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

Towards Advanced Mathematical Reasoning for LLMs via First-Order Logic Theorem Proving

Large language models (LLMs) have shown promising first-order logic (FOL) reasoning capabilities with applications in various areas. However, their effectiveness in complex mathematical reasoning involving multi-step FOL deductions is still under-researched. While LLMs perform competitively on established mathematical reasoning benchmarks, they struggle with multi-step FOL tasks, as demonstrated by Deepseek-Prover-V2-7B's low accuracy (4.2%) on our proposed theorem proving dataset. This issue arises from the limited exploration of diverse proof strategies and the potential for early reasoning mistakes to undermine entire proofs. To address these issues, we propose DREAM, a self-adaptive solution that enhances the Diversity and REAsonability of LLMs' generation strategies. DREAM incorporates an Axiom-Driven Strategy Diversification mechanism to promote varied strategic outcomes and a Sub-Proposition Error Feedback to help LLMs reflect on and correct their proofs. Our contributions include pioneering advancements in LLMs' mathematical reasoning through FOL theorem proving, introducing a novel inference stage solution that improves performance by 0.6% to 6.4%, and providing a curated dataset of 447 mathematical theorems in Lean 4 format for evaluation.

02.
arXiv (math.PR) 2026-06-16

Collapsibility in Multiparametric Models of Random Simplicial Complexes

Authors:

arXiv:2606.15276v1 Announce Type: cross Abstract: We study collapsibility in the multiparametric models of random simplicial complexes, namely the lower and upper models. In the upper model, we improve upon a result of Farber and Nowik, and assert that the homology is a.a.s concentrated in a single dimension by proving that the complex collapses to that \di. In the lower model, we prove that the complex a.a.s collapses to the \di\ with maximal non-trivial cohomology. We then compare this threshold to the ones derived previously for the special cases of the clique complex (by Kahle) and the Linial-Meshulam model.

03.
arXiv (quant-ph) 2026-06-16

Programmable Gauge-Field Textures with Ultracold Atoms in Momentum Space

arXiv:2606.15124v1 Announce Type: cross Abstract: Synthetic gauge fields with ultracold atoms offer a route to quantum matter in which electromagnetic environments can be designed rather than merely imposed. While the Harper-Hofstadter model has been realized in several cold-atom systems, existing implementations are largely limited to spatially uniform magnetic fluxes. Here we experimentally realize a highly programmable two-dimensional momentum-state lattice of ultracold atoms with local control over the Peierls phase pattern, enabling direct implementation of Harper-Hofstadter Hamiltonians with tunable and spatially structured synthetic gauge fields. We observe a crossover from ballistic to strongly flux-modified bulk dynamics with suppressed transport. By introducing a synthetic electric field through site-dependent energy gradients, we further demonstrate Hall-type transverse drift arising from the interplay between electric and magnetic fields. In addition, we engineer a synthetic flux domain wall separating regions with opposite magnetic fluxes and observe anisotropic propagation guided along the interface. These results move cold-atom gauge-field engineering from uniform magnetic backgrounds toward designer gauge textures, providing an experimental setting for transport across programmable topological interfaces.

04.
arXiv (CS.CV) 2026-06-24

Venice-H1: Failure-Aware Query Re-Ranking with Multi-Scale Grid Signatures for Referring Image Segmentation

Modern Referring Image Segmentation (RIS) systems generate multiple candidate masks per expression but rely on a simple heuristic–typically the argmax detection score–to select the final output. We identify query selection as a failure-case bottleneck: although heuristic selection succeeds on 82-93% of samples, the residual 7-18% of failures dominate the error budget, leaving a best-query selection gap of 3-11% mIoU. We introduce Venice-H1, a lightweight, backbone-decoupled post-hoc re-ranking module that encodes each candidate through multi-scale grid signatures–compact spatial descriptors pooled onto 4x4, 8x8, and 16x16 grids–and feeds them to a Transformer-based re-ranker with a Failure Gate (ROCAUC 0.78-0.82) that intervenes only when the default choice is likely suboptimal. Instantiated on DeRIS-L and DeRIS-B, Venice-H1 achieves delta_fail of +1.40 and +0.89 mIoU with strictly positive 95% CIs on all 16/16 (split, backbone) pairs and harmful-switch rates below 0.53%. Zero-shot transfer to medical referring segmentation (MS-CXR, M3D-RefSeg-2D) yields +1.16 and +0.51 mIoU without RIS-backbone fine-tuning. The module adds approximately 11.3M parameters and under 1 ms latency.

05.
arXiv (CS.LG) 2026-06-19

Full-Self Diagnostics (FSD): Physics-Grounded Visual Biomarker Inference from Smartphone Video via Inverse Problems and Operator Learning

arXiv:2606.19372v1 Announce Type: cross Abstract: We present Full-Self Diagnostics (FSD), a unified mathematical framework for recovering latent physiological states from unconstrained 9-second facial videos captured by consumer smartphones. The approach integrates five mutually reinforcing components: (1) a physics-based forward model derived from the radiative transfer equation and chromophore absorption that maps camera observables to biomarker concentrations; (2) an information-theoretic observability theory proving that multi-channel visual signals (spectral, pulse, respiratory, micro-expression, and oculomotor) contain strictly increasing mutual information with physiological state; (3) a stable, Tikhonov-regularized inverse problem with domain-uniform identifiability guarantees; (4) an operator-learning formulation that enables generalization across devices, resolutions, and populations; and (5) a supervised learning procedure, interpretable as stochastic variational inference, that continuously refines the model from paired biosensor ground truth with performance improving proportionally to one over the square root of the number of paired observations. Empirical validation on 38812 real-world paired scans across 59 subjects demonstrates practical performance. Self-collected data from the lead author (glucose range 35-550 mg/dL) yields MARD of 29.86 percent with 97.57 percent of predictions in Clarke Error Grid Zones A+B and only 0.27 percent in the dangerous Zone E. A well-managed diabetic participant achieves MARD of 17 percent in the narrower 70-180 mg/dL band. These results confirm that consumer-grade facial video encodes sufficient structured information for clinically relevant, non-invasive biomarker inference under fully unconstrained conditions, with performance scaling predictably as more paired data becomes available.

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

Policy-Embedded Graph Expansion: Networked HIV Testing with Diffusion-Driven Network Samples

arXiv:2601.16233v2 Announce Type: replace-cross Abstract: HIV is a retrovirus that attacks the human immune system and can lead to death without proper treatment. In collaboration with the WHO and the University of Witwatersrand, we study how to improve the efficiency of HIV testing with the goal of eventual deployment, directly supporting progress toward UN Sustainable Development Goal 3.3. While prior work has demonstrated the promise of intelligent algorithms for sequential, network-based HIV testing, existing approaches rely on assumptions that are impractical in our real-world implementations. Here, we study sequential testing on incrementally revealed disease networks and introduce Policy-Embedded Graph Expansion (PEGE), a novel framework that directly embeds a generative distribution over graph expansions into the decision-making policy rather than attempting explicit topological reconstruction. We further propose Dynamics-Driven Branching (DDB), a diffusion-based graph expansion model that supports decision making in PEGE and is designed for data-limited settings where forest structures arise naturally, as in our real-world referral process. Experiments on real HIV transmission networks show that the combined approach (PEGE + DDB) consistently outperforms baselines (e.g., 17.3% improvement in discounted reward and 15.4% more HIV detections with 25% of the population tested) and explore key tradeoffs that drive solution quality.

07.
arXiv (CS.CL) 2026-06-12

X-MADAM-RAG: Diagnosing and Handling Chinese-English Evidence Conflict in Retrieval-Augmented Generation

Retrieval-augmented generation (RAG) systems may receive evidence that is not merely noisy but mutually contradictory. This issue becomes particularly salient in multilingual settings, where retrieved Chinese and English evidence may support incompatible answer candidates. We study this problem through X-RAMDocs-ZHEN, a controlled Chinese-English benchmark derived from RAMDocs for diagnosing evidence conflict in RAG. The benchmark contains 300 examples across six balanced conditions, including monolingual support, bilingual agreement, reversed conflict directions, and conflict with optional noise. We further examine X-MADAM-RAG, an interpretable pipeline that decomposes evidence handling into per-document candidate extraction, visible-evidence repair, deterministic candidate grouping, and conflict-aware aggregation. On the original controlled benchmark with Qwen2.5-7B-Instruct, X-MADAM-RAG achieves 0.9667 strict accuracy and 0.9767 conflict-aware success, outperforming an evidence-normalized single-call baseline. However, a zero-call rule-only extractor reaches 1.0000 on the same benchmark, revealing strong template regularity. To probe this limitation, we construct a deterministic naturalized stress test that removes explicit answer templates while preserving candidate strings. On its 100-sample subset, rule-only extraction falls to 0.0000, but X-MADAM-RAG also drops to 0.3000 strict accuracy, below both naive and evidence-normalized baselines. A privileged oracle remains perfect, indicating that document-level extraction is the main bottleneck. These findings position X-RAMDocs-ZHEN and X-MADAM-RAG as diagnostic tools for controlled evidence conflict rather than as evidence of general hallucination detection or robustness to natural retrieval.

08.
arXiv (CS.AI) 2026-06-16

Phishing Email Detection Using Large Language Models

arXiv:2512.10104v2 Announce Type: cross Abstract: Email phishing is one of the most prevalent and globally consequential vectors of cyber intrusion. As systems increasingly deploy Large Language Models (LLMs) applications, these systems face evolving phishing email threats that exploit their fundamental architectures. Current LLMs require substantial hardening before deployment in email security systems, particularly against coordinated multi-vector attacks that exploit architectural vulnerabilities. This paper proposes LLMPEA, an LLM-based framework to detect phishing email attacks across multiple attack vectors, including prompt injection, text refinement, and multilingual attacks. We evaluate three frontier LLMs (e.g., GPT-4o, Claude Sonnet 4, and Grok-3) and comprehensive prompting design to assess their feasibility, robustness, and limitations against phishing email attacks. Our empirical analysis reveals that LLMs can detect the phishing email over 90% accuracy while we also highlight that LLM-based phishing email detection systems could be exploited by adversarial attack, prompt injection, and multilingual attacks. Our findings provide critical insights for LLM-based phishing detection in real-world settings where attackers exploit multiple vulnerabilities in combination.

09.
arXiv (quant-ph) 2026-06-11

Mixed-State Topological Order under Coherent Noise

arXiv:2411.03441v2 Announce Type: replace Abstract: Mixed-state phases of matter under local decoherence have recently garnered significant attention due to the ubiquitous presence of noise in current quantum processors. One of the key issues is understanding how topological quantum memory is affected by realistic coherent noise, such as random rotation noise and amplitude-damping noise. In this work, we investigate the intrinsic error threshold of the two-dimensional toric code (TC), a paradigmatic topological quantum memory, under these types of coherent noise by employing both analytical and numerical methods based on the doubled-Hilbert-space formalism. A connection between the mixed-state phase of the decohered TC and a non-Hermitian Ashkin-Teller-type statistical-mechanics model is established, and the mixed-state phase diagrams under the coherent noise are obtained. We find remarkable stability of mixed-state topological order under random rotation noise with axes near the $Y$-axis of qubits. We also identify intriguing extended critical regions at the phase boundaries, highlighting a connection with non-Hermitian physics. We argue that these phase boundaries provide upper bounds for the intrinsic error threshold, beyond which quantum error correction becomes impossible. We complement these findings by estimating the error thresholds for random rotation noise under standard quantum error correction, thereby providing lower bounds on the intrinsic error threshold.

10.
arXiv (CS.AI) 2026-06-16

Visual-Seeker: Towards Visual-Native Multimodal Agentic Search via Active Visual Reasoning

arXiv:2606.15231v1 Announce Type: new Abstract: Multimodal large language models (MLLMs) have demonstrated impressive capabilities in many visual tasks, but they often struggle with factual grounding when confronted with complex, open-world scenarios. While recent multimodal deep search agents attempt to address this issue by utilizing external tools, the visual-native search paradigm remains underexplored. Existing methods primarily rely on simple images with explicit semantics and text-only evidence trajectories, limiting the agent's ability to perform multi-hop, cross-modal reasoning and search. To address these limitations, we propose Visual-Seeker, a visual-native multimodal deep search agent via active visual reasoning. Rather than treating vision as a static input, our agent actively attends to fine-grained visual details, dynamically harvests visual evidence throughout the search process. To unlock its visual-native potential, we design an active visual reasoning data pipeline and synthesize 5K high-quality multimodal trajectories for model training. Extensive experiments demonstrate the state-of-the-art performance across five challenging multimodal search benchmarks, even surpassing several proprietary models, validating robust visual-native reasoning and search in real-world web environments. The code and data can be accessed at: https://github.com/ZhengboZhang/Visual-Seeker.

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

Beyond Averaging in John Ellipsoid Approximation: High-Accuracy Algorithms in the Leverage-Score Model

arXiv:2606.20082v1 Announce Type: cross Abstract: The John ellipsoid of a symmetric polytope $P=\{\mathbf{x}\in\mathbb{R}^d:\|\mathbf{A}\mathbf{x}\|_\infty\le1\}$, $\mathbf{A}\in\mathbb{R}^{n\times d}$, is computed by a long line of leverage-score algorithms, from Cohen, Cousins, Lee and Yang (COLT 2019) to its successors [WY24, CLS+25], all reaching a $(1+\varepsilon)$-approximation in $\Theta(\varepsilon^{-1}\log(n/d))$ iterations. We separate this complexity into three costs the modern line conflates (certification, identification, and accuracy) and locate the historical $\varepsilon^{-1}$ in the first alone. In the equivalent D-optimal-design form $\min_{\mathbf{p}\in\Delta_n}-\log\det(\sum_i p_i\mathbf{a}_i\mathbf{a}_i^\top)$, the leverage-score oracle is exactly the first-order oracle and the $(1+\varepsilon)$-John guarantee the Frank-Wolfe gap $g(\mathbf{p})\le\varepsilon d$; through this dictionary the costs come apart. The $\varepsilon^{-1}$ is a certification artifact: the uniform average of the iterates, the certificate used throughout the line, has gap exactly $\Theta(1/T)$, however cheap each iteration is made. Pointed instead at the last iterate the same oracle is fast: a warm-started accelerated method reaches the guarantee in $C(\mathbf{A})+O(\sqrt{\kappa}\log(1/\varepsilon))$ queries after an $\varepsilon$-independent setup $C(\mathbf{A})$, and once the optimal face is identified the facial problem is an unconstrained self-concordant minimization whose Hessian the oracle recovers exactly, so damped Newton needs only $O(\log\log(1/\varepsilon))$ steps, for a total of $C(\mathbf{A})+O(d^2\log\log(1/\varepsilon))$ queries. The accuracy dependence is thus doubly logarithmic after an $\varepsilon$-independent, condition-dependent setup; the open problem is the remaining identification cost (a condition-free bound on reaching the optimal face) and lower bounds. Accuracy is not the obstruction.

12.
arXiv (CS.AI) 2026-06-24

Disentangling Aleatoric and Epistemic Uncertainty in Physics-Informed Neural Networks. Application to Insulation Material Degradation Prognostics

arXiv:2601.03673v2 Announce Type: replace-cross Abstract: Physics-Informed Neural Networks (PINNs) provide a framework for integrating physical laws with data. However, their application to Prognostics and Health Management (PHM) remains constrained by the limited uncertainty quantification (UQ) capabilities. Most existing PINN-based prognostics approaches are deterministic or account only for epistemic uncertainty, limiting their suitability for risk-aware decision-making. This work introduces a heteroscedastic Bayesian Physics-Informed Neural Network (B-PINN) framework that jointly models epistemic and aleatoric uncertainty, yielding full predictive posteriors for spatiotemporal insulation material ageing estimation. The approach integrates Bayesian Neural Networks (BNNs) with physics-based residual enforcement and prior distributions, enabling probabilistic inference within a physics-informed learning architecture. The framework is evaluated on transformer insulation ageing application, validated with a finite-element thermal model and field measurements from a solar power plant, and benchmarked against deterministic PINNs, dropout-based PINNs (d-PINNs), and alternative B-PINN variants. Results show that the proposed B-PINN provides improved predictive accuracy and better-calibrated uncertainty estimates than competing approaches. A systematic sensitivity study further analyzes the impact of boundary-condition, initial-condition, and residual sampling strategies on accuracy, calibration, and generalization, and the influence of measurement noise on aleatoric uncertainty. Overall, the findings highlight the capability of Bayesian physics-informed learning to support uncertainty-aware prognostics and informed decision-making in transformer asset management by tracking aleatoric and epistemic sources of uncertainty.

13.
arXiv (CS.CV) 2026-06-16

CoIRL-AD: Collaborative-Competitive Imitation-Reinforcement Learning in Latent World Models for Autonomous Driving

End-to-end autonomous driving models trained with imitation learning (IL) often generalize poorly, particularly in long-tail scenarios where expert demonstrations are sparse. Reinforcement learning (RL) can provide complementary task-level supervision, but applying RL to real-world autonomous driving is challenging in offline settings without interactive simulators, where datasets are dominated by expert actions and provide limited behavioral diversity. We propose CoIRL-AD, a competitive dual-policy framework that integrates IL and RL under a unified offline training regime. CoIRL-AD decouples imitation and reward optimization into separate actors to alleviate objective conflicts, uses imagined future rollouts for long-horizon reward estimation, and introduces a competition mechanism that selectively transfers beneficial behaviors while keeping RL anchored to expert-like driving. Experiments on the nuScenes benchmark show that CoIRL-AD consistently improves robustness over strong IL-based baselines, with especially large gains in cross-city generalization and long-tail scenarios. Code is available at: https://github.com/SEU-zxj/CoIRL-AD.

14.
arXiv (math.PR) 2026-06-12

Quenched and Annealed CLTs for the one-periodic Aztec diamond in random environment

arXiv:2510.11846v2 Announce Type: replace Abstract: We study the asymptotic behavior of random dimer coverings of the one-periodic Aztec diamond in random environment. We investigate quenched limit theorems for the height function and we extend annealed limit theorems that were recently studied in [arXiv:2507.08560]. We consider more general choices of random edge weights (independence is not assumed) and we distinguish two cases where the random edge weights satisfy the Central Limit Theorem (CLT) under different scalings. For both cases, we prove convergence to the Gaussian Free Field for the quenched fluctuations. For the annealed version, it had been shown in [arXiv:2507.08560], that Gaussian Free Field fluctuations can be dominated by the much larger fluctuations of the random environment. To access quenched fluctuations we analyze the Schur process with random parameters in a way that allows to prove the annealed CLT for the height function for non i.i.d. weights. We consider specific examples where we determine the asymptotic fluctuations.

15.
medRxiv (Medicine) 2026-06-17

Frequency-dependent cognitive effects of Deep Brain Stimulation in Parkinson's Disease: A Systematic Review and Meta-Analysis

Background: Subthalamic nucleus deep brain stimulation (STN-DBS) improves levodopa-induced motor complications and cardinal motor symptoms of Parkinson's disease (PD), but stimulation frequency may differentially shape outcomes. This is evident for axial and gait symptoms, which may respond differently to lower-frequency stimulation. Whether frequency-dependent effects extend to cognition remains unclear. Objective: To investigate the cognitive effects of DBS at distinct frequencies in PD. Methods: We conducted a systematic review and meta-analysis (PROSPERO - CRD42024618253). PubMed, Web of Science, and EMBASE were searched for studies assessing cognitive outcomes under different stimulation frequencies. Eight cognitive domains were defined: verbal fluency, cognitive flexibility, executive control, working memory, attention, processing speed, episodic memory, and time processing. Multilevel random-effects meta-analyses were performed, with effect sizes expressed as Hedges' g. Results: Forty-three studies met the inclusion criteria, the majority (n = 31) involving STN-DBS. Twenty-one STN-DBS studies, including 355 patients, were included in the meta-analysis. Compared with HFS ([≥] 130 Hz), lower frequencies (4-80 Hz) were associated with better verbal fluency (g = 0.27) and cognitive flexibility (g = 0.38), with consistent effects across sensitivity and leave-one-out analyses. Accuracy-based executive control measures also favored lower-frequency stimulation. OFF-stimulation comparisons showed a concordant pattern. Evidence for other targets (PPN and NBM) was limited. Conclusions: Lower-frequency STN-DBS was associated with modest benefits in specific cognitive domains compared with HFS. These findings highlight the need for future research to determine how frequency interacts with stimulation location and symptom-specific networks to shape cognitive and cognitive-motor outcomes in PD.

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

PCBSchemaGen: Reward-Guided LLM Code Synthesis for Printed Circuit Boards (PCB) Schematic Design with Structured Verification

arXiv:2602.00510v2 Announce Type: replace Abstract: Most LLM code-synthesis benchmarks rely on unit tests as the reward oracle, but PCB schematic design has none: correctness is defined by structured physical constraints over real IC packages and pin-level assignments, per-task golden references are unavailable, and SPICE simulation does not validate schematic-level correctness. We introduce PCBSchemaGen, a training-free inference-time framework that turns a frozen LLM into a verifiable, repairable PCB schematic generator. The framework induces a domain schema from IC datasheets to ground LLM decoding, pairs it with a deterministic 5-layer continuous-reward verifier with pin-level error localization, and refines candidates through a Thompson Sampling arm-acquiring bandit. We evaluate on 2 PCB benchmarks covering 227 real-IC tasks across 22 unified circuit domains, including a public-schematic-derived suite that serves as a fully held-out generalization test (verifier, KG library, and prompts frozen before any evaluation). Under our framework, an open-weight 31B model (Gemma-4-31B) passes 81.3% of PCBBench tasks on average, and the same framework transfers across both benchmarks with zero verifier code changes; a Circuitron-style inference-time prompting baseline on the same Gemma-4-31B backbone collapses on hard system-level designs. This suggests inference-time refinement under a deterministic structural verifier is a general recipe for reference-free LLM code synthesis in domains without unit-test oracles. Our benchmarks and deterministic verifier are publicly available at https://github.com/HZou9/PCBSchemaGen_v2.

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

Multiple Descents in Deep Learning as a Sequence of Order-Chaos Transitions in LSTM Networks

arXiv:2505.20030v2 Announce Type: replace-cross Abstract: We observe a novel `multiple-descent' phenomenon during the learning process of a recurrent neural network called long-short-term memory (LSTM) networks during its training on real-world task, in which the performance goes through long cycles of up and down trends multiple times after the model is overtrained. By carrying out asymptotic stability analysis of the models, we found that the cycles in performance – indicated by loss function in test data – are closely associated with the phase transition process between order and chaos of the model, and the local optimal training step are consistently at the critical transition point between the two phases. More importantly, the most optimal point of the model usually occurs at the first transition from order to chaos, where the `width' of the `edge of chaos' is often the widest, allowing the best exploration of weight configurations for learning.

18.
arXiv (CS.CL) 2026-06-12

Attention Expansion: Enhancing Keyphrase Extraction from Long Documents with Attention-Augmented Contextualized Embeddings

Pre-trained language models (PLMs) have achieved strong performance in keyphrase extraction (KPE), largely due to their ability to generate rich contextualized representations. However, long-document KPE remains challenging because salient keyphrase evidence may be scattered across distant document sections that cannot be jointly captured within the limited context window of most PLMs. Although long-context large language models (LLMs) can process broader textual contexts, their computational cost limits their practicality for efficient and high-throughput KPE. To overcome this limitation, we propose an attention expansion mechanism that augments PLM token representations with information from surrounding out-of-context chunks using pre-trained word embeddings. The proposed mechanism expands the effective contextual scope of PLM-based KPE models without requiring full-document attention or expensive LLM-based inference. We evaluate our approach across five PLM backbones, including general-purpose, scientific, task-specific, and long-context encoders, using two training regimes and five benchmark corpora from scientific and news domains. Experimental results demonstrate that attention expansion consistently enhances KPE performance across all evaluation settings, outperforming state-of-the-art models and yielding notable improvements in F1 score. The improvements extend to domain-specific, task-specialized, and native long-context models, showing that the proposed mechanism provides complementary information rather than merely compensating for limited input length. These results establish attention expansion as an efficient and effective strategy for long-document KPE.

19.
medRxiv (Medicine) 2026-06-10

Estimating COVID-19 Cumulative Incidence from Seroprevalence Surveys accounting for Time-Varying Seroreversion: A Fully Bayesian Methodology

Seroprevalence surveys reveal the extent of humoral immunity against pathogens such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and under some circumstances represent cumulative incidence of prior infection. However, antibody waning - or seroreversion - biases these estimates by reducing assay sensitivity in a time-varying manner. Because assay sensitivity decays over time, naively using serosurveys can substantially bias estimates of SARS-CoV-2 cumulative incidence and fatality rates. The Bayesian assay-specific, time-varying sensitivity adjustment developed in this paper can reliably correct for this bias and account for the delay between infection and serosurvey. In seroprevalence studies conducted in the United States in 2020, adjusting for time-varying sensitivity increased cumulative incidence by up to 1.4-fold, with an adjustment of 1.08 for a national study. Our estimates contrast with a previously published 2-fold adjustment that did not account for assay design. This suggests that previous analyses overestimated cumulative incidence by applying seroreversion corrections that did not account for assay-specific effects, or underestimated cumulative incidence by not applying seroreversion corrections. These biases imply fatality rate underestimation and overestimation, respectively. Our model provides a framework for design-specific time-varying sensitivity corrections in seroprevalence surveys for other pathogens.

20.
medRxiv (Medicine) 2026-06-15

Neural Correlates of Human Food Memory link to Microbial, Homeostatic, and Hedonic Signals: Evidence from a Prebiotic Randomized Clinical Trial

Background Homeostatic and hedonic brain circuits regulate eating behavior but also shape how food memories are encoded and retrieved. Objective We examined neural correlates during food memory encoding and retrieval during functional MRI before and after a 14-day prebiotic intervention in a preregistered, double-blind crossover trial (NCT03829189). Design 55 healthy adults with overweight (19 females, age 28{+/-}6.5, BMI 25-30 kg/m2) underwent 3 Tesla task-based functional MRI before and after dietary intervention of prebiotic (30g inulin/day) or equicaloric placebo for 14 days. Peripheral metabolic, short-chain fatty acids (SCFA), and microbial markers using 16S rRNA analysis were assessed in fasting blood and feces. Results Food memory was enhanced by assigned reward value and engaged brain activity in hedonic regions, including the nucleus accumbens, orbitofrontal cortex, caudate, cingulate, dorsomedial prefrontal cortex, and ventral tegmental area, as well as homeostatic and memory-related such as the hypothalamus and the hippocampus. Higher neural activations during food encoding were related to higher Actinobacteriota abundance, fecal SCFA acetate, and creatinine levels, and lower ghrelin levels. Activations in reward-related and homeostatic brain areas partially correlated with insulin, glucagon-like peptide-1, leptin, and thyroid-stimulating hormone levels. Neural activations related to food memory decreased after prebiotic intervention. The prebiotic supplementation induced decrease of hippocampal activity during food encoding related to changes in gut microbiota Firmicutes abundance. Conclusions This study indicates that neuronal food-related memory processes depend on homeostatic and hedonic brain signals modulated by the gut-brain axis. Our findings raise implications for the treatment of obesity and substance use disorder.

21.
arXiv (CS.CL) 2026-06-24

Faithful by Construction: Claim-Anchored Attribution for Multi-Document Summarization

Authors:

End-to-end large language models (LLMs) produce fluent multi-document summaries but remain prone to hallucination, and the attributions they offer are typically coarse (whole documents or passages) and generated post hoc, leaving each summary statement hard to verify. We revisit the modular Extract–Select–Rewrite paradigm and recast its intermediate representation as the unit of attribution. We present CAMS, a Claim-Anchored Multi-document Summarization framework that (i) extracts atomic claims with token-level provenance from every source document, (ii) clusters equivalent claims across documents while flagging inter-source conflicts, (iii) selects a support-aware and salient subset, and (iv) rewrites the selection into a summary in which every sentence is anchored to a support-checked claim that links back to one or more source spans. Because content is localized before it is realized, the pipeline is attribution-oriented by construction and faithfulness-oriented by construction: it structurally preserves fine-grained, multi-source traceability while using support-aware selection, constrained rewriting, and verification to encourage, rather than guarantee, factual faithfulness. We evaluate quality, faithfulness, and localization on MultiNews, analyze conflict handling on DiverseSumm, and test zero-shot transfer on WCEP, using a two-regime protocol that separates reference-free citation quality from gold-aligned localization accuracy, and we add an evaluator-decoupled audit that tests citation precision with a support model never used for selection or verification. CAMS matches strong end-to-end and span-attribution baselines on summary quality while substantially improving faithfulness and citation precision, lifting multi-source attribution accuracy by roughly two-thirds, and exposing a controllable faithfulness–coverage trade-off that end-to-end models leave implicit.

22.
arXiv (CS.LG) 2026-06-16

Pushing the Boundaries of Natural Reasoning: Interleaved Bonus from Formal-Logic Verification

arXiv:2601.22642v2 Announce Type: replace Abstract: Large Language Models (LLMs) show remarkable capabilities, yet their stochastic next-token prediction creates logical inconsistencies and reward hacking that formal symbolic systems avoid. To bridge this gap, we introduce a formal logic verification-guided framework that dynamically interleaves formal symbolic verification with the natural language generation process, providing real-time feedback to detect and rectify errors as they occur. Distinguished from previous neuro-symbolic methods limited by passive post-hoc validation, our approach actively penalizes intermediate fallacies during the reasoning chain. We operationalize this framework via a novel two-stage training pipeline that synergizes formal logic verification-guided supervised fine-tuning and policy optimization. Extensive evaluation on six benchmarks spanning mathematical, logical, and general reasoning demonstrates that our 7B and 14B models outperform state-of-the-art baselines by average margins of 10.4% and 14.2%, respectively. These results validate that formal verification can serve as a scalable mechanism to significantly push the performance boundaries of advanced LLM reasoning.

23.
Nature Biotechnology 2026-06-19

Optimized R2 retroelement complexes for DNA insertion into plant genomes

Traditional approaches for DNA insertion into plant genomes using Agrobacterium tumefaciens result in random integration. Newer genetic engineering methods based on nucleases, prime editors, transposases and recombinases extend capabilities but remain constrained with low efficiencies, off-target integration or limited payload size. Here we adapt the avian Taeniopygia guttata R2 protein (R2Tg) for targeted DNA insertion into plant genomes by engineering R2Tg expression cassettes and RNA payloads carrying intron-disrupted reporters, with optimized ribosomal DNA homology arms and untranslated regions. In Arabidopsis thaliana protoplasts, Nicotiana benthamiana leaves and Solanum lycopersicum seedlings, our R2Tg editor system achieves targeted insertion of full-length payloads ranging from 2.2 kb to 5 kb. In Nicotiana benthamiana leaves, integration occurs, on average, at 1 copy per genome, which is 30 times more efficient than that achieved by Cas9 homology-directed repair. This work establishes an R2Tg ribonucleoprotein platform for targeted DNA insertion into plant genomes, using a multicopy genomic safe-harbor site to enable efficient addition of multikilobase genes. R2 retrotransposons are used to integrate DNA into plant and crop 25S ribosomal DNA sites.

24.
medRxiv (Medicine) 2026-06-22

Genetic modifiers of psychiatric, motor, and cognitive symptoms in Huntington's disease

The Enroll HD natural history platform provides rich longitudinal phenotypes enabling genome wide analyses across diverse clinical domains. Psychiatric symptoms are a major source of morbidity in Huntington's disease (HD), yet the genetic architecture underlying their onset is poorly understood. We analyzed ~18,000 people with HD (PwHD) to define genetic determinants of ages at psychiatric, motor, and cognitive symptom onset, and HD diagnosis. GWAS meta analysis recapitulated 11 established modifiers of motor onset and identified a novel locus spanning RAB3B/ZFYVE9 associated with age at violent/aggressive behavior onset. Exome wide analyses in Enroll HD participants implicated rare variants in FAN1, PMS1, POLD1, and HTT. Several HD modifiers of motor and cognitive symptom onset (MSH3, FAN1, HTT) also influenced psychiatric symptom onset, whereas PMS1 and POLD1 showed significant association with motor symptom onset. Psychiatric polygenic scores predicted psychiatric symptom onset, revealing a hybrid architecture combining psychiatric liability in general population with HD- or repeat expansion disease (RED) specific pathways.

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

AI Supply Chain Galaxy: 3D Visual Analytics for License Compliance

arXiv:2606.16292v1 Announce Type: cross Abstract: The rapid proliferation of machine learning model reuse has transformed the AI ecosystem into a highly interconnected supply chain. Traditional compliance tools and static reports struggle to navigate these massive, multi-hop dependency networks. To address this, we present AI Supply Chain Galaxy (AISCG), an interactive 3D visual analytics system for model provenance and compliance auditing. AISCG maps models into a 3D spatial layout, integrating explicit structural dependencies with a rule-based compliance engine. It supports multi-scale exploration, from global community detection to localized, path-aware lineage tracing. We demonstrate its efficacy through an ecosystem-scale empirical analysis of 908,449 models from Hugging Face. Our findings reveal a concerning landscape: 55.46% of models exhibit compliance risks or metadata conflicts/omissions. We also identified distinct risk patterns, including a 56.67% license omission rate in adapter derivations and an 8.05% "license drift" rate in fine-tuning. Through a case study on the complex Llama model family, we show how AISCG empowers analysts to intuitively trace inherited restrictive terms and identify root causes across deep topological networks, significantly reducing the cognitive load of compliance auditing.