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01.
arXiv (CS.LG) 2026-06-16

Information Gap and Feasibility-Aware Inference in Binomial Logistic Mixtures

arXiv:2606.15665v1 Announce Type: cross Abstract: This paper studies the information gap between mixture detection and label recovery in binomial logistic mixtures. Standard likelihood-based criteria such as the Bayesian information criterion (BIC) can detect the presence of two components, but this does not guarantee that the corresponding labels are recoverable. We show that this gap is intrinsic to binomial logistic mixtures with a fixed number of trials: observed-data evidence for mixture structure and per-observation information for label recovery have different local orders in the component separation, and only the former accumulates with the sample size. As a result, there exists a detectable-but-unrecoverable regime in which BIC selects two components while the posterior labels remain essentially uninformative. To address this issue, we propose two feasibility-aware inference procedures: a recoverability-aware BIC with a posterior-entropy penalty and an entropy-regularized estimator that mitigates the tendency of the maximum likelihood estimator to produce overly separated components and overly concentrated posterior responsibilities. Numerical experiments confirm the predicted gap and demonstrate that the proposed methods avoid misleading component selections and improve the calibration of posterior label probabilities.

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

Massive Open-Vocabulary Keyword Spotting

Automatic speech recognition systems have been shown to under-perform when it comes to transcribing words rarely seen in the training data, namely specialized terminology. Open-vocabulary keyword spotting, combined with contextual biasing, has been shown to mitigate this issue. However, existing systems can only handle glossaries of a few hundred terms without becoming an infeasible bottleneck. We propose a system that stores features with a memory footprint up to 128 times smaller than a comparable baseline and allows users to process massive databases while remaining open-vocabulary. Without fine-tuning the speech recognition model, our system achieves a comparable entity recall as uncompressed solutions, even in languages not seen during training.

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

CREDENCE: Claim Reduction for Decomposition & Enhanced Credibility – Semantic Metrics and Convergence Analysis

Decomposing compound sentences into atomic, verifiable claims is a prerequisite for reliable automated fact-checking. Prior work has relied on token-overlap (Jaccard) metrics that systematically underestimate decomposition quality for paraphrastic claims, and has lacked formal termination analysis for the repair loop. We present Credence, a revised claim decomposition and evaluation framework addressing both shortcomings. Our contributions are: (1) Semantic-F1: we use BGE-large cosine similarity fidelity metric that resolves Jaccard's penalisation and improves downstream fact-checking accuracy; (2) Convergence theorems: we formally characterise four properties of the repair pipeline, establishing that rule-based repair is monotone and finitely terminating under an oracle parser assumption; LLM-based self-repair is provably non-monotone and requires an early-exit guard; (3) Three evaluation benchmarks spanning social-media, encyclopaedic, and news domains for cross-domain generalisation measurement; (4) Multi-model benchmarking across four decomposer models (3.8B-12B) and a closed API model. Experiments on SocialClaimSplit, WikiSplitBench, and ClaimDecompBench show that Semantic-F1 outperforms Jaccard-F1 by +15-32pp. EPR ranges from 0.94 to 1.00 on SocialClaimSplit and WikiSplitBench, while ClaimDecompBench includes lower base EPR cases (down to 0.824) due to harder news-domain constructions, and rule-repair reduces the Atomicity Violation Rate (AVR) by 47-100% relative to the base model without degrading fidelity.

04.
medRxiv (Medicine) 2026-06-12

A Machine Learning Pipeline for Scalable Annotation of Patient-Ventilator Dyssynchrony from Bedside Ventilator Data

Objective: Patient-ventilator dyssynchrony (PVD) is a common and clinically consequential problem in critically ill patients receiving invasive mechanical ventilation. Yet automated identification of PVD subtypes at scale remains an unmet clinical need, owing to the lack of large annotated bedside waveform datasets. Methods: We developed and validated a semi-supervised algorithm for automated annotation of PVD. In two medical ICUs at a tertiary academic center, bedside devices continuously collected airway flow and pressure waveforms from the ventilators. We developed a software interface with an information retrieval system that grouped similar breaths for expert human review, yielding 1,542,296 labeled breaths across eight categories: 2 labels for breath delivery mode, 5 labels for PVD subtypes, and 1 label denoting a normal breath. Two pulmonary physicians with expertise in ventilator training and education provided the expert reference labels. We trained an initial classification model on a model-derivation set of 771,148 breaths (divided into training and validation) and evaluated it on a hold-out test set of 771,149 breaths A semi-supervised approach was utilized to extend labeling to an additional 12,965,000 unlabeled breaths. Results: The supervised model performed well across all labels, with Macro-F1 scores between 0.96 and 1.00. Semi-supervised learning across 12 rounds expanded the training set from 771,148 to 8,563,995 breaths without significant performance degradation. Conclusion: We developed a practical and scalable system for automated PVD annotation that performed well across all subtypes. This work provides a reproducible foundation for automated PVD labeling to support the development of machine-learning-based clinical decision support systems for identifying patient-level asynchrony.

05.
arXiv (CS.LG) 2026-06-17

MGUP: A Momentum-Gradient Alignment Update Policy for Stochastic Optimization

arXiv:2606.17526v1 Announce Type: new Abstract: Efficient optimization is essential for training large language models. Although intra-layer selective updates have been explored, a general mechanism that enables fine-grained control while ensuring convergence guarantees is still lacking. To bridge this gap, we propose MGUP, a novel mechanism for selective updates. MGUP augments standard momentum-based optimizers by applying larger step-sizes to a selected fixed proportion of parameters in each iteration, while applying smaller, non-zero step-sizes to the rest. As a nearly {plug-and-play} module, MGUP seamlessly integrates with optimizers such as AdamW, Lion, and Muon. This yields powerful variants such as MGUP-AdamW, MGUP-Lion, and MGUP-Muon. Under standard assumptions, we provide theoretical convergence guarantees for MGUP-AdamW (without weight decay) in stochastic optimization. Extensive experiments across diverse tasks, including MAE pretraining, LLM pretraining, and downstream fine-tuning, demonstrate that our MGUP-enhanced optimizers achieve superior or more stable performance compared to their original base optimizers. We offer a principled, versatile, and theoretically grounded strategy for efficient intra-layer selective updates, accelerating and stabilizing the training of large-scale models. The code is publicly available at https://github.com/MaeChd/MGUP.

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

Safety-Contract Graph Multi-Agent Reinforcement Learning for Autonomous Network Security Response

arXiv:2606.13832v1 Announce Type: cross Abstract: Autonomous network-security response systems promise to reduce Security Operations Centre (SOC) reaction latency, but reward-only multi-agent reinforcement learning (MARL) can improve security reward while remaining non-deployable. We present a safety-contract graph MARL framework and instantiate it as ACD$^3$-GAT (Adaptive Constrained Counterfactual Decisioning with a Graph Attention Network encoder), an architecture that separates simulator observations from reusable operational budgets, constrained optimization, graph state encoding, and counterfactual action screening. We evaluate the method in CAGE Challenge 4, where agents operate under budgets for Mean Time to Recover (MTTR), false-positive response, and firewall change-management disruption. Across the benchmark, every unconstrained method violates the SOC downtime budget in 100% of evaluated episodes, with mean downtime proxy costs of 311-430 against a budget of 50. This complements prior CAGE Challenge 4 findings by showing that reward-only learning lacks operational discipline. Constrained MAPPO-GAT (C-MAPPO-GAT) isolates Lagrangian operational-cost control and budget-aware screening, while ACD$^3$-GAT adds budget context, CVaR tail-risk estimation, opponent-belief state, and Graph Counterfactual Risk Propagation (G-CRP). The replicated comparison includes three 200-episode seeds for IPPO, MAPPO-GAT, C-MAPPO-GAT, and ACD$^3$-GAT. C-MAPPO-GAT reduces downtime violation from 100% to 0.3% and mean downtime cost from 355.4 to 15.5 relative to MAPPO-GAT. ACD$^3$-GAT reduces mean downtime cost to 48.2 with a 13.8% violation rate, placing it on the safety-contract frontier rather than at the most conservative compliance point. Topology-seed and coupled adaptive Red-process stress tests preserve this contrast and show lower worst adaptive degradation for safety-constrained policies than reward-only MAPPO-GAT.

07.
medRxiv (Medicine) 2026-06-15

Socioeconomic inequalities in smoking prevalence and intensity in Germany: A repeated cross-sectional analysis from 1998 to 2024

Background: Smoking inequalities by socioeconomic status have widened consistently in Germany, but sex-specific trends after 2013 and inequalities in daily cigarette consumption among smokers (intensity) are unknown. We analyzed trends in absolute and relative socioeconomic inequalities in smoking prevalence and intensity among German adults across three decades. Methods: We used 14 waves (1998-2024) of population-representative cross-sectional data from the German Socio-Economic Panel to estimate sex-specific trends in smoking prevalence and intensity in adults aged 25-64. Inequalities were quantified across strata of education, occupation, and equivalized household income using the absolute and relative concentration index with 95% bootstrap confidence intervals. Results: Overall smoking prevalence declined from 35.05% (CI: [33.90%, 36.20%] in 1998 to 22.19% (CI: [21.15%, 23.24%]) in 2024, and mean intensity from 17.49 (CI: [17.09,17.90]) to 13.33 (CI: [12.88, 13.79]) cigarettes/day. Over this period sex-differences in both outcomes narrowed almost completely. Absolute and relative inequalities in smoking prevalence widened across all SES dimensions, particularly for education and occupation. By 2024, inequalities were larger among women than men driven by a stagnating or rising smoking prevalence among low-SES women at least until 2018 alongside continued declines in higher-SES women and for men. Inequalities in smoking intensity, particularly related to income, were generally smaller than those in prevalence. Conclusion: Socioeconomic smoking inequalities in Germany widened from 1998 to 2024 primarily driven by reductions among higher-SES groups and increases in low-SES women. However, recent reductions in low-SES women may indicate a new phase in the smoking epidemic. Health equity considerations should be integrated into a targeted German tobacco control strategy.

08.
arXiv (CS.CV) 2026-06-19

SurgVista: Long-Horizon Surgical World Modeling with Plausible Instrument-Tissue Dynamics

Scaling robot policy learning for autonomous surgery is challenging, as expert demonstrations are expensive and in vivo exploration poses substantial safety risks. Surgical world models address this by generating realistic, action-conditioned future frames from an initial observation, but existing methods exhibit two persistent failure modes: spatial interaction incoherence, where visible instrument contact fails to induce spatially consistent tissue deformation, and temporal fidelity collapse, where prediction errors compound across autoregressive rollouts and progressively corrupt visual quality. We present SurgVista, a surgical world model that mitigates both failures through two training recipes. Deformation Consistency Regularization extracts scene-point trajectories from training videos and enforces cross-frame coherence through latent contrastive learning, strengthening physically consistent instrument-tissue dynamics. Drift Adaptation Training mitigates long-horizon drift by perturbing conditioning frames with online prediction residuals and photometric augmentations calibrated to long-horizon drift statistics, sustaining visual fidelity over extended rollouts. To enable rigorous evaluation, we further introduce SurgWorld-Bench, featuring diverse procedure types, long-range rollouts, and decoupled metrics for instrument-motion accuracy and tissue-response fidelity. Extensive experiments show that SurgVista consistently outperforms state-of-the-art methods across visual quality, temporal consistency, and interaction fidelity, with gains widening as the prediction horizon grows.

09.
arXiv (CS.CL) 2026-06-17

MLLP-VRAIN UPV system for the IWSLT 2026 Simultaneous Speech Translation task

This work describes the participation of the MLLP-VRAIN research group in the shared task of the IWSLT 2026 Simultaneous Speech Translation track. Our submission utilizes the recently released Parakeet and Qwen 3.5 models to create a robust, cascaded solution for long-form SimulST through the use of adaptive "black-box" policies. We explore relaxations of these policies to achieve better quality-latency trade-offs. Compared to last year, we participate on all language directions. In addition to this, for the En$\rightarrow${De, It, Zh} directions we also participate in this year's new context track employing a combination of ASR word-boosting and a RAG mechanism of offline pre-translated exemplars to guide generation and enrich our system with domain-specific context. Finally, we provide a detailed latency analysis of our system. Compared to last year, results on the MCIF En$\rightarrow$De test set shows a substantial quality improvement of +5.82 XCOMET-XL. Our context track processing further improves performance by +1.03.

10.
arXiv (CS.LG) 2026-06-12

ProtoX-AD: Self-Explainable Time Series Anomaly Detection and Characterization

arXiv:2606.13277v1 Announce Type: cross Abstract: Recent advances in time series anomaly detection (TSAD) have highlighted the effectiveness of self-supervised classification-based approaches. These methods apply transformations to normal training samples, training a classifier to recognize transformation-specific patterns that help identify anomalies through increased classification errors. Despite their strong performance, a significant challenge is their lack of explainability, as they provide limited insight into the characteristics of flagged anomalies. To address this limitation, we propose ProtoX-AD, a prototype-based self-explainable framework for self-supervised TSAD. ProtoX-AD learns transformation-aware latent representations alongside interpretable prototypes, enabling both accurate anomaly detection and the identification of distinct anomalous profiles through prototype-based explanations. Additionally, it allows for systematic analysis of how transformation design impacts detection performance and explainability. Experimental results on synthetic and real-world datasets demonstrate that ProtoX-AD achieves detection performance comparable to its black-box counterparts while offering more consistent and semantically meaningful explanations than existing explainable baselines. Our code is publicly available at https://github.com/Aitorzan3/ProtoX-AD.

11.
arXiv (CS.AI) 2026-06-19

AutoPass: Evidence-Guided LLM Agents for Compiler Performance Tuning

arXiv:2606.20373v1 Announce Type: cross Abstract: Large Language Models (LLMs) show promise for code compilation tasks, but applying them to runtime performance tuning is difficult due to complex microarchitectural effects and noisy runtime measurements. We present AutoPass, a multi-agent framework for compiler performance tuning that uses compiler and runtime evidence to guide LLM-generated optimization decisions. Rather than treating the compiler as a black box like prior auto-tuning schemes, AutoPass opens up the compiler to the LLM, enabling it to query compiler-internal optimization states and analyze the intermediate representation to orchestrate compiler options. The search process iteratively refines optimization configurations using measured runtime feedback to diagnose regressions and guide latency-improving edits. AutoPass operates in an inference-only, training-free setting and requires no offline training or task-specific fine-tuning, making it readily applicable to new benchmarks and platforms. We implement AutoPass on the LLVM compiler and evaluate it on server-grade x86-64 and embedded ARM64 systems. AutoPass outperforms expert-tuned heuristics and classical autotuning methods, achieving geometric-mean speedups of 1.043x and 1.117x over LLVM -O3 on x86-64 and ARM64, respectively.

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

Akasha 2: Hamiltonian State Space Duality and Visual-Language Joint Embedding Predictive Architectur

作者:

We present Akasha 2, a state-of-the-art multimodal architecture that integrates Hamiltonian State Space Duality (H-SSD) with Visual-Language Joint Embedding Predictive Architecture (VL-JEPA). The system leverages the Mamba-3 Selective State Space Model (SSM) augmented by a Sparse Mixture of Hamiltonian Experts (SMoE-HE) that enforces latent physical conservation laws through symplectic integration. For visual synthesis, we introduce Hamiltonian Flow Matching (HFM) and persistent 3D Gaussian Splatting (3DGS), enabling ultra-low latency (

13.
arXiv (math.PR) 2026-06-11

The Geometry of Admissible Short Selling in Discrete-Time Stochastic Portfolio Theory

arXiv:2606.11191v1 Announce Type: cross Abstract: While discrete-time Stochastic Portfolio Theory (SPT) provides a robust framework for market analysis, existing work on functional generation has predominantly focused on long-only portfolios defined on the entire unit simplex. This paper extends the geometric framework of functional generation to the broader class of bankruptcy-proof long-short portfolios defined on local market state spaces. We establish that, within this admissible setting, pseudo-arbitrage is fully characterized by the concavity of the generating function on the market state space, thereby relaxing the usual global domain requirement. A central contribution of this work is a geometric characterization of the short-selling mechanism. We prove that the presence of short selling is equivalent to the negativity of the maximal concave extension of the generating potential. This phenomenon is linked to the steepness of the logarithmic gradient as the market approaches a zero boundary nested inside the simplex. To systematically exploit this mechanism, we introduce the barycentric scaling transformation, a constructive methodology that maps classical long-only generating functions onto restricted domains to engineer admissible strategies with controlled short-selling exposure. Finally, through the analysis of specific shrunken portfolios, we identify a geometric phase transition: under suitable boundary conditions, admissible strategies exhibit a long-only core and a short-selling region in a qualitative sense (without asserting an exact partition of the state space). This provides a unified geometric perspective on relative arbitrage beyond the long-only constraint.

14.
arXiv (CS.CV) 2026-06-16

Post-Launch Capability Expansion of Vision-Language Models via Prompting for On-Orbit Spacecraft Inspection

Spaceborne inspection systems often deploy perception models prior to launch, after which updating model weights or expanding fixed label sets becomes operationally impractical. While supervised models can be integrated pre-flight, adding new semantic capabilities in orbit requires retraining and re-uploading parameters. We investigate whether prompt-driven vision–language models can enable post-launch semantic expansion, allowing new spacecraft components to be specified via natural-language prompts without modifying onboard weights. We evaluate zero-shot instance segmentation of spacecraft components under a strictly frozen, single-pass inference protocol on a test set of $129$ images of previously unseen satellites. Under fixed global thresholds and no post-processing, SAM3 achieves $0.385$ mAP@$0.5$ and $0.267$ mAP@$0.5{:}0.95$. Performance is strongly scale-dependent: large structural elements like spacecraft bodies ($0.639$ AP@$0.50$) and solar arrays ($0.598$ AP@$0.5$) localize reliably, while relatively small appendages like antennas ($0.221$ AP@$0.5$) and thrusters ($0.081$ AP@$0.5$) remain difficult. Prompt formulation influences performance, with structured prompts incorporating spatial and geometric descriptors yielding up to $82%$ improvement over short category-name prompts. The model operates within the memory and compute envelope of contemporary embedded GPUs, suggesting prompt-driven grounding can provide a practical mechanism for post-launch semantic extension of dominant spacecraft structures while highlighting limitations of zero-shot localization for fine-scale components under orbital domain shift.

15.
arXiv (quant-ph) 2026-06-16

Neural quantum states for entanglement depth certification from randomized Pauli measurements

arXiv:2512.13121v2 Announce Type: replace Abstract: Entanglement depth quantifies how many qubits share genuine multipartite entanglement, but certification typically relies on tailored witnesses or full tomography, both of which scale poorly with system size. We recast entanglement-depth and non-$k$-separability certification as likelihood-based model selection among neural quantum states whose architecture enforces a chosen entanglement constraint. A hierarchy of separable neural quantum states is trained on finite-shot local Pauli outcomes and compared against an unconstrained reference model trained on the same data. When all constrained models are statistically disfavored, the data certify entanglement beyond the imposed limit directly from measurement statistics, without reconstructing the density matrix. We validate the method on simulated six- and ten-qubit datasets targeting GHZ, Dicke, and Bell-pair states, and demonstrate robustness for mixed states under local noise. Finally, we discuss lightweight interpretability diagnostics derived from trained parameters that expose coarse entanglement patterns and qubit groupings directly from bitstring statistics.

16.
arXiv (CS.CV) 2026-06-16

Bridging Information Asymmetry: A Hierarchical Framework for Blind Face Restoration with Reduced Uncertainty

Blind face restoration remains a persistent challenge due to the inherent ill-posedness of reconstructing holistic structures from severely constrained observations. Current generative paradigms, while capable of synthesizing realistic facial details, remain limited by the under-constrained nature of blind restoration, where severely degraded inputs can be mapped to plausible yet identity-inconsistent outputs. To address this issue, we present Pref-Restore, a hierarchical framework for BFR with reduced restoration uncertainty. Our design is organized around three complementary principles: (1) Semantic Information Augmentation, where an auto-regressive semantic branch converts image and text cues into structured tokens that provide a stable high-level anchor; (2) Texture-level Fidelity Alignment, where the diffusion generator is trained under this anchor to recover identity-relevant details; and (3) Fidelity-constrained Preference Optimization, where a face-aware reward refines the diffusion trajectory while controlling the quality–fidelity trade-off. Extensive experiments on synthetic and real-world benchmarks show that Pref-Restore achieves state-of-the-art performance, with stronger identity-sensitive fidelity and lower restoration uncertainty across repeated sampling. Systematic ablations further attribute these gains to the proposed hierarchical design, showing the necessity of staged training, the robustness and quality dependence of the text pathway, and the benefit of fidelity-constrained preference optimization.

17.
arXiv (CS.AI) 2026-06-18

A DeepLearning Framework for Dynamic Estimation of Origin-Destination Sequence

arXiv:2307.05623v2 Announce Type: replace-cross Abstract: OD matrix estimation is a critical problem in the transportation domain. The principle method uses the traffic sensor measured information such as traffic counts to estimate the traffic demand represented by the OD matrix. The problem is divided into two categories: static OD matrix estimation and dynamic OD matrices sequence(OD sequence for short) estimation. The above two face the underdetermination problem caused by abundant estimated parameters and insufficient constraint information. In addition, OD sequence estimation also faces the lag challenge: due to different traffic conditions such as congestion, identical vehicle will appear on different road sections during the same observation period, resulting in identical OD demands correspond to different trips. To this end, this paper proposes an integrated method, which uses deep learning methods to infer the structure of OD sequence and uses structural constraints to guide traditional numerical optimization. Our experiments show that the neural network(NN) can effectively infer the structure of the OD sequence and provide practical constraints for numerical optimization to obtain better results. Moreover, the experiments show that provided structural information contains not only constraints on the spatial structure of OD matrices but also provides constraints on the temporal structure of OD sequence, which solve the effect of the lagging problem well.

18.
arXiv (CS.LG) 2026-06-15

Online Convex Optimization with Sublinear Noisy Probes

arXiv:2606.14640v1 Announce Type: new Abstract: We study Online Convex Optimization (OCO) over a convex set $K\subseteq \mathbb R^d$, where in each round $t$ the learner selects $x_t\in K$ and then observes a convex loss $f_t:K\to[0,1]$, with the goal of minimizing regret to the best fixed decision in hindsight. We introduce a unified probing model that generalizes two recent lines of work: sublinear best-expert queries in the experts setting, and pairwise (comparison-based) feedback available every round in OCO. In our framework, the learner has a budget of $k\le T$ pairwise probes; on a probed round it may query two points and learn which one has smaller loss. Our main result shows that even a sublinear and noisy probe budget can provably improve worst-case regret in the full feedback OCO regime. With $k$ $\delta$-noisy pairwise probes, we obtain: $ Reg_T \le O\left(\min\left\{\sqrt{dT\ln T},\; \frac{dT\ln T}{k|1-2\delta|}\right\}\right) $, which is tight (up to logarithmic factors in $T$) across $T$, $k$ and $\delta$. Specifically regarding the noise parameter $\delta \in [0,1]$, the regret guarantee smoothly degrades as the oracle response approaches a coin flip, i.e., $\delta$ is close to $\frac{1}{2}$. When applying the same techniques to a finite $K$ for the prediction with $d$ experts setting, the resulting rates are instead completely tight in all parameters, including $d$. Our analysis gives a streamlined treatment of pairwise probing in OCO by quantifying the benefit of probing via a variance reduction effect, combined with a second-order (variance-based) analysis of Continuous Exponential Weights.

19.
arXiv (CS.CV) 2026-06-16

From Frames to Temporal Graphs: In-Context Egocentric Action Recognition with Vision-Language Models

Action reasoning in egocentric video requires capturing fine-grained transitions of hand-object interactions, a task where general-purpose Vision-Language Models (VLMs) often struggle when operating directly on raw pixels. We propose to decouple visual perception from symbolic reasoning by converting videos into Temporal Action Graphs. In a multi-stage prompting pipeline, we first generate dense natural language narratives over short temporal windows as a semantic bottleneck, then formalize them into structured, open-vocabulary graph representations. On the EGTEA and Epic-Kitchens-100 datasets, the symbolic representation unlocks efficient in-context learning: few-shot graph demonstrations yield substantial accuracy gains over zero-shot frame and graph-based inference alike. Even in the zero-shot setting, graph-based reasoning remains competitive with pixel-based inference despite potential pretraining contamination favoring the latter. Across 11 open-weight VLMs from 6 model families ranging from 2B to 235B parameters, our findings indicate that current VLMs are more effective as symbolic reasoners than as direct visual observers. By projecting video into the language domain, we provide a scalable, fine-tuning-free alternative to end-to-end approaches that better leverages these models' latent reasoning strengths. The code will be made public.

20.
bioRxiv (Bioinfo) 2026-06-10

ECMME: an atlas of selection pressures on the mammalian extracellular matrix reveals contrasting evolutionary dynamics

The extracellular matrix (ECM) is a fundamental metazoan innovation that provides structural support and regulatory cues essential for multicellular life. While core matrisome components are subject to strong functional constraints, their evolutionary dynamics at the molecular level remain incompletely characterized. Here, we present a comprehensive per-residue analysis of selection pressures across 272 human core matrisome proteins using high-quality orthologous sequences from up to 228 placental mammal species. We developed an automated pipeline integrating ortholog identification, codon-aware alignments, and site-specific selection analyses with the MEME and FUBAR methods from the HyPhy suite. Results reveal pervasive strong purifying selection across the matrisome, consistent with its structural and functional indispensability. This is accompanied by episodic positive selection and rarer pervasive positive selection, with collagens exhibiting significantly elevated episodic positive selection compared to glycoproteins and proteoglycans. To facilitate community access, we developed ECMME (ECM Molecular Evolution) browser, an intuitive open-access web resource that visualizes selection metrics plotted directly onto protein topologies. ECMME allows researchers to seamlessly browse and investigate the data, providing a powerful framework for interpreting functional sites. It is available online and requires no local installation or set-up (https://izzilab-ecmme.share.connect.posit.cloud/).

21.
bioRxiv (Bioinfo) 2026-06-18

A data-driven rediscovery of the specificity-conferring code of adenylation domains in nonribosomal peptide synthetases

Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that assemble structurally diverse peptides, many of pharmacological importance, including antibiotics and immunosuppressants. Within each NRPS module, the adenylation (A) domain selects the substrate to be incorporated, a choice governed by a small set of residues lining the binding pocket. For two decades, computational prediction of A-domain substrate specificity has relied on residue sets - most prominently the Stachelhaus code and the 34-residue "8 Angstrom code" - that were defined by spatial proximity to the substrate rather than by demonstrated predictive value. Here we revisit which residues govern substrate specificity from a purely data-driven perspective. We assembled a non-redundant dataset of 5,366 A-domain sequences (4,693 bacterial and 673 fungal) and used information-theoretic measures to rank alignment positions by their statistical association with substrate identity, without restricting candidate positions to any predefined structural shell. This procedure yielded two compact, kingdom-specific codes: IG15B (15 positions) for bacterial and IG13F (13 positions) for fungal A-domains. Both match or exceed the predictive accuracy of the 34-residue 8 Angstrom code while using fewer than half its positions, and both independently recover the majority of the classical Stachelhaus positions. Notably, our analysis identifies four positions (242, 280, 281, and 284) that lie outside all conventional codes yet carry non-redundant specificity information and co-localize with classical determinants on two helices flanking the binding pocket. These positions provide new candidate sites for the rational engineering of A-domain specificity.

22.
arXiv (CS.CL) 2026-06-19

CATCH-ME if you RAG: a dataset of Contextually Annotated multi-Turn Counterspeech against Hate and Misinformation Exchanges

Online hate speech and misinformation frequently overlap, yet NLP research has mainly treated them in isolation. While LLMs represent a scalable solution for assisting humans in the generation of counterspeech for both threats, zero-shot models frequently generate repetitive and vague responses, underscoring the need for high-quality examples to steer model generation. However, existing counterspeech datasets against the overlap of hate and misinformation are scarce and limited to single-turn English dialogues, while real-life interactions span across multiple turns and languages. To bridge this gap, we introduce the first large-scale, expert-curated, multilingual dataset of dialogues tackling the intersection of hate and misinformation. To ensure factual grounding, the dialogues are also anchored in verified external knowledge (i.e., fact-checking articles and NGO reports) and include document- and chunk-level span annotations, making it directly applicable for RAG systems. Covering five languages and targeting hate directed at seven marginalized groups, this novel resource enables the training and evaluation of more persuasive, factually grounded counterspeech models.

23.
arXiv (CS.LG) 2026-06-15

Learning the Context of Errors: Black-Box Online Adaptation of Time Series Foundation Models

arXiv:2606.14222v1 Announce Type: new Abstract: The rapid evolution of Time Series Foundation Models (TSFMs) has advanced zero-shot forecasting across diverse domains. Inspired by the current form of Large Language Models, future TSFMs may be offered as commercialized, closed-source API services. However, many existing online adaptation methods still rely on white-box access for parameter fine-tuning or gradient backpropagation. This paradigm mismatch raises a question: In black-box online adaptation for TSFMs, what should we learn? We answer this with an insight: the predictive errors of the base model are conditioned on both the input and output of the base model (i.e., the context of errors). To validate this insight, we propose ORCA (Online Residual Contextual Adaptation). We conduct extensive experiments across 5 state-of-the-art TSFMs and 8 datasets to demonstrate the effectiveness of our approach. Furthermore, through ablation studies, we quantitatively analyze the impact of different adapter learning hypotheses on the final adaptation performance in black-box online adaptation. Code available at https://github.com/Fifthky/ORCA.

24.
arXiv (CS.CV) 2026-06-17

Visual Retrieval-Augmented Generation for Silhouette-Guided Animal Art

Generative AI has advanced the ability to render photorealistic or artistic images, yet it remains limited in a key aspect of human creativity: interpreting ambiguous shapes. This phenomenon, rooted in pareidolia, allows humans to perceive meaningful forms in random patterns such as clouds, stones, or leaves. To computationally replicate this imaginative process, we introduce Visual Retrieval-Augmented Generation (Visual-RAG), a framework that generates animal art directly from natural silhouettes. Our method retrieves structurally similar animal shapes from a curated corpus of 28,586 high-quality silhouettes and uses them as reference exemplars to guide diffusion-based generation with ControlNet and IP-Adapter. Ablation studies confirm that shape Context with RANSAC provides the most accurate alignment, while removing shape standardization reduces the inlier ratio to just 13.4\%, underscoring the importance of structural fidelity in Visual-RAG. A user study with 12 participants evaluated the outputs in terms of aesthetics, silhouette fidelity, and overall impression. Results reveal that while Visual-RAG provides plausible interpretations, challenges remain in achieving high perceptual impact. This work lays the foundation for computational pareidolia, showing how machines can contribute to the early stages of imaginative discovery.

25.
arXiv (CS.CL) 2026-06-16

SkillWiki: A Living Knowledge Infrastructure for Agent Skills

While knowledge is managed through Wikipedia and software through GitHub, agent skills still lack an infrastructure for large-scale production, governance, and evolution. SkillWiki is a living knowledge infrastructure that supports the organization, grounding, and continuous evolution of agent skills by transforming heterogeneous knowledge into reusable skill assets linked to their originating evidence. Our demonstration presents the complete skill lifecycle, from knowledge ingestion and skill production to provenance-aware exploration, governance, and execution-driven evolution. SkillWiki highlights a future in which knowledge, skills, and execution experience co-evolve within a shared infrastructure. The live demonstration and source code are publicly available at https://github.com/Huangdingcheng/SkillWiki.