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01.
arXiv (CS.AI) 2026-06-11

MoCA-Agent: A Market-of-Claims Code Agent for Financial and Numerical Reasoning

arXiv:2606.11537v1 Announce Type: new Abstract: Financial and tabular question answering requires more than fluent reasoning: answers must be grounded in the exact facts, formulas, units, signs, and scales that support them. A single misread cell or incorrect operation can silently produce a plausible but wrong result. We introduce \textsc{MOCA-Agent}, a market-of-claims code agent that replaces free-form multi-agent debate with claim-level verification. The system decomposes each question into typed atomic claims, asks specialist trader agents to buy or sell those claims, clears their orders into confidence-weighted accept/reject decisions, and synthesizes an executable Python program from market-supported evidence. A code-aware verifier then checks the program for execution, structural consistency, and common financial reasoning errors, with at most one market-aware repair round. Across ten public benchmarks spanning financial numerical reasoning, general tabular reasoning, ESG question answering, and multimodal chart reasoning, \textsc{MOCA-Agent} achieves strong performance using a fixed Qwen3.6-27B backbone, including $78.3\%$ on FinQA, $76.0\%$ on FinanceMath, $71.2\%$ on MultiHiertt, $86.9\%$ on ESGenius, and $85.6\%$ average on FinChart-Bench. These results show that aggregating evidence at the level of atomic claims, rather than whole answers, improves robustness in high-stakes numerical reasoning.\footnote{The code and data are available: https://github.com/UBC-NLP/MoCA-Agent.

02.
bioRxiv (Bioinfo) 2026-06-18

MorphoStat: A Statistics-Aware Pipeline for Morphological Profiling Analysis

作者:

High-content imaging produces thousands of morphological measurements per cell. Interpreting these measurements requires normalization to remove plate effects, statistical tests selected on the basis of data distribution, and control over false discoveries across many features tested at once. MorphoStat is an open-source Python pipeline that applies this sequence of steps automatically. Given a CSV file from CellProfiler or a compatible imaging platform, it removes low-quality wells, normalizes each plate against DMSO controls using a MAD-scaled z-score, routes each feature to a parametric or nonparametric test based on a distributional check, applies Benjamini Hochberg correction, and writes out results and publication-ready figures. On the BBBC021 benchmark (MCF-7 breast-cancer cells, 632 wells, 473 features), MorphoStat recovered 12 of 13 known mechanism-of-action classes in principal component space, confirming that the normalization and statistical routing work as intended. The tool is available at https://github.com/Almunthir334/morphostat (DOI: 10.5281/zenodo.20354069) under the MIT license.

03.
arXiv (math.PR) 2026-06-17

Decay of correlations and zeros for the hard-core model

arXiv:2603.17858v2 Announce Type: replace Abstract: In a recent paper the last author proved that absence of complex zeros of the partition function of the hard-core model near a parameter $\lambda>0$ implies a form of correlation decay called strong spacial mixing. In this paper we investigate the reverse implication. We introduce a strengthening of strong spatial mixing that we call very strong spatial mixing (VSSM). Our main result is that if VSSM holds at a parameter $\lambda>0$ for a family of graphs, this implies that the partition function has no zeros near that parameter for each graph in the family. We also demonstrate that a closely related variant of very strong spatial mixing does not imply zero-freeness. As a consequence of our main result, we moreover obtain that VSSM implies spectral independence. Our proof relies on transforming the problem to the analysis of an induced non-autonomous dynamical system given by Möbius transformations.

04.
arXiv (CS.AI) 2026-06-18

Leveraging Energy Features for Surface Classification with Deep Learning: A Comparative Analysis Across Three Independent Datasets

arXiv:2606.18698v1 Announce Type: cross Abstract: The energy-based method remains a comparatively underexamined approach for surface classification in mobile robotics, despite promising results in constrained environments. This study evaluated the viability of using energy-derived features as either a standalone classification modality or as supplementary input to inertial data. A comprehensive evaluation was conducted across three publicly available datasets, comparing the performance of modern deep learning architectures including recurrent neural networks, convolutional neural networks, encoder-only transformers, and Mamba state-space models, under automated hyperparameter tuning and input sequence length optimization. The models achieved higher accuracy than previously reported values on all evaluated datasets, with the convolutional neural network yielding the highest overall performance. When relying exclusively on energy-based features, the models attained classification accuracies in the range of 85-90%, approximately 5-10% lower than those achieved when combined with inertial features (96-99%). Augmenting inertial data with energy features resulted in a consistent mean accuracy improvement of 1-2%. These findings indicate that classifiers relying solely on energy features offer sufficient accuracy for standalone deployment, while also providing a consistent gain when used in combination with other sensing modalities.

05.
medRxiv (Medicine) 2026-06-15

Data-Driven Stochastic Model for Detecting Patientswith Alzheimer's Disease

Alzheimer s disease (AD) is a critical neurological disorder that causes the brain to shrink and leads to the eventual death of brain cells, adversely affecting a person s ability to function. AD is a fast-growing disease in the United States and was the fifth leading cause of death among Americans 65 years of age or older in 2023. In the United States 6.9 million people aged 65 or older were diagnosed with AD, along with a high rate of undiagnosed patients. Thus, the objective of our study is to develop a real data-driven predictive model to identify a patient with AD based on eight risk factors: Age, Gender, ADAS-Cog13, Entorhinal, Fusiform, Intracranial Volume (ICV), Amyloid-Beta, and Tau Protein, with a high degree of accuracy. The quality of the model was evaluated using well-established and sophisticated statistical measures: the area under the receiver operating characteristic curve, calibration plot, Hosmer-Lemeshow goodness-of-fit test, and K-fold cross-validation. If a patient is given information on the above risk factors, our proposed binary logistic regression model can classify the patient as having AD or not with at least 98% accuracy.

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

Phase-Aware Guidance Injection for Recurrent MAPPO in Assembly-Line Disruption Recovery

arXiv:2606.16330v1 Announce Type: new Abstract: Disruption recovery in industrial assembly lines requires timely decisions under machine faults, worker absence, and emergency orders. Existing methods either rely on rigid handcrafted recovery logic or learn adaptive policies that do not readily exploit heterogeneous external recovery knowledge at decision time to reduce abnormal recovery time (ART) and preserve on-time delivery (OTD). To address this gap, we propose a phase-aware guidance injection framework that augments a trained recurrent MAPPO (RMAPPO) scheduling policy through logit-level action bias during evaluation. The framework provides a unified decision-time interface for rule-based, replay-based, and online LLM-based guidance, while activating intervention only during abnormal and recovery phases. Experiments on a custom AssemblyLineEnv show that high-quality rule guidance yields the strongest gains, replay-based guidance degrades smoothly under imperfect availability, and online LLM guidance still provides useful intermediate improvements. These results show that decision-time guidance injection can exploit heterogeneous recovery hints without redesigning the actor.

07.
arXiv (CS.LG) 2026-06-19

A deep learning framework for jointly solving transient Fokker-Planck equations with arbitrary parameters and initial distributions

arXiv:2604.06001v2 Announce Type: replace-cross Abstract: Efficiently solving the Fokker-Planck equation (FPE) is central to analyzing complex parameterized stochastic systems. However, current numerical methods lack parallel computation capabilities across varying conditions, severely limiting comprehensive parameter exploration and transient analysis. This paper introduces a deep learning-based pseudo-analytical probability solution (PAPS) that, via a single training process, simultaneously resolves transient FPE solutions for arbitrary multi-modal initial distributions, system parameters, and time points. The core idea is to unify initial, transient, and stationary distributions via Gaussian mixture distributions (GMDs) and develop a constraint-preserving autoencoder that bijectively maps constrained GMD parameters to unconstrained, low-dimensional latent representations. In this representation space, the panoramic transient dynamics across varying initial conditions and system parameters can be modeled by a single evolution network. Extensive experiments on paradigmatic systems demonstrate that the proposed PAPS maintains high accuracy while achieving inference speeds four orders of magnitude faster than GPU-accelerated Monte Carlo simulations. This efficiency leap enables previously intractable real-time parameter sweeps and systematic investigations of stochastic bifurcations. By decoupling representation learning from physics-informed transient dynamics, our work establishes a scalable paradigm for probabilistic modeling of multi-dimensional, parameterized stochastic systems.

08.
arXiv (CS.LG) 2026-06-11

Scaling Laws of Global Weather Models

arXiv:2602.22962v2 Announce Type: replace Abstract: Data-driven models are revolutionizing weather forecasting. To optimize training efficiency and model performance, this paper analyzes empirical scaling laws within this domain. We investigate the relationship between model performance (validation loss) and three key factors: model size ($N$), dataset size ($D$), and compute budget ($C$). Across a range of models, we find that Aurora exhibits the strongest data-scaling behavior: increasing the training dataset by 10x reduces validation loss by up to 3.2x. GraphCast demonstrates the highest parameter efficiency, yet suffers from limited hardware utilization. Our compute-optimal analysis indicates that, under fixed compute budgets, allocating resources to more total training data yields greater performance gains than increasing model size. Furthermore, we analyze model shape and uncover scaling behaviors that differ fundamentally from those observed in language models: weather forecasting models consistently favor increased width over depth. These findings suggest that future weather models should prioritize wider architectures and larger effective training datasets to maximize predictive performance.

09.
arXiv (CS.LG) 2026-06-19

Judging to Improve: A De-biased VLM-as-3D-Judge Protocol for Single-Image 3D Generation

arXiv:2606.20364v1 Announce Type: new Abstract: A companion study established a de-biased, cross-model VLM-as-3D-judge that reliably ranks single-image-to-3D mesh quality where cheap geometry and CLIP proxies fall short. This paper asks: can that judge's preferences specialize a strong open generator, TRELLIS, on one asset class (furniture), cheaply and without human labels? Taking the judge from ranking to optimization is where the work lives. Pushing a VLM judge into the training and evaluation loop exposes failure modes ranking never triggered, so our contribution is an optimization-grade hardening of the judge: a training judge (Qwen2.5-VL-7B) held distinct from an evaluation judge (InternVL3-8B) to break circularity; position-bias correction; and fixes for three failure modes (image overload, geometry-hiding splat renders, and reference-free judging that rewards clean-but-wrong outputs), with calibration evidence (clear-gap win-rate 0.83-1.0; base-vs-base ~0.5). Using this protocol as an independent evaluator, and working only from public models and data with lightweight parameter-efficient adaptation, we find our methods match the strong base rather than exceed it. Independent base samples carry essentially no learnable preference (0.94 order-flip rate), so signal must be engineered by quality-contrastive construction. Across six adaptation methods, two input regimes, and a severity sweep, the most targeted - conditioner repair under severe degradation - reaches parity (0.50) with the base, while no method clears the >=65% win-rate target. The result is mechanistic: clean inputs saturate the judge, flow-DIT fine-tuning washes out through the sampler, and conditioning repair is the locus that moves geometry. Win-rates are directional at n=8 objects. Matching a strong public-data base with cheap adaptation is itself informative: exceeding it needs more than lightweight PEFT on public data, and the judge protocol is reusable.

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

SafeLLM: Extraction as a Hallucination-Resistant Alternative to Rewriting in Safety-Critical Settings

Large language models (LLMs) are increasingly used to access organisational documentation, including standard operating procedures (SOPs), HR policies and institutional guidelines. However, retrieval-augmented generation (RAG) systems that rely on free-form rewriting can introduce hallucinations and unstable trade-offs between completeness and conciseness, particularly in safety- and compliance-critical settings. Objectives: To evaluate extraction as a hallucination-resistant alternative to rewriting-based RAG and compare strategies that balance precision, recall and safety across document types and model scales. Methods: We compare multiple prompting strategies, including line-number-based source selection, extraction of relevant guideline sentences with explicit safety annotations, and a multi-stage pipeline that refines draft answers using supporting evidence from source guidelines. Experiments are conducted on documents of varying length and structure, including local NHS acute care and oncology guidelines and UK-wide NICE guidelines, using both frontier-scale and locally deployable models. Performance is assessed using automatic metrics and human expert evaluation of relevance and completeness. Results: Line-number selection achieves the strongest results, outperforming direct copying and safety-focused strategies across both large and small models while maintaining high term recall (up to 95%) and close alignment with source text. Safety-oriented approaches improve precision but introduce systematic omissions, while multi-stage filtering further amplifies this trade-off. Performance varies with document structure: line-based extraction excels in protocol-like content, whereas alternative strategies perform better on more verbose documents (up to 97% term recall).

11.
Nature (Science) 2026-06-17

Towards Conversational AI for Disease Management

While large language models (LLMs) have shown promise in diagnostic dialogue1, their capabilities for effective management reasoning—including disease progression, therapeutic response, and safe medication prescription—remain under-explored. We advance the previously demonstrated diagnostic capabilities of the Articulate Medical Intelligence Explorer (AMIE)1−3 through a new LLM-based agentic system optimized for multi-visit clinical management and dialogue. To ground its reasoning in authoritative clinical knowledge, AMIE leverages Gemini’s long-context capabilities4, combining in-context retrieval with structured reasoning to align its output with up-to-date clinical practice guidelines and drug formularies. In a randomized, blinded virtual Objective Structured Clinical Examination (OSCE) study, AMIE was compared to 21 primary care physicians (PCPs) across 100 multi-visit case scenarios designed to reflect UK NICE Guidance and BMJ Best Practice guidelines. AMIE was non-inferior to PCPs in management reasoning as assessed by specialists and scored better in both preciseness of treatments and investigations, and in its alignment with and grounding in clinical guidelines. To benchmark medication reasoning, we developed RxQA, a multiple-choice question benchmark derived from two national drug formularies (US, UK) and validated by board-certified pharmacists. Though AMIE and PCPs both benefited from the ability to access external drug information, AMIE outperformed PCPs on higher difficulty questions. While further research would be needed before real-world translation, AMIE’s strong performance across evaluations marks a significant step towards conversational AI as a tool in disease management.

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

Computational Safety for Generative AI: A Hypothesis Testing Perspective

作者:

arXiv:2502.12445v2 Announce Type: replace Abstract: AI safety is a rapidly growing area of research that seeks to prevent the harm and misuse of frontier AI technology, particularly with respect to generative AI (GenAI) tools that are capable of creating realistic and high-quality content through text prompts. Examples of such tools include large language models (LLMs) and text-to-image (T2I) diffusion models. As the performance of various leading GenAI models approaches saturation due to similar training data sources and neural network architecture designs, the development of reliable safety guardrails has become a key differentiator for responsibility and sustainability. This paper presents a formalization of the concept of computational safety, which is a mathematical framework that enables the quantitative assessment, formulation, and study of safety challenges in GenAI through the lens of signal processing theory and methods. In particular, we explore two exemplary categories of computational safety challenges in GenAI that can be formulated as hypothesis testing problems. For the safety of model input, we show how sensitivity analysis and loss landscape analysis can be used to detect malicious prompts with jailbreak attempts. For the safety of model output, we elucidate how statistical signal processing can be used to detect AI-generated content. Finally, we discuss key open research challenges, opportunities, and the essential role of signal processing in computational AI safety.

13.
arXiv (CS.AI) 2026-06-19

Triangular Consistency as a Universal Constraint for Learning Optical Flow

arXiv:2606.19938v1 Announce Type: cross Abstract: We propose triangular consistency as a first-principled constraint for optical flow, which is agnostic to network architecture, supervision type, and dataset, and applies to both image-pair and multi-frame settings. This simple but powerful constraint is to compose two flows to induce a third flow and enforce consistency among the three. The composed flows may arise from (i) image pairs, yielding cycle consistency; (ii) multiple video frames, producing longer-range motion through temporal chaining; or (iii) image pairs combined with controlled synthetic transformations, which becomes data augmentation. This triangular consistency introduces negligible computational overhead and requires no additional annotations. Since it is derived directly from the geometry of optical flow, it does not rely on model-specific assumptions and serves as a ``universal'' plug-and-play component for optical flow training. Experiments show consistent improvement across supervised, unsupervised, and transfer learning settings.

14.
bioRxiv (Bioinfo) 2026-06-11

Viability of engineered AAVs via protein language models

Capsid engineering has greatly improved the performance of recombinant AAV vectors used for gene therapy. One commonly used strategy is the insertion of a short, 7-mer, peptide into surface-exposed loops to modify receptor interactions and enhance cell entry. While effective in receptor retargeting and improved transduction, these insertions might destabilize the capsid protein, hinder assembly, and thus limit production. While previous attempts have used deep mutational scanning and AI to predict which insertions are viable, there is lack in understanding the structural consequences of these peptide insertions at the amino-acid level. Here we combined experiments, deep sequencing and large protein language models to gain insight on the impact of 7-mer insertions on the VR-VIII region. We first characterize the biochemical properties of viable insertions, thus identifying which residues are well tolerated, and which should instead be avoided. We then focus on the nearby context of those insertions, by studying the effect of the linkers, either for highly diverse libraries or for individual variants known for their efficiency. Next, we study the broader context, by extending our analysis to the whole capsid sequence, and identifying regions that can tolerate insertions without long-ranged structural deformations that could affect capsid functionality. We conclude with a cross-serotype comparison and a viability analysis of tens of previously engineered variants. Our work showcases how AI can uncover structure-function rules governing the success of engineered AAV capsids.

15.
arXiv (CS.AI) 2026-06-16

The Quality-Utility Paradox: Why High-Reward Data Impairs Small Model Mathematical Reasoning

arXiv:2606.16152v1 Announce Type: new Abstract: Knowledge distillation from powerful reasoning models is widely used to improve Small Language Models (SLMs) on mathematical reasoning, often assuming that traces with higher reward model scores provide more useful supervision. We identify a counterintuitive Quality-Utility Paradox in mathematical reasoning distillation. Data refined or synthesized by a stronger Oracle obtains higher perceived quality according to reward models, yet consistently underperforms traces generated by the SLM itself and selected through rejection sampling across Qwen2.5, LLaMA-3, and DeepSeek families. Our analysis shows that Oracle refinement couples logical repair with distributional drift away from the SLM's native reasoning distribution. This drift increases the learner's adaptation cost and can outweigh the benefit of improved reasoning logic. To test this mechanism, we introduce Style-Aligned Refinement, which preserves the native trajectory of the SLM while retaining logical repair from the Oracle. This intervention lowers adaptation cost and restores downstream utility. These findings suggest that effective mathematical reasoning distillation should jointly optimize perceived solution quality and learner-data compatibility, rather than relying solely on reward-model scores. The datasets and code are available at https://github.com/Dracoqhl/Quality-Utility-Paradox.

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

Med-R2: Perception and Reflection-driven Complex Reasoning for Medical Report Generation

Automated medical report generation (MRG) is increasingly used to reduce the burden of manual reporting and for decision support. Large vision-language models (LVLMs) hold great promise for automated MRG due to their fine-grained image-text alignment and advanced text-generation capabilities. Currently, state-of-the-art MRGs primarily focus on adapting pre-trained LVLMs with direct supervised fine-tuning (SFT), a fine-tuning strategy with medical image-report pairs. However, several factors limit the performance of these LVLMs. Firstly, direct SFT enables LVLMs to generate medical reports directly without an intermediate thinking process of pathological feature perception and diagnostic reasoning. This causes a potential failure to perceive pathological features and thus leads to misdiagnosis. Secondly, direct SFT lacks the incorporation of radiology-specific knowledge guidance, causing LVLMs to misinterpret perceived pathological features and make incorrect diagnoses. To address these gaps, we propose a novel fine-tuning strategy named Med-R2. We introduce a perception-driven long reasoning process that precedes report generation and incorporates radiology-specific knowledge as guidance. Additionally, to alleviate potential perceptual errors in complex reasoning, a reflection mechanism is introduced to refine the perception of pathological features and the generated report. Our experiments demonstrate that Med-R2 effectively enhances the capability of pathological features perception and diagnosis accuracy for MRG via fine-tuned LVLMs.

17.
arXiv (quant-ph) 2026-06-12

Matrix phase-space representations for gaussian boson sampling

arXiv:2503.12749v2 Announce Type: replace Abstract: We introduce coherent matrix phase-space distributions. These use conservation laws and symmetries to improve the accuracy and speed of quantum phase-space representations. As an example, this is applied to validation of low-loss Gaussian boson sampling (GBS) quantum computational advantage experiments, where classical generation of the random photon-number counts is exponentially hard. Large improvements in sampling errors are demonstrated compared to previous methods. Matrix phase-space representations also provide a large numerical speed-up, due to their (at worst) quadratic scaling, compared to other methods for validating total count probabilities of large-scale, low-loss GBS networks.

18.
arXiv (CS.CV) 2026-06-16

Multi-view feature High-order Fusion for Space Weak Object Detection and Segmentation

Weak objects are common in images and videos of space applications. However, it is hard to learn proper representations from their limited appearance information. Inspired by multi-view learning, we develop simple multi-view attentions, treating their outputs as multi-view features. We also propose a multi-view feature high-order fusion method (MHF) to aggregate more accurate and richer features of weak objects. Our MHF extends the commonly used low-order feature fusion method to higher orders. It enhances the model's capacity to capture relevant and complementary information about weak objects. This is achieved by introducing high-order multi-view features perception and a recursive task-contribution gated selection of multi-view features. The new operation is highly flexible and customizable. It is compatible with various variants of multi-view feature representations. We conduct extensive experiments on two newly constructed space science datasets and an open, large-scale satellite video dataset. Our MHF serves as a plug-and-play module and significantly improves various vision transformers and convolution-based detection and segmentation models. We achieve all state-of-the-art accuracies on both tasks across three datasets. Our MHF can be a new basic module for visual modeling that effectively represents weak objects in terms of multi-view learning. The code will be available at https://github.com/Kingdroper/MHF.

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

Context-Aware Multimodal Claim Verification in Spoken Dialogues

Every day, millions absorb claims from podcasts and streams that no fact-checker ever sees. Spoken misinformation is built through conversation, where credibility comes not from facts alone but from how claims are framed, reinforced, or left unchallenged across turns. Yet fact-checking has focused on isolated text, leaving dialogue audio under-studied. We introduce MAD2, a new Multi-turn Audio Dialogues benchmark for spoken claim verification, containing 1,000 two-speaker dialogues with 3,368 check-worthy claims and approximately 10 hours of audio, and propose calibrated multimodal fusion of a context-aware audio encoder and a dialogue-aware text model. Across settings, adding dialogue context improves verification, but the gains depend on scenario type. Using only preceding context often matches offline performance, supporting live-moderation settings, and audio contributes most when transcript-based models are destabilized by additional context. Overall, conversational structure matters more for verification than misinformation framing.

20.
arXiv (CS.CV) 2026-06-18

Geometry-Aware Dataset Condensation for Diffusion Model Training

Dataset condensation aims to construct compact datasets from real data via synthesis or selection. However, existing approaches are ill-suited for diffusion model training: synthetic data generation often yields low-fidelity samples unsuitable for authentic modeling, while real subset selection typically fails to preserve the distributional geometry required by diffusion likelihood objectives. To address this, we propose to reformulate real subset selection as a geometry-aware distribution alignment problem. By incorporating one-sided partial optimal transport, our method selectively aligns a compact subset with the full data distribution while allowing unmatched mass in low-density regions, ensuring the preserved geometric structure necessary for effective diffusion model training. To further ensure distributional fidelity, we complement geometric alignment with lightweight feature-statistics and semantic consistency regularization. An efficient two-stage discrete optimization strategy is proposed to achieve this alignment objective. Extensive experiments across diffusion variants, subset sizes, image resolutions, and training rounds show that our method achieves superior fidelity and distributional coverage in diffusion model training. Codes are available at https://github.com/2018cx/GADC.

21.
arXiv (CS.AI) 2026-06-18

As You Wish: Mission Planning with Formal Verification using LLMs in Precision Agriculture

arXiv:2606.18519v1 Announce Type: cross Abstract: Though robotic systems are now being commercialized and deployed in various industries, many of these systems are highly specialized and often require an advanced skill set to operate and ensure they perform as instructed. To mitigate this problem, we recently introduced a mission planner leveraging LLMs to synthesize mission plans in precision agriculture based on mission descriptions provided in natural language. While the system demonstrates impressive performance, it also suffers from the inherent ambiguities of natural language. In this paper, we extend our system to address this issue by introducing multiple feedback loops in the planning architecture that leverage linear temporal logic (LTL) to ensure the mission planning system meets the specifications formulated by the user while still using natural language. To mitigate potential bias, this is achieved by using two different commercial LLMs in charge of the specification and verification subtasks. Through extensive experiments, we highlight the strengths and limitations of integrating mission verification into a fully autonomous pipeline, particularly regarding an LLM's ability to generate valuable LTL formulas, and show how our proposed implementation addresses and solves these challenges.

22.
PLOS Computational Biology 2026-05-29

A prototype-augmented graph representation learning framework for identifying brain disorder-associated genes and facilitating drug repurposing

作者:

by Jiafang Li, Yifei Li, Siying Lin, Jiahua Rao, Huiying Zhao Many genetic loci were identified as associated with neuropsychiatric disorders and neurodegenerative disorders by Genome-wide association studies (GWAS). How these loci impact these diseases is unclear. Advances in deep-learning approaches and multi-omics data have the potential to link GWAS findings with disease mechanisms. Here, we proposed the Multi-omics Graph Transformer Network (MOGT), a semi-supervised graph neural network that leverages graph representation learning to model biological networks derived from multi-omics data to predict disease-associated genes. MOGT outperforms the current approaches in disease gene prediction for two psychiatric disorders and three neurodegenerative/neurological diseases. High-risk genes (HRGs) for Parkinson’s disease (PD) predicted by MOGT were used to drug discovery by integrating with the CMAP database. Finally, 10 drugs were identified as potential candidates. Among them, the effect of drug UK-356618 was experimentally verified in a primary neuron model, showing that UK-356618 reversed the abnormal expression of PD-associated genes and improved the cell-level phenotypes of PD. Together, these results indicate that MOGT can be used to identify HRGs for brain disorders, and these predicted HRGs provide high-level insights into the mechanisms and treatments of brain disorders.

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

Execution-bound advisory automation for agentic AI: a reproducible AIBOM-driven CSAF-VEX framework

arXiv:2606.19390v1 Announce Type: cross Abstract: A protocol driven framework is presented that binds SBOM and AIBOM artefacts to deterministic environment capture and structured runtime telemetry. Exploitability is computed from declared artefacts, observed activation conditions, and enforced execution policies. CSAF VEX advisories are generated from combined static and runtime evidence, cryptographically signed, and validated through deterministic replay. Evaluation uses approximately 10000 component entries across synthetic Agentic AI workloads 50 to 5000 components, incorporating OSV, GitHub Advisory, KEV, and EPSS datasets.

24.
arXiv (CS.LG) 2026-06-16

Filtered ANN as a Phase Transition: When Selectivity-Estimation Error Causes Plan Regret

arXiv:2606.16341v1 Announce Type: new Abstract: A filtered approximate-nearest-neighbor (ANN) query returns the k nearest vectors among those satisfying an attribute predicate P of selectivity s. The best execution strategy – pre-filter, post-filter, or in-filter – changes with s, so a system must estimate s and choose. We model this as an argmax over a landscape with phases (regions where each strategy wins) separated by boundaries, and show that selectivity-estimation error produces plan regret – recall lost versus the oracle strategy – only in the critical regions around those boundaries. The regret is a wedge of log-width equal to the multiplicative estimation error epsilon and height equal to the local cliff |V'(s*)| epsilon; the flip-margin 1/|V'(s*)| is the condition number of a sibling cardinality-estimation study reappearing as the local boundary theory. The two phase boundaries follow from independent mathematics: order statistics place the post-filter cliff at s ~ k/K, and site percolation places the in-filter cliff at s_c ~ 0.83/M for graph degree M (corpus-size independent). Criticality exists only under a constrained budget B < sqrt(k n). Under pre-registered decision rules we confirm, on synthetic sweeps and real SIFT1M, that regret concentrates ~290x at the boundary and that the regret curves obey a finite-size scaling collapse onto one universal wedge across two decades of corpus size. A real approximate index does not mis-locate the boundary, but a biased cost model opens a persistent miscalibration band that estimation-error robustness cannot fix. The contribution is a characterization, not a new index. Code and the full pre-registration are public.

25.
medRxiv (Medicine) 2026-06-17

Non-Medical COVID-19 Impacts and Hearing Status: A Global Study of Differential Health Impact Among Deaf, Hard of Hearing, and Hearing Populations

Background: Deaf and hard of hearing (HoH) experienced complex challenges during the COVID19 pandemic, including obscured visual communication from mask mandates, inaccessible public health messaging, and inadequate interpreter availability. We examined whether hearing status predicted nonmedical COVID19 impact on a global level. Methods: We conducted a nested cross-sectional analysis within a global study collecting data across two waves (April to May 2020 and July to August 2022) from 184 countries. Participants (N=7,998) were categorized as Deaf (n=304), Hard of Hearing (HoH; n=951), or Hearing (n=6,743). The primary outcome was a composite COVID-related non-medical Personal Impact TScore derived from 14 items across employment, resource access, and healthcare domains. Multinomial logistic regression models progressively adjusted for demographic, structural, and psychosocial variables. Results: Deaf participants reported substantially higher rates of pandemic-related job loss (28.9% vs. 9.6% hearing), healthcare cancellations (39.9% vs. 24.6%), and inability to obtain basic supplies. Over half (55.9%) of Deaf participants scored above the median composite impact index, compared to 39.2% of hearing participants. In the fully adjusted model, Deaf status remained an independent predictor of high non-medical impact (aOR=1.6, 95% CI: 1.1 to 2.4). HoH status showed no statistically significant difference from hearing participants in any model. Conclusions: People identifying as Deaf experienced significant disparities during COVID19 when compared with HoH or hearing people, driven by language access barriers and institutional exclusion rather than hearing loss per se. These experiences underscore the importance for systemic interventions centering on accessible communication, Deaf-centered needs, and reducing audism in Deaf-hearing interaction.