairwise statistical features derived from classical asymmetry measures are injected through statistics-conditioned attention, guiding the model toward known causal signals. A factorized decoder separates edge existence from direction, while a triangular refinement module enables reasoning over higher-order causal motifs such as chains and colliders. In addition, a dedicated confounder module based on learnable latent tokens explicitly models hidden common causes, and the model explicitly handles missing data via its masked input representation. To our knowledge, FoundCause is the first amortized causal discovery approach to explicitly model latent confounding. FoundCause outperforms 11 classical non-amortized methods (e.g., PC, GES, NOTEARS-style optimization) and 4 amortized causal discovery methods on 15 real-world datasets, achieving +9.6% improvement in $F_1$, +1.2% in AUROC, and an 18.9% reduction in structural Hamming distance relative to the strongest non-amortized methods, while performing inference in a single forward pass.

21.
bioRxiv (Bioinfo) 2026-06-17

Correcting spatial transcriptomics data affected by a prevalent transcript leakage problem across platforms, species, and tissues

Spatial transcriptomics has been widely applied to study the spatial distribution of cell types, cell states, and specific gene expression in tissue samples. However, we show that there is a prevalent transcript leakage problem in spatial transcriptomics data, where transcripts expressed by a cell diffuse to its neighborhood and are recurrently detected in the nearby cells. By analyzing published data sets, we show that this problem is general across data produced from different tissues and different species using different imaging-based and sequencing-based spatial transcriptomics platforms. It affects both upstream tasks such as expression quantification as well as downstream tasks such as cell-type annotation and detection of spatially-dependent gene expression. To tackle the transcript leakage problem, we propose a reference-free Bayesian model-based method, DeLeakage, which cleans up the data much more effectively than existing denoising methods. DeLeakage also improves cell-type annotation and avoids false detection of spatially dependent expression.

22.
arXiv (CS.LG) 2026-06-17

Regularized Machine Learning for System Identification of Ship Free-Running Manoeuvres from CFD-Based Synthetic Data: A Comparative Study

arXiv:2606.17121v1 Announce Type: cross Abstract: This study investigates supervised machine learning techniques for identifying ship hydrodynamic coefficients from CFD-generated data from free-running simulations. Specifically, ordinary least squares and regularized regression methods are applied to Abkowitz-type manoeuvring models. Training and validation datasets are derived from URANS simulations of zig-zag and turning circle manoeuvres, which are validated against experimental benchmark data. The analysis evaluates the effects of coefficient set size, minimum training length required for predictive model training, and manoeuvre combinations on model performance. Results demonstrate the suitability of large-angle zig-zag manoeuvres for hydrodynamic system identification, provided that multicollinearity is addressed through appropriate coefficient selection, regression models, or input data variability. Larger coefficient sets offer greater model flexibility for variable conditions but are more prone to multicollinearity. Regularized regression techniques effectively mitigate multicollinearity and notably enhance prediction accuracy, as does incorporating more diverse manoeuvring data. Among tested models, Ridge regression provided the best compromise between computational efficiency and prediction accuracy.

23.
arXiv (CS.CL) 2026-06-19

How Linear Is a Transformer Feed-Forward Block? Per-Block Linear Recoverability Is Learned, Not Architectural

作者:

Transformer feed-forward networks (FFNs) are often treated as nonlinear stores of computation, yet how nonlinear a trained FFN block actually is has rarely been measured. We treat each FFN as a position-wise input-to-output map and split it into the exact least-squares linear approximation plus a residual. The held-out variance the closed-form linear map explains defines a block's linear recoverability (R^2_lin), an optimiser-free measure of its linearity. Across all twelve blocks of GPT-2, Pythia-160m, and llama-160m, R^2_lin is highly heterogeneous and non-monotone with depth, ranging from near-linear (>0.99) to strongly nonlinear (

24.
arXiv (CS.CV) 2026-06-15

One Layer's Trash is Another Layer's Treasure: Adaptive Layer-wise Visual Token Selection in LVLMs

Large Vision-Language Models (LVLMs) have achieved remarkable success across diverse multimodal tasks, yet their practical deployment remains constrained by the computational burden arising from lengthy visual tokens. While visual token pruning has emerged as a promising solution, existing methods suffer from a fundamental limitation: once tokens are pruned at a specific layer, they become inaccessible to all subsequent layers, leading to premature information loss that can compromise model performance. Through empirical studies, we observe that different layers exhibit distinct visual region focus, indicating a varying optimal token subset across layers. Motivated by this insight, we propose Adaptive Layer-wise Visual Token Selection (ALVTS), a novel framework that breaks away from the conventional static token pruning paradigm. ALVTS incorporates a lightweight token selector to identify and route important tokens for further processing, while allowing less important tokens to skip the layer, thus minimizing computational redundancy. These two streams of tokens are seamlessly reintegrated before being fed into subsequent layers, facilitating adaptive compression across the entire model. Grounded in our importance consistency constrained low-rank approximation, the proposed token selection module closely emulates the full attention mechanism, effectively capturing its essential patterns without requiring model retraining. Extensive experiments on LLaVA-1.5, LLaVA-NeXT, and Qwen2.5-VL validate the effectiveness of our method. With an 89% token compression ratio, ALVTS retains 96.7% of the original model's accuracy, achieving a superior efficiency-accuracy trade-off for LVLM inference.

25.
arXiv (CS.CV) 2026-06-12

Trajectory-Level Redirection Attacks on Vision-Language-Action Models

Vision-language-action (VLA) policies bring natural language into closed-loop robot control, enabling robots to execute manipulation tasks directly from text instructions. The same interface gives text a recurring role in control because the prompt is reused at every replanning step, and each prompt-conditioned action changes the future observations on which the policy acts. Existing VLA attacks study adversarial prompts that elicit targeted low-level actions or make such actions persist across changing images. We identify a stronger trajectory-level failure mode: a prompt that still $appears$ to specify the intended task but redirects the final physical outcome. We mathematically formalize this setting as $command-preserving trajectory redirection$, a prompt-only threat model in which the attacker chooses one prompt before the episode, all policy and environment components remain fixed, and the prompt must stay close to the benign instruction while omitting target words and correction language. To find such prompts, we introduce an on-policy prompt search method that uses rollouts to discover perturbations whose closed-loop behavior tracks a target task while satisfying the command-preserving constraints. Experiments in simulation and on hardware show that near-benign prompt perturbations can redirect VLA rollouts to attacker-specified targets. These results expose a trajectory-level vulnerability in VLA instruction grounding: text that appears to preserve the intended command can still give an adversary control over the robot's final physical outcome. Project website: https://vla-redirection-attack.github.io/