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01.
arXiv (quant-ph) 2026-06-16

Conditions for Unitarity in Timeless Quantum Theory

arXiv:2504.01579v3 Announce Type: replace Abstract: Quantum timeless approaches solve the problem of time by recovering the usual unitary evolution of quantum theory relative to a clock in a stationary quantum Universe. For some Hamiltonians of the Universe, such as those including an interaction term with the clock, the dynamics is substantially altered and can be non-unitary. This work derives necessary and sufficient conditions for the relative dynamics to be unitary and finds the general form of the unitary evolution operator. A physical interpretation of these conditions is given in terms of the clock's rate. Unitary dynamics is associated with rates that are constant in time and independent of the clock's internal structure.

02.
arXiv (CS.CL) 2026-06-24

Transformer-Based Language Models Across Domain Verticals: Architectures, Applications and Critical Assessment

Transformer-based language models have become the default substrate for natural language processing and the pace of new releases has made it hard for practitioners to separate durable ideas from the noise of incremental announcements. This review works at two levels. At the level of mechanism, we organise the main transformer families into a working taxonomy, covering encoder-only, decoder-only, encoder-decoder, long-context, permutation-based, and generator-discriminator variants. We then extend the discussion to post-2023 developments that changed the picture in practice: instruction tuning, reinforcement learning from human feedback, direct preference optimisation, mixture-of-experts scaling, retrieval augmentation and the current flagship model families from OpenAI, Anthropic, Google, Meta, Mistral and DeepSeek. At the level of use, we survey deployments across healthcare, finance, legal, education, customer service, creative writing and scientific work. Based on this we link each to the specific capabilities that make a transformer the appropriate tool. The contribution of this paper is a critical assessment that is based on the survey. We compare architectures on four axes that matter to deployment decisions, we quantify the trade-off between parameter count and energy cost. We also discuss how alignment methods, data provenance and benchmark saturation change what it means to call a model "state of the art". The final section lists the research questions that we think deserve more attention.

03.
arXiv (quant-ph) 2026-06-15

Universal Crossovers of Stabilizer Entropy Beyond Criticality

arXiv:2606.13810v1 Announce Type: new Abstract: Stabilizer Rényi entropy has emerged as a probe of nonstabilizerness in quantum many-body systems, but its scaling structure beyond critical points remains poorly understood compared with entanglement entropy. Recent field-theory approaches indicate that stabilizer entropy contains universal critical data and boundary-sensitive terms, raising the question of how these structures extend into massive and crossover regimes. We address this problem for a broad class of finite-range spin chains at Rényi index one-half. We derive exact finite-size formulas for both full periodic chains and finite intervals of the infinite chain, making the universal crossover from critical to noncritical behavior analytically accessible. In periodic geometry, the entropy obeys a volume law away from criticality and exhibits a universal finite-size crossover controlled by the competition between system size and correlation length. We also show that the large-scale SRE density develops a cusp across the field-tuned critical line, while the XX endpoint is governed by a distinct scaling regime associated with the saturation point. In the subsystem geometry, the interval entropy separates bulk critical behavior from boundary contributions generated by the way the finite region cuts the infinite chain. The crossover from critical to massive behavior is then encoded in boundary constants and universal functions controlled by the correlation length. Through exact stabilizer-entropy correspondences, the scaling theory extends to internal XY reductions, Finite-range spin chains, and Cluster–Ising representatives. Our results provide an exact lattice benchmark for the emerging QFT description of stabilizer entropy beyond isolated conformal points.

04.
medRxiv (Medicine) 2026-06-22

Nutrient Composition of Foods Represented in the U.S. Food and Nutrient Database for Dietary Studies, 2013-2023

Background: The U.S. Food and Nutrient Database for Dietary Studies (FNDDS) is updated across NHANES dietary cycles and is central to U.S. nutrition surveillance. However, multi-cycle food-code-level changes in nutrient composition have not been comprehensively characterized across the full WWEIA nutrient panel. Objective: To characterize ten-year temporal patterns in nutrient composition across five FNDDS cycles, evaluate pandemic-period food-code compositional stability, and distinguish exploratory mean-level signals from distributional heterogeneity that may reflect reformulation, database coverage, or food-code definition changes. Methods: We analyzed five consecutive FNDDS biennial releases: 2013-14, 2015-16, 2017-18, 2019-20, and 2021-23. Nutrient values were extracted from the public FNDDS/FoodData Central release files and standardized to per-100-g food-code-level records. Cycle midpoints, 2013.5, 2015.5, 2017.5, 2019.5, and 2022.0, served as the independent variable in an exploratory ordinary least squares (OLS) regression. Mann-Kendall testing assessed monotonic rank trends, Welch's ANOVA assessed food-code-level distributional heterogeneity, and pairwise Welch comparisons with Cohen's d summarized pre-pandemic, pandemic-period, and post-pandemic differences. Equivalence testing using TOST with +/-10% bounds was restricted to the 2019-20 versus 2021-23 stability comparison. OLS sensitivity analyses were repeated after excluding the structurally atypical 2017-18 cycle. Results: Sixty-three nutrients were analyzed. Eight nutrients showed nominal OLS trends, p < 0.05, but none remained significant after Bonferroni correction. Mann-Kendall testing identified two nominal monotonic signals, and none after adjustment. Welch's ANOVA detected cycle-level distributional differences for 61 of 63 nutrients at nominal p < 0.05 and 57 of 63 after adjustment. Pairwise pandemic-period analyses showed many adjusted differences when the pre-pandemic baseline was compared with 2019-20 or 2021-23, but standardized effects were small, with all absolute Cohen's d values < 0.20. No nutrient differed after adjustment between 2019-20 and 2021-23, and 39 of 48 primary analytes met +/-10% TOST equivalence criteria for that comparison. Slope estimates were directionally stable after excluding 2017-18, but nominal significance status remained sensitive to the short time series. Conclusions: FNDDS food composition varied across cycles, but there was no clear decade-long linear trend for most nutrients. The main signal was a possible increase in total PUFA and linoleic acid, which may reflect changes in fat quality. The 2021-23 cycle was very similar to 2019-20, suggesting no major post-pandemic shift in the foods represented. These findings should be interpreted as food-database signals, not as direct estimates of what people consumed.

05.
arXiv (CS.LG) 2026-06-18

A Streaming Sparse Cholesky Method for Derivative-Informed Gaussian Process Surrogates Within Digital Twin Applications

arXiv:2511.00366v2 Announce Type: replace-cross Abstract: Digital twins are developed to model the behavior of a specific physical asset (or twin), and they can consist of high-fidelity physics-based models or surrogates. A highly accurate surrogate is often preferred over multi-physics models as they enable forecasting the physical twin future state in real-time. To adapt to a specific physical twin, the digital twin model must be updated using in-service data from that physical twin. In this paper, we combine and extend several previous surrogate-related advancements with the goal of demonstrating an end-to-end digital twin (DT) solution for predicting performance of an aircraft structure (the physical asset). To this end, we extend Gaussian process (GP) models to include derivative data, for improved accuracy, with dynamic updating to ingest physical twin data during service. Including derivative data, however, comes at a prohibitive cost of increased covariance matrix dimension. We circumvent this issue through our modified dynamic sparse Cholesky linear system solver. Numerical experiments demonstrate that the prediction accuracy of the derivative-enhanced sparse Cholesky GP method produces improved models upon dynamic data additions. Lastly, we demonstrate the developed algorithm within a DT framework to model fatigue crack growth in an aerospace vehicle, thereby exhibiting through our assembled engineered system how digital twin technologies can be combined in practice.

06.
arXiv (quant-ph) 2026-06-19

Optimizing resource allocation for accuracy in noisy variational quantum algorithms

arXiv:2606.20153v1 Announce Type: new Abstract: For quantum algorithms to achieve their full potential, we need methodologies to optimize them, such as reaching a given output accuracy with minimal resource costs. Here, we develop such a methodology for a class of Noisy Intermediate-Scale Quantum (NISQ) algorithms. We leverage simulations of a Variational Quantum Eigensolver (VQE) to propose a phenomenological model of such algorithms that captures the complex relationship between algorithmic accuracy, algorithmic resource costs, and the noise that exists in realistic quantum hardware. For this, we take the algorithmic resource cost to be the total number of quantum gate-operations in the algorithm; minimizing this cost typically makes the algorithm faster and more energy-efficient. We consider the subtle trade-off between quantum circuit size (small circuits are too imprecise, but large ones are too noisy), and the number of iterations of that quantum circuit for the full algorithm to sufficiently converge. Using a noise-metric-resource methodology, we identify the sweet spot (of circuit size versus iterations) that minimizes the algorithmic resource costs for a desired algorithm accuracy. It also gives the circuit size that maximizes algorithm accuracy for a fixed resource cost. Our methodology provides a practical guideline for near-term deployment of variational algorithms on realistic noisy hardware, including hardware that uses error mitigation.

07.
arXiv (CS.AI) 2026-06-15

Capability Minimization as a Safety Primitive: Risk-Aware Causal Gating for Least-Privilege LLM Agents

arXiv:2606.13884v1 Announce Type: new Abstract: Modern decision systems increasingly rely on learned components whose outputs may be confident yet wrong, exposing downstream actions to costly errors. We introduce Risk-Aware Causal Gating (RACG), a framework that decides whether to act on, defer, or abstain from a model's prediction by combining causal effect estimation with calibrated risk control. RACG models the causal pathway from candidate actions to outcomes and gates each decision according to an estimated counterfactual risk rather than raw predictive confidence. To make gating reliable, we derive distribution-free bounds on the probability of acting under high-risk conditions and show how these bounds translate into operating thresholds that satisfy user-specified safety constraints. We further propose an adaptive gating policy that adjusts to distribution shift by monitoring discrepancies between predicted and realized outcomes, tightening the gate when causal assumptions appear violated. Across simulated interventions and real-world decision benchmarks, RACG reduces high-cost errors substantially while preserving most of the utility of an ungated policy, and it outperforms confidence-based and selective-prediction baselines at matched abstention rates. Our results indicate that explicitly separating causal risk from predictive uncertainty yields decision systems that are both safer and more transparent, offering a principled mechanism for trustworthy automation in high-stakes settings.

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

Structured vs. Unstructured Pruning: An Exponential Gap

arXiv:2603.02234v3 Announce Type: replace-cross Abstract: The Strong Lottery Ticket Hypothesis (SLTH) states that large, randomly initialized neural networks contain sparse subnetworks capable of approximating a target function at initialization without training, suggesting that pruning alone is sufficient. Pruning methods are typically classified as unstructured, where individual weights can be removed from the network, and structured, where parameters are removed according to specific patterns, as in neuron pruning. Existing theoretical results supporting the SLTH rely almost exclusively on unstructured pruning, showing that logarithmic overparameterization suffices to approximate simple target networks. In contrast, neuron pruning has received limited theoretical attention, despite its practical appeal for direct hardware speedups. In this work, we consider the problem of approximating a single bias-free ReLU neuron by pruning hidden units of a randomly initialized two-layer ReLU network, effectively isolating the intrinsic limitations of neuron pruning. We show that achieving an $\varepsilon$-approximation requires a starting network size of $\Omega(1/\varepsilon)$ for neuron pruning, whereas weight pruning succeeds with only $O(\log(1/\varepsilon))$ hidden units, revealing an exponential separation between the two approaches.

09.
arXiv (CS.LG) 2026-06-24

GRACE: Gated Refinement for Accurate Causal Edge Discovery in High-Dimensional Time Series

arXiv:2606.23880v1 Announce Type: new Abstract: From climate teleconnections to gene regulation, modern time-series datasets encompass tens or hundreds of interacting variables, making causal discovery increasingly challenging. Constraint-based methods offer statistical rigor but their nonlinear CI tests are infeasible at scale, while score-based alternatives avoid CI testing but require arbitrary thresholds to binarize continuous edge scores. We propose GRACE ($G$ated $R$efinement for $A$ccurate $C$ausal $E$dge discovery), which refines constraint-based discovery using Hard Concrete gates with $L_0$ regularization: each candidate edge has an independent gate whose values concentrate near 0 or 1, yielding a clean bimodal separation that makes the binary decision robust, unlike the narrow, overlapping score distributions produced by $L_1$ and attention-based methods. A fast linear CI skeleton provides high-recall candidates; a single gated model then prunes false positives by learning which edges genuinely improve prediction, with automatic regularization adapted to problem dimensions and skeleton density. Systematic experiments on synthetic benchmarks, spanning diverse graph topologies (scale-free, Erdős-R'enyi, small-world) and dimensionalities up to $d=100$, show that GRACE substantially improves F1 over its base CI method while maintaining high precision, and outperforms attention-based and score-based alternatives. GRACE matches or exceeds expensive nonlinear CI tests at a fraction of the cost ($75\times$ faster). On a real-world river flow dataset, where rainfall confounders, variable propagation lags, and distributional shifts violate standard assumptions, a temporal bootstrap variant of GRACE recovers 9 of 11 causal edges along the Elbe River with only 1 false positive ($F_1 = 0.86$, AUROC${} = 0.99$), reducing the skeleton's 106 false positives by 99%.

10.
bioRxiv (Bioinfo) 2026-06-13

Virus-human protein-protein interactions predict viral phenotypes

Viral phenotypes such as host and tissue tropism are critical determinants of viral infection and transmission. Inferring viral phenotypes presents unique challenges compared to cellular organisms, as viruses rely entirely on host machinery for replication and survival. Current methods for predicting viral phenotypes mainly rely on viral genomic data, often overlooking host-related information. Here, we evaluated the utility of predicted virus-human protein-protein interactions (PPIs) in inferring diverse viral phenotypes using machine-learning algorithms. For predicting human infectivity, a PPI-based machine learning model outperformed both virus genomic and protein sequence-based models that used large language model embeddings. It also surpassed previous methods that incorporated both viral and host genomic data. The human proteins identified by the model were significantly enriched in functions related to viral infection and immune response. In predicting various phenotypes of human RNA viruses, PPI-based models performed better than virus sequence-based models in forecasting virulence, human transmissibility and transmission routes, while showing comparable performance to genomic sequence-based models in predicting tissue tropism. Finally, we demonstrated that a PPI-based model could distinguish high-risk HPV genotypes from low-risk ones. Proteins associated with high-risk HPV were involved in apoptosis and immune regulation, whereas those linked to low-risk HPV were enriched in telomere maintenance and DNA repair. Collectively, this study is the first to demonstrate the value of predicted virus-human PPIs in inferring viral phenotypes, thereby enhancing our understanding of the molecular mechanisms underlying these phenotypes. It also provides effective tools for risk assessment of emerging viruses, contributing to improved pandemic preparedness.

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

From Physics to Representation: Audio Learning with Synthetic Pre-training via Procedural Generation

arXiv:2606.14791v1 Announce Type: cross Abstract: Self-supervised learning advances audio representation for multimedia analysis. However, prevailing data-centric approaches rely on massive real-world corpora, increasing training costs, curation burdens, and privacy barriers. To address this, we present AudioPG, a procedural synthesis framework eliminating real audio recordings during pre-training. AudioPG trains a Transformer-based masked autoencoder on waveforms generated on-the-fly from basic acoustic primitives and composition rules. The encoder transfers effectively to real audio benchmarks, achieving 90.60% accuracy on ESC-50, 0.546 mAP on FSD50K, 88.17% on UrbanSound8K, and 97.03% on Speech Commands V2. Notably, pre-training completes in under 20 minutes on a single GPU. Latent space analysis reveals physical factors, including fundamental frequency and relative intensity, emerge in orthogonal subspaces, making representations linearly decodable. These results establish procedural synthesis as an efficient, interpretable pre-training signal when large-scale corpora are unavailable. Our code is available at: https://github.com/Freyliu0516/audioPG.

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

Agentic Electronic Design Automation: A Handoff Perspective

arXiv:2606.19795v1 Announce Type: cross Abstract: Electronic design automation (EDA) is inherently multi-stage and handoff-heavy. Design artifacts, flow scripts, and engineering decisions cross tool, session, and organizational boundaries before final implementation, signoff, or release. Each transfer carries explicit and implicit requirements that may not be fully captured by stage-local checks. LLM-based agents now invoke EDA tools directly, embed retrieved knowledge in executable scripts, and hand off state across sessions and stages. Once their outputs condition downstream engineering decisions, the transferred object must satisfy a handoff contract and meet the assumptions of its next consumer. This survey introduces handoff validity as its organizing principle. A handoff is valid when the transferred object satisfies the consumer's acceptance conditions and carries sufficient context, evidence, and provenance for downstream use. We review 82 systems and classify them into three boundary classes. Stage-Bound systems establish validity within a single EDA stage or bounded verification task. Flow-Bound systems preserve coherent workflow state across tools, invocations, and sessions. Organization-Bound systems maintain source grounding, provenance, scope, and admissibility across knowledge and authority boundaries. For each class, we analyze handoff contracts, handoff objects, coordination mechanisms, and open questions. These analyses motivate a five-layer EDA agent communication protocol (EACP), covering the agent discovery, agent message, tool invocation, workflow orchestration, and security and IP protocols. We aim to provide a common vocabulary and research agenda for trustworthy agentic EDA.

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

Steering the Noise: Turning Random Perturbations into Effective Descent for Memory-Efficient LLM Fine-Tuning

Fine-tuning large language models (LLMs) achieves strong performance but is often limited by the memory overhead of backpropagation. Zeroth-order (ZO) optimization avoids this overhead by estimating gradients through forward passes alone, yet it typically converges slowly because random Gaussian perturbations yield high-variance gradient estimates in high-dimensional parameter spaces. In this paper, we propose a plug-and-play framework that turns random perturbations into more effective descent directions. The key idea is to draw a small pool of candidate perturbations, evaluate their loss values, and then select or combine those that are best aligned with the optimization objective. We develop two instantiations of this idea: MeZO-GV, which forms a guiding vector from the contrast between low-loss and high-loss perturbation groups, and MeZO-Greedy, which keeps the single best perturbation within a fixed evaluation budget. We theoretically show that both strategies yield a larger per-step reduction in the objective than standard ZO estimation, leading to improved convergence rates. Experiments on LLMs of different scales and architectures confirm that the proposed methods integrate naturally with existing ZO optimizers and consistently improve convergence speed and task accuracy. On OPT-13B, our approach outperforms all ZO baselines across 11 benchmarks and exceeds gradient-based methods on 9 of them, while retaining the memory efficiency of forward-only optimization.

14.
arXiv (quant-ph) 2026-06-12

Unifying spacetime approaches to quantum mechanics

arXiv:2606.12539v1 Announce Type: new Abstract: Recent efforts to formulate quantum mechanics in a way that treats space and time on a more equal footing have led to a large variety of spacetime-oriented approaches. In this work we present a detailed study of spacetime states, the objects that play the role of quantum states in the recently introduced framework of spacetime quantum mechanics, and show that the main proposals in the literature are different manifestations of the same underlying object. Path integrals, quantum states over time, pseudo-density matrices, the Page and Wootters mechanism, superdensity operators, and timelike-entanglement proposals all arise from spacetime states through particular evaluations, reduced information, linear maps, or quantum channels. This unification provides explicit mathematical representations of these formalisms, reveals relations among them, and clarifies the spacetime information each one captures. We also study the broader relevance of the spacetime-state point of view for Leggett-Garg inequalities, OTOCs, temporal tensor networks, fermionic systems, relativistic QFTs, quantum reference frames, and classical physics, together with additional insights and perspectives revealed by the common unifying framework.

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

Open-World Video Segmentation

While video segmentation has advanced rapidly on short clips and closed-set benchmarks, open-world video segmentation remains largely unexplored. The challenge is twofold: (1) existing methods are not designed to support object discovery and identity maintenance in long videos of dynamic ego-motion, and (2) existing evaluation protocols rely on a rigid 1:1 matching that unfairly penalizes semantically valid predictions with mismatched granularity. To address both gaps, we introduce Savvy, a practical and strong system for zero-shot open-world long-horizon video segmentation. Savvy combines hierarchical mask discovery, deferred admission, and track consolidation to support persistent object discovery, safe track promotion, and stable long-range identity maintenance. We further propose OGA, a granularity-aware evaluation suite for open-world video segmentation. Built on a Granularity-Agnostic (GA) matching protocol, OGA relaxes conventional 1:1 matching to an n:1 mapping, but still enforces temporal rigor by detecting support discontinuities through sever points and scoring each reference object through its dominant coherent fragment. This prevents fragmented or flickering support from being over-rewarded while enabling GA-adapted metrics and structural diagnostics: identity persistence (IP), and identity concentration (IC). On VIPSeg, we show that standard 1:1 evaluation substantially underestimates open-world methods, whereas GA evaluation recovers much of their suppressed performance. On the more realistic long-horizon benchmarks: ScanNet and HM3D, Savvy consistently outperforms strong baselines across both classical and proposed metrics, including STQ, VPQ$_\infty$, IP and IC. Together, these results establish a practical benchmark and a strong baseline for open-world long-horizon video segmentation.

16.
PLOS Computational Biology 2026-05-29

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

Authors:

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.

17.
bioRxiv (Bioinfo) 2026-06-11

A Deep Hypergraph Learning Model for Predicting Antimicrobial Combination Effects Across Bacterial Targets

Antimicrobial resistance (AMR) creates an urgent need for efficient strategies to identify effective antibacterial combinations. Combination therapy, including antimicrobial peptides (AMPs) paired with conventional antibiotics, is a promising approach, but exhaustive experimental screening across drug pairs and bacterial targets is impractical. This study introduces a hybrid GCN-based hypergraph neural network (HGNN) for predicting antimicrobial-agent combination outcomes against bacterial targets. Each antimicrobial-agent-antimicrobial-agent-bacterium triplet is represented as a ternary hyperedge, enabling the model to learn context-dependent interaction patterns. The framework integrates SMILES-derived molecular graph embeddings for antimicrobial agents, including conventional antibiotics and AMPs, with taxonomy-derived bacterial representations. The prediction task was formulated as a three-class classification problem: synergy, antagonism, and non-interaction. The non-interaction class included experimentally verified indifferent records and synthetic presumed non-interaction triplets generated by negative sampling. Model development used drug-pair-grouped splitting, five-fold grouped cross-validation within the training/validation partition, and final evaluation on a held-out test set. On the held-out three-class test set, the selected GCN-based HGNN achieved an accuracy of 0.83, weighted F1-score of 0.84, macro F1-score of 0.80, and ROC-AUC of 0.95. Per-class evaluation showed accuracies of 0.80 for synergy, 0.92 for antagonism, and 0.85 for non-interaction. Pair-type analysis showed strong performance across AMP-AMP, AMP-conventional antibiotic, and conventional antibiotic-conventional antibiotic combinations. These findings suggest that hypergraph-based representation learning can support computational prioritization of antimicrobial combinations for experimental follow-up. Further studies will be needed to improve model interpretability and to perform prospective validation of predicted synergistic combinations.

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

Let LLMs Judge Each Other: Multi-Agent Peer-Reviewed Reasoning for Medical Question Answering

Objective: To enhance the accuracy, interpretability, and robustness of large language models (LLMs) in medical question answering (MedQA). Method: We designed a multi-agent peer-reviewed reasoning method in which multiple LLM agents independently generate chain-of-thought reasoning with candidate answers, then act as peer reviewers to evaluate each other's reasoning for factual correctness and logical soundness. The highest-rated reasoning chain is selected to produce the final answer. Experiments were conducted with five state-of-the-art LLMs (Llama-3.1-8B, Qwen2.5-7B, Phi-4, DeepSeek-LLM-7B, GPT-oss-20B) on three benchmark datasets: HeadQA, MedQA-USMLE, and PubMedQA. Performance was compared against single-model chain-of-thought reasoning and chain-of-thought-based majority voting. Results: Peer-reviewed reasoning consistently outperformed both baselines. The best model combination achieved an average accuracy of 0.820 across datasets, exceeding the strongest single model (0.777) and majority voting ensembles (up to 0.789). The method also scaled effectively with more participating models, while peer assessments reliably distinguished high- from low-quality reasoning chains. Conclusion: The proposed multi-agent peer-reviewed reasoning method enables LLMs to act as both solvers and evaluators, yielding superior performance in MedQA. By emphasizing reasoning quality rather than answer agreement alone, this approach improves accuracy, interpretability, and robustness, offering a promising direction for trustworthy biomedical AI systems.

19.
PLOS Computational Biology 2026-06-03

IsoPepTracker: An interactive web application for peptide-driven isoform analysis

Authors:

by Araf Mahmud, Chen Huang Alternative splicing affects 95% of multi-exon genes, generating protein isoforms with distinct functions. While current alternative splicing analyses effectively identify splice events at the RNA level, they provide limited protein-level insight. To address this gap, we developed IsoPepTracker (https://www.isopeptracker.org), a user-friendly web application for analyzing and visualizing differential peptides across canonical and novel isoforms that are theoretically detectable by shotgun mass spectrometry-based proteomics. IsoPepTracker features four modules: Canonical Isoform Analysis, Novel Isoform Discovery, Peptide Sequence Search, and Alternative Splicing Analysis. Each module is tailored for distinct and complementary proteogenomics analyses. Users can input genes, novel cDNA sequences, peptides, or alternative splicing results to pinpoint peptides of interest and identify their associations with target genes or isoforms. We demonstrate the straightforward application of IsoPepTracker in proteogenomics through case studies. IsoPepTracker not only provides informative peptide signatures to understand the protein-level consequences of alternative splicing but also supplies peptide candidates for validation in shotgun proteomics.

20.
arXiv (CS.AI) 2026-06-24

Dual-Anchoring: Addressing State Drift in Vision-Language Navigation

arXiv:2604.17473v4 Announce Type: replace-cross Abstract: Vision-Language Navigation(VLN) requires an agent to navigate through 3D environments by following natural language instructions. While recent Video Large Language Models(Video-LLMs) have largely advanced VLN, they remain highly susceptible to State Drift in long scenarios. In these cases, the agent's internal state drifts away from the true task execution state, leading to aimless wandering and failure to execute essential maneuvers in the instruction. We attribute this failure to two distinct cognitive deficits: Progress Drift, where the agent fails to distinguish completed sub-goals from remaining ones, and Memory Drift, where the agent's history representations degrade, making it lose track of visited landmarks. In this paper, we propose a Dual-Anchoring Framework that explicitly anchors the instruction progress and history representations. First, to address progress drift, we introduce Instruction Progress Anchoring, which supervises the agent to generate structured text tokens that delineate completed versus remaining sub-goals. Second, to mitigate memory drift, we propose Memory Landmark Anchoring, which utilizes a Landmark-Centric World Model to retrospectively predict object-centric embeddings extracted by the Segment Anything Model, compelling the agent to explicitly verify past observations and preserve distinct representations of visited landmarks. Facilitating this framework, we curate two extensive datasets: 3.6 million samples with explicit progress descriptions, and 937k grounded landmark data for retrospective verification. Extensive experiments in both simulation and real-world environments demonstrate the superiority of our method, achieving a 15.2% improvement in Success Rate and a remarkable 24.7% gain on long-horizon trajectories. To facilitate further research, we will release our code, data generation pipelines, and the collected datasets.

21.
medRxiv (Medicine) 2026-06-22

How knowledge shapes community stigma and social support for women seeking abortion in the Democratic Republic of Congo: A cross-sectional study.

Background The Democratic Republic of Congo (DRC) bears one of the highest maternal mortality ratios globally (746 per 100,000 live births), with nearly 11% of deaths attributable to complications of unsafe abortion. Despite ratification of the Maputo Protocol and related national policies, access to safe abortion remains limited, largely due to entrenched stigma. Social support, encompassing emotional, informational, and instrumental assistance, is critical in shaping womens abortion-seeking behaviors and health outcomes. This study examines the influence of community-level knowledge on stigma and social support for women seeking abortion care. Methods A cross-sectional survey was conducted from May 2024 to June 2024 among 1,715 adults in Kinshasa and North Kivu provinces. Analyses focused on a sub-sample of 574 respondents reporting familiarity with women who had undergone abortion. Structural Equation Modeling (SEM) was applied to estimate direct and indirect pathways linking community knowledge, stigma, and social support. Results Two core knowledge indicators, recognition of abortion as a safe medical procedure and awareness of legal conditions for access, were significantly associated with outcomes. A one-unit increase in knowledge corresponded to a 0.39-point increase in social support and a 0.19-point reduction in stigma. Enhanced knowledge promoted empathetic attitudes, reinforced practical support, and mitigated moralizing judgments toward women seeking abortion. Conclusions Strengthening community knowledge emerges as a strategic lever to reduce abortion-related stigma and enhance social support in the DRC. These findings underscore the importance of integrating stigma-reduction and knowledge-enhancement interventions into reproductive health programs to improve womens access to safe and dignified abortion care.

22.
arXiv (CS.LG) 2026-06-12

DeepJEB++: Foundation Model-Driven Large-Scale 3D Engineering Dataset via 2D Latent Space Augmentation

arXiv:2606.12994v1 Announce Type: new Abstract: Data-driven engineering design is constrained by the lack of large-scale 3D datasets that pair geometry with physics-based performance labels. In particular, existing 3D data augmentation techniques have limitations in preserving subtle and diverse geometric variations, and it remains difficult to automate the subsequent simulation-labeling process, where boundary conditions vary depending on the generated geometry. We present DeepJEB++, a foundation-model-driven data-augmentation framework that expands a small seed set of jet engine brackets into a large, simulation-labeled 3D dataset under constrained resources. Our key idea is to augment in the data-rich 2D latent space, then transfer to 3D. In Stage 1, we fine-tune a pretrained 2D latent diffusion model on multi-view renders and synthesize novel views by latent interpolation, retaining manufacturable designs through a vision-language-model (VLM) quality filter. In Stage 2, the validated images are lifted to 3D meshes by a domain-adapted generative foundation model. In Stage 3, an automated pipeline recognizes the load and bolt interfaces on each mesh and assigns finite-element labels – mass, stress, and displacement – without manual intervention. We assess augmentation quality along three intrinsic axes: manufacturability, label fidelity against the SimJEB ground truth, and distributional consistency. Starting from fewer than 400 seed designs, DeepJEB++ yields 15,360 simulation-labeled 3D brackets – a 40x expansion – using a single GPU per stage. The dataset will be made publicly available to support reproducible engineering-AI research.

23.
arXiv (CS.LG) 2026-06-11

Mirror Descent Beyond Euclidean Stability: An Exponential Separation in Initialization Sensitivity

arXiv:2606.11431v1 Announce Type: new Abstract: Mirror Descent (MD) extends Gradient Descent (GD) beyond Euclidean geometry and has recently reappeared as a lens for KL-regularized policy optimization in reinforcement learning and LLM post-training. This raises a basic robustness question, crucial to reproducibility and reliability: how sensitive are MD dynamics to their inputs? We focus on initialization, often itself a pretrained or previously aligned model. Quadratic-regularized MD, including GD and Mahalanobis geometries, is well-known to be stable for convex smooth objectives. We show a sharp contrast: once the regularizer is non-quadratic, MD can be exponentially more sensitive to initialization than GD, even with a well-conditioned regularizer in Euclidean norm. We give a three-dimensional construction with a convex, smooth objective and a strongly convex, smooth, well-conditioned regularizer where an initial $\varepsilon$ perturbation is quickly amplified to $\min\{polylog^{-1}(1/\varepsilon), \varepsilon e^{\Omega(\eta T)}\}$ after $T$ iterations of MD with step size $\eta$. For canonical KL-regularized MD on the simplex, we show that even linear objectives can amplify an initial $\varepsilon$ perturbation exponentially fast in high-dimensional or near-boundary regimes. Finally, we show that adding a Bregman regularization term toward an anchor point can stabilize the dynamics while largely preserving the optimization guarantees, and that the choice of anchor is crucial: anchoring at the initialization only partially mitigates the instability, whereas anchoring at a fixed point yields a more stable mechanism.

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

Rapid FinFET Modelling Using an Autoencoder

arXiv:2606.24046v1 Announce Type: cross Abstract: This work presents a machine learning framework that leverages an autoencoder (AE) for the efficient modeling of FinFET. We first calibrated a BSIM-CMG model to generate a dataset of current-voltage (ID-VG) characteristics. This data was used to train an autoencoder that compresses full I-V curves into a low-dimensional latent space, which intrinsically encodes key device physics. A key innovation is the explicit incorporation of parameter such as drain to source voltage (VDS) as an input feature, enhancing the model ability to capture bias dependent variation. The trained model successfully reconstructs full I-V curves and directly extracts critical device metrics including threshold voltage (VTH), subthreshold slope (SS), and peak transconductance (gm). This approach demonstrates that data driven compact models, built from actual characterization data, can achieve high accuracy with minimal training data, providing a powerful tool for rapid device characterization, modelling and circuit level simulation.

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

Neural Bayesian Anomaly Mitigation: A Robust Loss that Doubles as an Unsupervised Contamination Classifier

arXiv:2606.16524v1 Announce Type: new Abstract: Engineered robust losses such as Huber, Student-$t$, and generalised cross-entropy make supervised models tolerant of contamination but cannot answer which observations are corrupted. We introduce Neural Bayesian Anomaly Mitigation (NBAM), a general-purpose drop-in loss derived from a Bayesian latent-switch mixture model: the marginal likelihood defines a robust supervised loss, and the associated posterior defines an unsupervised contamination classifier. Like Huber or Student-$t$, NBAM can replace the standard training loss in any supervised pipeline; unlike them, it additionally learns a structured contamination model and returns a calibrated per-sample contamination posterior. A learned input-dependent prior $\pi_\phi(x)$ captures the spatial locality of contamination, so that samples near known corruptions are more likely to be flagged, while an Occam penalty emerges automatically and regularises against over-flagging. On CIFAR-10 with asymmetric label contamination, NBAM recovers the structure of the corruption process without supervision: the contamination posterior separates clean from corrupted samples, and the learned anomaly head identifies the direction of every label-flip pair. Alongside these capabilities, NBAM outperforms the four robust-loss baselines considered here at contamination rates 0.2-0.6.