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01.
medRxiv (Medicine) 2026-06-18

Evaluating Deep-Learning Based Quantification of Breast Arterial Calcification on Mammography for Cardiovascular Risk Assessment

Purpose: To develop and evaluate a deep learning model for automated quantification of breast arterial calcification (BAC) on screening mammography and to assess whether AI-derived BAC burden predicts major adverse cardiovascular events (MACE) in women. Methods: In this retrospective study, 202,006 women who underwent screening mammography without history of MACE were included. A BAC segmentation model was trained on an expert-annotated dataset using a multi-task U-Net with a ResNet-18 encoder to detect and segment BAC. BAC burden was quantified as area (mm{superscript 2}) from model-generated masks using DICOM pixel spacing and categorized by tertiles into low, intermediate, and high. The PREVENT score and incident MACE were identified from electronic health records. Cox proportional hazards models were developed to evaluate AI-derived BAC burden and PREVENT score alone, and combined models for 5 - and 10-year cardiovascular risk prediction. Results: Among 202,006 women (mean age 54.8{+/-}11.7 years), 23.1% had AI-detected BAC, and 7,701 (3.8%) developed incident MACE during a median follow - up of 7.5 years. On the geographically held-out test set, the BAC model achieved an AUROC of 0.97, Dice score of 0.6678, and Pearson correlation of 0.961 between AI-derived and manually annotated BAC burden. BAC burden increased with age and was higher among women who developed MACE. Five - year MACE incidence increased across BAC categories from 1.5% in women without BAC to 6.9% in those with high BAC burden. BAC burden alone showed modest prediction of MACE, with 5-year and 10-year AUROCs of 0.661 and 0.650, respectively, while PREVENT achieved AUROCs of 0.781 and 0.771. Adding BAC to PREVENT produced minimal improvement in discrimination. Conclusion: Deep learning-based BAC quantification from routine mammography is feasible, accurate, and associated with future cardiovascular risk. Although BAC added little to PREVENT for overall discrimination, it may serve as a scalable opportunistic imaging biomarker to identify women at elevated cardiovascular risk and support preventive care.

02.
arXiv (quant-ph) 2026-06-24

Quantum Adaptive Self-Attention for Quantum Transformer Models

arXiv:2504.05336v4 Announce Type: replace Abstract: A recurring weakness in quantum machine learning (QML) is that reported ``quantum advantages'' are seldom tested against a capacity-matched classical control, leaving it unclear whether a gain comes from the quantum substrate or from the architectural change that accompanies it. Our primary contribution is methodological: a protocol for attributing such gains honestly – a capacity-matched classical bottleneck of identical parameter budget, transparent reporting of where quantum does not help, and validation on real quantum hardware – which we develop and apply through a concrete case study. That case study is Quantum Adaptive Self-Attention (QASA), a hybrid Transformer that replaces the value projection of a single encoder layer with a 36-parameter parameterized quantum circuit (PQC), keeping all other layers classical. Across nine synthetic benchmarks and the real-world ETTh1 dataset, QASA improves on a full-capacity classical Transformer for chaotic and trend-dominated signals. To ask whether this is a genuinely quantum effect, we introduce a control rarely applied in quantum machine learning – a capacity-matched classical bottleneck with the same parameter budget – and find that it matches the PQC on the error metrics. The gain is therefore attributable to the low-rank value-projection bottleneck (an architectural parsimony principle), not to quantumness; adding further quantum layers only degrades performance and trainability. We accordingly position the quantum layer not as a source of accuracy advantage but as a competitive instantiation of this principle: its low-rank compression onto the signal's intrinsic dimensionality is matched by a classical bottleneck, so the gain is architectural rather than quantum.

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

From Tokens to Faces: Investigating Discrete Speech Representations for 3D Facial Animation

The choice of speech representation is critical in speech-driven 3D facial animation. Representations differ in what they encode: SSL features emphasize segmental and semantic cues, neural codecs yield latents optimized for acoustic reconstruction, and ASR-style objectives produce label-based spaces. We evaluate four speech representation families for 3D facial synthesis, comparing their facial reconstruction quality across two facial decoders using objective metrics and a perceptual evaluation. We additionally conduct probing analyses that relate tokenized representations to phonetic units and to articulatory deformations. We found that encoding phonetic classes is beneficial for accurate facial animation prediction on both semantic and label-based representations with comparable facial animation quality. From the latter, we introduce an Audio Visual Text-to-Speech (AVTTS) pipeline that leverages, as a shared space, discrete representations to decode speech and 3D facial motion.

04.
arXiv (CS.LG) 2026-06-17

Public transit gains and spatially uneven travel demand changes after NYC congestion pricing

arXiv:2606.17530v1 Announce Type: cross Abstract: New York City implemented the nation's first cordon-based congestion pricing program in January 2025, providing an opportunity to evaluate how system-wide urban mobility responds to large-scale pricing interventions. Because such policies generate spillovers across modes and locations, credible control groups are difficult to construct. We address this challenge using time series foundation models to generate probabilistic counterfactual demand forecasts with calibrated uncertainty. Applying this framework to bus, subway, and aggregate trip volume data, we find that post-policy bus and subway ridership increased significantly relative to expected no-policy demand, while overall travel demand decreased modestly. The effects are spatially heterogeneous: while reductions in overall travel demand are concentrated within the Congestion Relief Zone, transit gains extend beyond Manhattan's core. Socio-demographic analyses further reveal uneven adaptation across neighborhoods, highlighting spatial equity implications. Our framework provides a scalable approach for the uncertainty-aware evaluation of system-wide urban interventions when clean control groups are unavailable.

05.
arXiv (CS.AI) 2026-06-12

When Does Delegation Beat Majority? A Delegation-Based Aggregator for Multi-Sample LLM Inference

arXiv:2606.08098v2 Announce Type: replace Abstract: Majority voting over sampled answers is the dominant unsupervised aggregator for multi-sample LLM inference. In this paper, we show a delegation-based aggregator (Propagational Proxy Voting, PPV; Sakai et al., 2025) yields an unsupervised consensus rule that beats majority on MMLU-Pro by +1.5 pp overall and +2.24 pp on the non-trivial subset (paired McNemar p ~ 1.0e-14, n = 8,099). Majority discards two signals that every sample carries: within-group letter entropy and between-group reasoning geometry. PPV exposes per-voter levers that consume exactly these two signals: When (how much weight a voter keeps on its own pick) and Whom (how it splits the remainder across peers). We drive When with letter entropy and Whom with per-question-centered embedding cosine. Our method needs no gold labels and no auxiliary training: per-question, we partition 128 sampled generations into 16 groups, compute each group's letter-level semantic entropy and reasoning embedding centroid, and feed both into a stochastic delegation matrix whose stationary distribution selects the consensus answer. We walk through an example in which PPV overturns a clear 10-6 majority for the wrong letter: the 10-voter majority cluster is geometrically incoherent (mean within-cluster cosine -0.02) while the 6-voter minority is tight (+0.26), so propagated delegation mass concentrates on the minority's answer even though entropy alone would keep the majority ahead. We further report delegation strategies with negative results that constrain the design space for unsupervised LLM aggregation. No within-question ensemble of confidence modes closes the oracle gap.

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

Integrated expectile-based measures of inequality

arXiv:2606.12333v1 Announce Type: cross Abstract: Expectiles provide a class of asymmetric location functionals that incorporate the magnitude of deviations and admit a natural geometric interpretation. Building on their structural consistency with the convex stochastic order, this paper introduces a family of integrated expectile functionals for measuring risk, dispersion, and inequality. The proposed functionals admit analytical representations as integrals of expectiles across asymmetry levels. For a distinguished subclass of these constructions, a geometric representation is available: the resulting quantities can be expressed as weighted areas of star-shaped sets encoding the distributional asymmetry of a random variable. This approach yields a new class of expectile-based inequality indices, constituting a natural counterpart to classical Gini-type measures while preserving desirable monotonicity and consistency properties. Empirical counterparts are derived in closed form and admit explicit decompositions over finite samples. The framework extends naturally to multivariate settings through directional expectile constructions, leading to measures capable of capturing genuinely joint forms of multivariate dispersion and inequality.

07.
arXiv (quant-ph) 2026-06-16

Long-range nonstabilizerness of topologically encoded states from mutual information

arXiv:2605.22424v2 Announce Type: replace Abstract: We study long-range nonstabilizerness (LRN), namely the obstruction to remove nonstabilizerness with shallow-depth local quantum circuits. In one-dimensional settings, the mutual information between disconnected spatial regions has proven to be a powerful tool to diagnose LRN. In this work, we focus on encoded states of two-dimensional topologically-ordered systems, and explore the ability of the mutual information to serve as a diagnostic of LRN. Focusing on the concrete setting of lattice models defined on a torus, we show that information about LRN can be gained from the analysis of the mutual information between non-overlapping regions containing non-contractible loops, and of the change of such mutual information under modular real-space transformations. We exemplify this idea in the toric code and the non-abelian string-net model with doubled Fibonacci topological order. In the former case, we show that the mutual information provides a full classification, certifying LRN for all encoded non-stabilizer states. In the latter case, instead, our approach does not lead to a full classification, as it detects LRN for all states except from a finite subset with special transformation properties under the modular group. Finally, we discuss how our results on LRN constrain the logical gates that can be implemented fault-tolerantly on the torus.

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

Circuit Synchronization Precedes Generalization: Causal Evidence from Fourier Structure in Grokking Transformers

arXiv:2606.12966v1 Announce Type: new Abstract: Grokking – where a transformer on modular arithmetic suddenly transitions from near-chance to near-perfect validation accuracy – is attributed to a Fourier circuit, but its timing, causal structure, and controllability remain poorly understood. We introduce the Frequency Synchronization Degree (FSD), a normalised, permutation-tested metric for Fourier circuit synchronisation requiring no prior circuit knowledge. Across nine modular addition configurations (primes p in {53, 71, 97, 113, 131}, three seeds), FSD synchronises 500-3,000 steps before grokking (mean lead +1,722 steps; all nine positive, sign-test p~0.004), and precedes a restricted-logit loss baseline (Nanda et al.'s excluded loss) in all nine cases, making it the earliest available predictor. We provide direct causal evidence that the inter-phase gap is a regularisation phenomenon: forking training at the FSD-ceiling step and varying weight decay lambda produces strictly monotone earlier grokking, with Delta_t proportional to 1/lambda. This law replicates across three primes (p in {53,97,131}; R^2=1.00 and R^2=0.99 for two clean cases), captured as Delta_t ~ C/lambda, consistent with (1/lambda)*log(||W_mem||/tau). Architecture ablations show an attention-only model groks with a strong FSD precursor; an MLP-only model never groks; a single-layer model's FSD lags, confirming the precursor is a multi-block circuit property.

09.
arXiv (CS.CV) 2026-06-11

Semantically-Aware Diver Activity Recognition Framework for Effective Underwater Multi-Human-Robot Collaboration

Effective multi-human-robot collaboration is essential for expanding human-led operations in the challenging and high-risk underwater environment. For autonomous underwater vehicles (AUVs) to become true teammates, they must be able to comprehend their surroundings and recognize a diver's activities to offer assistance and ensure safety. Towards this goal, we introduce DAR-Net, a novel transformer-based framework that analyzes complex underwater scenes to classify diver activities. Our contribution lies in a semantically guided learning formulation that couples transformer-based temporal reasoning with pixel-level scene supervision. This multi-loss training strategy explicitly aligns global activity recognition with local human-robot interaction semantics, which is particularly critical in low-visibility underwater conditions. To address the significant challenge of data scarcity in this domain, we present the first-ever Underwater Diver Activity (UDA) dataset, a foundational resource containing over 2,600 annotated images with pixel-level masks. Through rigorous experimental evaluations in a controlled environment, we demonstrate that DAR-Net achieves promising accuracy in recognizing six distinct diver activities, outperforming state-of-the-art models. While this dataset provides a crucial baseline, our work serves as a pioneering step, laying the groundwork for future research and facilitating the development of more intelligent, collaborative underwater robotic systems.

10.
arXiv (CS.CV) 2026-06-24

Modality-Aware Out-of-Distribution Detection for Multi-Modal Action Recognition

The incorporation of additional modalities into action recognition models increases their performance across a wide range of settings. However, how this additional information can contribute to making the models more robust remains underexplored, particularly for the case of multi-modal out-of-distribution (OOD) detection. While methods exist that regularize the multi-modal training process with OOD detection in mind, they still apply off-the-shelf OOD detectors designed for the uni-modal case during inference, discarding important information. Based on an interesting relationship we find between the multi-modal and uni-modal predictions, we propose to use this signal to build a post-hoc detector explicitly designed for the multi-modal scenario. We combine this new source of information with a feature-space score, which detects off-manifold samples in the multi-modal space, and normalize them by the multi-modal logits. In doing so, the proposed hybrid detector is compatible with existing training-time approaches and consistently improves performance. Experiments on a wide range of established datasets from the MultiOOD benchmark show that, on average, our approach outperforms the state of the art. Our results show the importance of explicitly considering the different modalities at inference time for multi-modal OOD detection.

11.
arXiv (CS.CV) 2026-06-24

Generative Manifold Distillation: Aligning Restoration Trajectories with Natural Image Prior

Pre-trained image restoration models often fail on out-of-distribution (OOD) real-world degradations. Adapting to these domains is challenging as real-world data lacks paired ground truth, and unsupervised methods often require unstable architectural changes. We propose Generative Manifold Distillation (GMD), which reframes domain adaptation as geometric manifold alignment. GMD operates in a strictly unpaired setting, requiring only low-quality (LQ) target observations. By leveraging the flow-matching dynamics of a frozen text-to-image foundation model, GMD projects off-manifold restorations onto the natural image manifold to generate high-quality pseudo-targets. To ensure stability, a quality-gated manifold filter rejects off-manifold samples, while source-anchored trajectory regularization prevents error accumulation. Ultimately, GMD distills a powerful generative prior into an efficient restoration network. Experiments demonstrate that GMD seamlessly adapts to new distributions using only LQ inputs, drastically improving perceptual quality with zero architectural modifications or added inference latency.

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

StagePilot: Stage-Level Planning for Long-Horizon Dialogue Simulation in Cybergrooming

Cybergrooming is an evolving threat to youth, requiring proactive educational interventions. We address this by modeling dialogue progression as a structured planning problem over stage-wise interactions. We propose StagePilot, a dialogue framework that separates stage-level planning from response generation, in which the model selects the next stage under constrained transitions and generates responses conditioned on it, enabling coherent and realistic progression. Reinforcement learning is used to learn stage-level policies from offline data, optimizing for both emotional alignment and goal-consistent progression. Our empirical experiments show that StagePilot generates more structured, coherent dialogue trajectories and reduces conversational stagnation compared to baselines; notably, the IQL+AWAC variant reaches the final stage more often while maintaining over 70% positive or neutral responses, yielding a 43% relative improvement.

13.
arXiv (CS.LG) 2026-06-18

SCAN: Enhance Time Series Anomaly Detection via Multi-Scale Neighborhood-Centered Clustering

arXiv:2606.19255v1 Announce Type: new Abstract: Time series anomaly detection plays a crucial role in a wide range of real-world applications. Reconstruction-based methods have become the mainstream paradigm, but they suffer from over-generalization and under-generalization problems, which are challenging to balance. To address this, we introduce multi-scale clustering to enhance reconstruction-based methods. At the representation level, we integrate the cluster center representations of normal patterns to constrain the model to target representative normal patterns for reconstruction, preventing dominance of powerful capacity and representation capability. At the anomaly criterion level, we derive anomaly confidence score based on cluster membership probability and combine it with reconstruction error, providing dual criteria for detection. Furthermore, the effectiveness of the cluster center representations and anomaly confidence score depends on the clustering performance. Accordingly, we extract neighborhood-centered representations for multi-view clustering to improve clustering performance. Extensive experiments on multiple real-world datasets from diverse application domains demonstrate the state-of-the-art performance of SCAN.

14.
arXiv (CS.AI) 2026-06-12

A Mathematical Forum Platform for Collaborative Problem Solving and Dataset Generation for AI Reasoning

arXiv:2606.12976v1 Announce Type: new Abstract: Sharing mathematical content in online forums remains a significant friction point for students and educators: writing raw LATEX is error-prone, standalone optical character recognition tools require platform switching, and current forum software offers no integrated path from a photograph of a formula to a rendered post. We present a unified system that eliminates this friction by embedding an image to LATEX conversion pipeline directly inside a forum posting interface. A user uploads or captures an image of a mathematical expression; the system routes it through the Mathpix OCR API, detects whether the returned output is LATEX or plain text containing inline math, applies the appropriate delimiter normalisation, and renders a live preview in either LATEX or Markdown mode before the post is committed to the database. The architecture is organized in three loosely coupled layers: image processing, rendering, and storage, and supports both desktop and mobile clients. A provisional US patent application has been filed covering the core methods. We describe the full system design, each component in detail, the data schema, and the key technical innovations, and we position the work against existing standalone tools and forum platforms to demonstrate the practical gap it closes. Beyond immediate usability, we argue that a deployed platform of this kind constitutes a continuously growing, community-validated dataset of mathematical problems and step-by-step solutions, a resource that can be used to train and benchmark AI systems for accurate mathematical reasoning

15.
medRxiv (Medicine) 2026-06-10

A Heterogeneous Graph Neural Network Framework for Multi-Horizon Stroke Mortality Prediction

Background: Machine learning models for stroke mortality prediction typically treat each time horizon independently and use flat tabular features that ignore the relational structure of electronic health records (EHRs). In this pilot study, we leveraged graph-based machine learning models to predict post stroke all-cause-mortality across three different time horizons. Methods: We developed Stroke Temporal Heterogeneous Graph (StrokeTHG), a heterogeneous graph neural network model for simultaneous multi-horizon stroke mortality prediction (30-day, 90-day, 1-year) using EHR data from Penn State Health System. The model encodes various relations among EHR entities (e.g., patient, diagnosis, comorbidity) and temporal encoding of admission time to better predict stroke mortality. We compared our proposed approach against various baseline methods, including Logistic Regression, Random Forest, and XGBoost. We also performed ablation and subgroup analyses, evaluated the quality of learned graph embeddings, and assessed the importance of different edge types in the graph. Results: We included 4,144 stroke patients (mean age 69.2 years; 54.3% men), of whom 3,332 (80.4%) survived their stroke after one year. 30-day, 90-day, and 1-year mortality rates were 9.7%, 13.7%, and 19.6%, respectively. Our proposed approach, StrokeTHG, achieved AUROC of 0.872, 0.878, and 0.837 across horizons, outperforming all tabular baselines. At [≥] , 75% specificity, the model identified 5-10 percentage points more mortality cases than the best baseline at each horizon. Subgroup analysis demonstrated consistent performance across sex subgroups and the largest discriminative gains in the Age 65-80 stratum. Edge-type ablation identified phenotype-patient and admission-patient edges in the constructed EHR graph as the most influential relational edges for mortality prediction. StrokeTHG embeddings outperformed all graph and matrix factorization baselines under an identical downstream classifier, confirming that performance gains stem from representation quality rather than classifier capacity. Conclusions: StrokeTHG demonstrates that heterogeneous graph representations of EHR data provide a consistent improvement over flat tabular models for multi-horizon stroke mortality prediction, with particular advantage at clinically actionable sensitivity thresholds and novel multi-horizon monotonic prediction capability. This methodological framework may be adaptable to other EHR-based clinical research studies seeking to leverage heterogeneous relational structures for predictive modeling.

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

Trait, Not State: The Durability of Reading Identity in Social Highlighting

Prior work on a social web highlighter located individuality in selection – which documents a person chooses to highlight – but measured it cross-sectionally. We ask the temporal question: is a reader's selection signature a trait or a state? We freeze each reader's first six months of highlighting as a profile and track its own-vs-other advantage on their later selections at growing gaps (to 24+ months), with negatives drawn from the same calendar era – so supply drift cannot masquerade as personal drift – at a coarse global level and at a fine level whose negatives and controls come from the reader's own interest neighborhood; the anchor cell reproduces the prior cross-sectional level (+0.188 vs +0.169), validating the harness. Four results. Within the same users, the fine-layer advantage shows no statistically detectable paired decline at any horizon (6-12 month retention R = 1.00 [0.85, 1.18], n = 212; the farthest bin is compatible with a modest decline; the only contrast whose interval excludes zero is the coarse layer at 12-24 months, about 13%). The signal is not reducible to repeated domains (~90% survives excluding all profile sources). Within-person drift is slow (a recent-half profile beats the old half by +0.042). Prospectively, personal profiles – even one built from a reader's earliest documents, median 20 months before evaluation – rank their next reads at roughly 3x the AP of every simple non-personal prior tested. We use "trait" operationally (a stable signature under continued engagement); the scope is heavy, long-tenured readers of one platform, and exposure is not separable from choice.

17.
arXiv (CS.CL) 2026-06-11

DEFINED: A Data-Efficient Computational Framework for Fine-Grained Creativity Assessment in Debate Scenarios

Human creativity has emerged as a critical competency in the era of large language models. Assessing creativity in complex, open-ended environments is a grand challenge in data mining, currently hindered by a reliance on standardized simple tasks and the scarcity of fine-grained expert data. As an ecologically valid assessment context, debate reflects multiple dimensions of creativity, encompassing both divergent thinking and convergent thinking. Moreover, debate is a data-rich domain, with a large volume of publicly accessible materials. Current mainstream automated scoring methods are poorly suited to complex settings such as debate, and therefore still rely on costly human evaluation. To this end, this paper proposes DEFINED, a data-efficient computational framework for fine-grained creativity assessment in debate scenarios. DEFINED operationalizes debate creativity through a hierarchical eight-dimensional metric system, implemented via a pre-trained autoregressive language model with a hierarchical scoring head that supports both fine-grained and coarse-grained evaluation. Statements and their associated expert scores were obtained from authentic debate competitions, and a constrained data augmentation strategy was employed to address the elite bias inherent in the original data. DEFINED adopts a mixed-granularity training strategy enabling robust learning from limited fine-grained supervision annotated by trained graduate experts. To rigorously validate ecological validity beyond synthetic benchmarks, we incorporate an empirical study with debate-naive participants, utilizing these authentic data to serve as a qualitative case study for mid-to-low proficiency populations. Across our evaluation protocol, our scoring model achieves accurate and stable scoring, outperforming prompt-based large language model evaluators and existing debate scoring methods.

18.
arXiv (CS.AI) 2026-06-24

video-SALMONN-R$^3$: Learning to ReWatch, ReAsk, and ReAnswer for Efficient Video Understanding

arXiv:2606.24477v1 Announce Type: cross Abstract: Video large language models (LLMs) are often constrained by computation and memory budgets, leading them to use reduced frame rates and spatial resolutions, which may cause them to miss critical information for question answering (QA). A practical and efficient solution is a two-stage paradigm: first perform coarse video understanding to localize relevant segments, and then re-watch these segments at higher temporal or spatial fidelity. In this paper, we present video-SALMONN-R$^3$, the first end-to-end video-LLM that enables re-watch through reinforcement learning without relying on chain-of-thought (CoT) cold-start. This design removes the need for costly CoT data annotations and avoids CoT-based supervised fine-tuning (SFT), which can otherwise degrade the pretrained video understanding abilities. To address the mismatch between the reasoning-first behavior induced by re-watch and the answer-first tendency of pretrained video-LLMs, we propose a re-answer strategy, in which the model first produces a direct answer in the first watch and then refines it after re-watching. Finally, to improve question adherence during re-watching, we propose a re-ask mechanism that re-injects the query when revisiting localized segments. Experimental results show that video-SALMONN-R$^3$ consistently outperforms both the base model and the QA-SFT baseline, while surpassing prior re-watch-based approaches with significantly lower computational cost. Code, models, and data will be publicly released upon acceptance.

19.
medRxiv (Medicine) 2026-06-24

Uncovering the fitness of endemically circulating Zika virus strains

Zika virus (ZIKV) is an arbovirus that usually causes few symptoms and has circulated endemically in Asia for decades. However, a large outbreak in South America in 2015 uncovered the serious risk of congenital Zika syndrome in infants born from ZIKV infected mothers. It is unknown whether a lineage with distinct pre-existing fitness advantage emerged from Asia to cause the South American outbreak, and whether there is ongoing evolution that can result in future globally fit strains. Here we used 107 sequences from a single setting (Thailand) collected over an 18 year period (2006-2023). We used novel analytical tools to identify distinct lineages that have circulated in the population and estimated their relative epidemiological fitness. We found there have been six lineages circulating sequentially in the country, with regular emergence and replacement of lineages showing higher fitness than their predecessors. We identified 15 lineage-defining amino acid changes, including four well-documented fitness-enhancing mutations, and two UTR substitutions. The lineage that emerged in South America was evolutionarily linked to the highest-fitness lineage in Thailand, carrying seven of our lineage-defining substitutions acquired during endemic circulation there, and subsequently accumulating four additional changes. After the global pandemic, endemic ZIKV in Thailand continued to evolve, with newly emerged lineages showing novel mutations and increased fitness. Our findings have key implications for the monitoring of ZIKV and can help identify the pathway to increased transmissibility of this globally important pathogen.

20.
arXiv (CS.AI) 2026-06-11

MLaGA: Multimodal Large Language and Graph Assistant

arXiv:2506.02568v2 Announce Type: replace Abstract: Large Language Models (LLMs) have demonstrated substantial efficacy in advancing graph-structured data analysis. Prevailing LLM-based graph methods excel in adapting LLMs to text-rich graphs, wherein node attributes are text descriptions. However, their applications to multimodal graphs–where nodes are associated with diverse attribute types, such as texts and images–remain underexplored, despite their ubiquity in real-world scenarios. To bridge the gap, we introduce the Multimodal Large Language and Graph Assistant (MLaGA), an innovative model that adeptly extends LLM capabilities to facilitate reasoning over complex graph structures and multimodal attributes. We first design a structure-aware multimodal encoder to align textual and visual attributes within a unified space through a joint graph pre-training objective. Subsequently, we implement a multimodal instruction-tuning approach to seamlessly integrate multimodal features and graph structures into the LLM through lightweight projectors. Extensive experiments across multiple datasets demonstrate the effectiveness of MLaGA compared to leading baseline methods, achieving superior performance in diverse graph learning tasks under both supervised and transfer learning scenarios.

21.
medRxiv (Medicine) 2026-06-18

Antimicrobial-resistant E. coli in human, animal and environmental reservoirs in rural Bangladeshi households with young children

In low-income countries, ESBL-producing Escherichia coli (ESBL-EC) is frequently detected in humans, animals and household environments, indicating widespread exposure to antimicrobial resistance (AMR). Established risk factors such as antibiotic use do not explain the high community carriage of AMR in all settings; identifying the dominant exposure pathways can inform interventions against AMR. We aimed to investigate (i) animal-human-environment sharing of AMR by assessing associations between the abundance of ESBL-EC in the household environment, domestic animal feces and young children's stool and (ii) household factors associated with ESBL-EC abundance in these reservoirs. We enrolled 112 households from the CRADLE trial in rural Bangladesh. We enumerated ESBL-EC in drinking water, food, child hand rinses, outdoor soil, indoor floor swabs, chicken and cow feces, and stool from children aged 6 months. We recorded indicators of sanitation, animal ownership/management, human and animal antibiotic use, and child exposure behaviors using structured questionnaires and spot checks. The highest prevalence of ESBL-EC was in child stool (95.6%) and animal feces (82.3-96.9%), followed by soil (48.2%) and floors (36.6%); < 10% of food, child hands and drinking water harbored ESBL-EC. The abundance of ESBL-EC in child stool was not associated with its abundance in any sampled matrix; the abundance in chicken but not cow feces showed positive correlations with soil, floors, child hands, and drinking water (correlation coefficients: 0.19-0.39, p-values < 0.05). Higher-quality latrines (improved, pour-flush, with slab) were associated with lower ESBL-EC abundance across matrices; unsafe animal management (animals roaming or spending the night inside the home) was associated with higher abundance. Child antibiotic use and exposure behaviors (soil ingestion, time spent on floor) were not associated with ESBL-EC abundance in child stool. We observed high AMR colonization among young children and domestic animals in rural Bangladesh not explained by traditional fecal-oral exposure pathways. Future studies should explore additional pathways and assess whether sanitation and animal management improvements can reduce AMR.

22.
bioRxiv (Bioinfo) 2026-06-14

Systematic AI-Driven Drug Repurposing via Clinical Trial Data Mining: A Framework and Six Cross-Therapeutic Case Studies.

作者:

Drug repurposing, the application of approved or shelved compounds to new therapeutic indications, offers a cost- and time-efficient alternative to de novo drug discovery. However, the systematic identification of repurposing candidates from the rapidly expanding body of clinical trial data remains a significant challenge. Here we present a publicly accessible AI-powered tool that mines the ClinicalTrials.gov registry to identify approved drugs with under-explored therapeutic potential in high-value disease areas. The tool integrates natural language processing, mechanism-of-action pathway analysis, and trial density scoring to surface candidates where biological plausibility is high and clinical trial coverage is sparse. We demonstrate the tool's utility across six cross-therapeutic case studies spanning oncology, cardiology, neurology, rare diseases, immunology, and infectious disease. Key findings include: the identification of Zonisamide as an under-explored combination candidate for obesity alongside GLP-1 receptor agonists; mechanistic validation of SGLT2 inhibitors in heart failure with preserved ejection fraction (HFpEF); and a novel cross-domain mapping of anti-TNF biologics to early-stage neurodegeneration via shared neuroinflammatory pathways. The tool is freely accessible and designed to lower the barrier for academic and industry researchers to systematically pursue repurposing opportunities.

23.
arXiv (quant-ph) 2026-06-11

Logical error estimation from syndrome data of surface-code experiments

arXiv:2606.11496v1 Announce Type: new Abstract: Decoders for quantum error correction (QEC) experiments rely on detector error models (DEMs), which encode, for each error, its probability and the detectors and logical observables it flips. Here we show that estimating DEM event probabilities from experimental syndromes is feasible, avoids independent device benchmarking, and produces useful decoder priors for estimating and reducing decoded logical error probabilities. We evaluate our methods using open-source data from surface-code memory experiments performed on Google's Willow chip, and we carry out analogous surface-code experiments on IBM's \texttt{ibm\_miami} processor. Despite the different physical error scales of the Google and IBM devices, in both cases our estimated DEMs improve logical error probabilities relative to baseline device-informed DEMs, typically at the $5\%-10\%$ level and with larger gains in some IBM cases, without additional calibration circuits, decoder fine-tuning, or supervised fitting to logical outcomes.

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

Conservation Laws for Modern Neural Architectures

arXiv:2606.17816v1 Announce Type: cross Abstract: Understanding gradient descent dynamics is key to explaining the success of over-parameterized models, where implicit bias manifests through conservation laws in gradient flow. While such laws are well understood for linear and ReLU networks, they remain largely unexplored for modern architectures. This work develops a unified framework to characterize conservation laws for contemporary models, including feedforward networks with GELU, SiLU, and SwiGLU activations, multihead attention with sinusoidal and rotary positional encodings, and Mixture-of-Experts architectures under diverse gating designs. Our theoretical findings are supported by experiments that validate the predicted invariants.

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

VGPT-RSI for RH-Adjacent Formal Progress: Boundary Certificates, Verified Finite Lagarias Inequalities, and Explicit Failure Localization

arXiv:2606.15096v1 Announce Type: new Abstract: The Riemann Hypothesis remains one of the central unsolved problems in mathematics. Rather than claiming proof, we investigate whether a verifiable AI-assisted reasoning system can produce reliable, formally checked partial progress while explicitly identifying the remaining mathematical obstructions. We apply the Verifiable Growing Physical Transformer with Recursive Self-Improvement (VGPT-RSI) to two RH-adjacent certification tasks. First, we construct and verify a finite RH-boundary certificate for inequality on a parameterized safe lower curve over a region. The numerical boundary curve is converted into a certificate-backed lower curve, audited using outward-rounded interval arithmetic and Arb/FLINT ball arithmetic, and then checked in Rocq/CoqInterval for the parameterized theorem. Second, we initiate a formal Lagarias-route certificate. Lagarias criterion states that RH is equivalent to the global inequality. We formalize the finite quantity and produce a Coq-checked finite certificate. The final system identifies the exact unresolved mathematical bottlenecks: formalizing the Lagarias equivalence, proving the global tail theorem beyond any finite cutoff, and potentially reducing counterexamples to colossally abundant or related extremal integers. These results demonstrate that VGPT-RSI can produce certified RH-adjacent formal progress, organize proof dependencies, and avoid overclaiming when the remaining obstruction is genuinely mathematical.