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01.
bioRxiv (Bioinfo) 2026-06-16

OmicOS: A Comprehensive Omics Ecosystem Infrastructure and Agent System for the AI Era

Authors:
Zeng↗Meng↗Hu↗Li↗Liu↗Shi↗Ma↗Gao↗Wang↗Luo↗Zheng↗Xian↗…

Biology has accumulated a vast ecosystem of omics methods, but much of this ecosystem remains built for expert humans rather than scientific agents. Methods are scattered across Python packages, R/Bioconductor and CRAN workflows, command-line tools, incompatible data containers and implicit object states, making even routine analyses difficult for an AI system to choose, execute and verify reliably. Here we introduce OmicOS, a comprehensive omics ecosystem infrastructure and agent system that turns OmicVerse V2, an open-source omics community, into an executable foundation for agentic biology. OmicVerse V2 provides the community substrate: scalable AnnDataOOM-compatible rust backends, agent-friendly Python algorithms for single-cell, spatial, bulk and multi-omics analysis, interfaces to single-cell foundation models, and Python-native reconstructions of historically R-centred Bioconductor/CRAN-style workflows. OmicOS makes this substrate actionable by registering analytical functions as state-aware capability contracts, allowing agents to inspect live data objects, select valid methods, execute controlled workflows and record provenance. The result is not a fixed pipeline, but a programmable omics environment in which agents compose real analyses from verified community methods rather than inventing tools. Across external and purpose-built benchmarks, OmicOS ranked first among the evaluated systems, reaching 81.2% on BiomniBench. Adding OmicVerse to a minimal agent improved task completion by up to 34.2 percentage points with qwen-3.6-35b, and controlled ablations showed that the gains came from registry-grounded execution rather than from larger models, documentation retrieval or unrestricted tool exposure. The same infrastructure scaled to atlas-sized data, reproduced R-centred workflows in Python and converted external pathology software into agent-usable skills. In a discovery task starting from a whole-body spatial map and the term Alzheimer disease, OmicOS composed a non-canonical workflow that integrated spatial expression, genetic association, eQTL and colocalization evidence to nominate a colon epithelial risk axis centred on PICALM, CD2AP and CR1. Together, OmicVerse and OmicOS define an open foundation for AI-era omics, showing how a community of biological methods can be transformed into a reliable, extensible and agent-operable system for discovery.

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02.
arXiv (CS.CV) 2026-06-16

An Adaptive Data cleaning Framework for Noisy Label Detection

Authors:
Chen-Hsuan Fang↗Wei-Hsinag Chen↗Pin-Hsuan Yu↗Jung-Hua Wang↗Tsung-Wei Pan↗

Deep neural networks (DNNs) excel in computer vision tasks given large annotated datasets. In real-world applications, however, labels are often corrupted by ambiguity, human error, or dynamic environments. Over-parameterized DNNs easily memorize these noisy labels during training, degrading model accuracy and generalization. Existing data-cleaning and sample-selection strategies often rely on manually specified thresholds, prior knowledge of the noise ratio, or a single metric (either learning dynamics or geometric structure), making them unstable in complex data regimes. This paper proposes a self-adaptive data-cleaning framework that integrates local, global, and learning dynamics cues for robust noisy-label detection. Samples are mapped into a unified low-dimensional feature space through a modular feature concatenation paradigm. We provide two instantiations: a 2D metric integrating class-adaptive KNN-based local disagreement with k-means-based global centroid distance, and a 3D multi-metric that additionally incorporates a z-normalized score. Unlike conventional 1D Gaussian Mixture Models applied to a single scalar metric, our framework performs multi-metric clustering on the feature space to adaptively partition samples into clean-dominant and noise-dominant components without requiring manual thresholds or noise priors. Experiments on CIFAR-10, MNIST, and ImageNet-100 with 5% to 40% symmetric label noise show high recall across settings, including near-perfect recall (>=98%) on ImageNet-100 at 40% noise. Subsequent training yields accuracy gains across evaluated settings, especially under severe corruption on ImageNet-100. These findings suggest that multi-metric integration provides a threshold-free, practical, and low-tuning strategy for noisy label detection.

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03.
arXiv (CS.CV) 2026-06-12

Learning Task-Aware Sampling with Shared Saliency through Density-Equalizing Mappings

Authors:
Tsz Lok Ip↗Han Zhang↗Lok Ming Lui↗

In image and surface-based learning tasks, convolutional features are typically extracted using receptive fields that are sampled uniformly across the entire domain. However, informative structures are rarely distributed uniformly in practice and are often concentrated in localized regions. Such phenomena are particularly common in medical imaging, where pathological changes are spatially confined. Consequently, uniform convolution allocates equal computational effort to both informative and uninformative regions, resulting in inefficient feature extraction and suboptimal utilization of model capacity. To address this issue, we propose a framework for task-adaptive sampling that dynamically redistributes computational attention according to the spatial importance of the data. Specifically, we introduce the Density-Equalizing Convolutional Neural Network (DECNN), which employs density-equalizing mappings to guide convolution through a learned density function. The density function encodes the relative importance of different regions and induces a transformation that enlarges informative areas while compressing less relevant ones. As a result, convolutional receptive fields are redistributed non-uniformly over the domain, enabling denser sampling in task-relevant regions. By coupling this importance-driven transformation with convolution, DECNN performs adaptive feature extraction that focuses computational resources on informative structures. This leads to more efficient use of model capacity, yielding a lightweight yet expressive architecture while simultaneously producing an interpretable saliency map. Experiments on image classification and craniofacial surface analysis demonstrate that DECNN achieves competitive or superior performance with fewer parameters, accurately identifies task-relevant regions, and remains robust under complex geometric variations.

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04.
arXiv (quant-ph) 2026-06-16

Adaptively secure unitary designs with constant non-Clifford cost

Authors:
Lennart Bittel↗Lorenzo Leone↗

arXiv:2510.08129v2 Announce Type: replace Abstract: Randomness is a fundamental resource in quantum information, with crucial applications in cryptography, algorithms, and error correction. A central challenge is to construct unitary $k$-designs that closely approximate Haar-random unitaries while minimizing the costly use of non-Clifford operations. In this work, we present a protocol able to generate unitary $k$-designs on $n$ qubits, secure against any adversarial quantum measurement, with a system-size-independent number of non-Clifford gates. Our construction applies a $k$-design only to a subsystem of size $\Theta(k)$, independent of $n$. This ``seed'' design is then ``diluted'' across the entire $n$-qubit system by sandwiching it between two random Clifford operators. The resulting ensemble forms an $\varepsilon$-approximate unitary $k$-design on $n$ qubits. We prove that this construction achieves full quantum security against adaptive adversaries using only $\tilde{O}(k^2 \log\varepsilon^{-1})$ non-Clifford gates. If one requires security only against polynomial-time adaptive adversaries, the non-Clifford cost decreases to $\tilde{O}(k + \log^{1+c} \varepsilon^{-1})$. This is optimal, since we show that at least $\Omega(k)$ non-Clifford gates are required in this setting. Compared to existing approaches, our method significantly reduces non-Clifford overhead while strengthening security guarantees to adaptive security as well as removing artificial assumptions between $n$ and $k$. These results make high-order unitary designs practically attainable in near-term fault-tolerant quantum architectures.

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05.
arXiv (CS.AI) 2026-06-16

Retro-Expert: Collaborative Reasoning for Interpretable Retrosynthesis

Authors:
Xinyi Li↗Sai Wang↗Yutian Lin↗Yu Wu↗

arXiv:2508.10967v3 Announce Type: replace-cross Abstract: Retrosynthesis prediction aims to infer the reactant molecules based on a given product molecule, which is a fundamental task in chemical synthesis. However, existing methods rely on a static pattern-matching paradigm, which limits their ability to perform effective logical decision-making from chemical data, leading to a black-box process. We propose Retro-Expert, an interpretable retrosynthesis framework that performs collaborative reasoning by combining the complementary strengths of Large Language Models and specialized models via pure reinforcement learning. It outputs natural language explanations grounded in chemical logic through three components: (1) specialized models provide chemical knowledge that is distilled into a high-quality chemical decision space, (2) LLM-driven critical reasoning to generate predictions with an interpretable reasoning path, and (3) knowledge-grounded policy optimization refines the interpretable decision policy. Experiments show that Retro-Expert surpasses both LLM-based and specialized models across different metrics, while generating chemically grounded explanations that enhance chemists' trust in practice. The source code for this paper is available at https://github.com/MagixRab-ll/Retro-Expert.

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

Are Frontier LLMs Ready for Cybersecurity? Evidence for Vertical Foundation Models from Dual-Mode Vulnerability Benchmarks

Authors:
Vivek Dahiya↗Sunny Nehra↗Vipul Dholariya↗Bhavik Shangari↗Chandra Khatri↗

arXiv:2605.23243v2 Announce Type: replace-cross Abstract: We evaluate whether frontier LLMs are ready for cybersecurity through a dual-mode benchmark: white-box function-level vulnerability detection (VulnLLM-R, across C/Java/Python) and black-box web application security testing (five production-style applications with 118 ground-truth vulnerabilities across 20+ CWE families, which we will open-source). We test six frontier models (GPT-5.4, Codex~5.3, Claude Opus~4.6, Sonnet~4.6, Gemini~3.1~Pro and Gemini~3~Flash) and two domain-specialized models across four testing paradigms. Our findings are sobering: (1)~every frontier model produces 10-50% false positive rates in white-box detection, systematically over-predicting vulnerabilities; (2)~in black-box testing, frontier models achieve only 4-8% ground-truth coverage, improving to just 10-19% even with external security tools (Playwright MCP, Burp Suite MCP); (3)~structured penetration-testing methodology encoded in domain-specialized agents raises per-family detection above 50%, demonstrating that methodology, not scale, is the primary lever; and (4)~a domain-specialized defense model achieves the highest precision (0.904) and lowest false positive rate (9.7%) among all models, on a single GPU. We identify the absence of structured security testing traces end-to-end request/response sequences, failure-heavy data, and multi-step attack chains as the fundamental training data bottleneck, and propose self-play security testing as a data generation strategy. Our results make the case for vertical foundation models purpose-built for cybersecurity.

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07.
arXiv (CS.LG) 2026-06-16

Graph Learning Should Move Beyond Restrictive Views of Spectral and Message-Passing GNNs

Authors:
Antonis Vasileiou↗Juan Cervino↗Pascal Frossard↗Charilaos I. Kanatsoulis↗Christopher Morris↗Michael T. Schaub↗Pierre Vandergheynst↗Zhiyang Wang↗Guy Wolf↗Ron Levie↗

arXiv:2602.10031v2 Announce Type: replace Abstract: Graph neural networks (GNNs) are commonly divided into message-passing neural networks (MPNNs) and spectral GNNs, reflecting two largely separate research traditions in machine learning and signal processing. While MPNNs have a precise definition, there is no widely accepted criterion for what makes a mapping a spectral GNN. Most existing work restricts spectral GNNs to layered architectures based on linear spectral filters. Under this restriction, we show that spectral and spatial GNNs have largely equivalent expressive power. To promote progress in the field, we propose a precise definition of spectral GNNs based on eigenbasis symmetries, in contrast to the definition of MPNNs via neighborhood permutation symmetries. We further argue that the two perspectives offer complementary strengths. MPNNs provide a natural language for discrete structure and expressivity analysis through tools from logic and graph isomorphism, while the spectral perspective offers principled tools for understanding smoothing, bottlenecks, stability, and community structure. Overall, we argue that progress in graph learning will be accelerated by clarifying the similarities and differences between these perspectives and by moving toward a unified theoretical framework.

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08.
bioRxiv (Bioinfo) 2026-06-16

Evidence for recombination in dengue virus genomes

Authors:
de Paula Oliveira↗Jacob Machado↗Prieto Oliveira↗Ocana↗

Recombination is a key driver of RNA virus evolution, yet its extent and evolutionary implications in dengue virus (DENV) remain incompletely understood. We conducted a comprehensive, genome-wide recombination screen across 6,905 complete DENV genomes representing all four serotypes, 82 countries, and eight decades of sampling (1944-2023) retrieved from the Bacterial and Viral Bioinformatics Resource Center. Using seven complementary recombination detection methods implemented in RDP5, we identified 66 recombination events across 53 unique recombinant sequences, of which 29 are newly described. Events included intra-genotypic (n = 18), inter-genotypic (n = 32), and inter-serotypic (n = 16) exchanges spanning 14 genotypes and four continents, with no meaningful serotype-level enrichment (Cramer's V = 0.054). Recombination was concentrated in non-structural genes, most frequently NS3 (19 events), NS5 (17), and NS2 (12), while the capsid gene contained no recombination events, consistent with strong functional constraint. Single-nucleotide polymorphism analyses confirmed low divergence between recombinants and their inferred parents in both recombinant and non-recombinant regions. Phylogenomic analysis of 6,642 sequences revealed that recombinants cluster significantly closer to their major parents (p = 8.9 x 10-6 ) and that their removal does not significantly alter tree topology (p = 0.898), suggesting that the short length of recombinant regions limits phylogenetic conflict. We also introduce RECOSIM, an unsupervised machine-learning tool for recombination detection that achieved higher precision than RDP5 on both simulated (93.4% vs. 80.0%) and empirical (98.1% vs. 39.3%) datasets. Collectively, these results establish recombination as a widespread, pan-serotypic phenomenon in DENV with implications for genomic surveillance, vaccine evaluation, and evolutionary inference.

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09.
arXiv (quant-ph) 2026-06-15

An integrated ultrahigh vacuum cluster tool for diamond surface science and single nitrogen-vacancy center measurements

Authors:
Zhiyang Yuan↗Sorawis Sangtawesin↗Lila V. H. Rodgers↗Kalliope Zervas↗James J. Allred↗Jared Rovny↗Patryk Gumann↗Nathalie P. de Leon↗

arXiv:2606.13961v1 Announce Type: new Abstract: We present a custom-designed ultrahigh vacuum (UHV) cluster tool developed for studying shallow nitrogen-vacancy (NV) centers in diamond, enabling in situ diamond surface preparation, characterization, and single NV center dynamics measurements within a single connected platform. The system combines a surface science chamber for controlled surface modification and analysis with a cryogenic confocal microscope chamber dedicated to NV spin and optical measurements. This integrated approach enables a direct correlation between diamond surface chemistry and the resulting NV spin and charge properties. The instrument provides a versatile platform for systematic studies of surface-induced decoherence mechanisms and charge dynamics for shallow NV centers, and establishes a pathway toward reproducible surface engineering for quantum sensing applications.

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10.
arXiv (CS.CV) 2026-06-11

ISAP-3D: Identity-Slot Aligned Part-Aware 3D Generation

Authors:
Junlin Hao↗Haoshuai Fu↗Xibin Song↗Wei Li↗Ruigang Yang↗Xinggong Zhang↗Jinchuan Zhang↗

Part-aware 3D generation aims to synthesize structured objects with semantically meaningful components, yet often suffers from structural ambiguity due to identity-layout entanglement. Existing methods either infer part identity and spatial layout implicitly, which can lead to unstable part allocation (e.g., slot swapping or part merging), or rely on strong layout conditions that are difficult to obtain in practice. We attribute this ambiguity to identity-slot permutation freedom: without explicit identity-slot alignment, the correspondence between semantic parts and generation slots is not identifiable during training, allowing multiple slot assignments to fit the same supervision and leading to inconsistent decomposition. Based on this insight, we argue that stable part-aware generation requires identity-aligned one-to-one slot modelling. We therefore propose an identity-slot aligned framework, ISAP-3D, which anchors each part with semantic identity tokens and performs identity-conditioned one-to-one layout prediction, followed by layout-conditioned geometry synthesis. Structured local-global conditioning maintains identity alignment across semantic, spatial, and geometric stages. We also construct a part-level dataset with a unified semantic protocol to enable learnable and consistent identity-slot alignment. Extensive experiments demonstrate improved structural stability, controllability, and robustness over state-of-the-art part-aware generation baselines.

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11.
arXiv (quant-ph) 2026-06-12

Entropic order parameters and topological holography

Authors:
Hua-Chen Zhang↗Germ\'an Sierra↗Javier Molina-Vilaplana↗

arXiv:2512.24225v2 Announce Type: replace-cross Abstract: We show that the symmetry topological field theory (SymTFT) construction, also known as the topological holography, provides a natural and intuitive framework for the entropic order parameter characterising phases with (partially) broken symmetries. Various examples of group and non-invertible symmetries are studied. In particular, the origin of the distinguishability of the vacua resulting from spontaneously broken non-invertible symmetries is made manifest with an information-theoretic perspective, where certain operators in the SymTFT are excluded from observation.

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

GetNetUPAM: Ecologically Informed Nested Cross-Validation and Noise-Robust Attention for Marine Bioacoustic Monitoring

Authors:
Nicholas R. Rasmussen↗Rodrigue Rizk↗Longwei Wang↗KC Santosh↗

Deploying reliable bioacoustic monitoring systems requires models that generalize under high-noise, low-SNR conditions and evaluation protocols that expose deployment-relevant failure modes, gaps largely unaddressed in current UPAM practice. Intrinsic noise, variable propagation, and mixed biological and anthropogenic sources induce distribution shifts that conventional models and single-split evaluations obscure, inflating performance and masking instability. We introduce GetNetUPAM, a hierarchical nested cross-validation framework that uses the nested stage to quantify model stability rather than tune for inflated hold-out scores. By partitioning data into site-year blocks, GetNetUPAM preserves ecological heterogeneity and forces each outer fold to represent a distinct environmental regime, preventing overfitting to localized noise or sensor artifacts. Inner stratified folds measure generalization across the full UPAM signal distribution, enforcing strict separation between model development and the outer held-out deployment condition. Using GetNetUPAM, we evaluate the Adaptive Resolution Pooling and Attention Network (ARPA-N), a CNN architecture for irregular spectrogram dimensions. ARPA-N integrates CBAM spatial attention as a learned noise suppressor, producing attention maps that localize true call structure and avoid the global, non-biological cues exploited by standard CNNs on long-window data. Under GetNetUPAM, ARPA-N generalizes robustly across diverse environmental regimes. In the zero-training support Balleny Islands region, it reduces false positives per hour by over an order of magnitude (approximately 10x) at fixed 90 percent recall, yielding consistently improved metrics across folds. These advances provide a reproducible benchmark and move UPAM toward scalable, deployment-reliable ecological monitoring.

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13.
arXiv (CS.CV) 2026-06-11

LAST: Bridging Vision-Language and Action Manifolds via Gromov-Wasserstein Alignment

Authors:
Huaihai Lyu↗Chaofan Chen↗Yuheng Ji↗Xiansheng Chen↗Pengwei Wang↗Shanghang Zhang↗Changsheng Xu↗

We take a Gromov-Wasserstein perspective on Vision-Language-Action (VLA) learning, where the goal is to make the relational geometry of action representations compatible with the semantic geometry of VL embeddings. However, this alignment is non-trivial due to the mathematical heterogeneity between the domains: the semantic space of vision-language is topologically linear and isotropic, whereas the physical manifold of robotic action is non-Euclidean and anisotropic. Their disjoint metric structures render direct regression ill-posed. To resolve this incompatibility, we introduce LAST (Lie-algebraic Action Space Tokenizer), which reconstructs the action space to establish local metric compatibility with the VL modality via a two-stage transformation: (1) Global Topological Linearization: linearizing the action manifold via Lie-algebraic mapping, converting trajectories into a fixed-length, physically additive representation. (2) Local Metric Discretization: hierarchically discretizing the representation into schemas and whitened residuals, yielding approximately isotropic local charts that are statistically aligned with the semantic metric. By resolving the structural mismatch at both global and local levels, LAST enables VLA models with superior convergence and generalizability.

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14.
arXiv (CS.CV) 2026-06-15

Towards Mitigating Hallucinations in Large Vision-Language Models by Refining Textual Embeddings

Authors:
Aakriti Agrawal↗Gouthaman KV↗Rohith Aralikatti↗Gauri Jagatap↗Jiaxin Yuan↗Sarvesh Baskar↗Vijay Kamarshi↗Andrea Fanelli↗Furong Huang↗

Hallucinations in Large Vision-Language Models (LVLMs) remain a persistent challenge, often stemming from inadequate integration of visual information during multimodal reasoning. A key cause is the model's over-reliance on textual priors and underutilization of visual cues, leading to outputs that are linguistically fluent but visually inaccurate. For example, given an image of an empty kitchen countertop, an LVLM might hallucinate a "bowl of fruit" or "cup of coffee", relying on language associations rather than visual evidence. Most LVLMs incorporate visual features by appending them to the input stream of a pre-trained LLM and training on large-scale vision-language datasets. Our systematic analysis reveals that this strategy often leads to over-dependence on textual information due to the inherent bias of LLMs towards language-dominant representations. This imbalance skews attention towards the text over visual content, weakening the model's ability to ground outputs in visual inputs. To address this, we propose a simple yet effective visual feature incorporation method that encourages the model to learn visually-informed textual embeddings distinct from those of the base LLM and promotes a more balanced attention distribution. Experimental results across multiple hallucination benchmarks demonstrate that our method significantly reduces hallucinations and fosters more balanced multimodal reasoning. Notably, our approach achieves substantial gains, including +9.33% on MMVP-MLLM, +2.99% on POPE-AOKVQA, up to +3.4% on Merlin, and +3% on the hard-data split of HallusionBench.

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15.
arXiv (CS.CV) 2026-06-12

CD-RCM: Generalizable Continuous-Depth Novel View Synthesis for Reflectance Confocal Microscopy

Authors:
Tooba Imtiaz↗Milind Rajadhyaksha↗Kivanc Kose↗Jennifer Dy↗

Reflectance confocal microscopy (RCM) provides noninvasive, cellular-resolution "optical biopsies" of human skin in vivo by acquiring en-face images at successive depths, forming a sparse z-stack. Due to optical limitations, these stacks are anisotropic 3D volumes with lateral resolution (0.5 $\mu$m) $\sim$6 times higher compared to axial resolution, which is defined by the optical sectioning (3 $\mu$m), limiting the interpretation of tissue. Our goal is to provide continuous-depth visualization by interpolating intermediate sections and making the 3D volume isotropic. Such a representation permits arbitrary-direction sectioning, including histopathology-like cross-sectional examination, without requiring per-patient optimization. To that end, we introduce the first RCM-specific novel-view synthesis (NVS) approach, CD-RCM, a feedforward model that predicts realistic, unseen depths from sparsely sampled RCM stacks. Classical neural rendering methods focus on reconstruction from surface-level multi-view observations. In contrast to surface-level camera views, RCM can acquire optically sectioned en-face images of tissue beyond the surface up to 200 $\mu$m. However, during visualization of the RCM stacks, observations of the shallower sections (towards the surface) obscure the deeper ones. This unique axial imaging geometry and layer-dependent anatomical organization motivated our development of a tailored architectural and training framework that explicitly accounts for RCM's depth-resolved, occlusive imaging physics. Experiments demonstrate that CD-RCM achieves high-fidelity novel-view synthesis with sub-second inference time.

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

Imperfect Visual Verification for Code Edition : A Case Study on TikZ

Authors:
Charly Reux↗Mathieu Acher↗Djamel Eddine Khelladi↗Cl\'ement Quinton↗Olivier Barais↗

arXiv:2606.15693v1 Announce Type: cross Abstract: LLMs have significantly advanced code generation, enabling the synthesis of functional programs. While recent systems achieve strong performance on many coding benchmarks, tasks involving programs such as TikZ that generate visual artifacts remain challenging, in particular on visual code customization. Unlike generation from scratch, customization requires localized, semantics-preserving edits: the model must locate relevant code, modify it according to the instruction, and preserve the remaining structure and rendering. Approaches based on post-hoc iterative refinement/correction where a verifier provides feedback to guide corrections, have shown promise. However, in the case of programs with a visual outcome such as in TikZ, where correctness is harder or likely impossible to formalize and evaluate automatically, deterministic verifiers do not exist. Hence, developers can only rely on imperfect verifiers. In this paper, we conduct an empirical study to answer:to what extent can iterative refinement remain effective when the verifier itself is unreliable?} We use TikZ as a focused case study that isolates the core difficulties of the problem (weak code structure, fine-grained visual semantics, and difficult feature localization) in a controlled and challenging setting. We define visual code customization as an iterative editing problem with an imperfect oracle, and introduce a framework for analyzing such iterative refinements. We conduct a large-scale study and evaluate multiple LLM-based and tool-augmented visual verifiers within iterative refinement pipelines, and perform extensive manual annotation of refinement trajectories to assess verifier behavior and feedback quality. Our findings show that even imperfect verifiers can determine with moderate accuracy whether visual instructions are applied to code, achieving F1-scores up to 0.815. Feedback improves iterative refinement, especially for weaker models, adding 11–20 perfect customizations for Qwen3-vl-30b-a3b-Instruct, while stronger models like Gemini-3 gain fewer improvements (+5) but benefit more from accurate verification that prevents premature acceptance. Feedback is effective only when it precisely identifies image issues, provides actionable guidance, addresses all relevant problems, and remains grounded in the original instruction.

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

SkillVetBench: LLM-as-Judge for Multi-Dimensional Security Risk Evaluation in Open-Source LLM Agent Skills

Authors:
Ismail Hossain↗Sai Puppala↗Md Jahangir Alam↗Tanzim Ahad↗Sajedul Talukder↗

arXiv:2606.15899v1 Announce Type: cross Abstract: Open-source LLM agent ecosystems are growing rapidly, yet the security of community-contributed skills - modular tool definitions that extend agent capabilities - remains largely unvetted. The gap we fill: existing scanners operate at the code layer and are structurally blind to instruction-layer and multi-agent risk - natural-language directives that hijack an agent, exfiltrate data through encoded side channels, or chain harm across pipelines - so what is needed is a semantic, multi-dimensional vetting system rather than another signature matcher. We present SKILLVETBENCH, a live public leaderboard on Hugging Face that uses an LLM-as-Judge to vet agent skills. What is new: SARS (Skill Agentic Risk Score), a five-dimensional agentic-risk metric with a principled weighted formula for instruction-following systems. What is integrated: full CVSS v4.0 vector decomposition and a ClawHub dual-view that places our LLM-generated review beside the official marketplace verdict. What is demonstrated: drawing on our companion benchmark paper [ 1], the LLM-as-Judge stage achieves zero false negatives across 78 confirmed-malicious skills and zero false positives across 22 benign controls, while the best static baseline (SKILLSIEVE) still misses 15%; for instruction-layer categories such as Prompt Injection and Memory Poisoning, conventional tools miss between 89% and 100% of threats (e.g., CODEBERT detects none of nine memory-poisoning skills). Detection rates vary from 35% to 95% across four LLM evaluators, motivating ensemble scoring in production deployments.

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18.
arXiv (math.PR) 2026-06-19

Establishing an $\Omega(\sqrt{d})$ complexity lower bound for PDMP samplers and how to break it: a sub-$\sqrt{d}$ algorithm for Gaussian-tailed targets

Authors:
Augustin Chevallier↗

arXiv:2606.19909v1 Announce Type: cross Abstract: Despite the theoretical appeal of their non-reversibility, to date, no Piecewise Deterministic Markov Process (PDMP) samplers have been developed that scale better than $\mathcal{O}(\sqrt{d})$ in computational complexity with respect to the target dimension $d$. We prove that this is a fundamental limitation by establishing an $\Omega(\sqrt{d})$ lower bound on the algorithmic complexity of PDMP samplers in a standard setup. By relaxing the assumption that the target density must remain invariant at all continuous times, we then demonstrate how to bypass this barrier. Specifically, we introduce a novel PDMP sampling scheme and show that it achieves an empirical complexity of $\mathcal{O}(d^\alpha)$, where $\alpha \in [0.2, 0.3]$ for Gaussian-tailed targets. In addition, this PDMP scheme is locally adaptive in both trajectory length and distance between velocity updates.

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

SAGE-OPD: Selective Agent-Guided Intervention for Multi-Turn On-Policy Distillation

Authors:
Yuhang Zhou↗Lizhu Zhang↗Yifan Wu↗Mingyi Wang↗Bo Peng↗Jiayi Liu↗Xiangjun Fan↗Zhuokai Zhao↗

On-policy distillation (OPD) improves student models by training them on trajectories induced by their own policy, making it a promising approach for mitigating exposure bias in agent training. However, most OPD studies focus on single-turn settings, while realistic LLM agents interact with environments over multiple turns. In this regime, early errors can alter future observations and compound across the trajectory, and standard dense token-level OPD becomes brittle, as it may over-penalize semantically valid alternatives, reinforce local degeneracies such as repeated actions, and propagate unreliable teacher supervision on off-distribution histories. We propose SAGE-OPD, a verifier-free selective intervention framework specifically designed for multi-turn OPD. Instead of applying teacher supervision uniformly across all turns, SAGE-OPD first observes environment feedback and uses teacher judgment to decide whether each student response should be skipped or intervened on. To further address compounding errors, SAGE-OPD weights token-level distillation by teacher confidence, reducing the influence of uncertain teacher distributions on corrupted or ambiguous histories. Finally, SAGE-OPD applies loss normalization to preserve the overall loss scale of standard OPD while retaining selective turn-level weighting. Experiments on agent tasks show that SAGE-OPD consistently improves over baselines, achieving up to a 13.3% relative improvement in ALFWorld unseen success rate over standard OPD. Ablation studies further demonstrate that turn-level intervention, teacher confidence weighting, and loss normalization provide complementary benefits. Our results suggest that effective multi-turn OPD should remain on-policy, but teacher supervision should be selectively allocated to turns where intervention is necessary and reliable.

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21.
arXiv (CS.CL) 2026-06-11

M4FC: a Multimodal, Multilingual, Multicultural, Multitask Real-World Fact-Checking Dataset

Authors:
Jiahui Geng↗Jonathan Tonglet↗Iryna Gurevych↗

Existing real-world datasets for multimodal fact-checking have multiple limitations: they contain few instances, cover on only one or two languages, focus only on one task, or rely on external news article sets for sourcing true claims. To address these shortcomings, we introduce M4FC, a new real-world dataset comprising 4,982 images paired with 6,980 claims. The images, verified by professional fact-checkers from 22 organizations, represent a diverse range of cultural and geographic contexts. Each claim is available in one or two out of ten languages. M4FC spans six multimodal fact-checking tasks: visual claim extraction, claimant intent prediction, fake image detection, image contextualization, location verification, and verdict prediction. We provide baseline results for all tasks and analyze how combining intermediate tasks affects verdict prediction performance. We make our dataset and code publicly available.

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22.
arXiv (CS.CL) 2026-06-11

When Generic Prompt Improvements Hurt: Evaluation-Driven Iteration for LLM Applications

Authors:
Daniel Commey↗

Evaluating Large Language Model (LLM) applications differs from conventional software testing because outputs are probabilistic, semantically variable, and sensitive to prompt and model changes. This technical report proposes the Minimum Viable Evaluation Suite (MVES), an audit-oriented structure for application-level LLM evaluation. MVES links application categories to failure modes, metrics, required artifacts, and validation evidence across general LLM applications, retrieval-augmented systems, and agentic workflows. We pair the framework with a reproducible local evaluation harness covering structured extraction, RAG citation/content-compliance, and instruction-following checks. Using Ollama with Llama 3 8B Instruct and Qwen 2.5 7B Instruct, we evaluate five prompt conditions over expanded 30-case-per-suite ablations. The results show that, in the tested local conditions, generic prompt additions do not produce monotonic improvements: stronger output-contract prompts improve strict extraction for both models, while RAG citation/content-compliance declines under some generic-rule conditions. The largest observed decline occurs for Qwen 2.5 on RAG when generic rules are appended to the user prompt, from 26/30 to 9/30. These findings support evaluation-driven prompt iteration: prompt changes should be treated as potential regression risks and tested against task-specific suites before deployment. The accompanying repository contains the test suites, prompt variants, evaluation harness, raw result logs, and scripts needed to reproduce the reported local ablations.

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23.
arXiv (CS.AI) 2026-06-17

SoK: AI-Augmented Binary Reversing

Authors:
Yujeong Kwon↗Yiyue Zhang↗Shakhzod Yuldoshkhujaev↗Kexin Pei↗Dokyung Song↗Hyungjoon Koo↗

arXiv:2606.17398v1 Announce Type: cross Abstract: Binary reversing is fundamental to software understanding, vulnerability discovery, malware investigation, and firmware auditing. However, it remains inherently challenging due to the irreversible loss of semantic information during compilation. Recent advances in machine learning, large language models (LLMs), and agentic AI systems have accelerated the adoption of AI-augmented binary reversing. Yet, the resulting body of work has become increasingly fragmented across reversing domains, artifact representations, learning approaches, and evaluation practices. This paper presents the first comprehensive systematization of knowledge on AI-augmented binary reversing. We analyze 144 research papers published since 2015, and organize them into 22 binary reversing domains according to the inference tasks. We further introduce a unified taxonomy spanning conventional and AI-augmented reversing pipelines. Our taxonomy connects traditional analysis techniques, binary-derived artifacts, representation strategies, learning paradigms, and downstream inference tasks, while clarifying the emerging roles of LLMs and agentic AI systems. By establishing a common vocabulary and structured framework, we provide a holistic view of the field's evolution over the past decade. Our study reveals common structures underlying seemingly disparate approaches, highlights persistent technical challenges and evaluation gaps, and identifies promising opportunities for future research. Collectively, these insights clarify the current state of the field and provide a foundation for the next generation of reliable and scalable AI-augmented binary reversing systems.

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24.
arXiv (quant-ph) 2026-06-11

Collective Emission in LH2 Assembly Beyond the Point-Dipole Approximation

Authors:
Javed Akhtar↗Himangshu Prabal Goswami↗

arXiv:2606.11227v1 Announce Type: cross Abstract: Collective emission in light-harvesting assemblies is governed by the local transition dipole and finite geometry of emitting units, a fact that point-dipole approximation obscures. To go beyond this picture, we develop a non-Hermitian Hamiltonian using the quantum electrodynamic dyadic Green's tensor for a purple bacteria. We construct it for the isolated 24-bacteriochlorophyll conical frustum and its P42$_1$2 crystallographic assembly. The P42$_1$2 unit-cell symmetry is found to invert the bright-dark ordering of the single ring, placing subradiant states at the low-energy end and revealing the entire crystal to be the energy-harvesting entity. Tilt-driven switching is activated only in crystal geometries where the finite dipole-carrier (LH2) lies perpendicular to the growth plane. Vacancy and orientational disorder work only in cooperation to renormalize the switching threshold from higher polar angles to lower values.

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25.
arXiv (CS.AI) 2026-06-18

Structured Cognitive Loop for Behavioral Intelligence in Large Language Model Agents (Extended Revision: From Behavioral Architecture to Epistemic Accountability)

Authors:
Myung Ho Kim↗

arXiv:2510.05107v5 Announce Type: replace Abstract: The central challenge for AI agents is not only performance but accountability. Agents that act through opaque prompt sequences may produce correct outputs, but they provide little basis for verifying why an action was permitted, where an error occurred, or how responsibility should be assigned. This paper presents the Structured Cognitive Loop as an architecture for accountable behavior in large language model agents. SCL separates cognition, memory, control, and action into distinct modules. The language model proposes. External memory preserves verified state. A lightweight controller checks preconditions, prevents redundant actions, and authorizes execution before tools are used. We evaluate SCL against ReAct and common LangChain agent variants across travel planning, conditional email drafting, and constraint guided image generation. Across 360 episodes, SCL achieves 86.3 percent task success compared with 70.5 to 76.8 percent for prompt based baselines. It also improves goal fidelity, reduces redundant tool calls, increases reuse of intermediate state, and lowers unsupported assertions. This extended revision situates SCL within a broader architecture of epistemic accountability. Subsequent extensions integrate context aware Human in the Loop control, Pool Gated Retrieval, and the Horizon Warrant Commitment framework. Together these components define an agent architecture in which the model proposes, structure decides, evidence is warranted before use, and human judgment is embedded in the trace rather than imposed after the fact. The result is a foundation for AI agents whose decisions are not only effective but also authorized, inspectable, and accountable.

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