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01.
arXiv (CS.AI) 2026-06-12

Understanding the Rejection of Fixes Generated by Agentic Pull Requests – Insights from the AIDev Dataset

Authors:
Mahmoud Abujadallah↗Ali Arabat↗Mohammed Sayagh↗

arXiv:2606.13468v1 Announce Type: cross Abstract: AI coding agents are increasingly used to generate pull requests (PRs) that propose code fixes in software projects. From a first exploration of the AIDev dataset, we find that 46.41\% of the fixes proposed by the agents Copilot, Devin, Cursor, and Claude are rejected. This represents a significant amount of wasted resources that require human reviews, verifications, and running tests and validations for fixes that are merely discarded. Our goal in this paper is to understand the failure modes of AI-agents, an understanding that is crucial for better integrating AI-agents as efficient teammates. In this paper, we conduct a qualitative study on a representative sample of 306 non-merged pull requests created or co-authored by the agents mentioned earlier, followed by a quantitative analysis of the reasons for rejection. Our qualitative findings identify 14 reasons divided into four high-level categories for rejecting AI-agent fixes. We observe that developers can reject fixes due to fixes whose implementation is incorrect (e.g., incomplete, wrong approach), fixes that do not pass the continuous integration (CI) pipelines and fail tests, fixes for which the agent is unable to perform the implementation (e.g., no code generated, sessions lost), and fixes whose priority is low. Our results shed light on the importance of better guiding the model at these levels: (1) proposing hints about the approach to follow for fixing an issue, (2) outlining constraints or limitations regarding the approaches that should not be taken, and (3) instructing the agent on how to validate the implementation through CI pipelines and without introducing a breaking change. Our results suggest the need for good prioritization of tasks so that generated fixes do not lead to wasted human review efforts or wasted agent resources (e.g., tokens, compute, or allowed number of requests).

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02.
arXiv (CS.LG) 2026-06-17

A Closer Look at Failure Modes in Temporal Understanding of Large Audio-Language Models

Authors:
Apoorva Kulkarni↗Kaousheik Jayakumar↗Sreyan Ghosh↗Sarah Wiegreffe↗Dinesh Manocha↗Ramani Duraiswami↗

arXiv:2606.17417v1 Announce Type: cross Abstract: Large Audio Language Models (LALMs) achieve strong performance on a variety of audio understanding tasks but continue to struggle with temporal reasoning, a fundamental capability central to human auditory perception. Understanding the causes of these failures remains challenging as existing benchmarks report performance gaps without probing underlying mechanisms. To address this, we introduce a benchmark with 1,657 questions across three foundational tasks designed specifically for mechanistic analysis. Examining model outputs across varying input settings (behavioral analysis) reveals that models often under-utilize audio when textual cues are available. We also provide the first causal mechanistic analysis of temporal reasoning failures in LALMs. Comparing attention upweighting against scaling, we find that redistributing attention across audio tokens is more effective than increasing audio attention. Targeting task-relevant tokens yields further gains. These findings suggest that modality imbalance alone cannot explain failures. Attention scaling at bottleneck layers improves accuracy from 55.9% to 59.1% without fine-tuning, demonstrating a promising direction for future work.

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03.
arXiv (CS.LG) 2026-06-18

Learning from Your Own Mistakes: Constructing Learnable Micro-Reflective Trajectories for Self-Distillation

Authors:
Zhilin Huang↗Hang Gao↗Ziqiang Dong↗Yuan Chen↗Yifeng Luo↗Chujun Qin↗Jingyi Wang↗Yang Yang↗Guanjun Jiang↗

arXiv:2606.18844v1 Announce Type: new Abstract: Self-distillation improves reasoning in large language models by using the model's own rollouts as training signal, typically through implicit logit-level alignment that minimizes KL divergence toward a privileged target distribution. However, because this supervision is generated via uncontrolled sampling, it provides no diagnostic insight into the model's specific errors or corrective guidance for its individual failure patterns. Consequently, the model learns to imitate a privileged distribution rather than receiving fine-grained corrections that pinpoint where and why its reasoning fails. In this paper, we propose Trajectory-Augmented Policy Optimization (TAPO), which advances self-distillation from implicit distributional alignment to explicit trajectory construction. During RL training, the model produces both correct and incorrect rollouts to the same query, and TAPO leverages this contrastive structure to construct micro-reflective corrections, new training trajectories that retain the model's erroneous reasoning up to the point of failure, then insert a natural-language diagnosis and corrected reasoning guided by a correct reference from the same sampling group. Since each trajectory is anchored in the learner's own prefix and solutions, the corrective signal preserves the model's on-policy distribution to a greater extent than the position-wise alignment imposed by KL-based methods. To integrate these trajectories, TAPO introduces difficulty-aware candidate selection at the model's capability boundary and decoupled advantage estimation to prevent gradient contamination. Experiments on AIME 2024, AIME 2025, and HMMT 2025 show that TAPO achieves consistent improvements over GRPO under the same number of training steps. Further analysis demonstrates that TAPO strengthens both first-pass reasoning and error-correction effectiveness.

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04.
arXiv (CS.CL) 2026-06-11

PoQ-Judge: A Multi-Architecture Evaluation Framework for Cost-Aware Proof-of-Quality in Decentralized LLM Inference

Authors:
Arther Tian↗Alex Ding↗Frank Chen↗Simon Wu↗Aaron Chan↗

Decentralized LLM inference networks need lightweight, reference-free quality evaluation for Proof of Quality (PoQ). We present PoQ-Judge, a framework that trains dedicated judge models to score query-output pairs without ground-truth references. We study three architectures across the quality-cost tradeoff: a TextCNN judge, a MiniLM cross-encoder, and a DeBERTa judge. Using two-stage training on UltraFeedback plus GPT-labeled in-domain data, the best model reaches 0.747 Pearson correlation with the ground-truth proxy on a held-out test set, outperforming reference-based evaluators from prior work. As a reference-free component in composite scoring, it achieves 0.645 Pearson correlation, matching the best single reference-based evaluator while removing the need for reference answers. We also show that online calibration identifies semantic quality as the dominant dimension and that cascade evaluation reduces cost by 72.7 percent with only modest quality loss. Results are much stronger on QA than summarization, pointing to proxy quality as the main remaining limitation.

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

KCSAT-ML: Probing Reasoning Models with Nationwide-Cohort Human Difficulty

Authors:
Sanghee Park↗Geewook Kim↗Kee-Eung Kim↗

Math reasoning benchmarks have proliferated, yet most lack a per-item difficulty signal grounded in actual human performance. We introduce KCSAT-ML, a decade (2014-2025) of Korean College Scholastic Ability Test (KCSAT; Suneung) mathematics: 664 problems with a 339-item core set carrying official per-item error rates from nationwide cohorts of hundreds of thousands of examinees. We pair the benchmark with Difficulty-aligned Reasoning Gain (DRG): a score-orthogonal metric that asks whether a model's mistakes concentrate on the items humans found hard, or on items humans found easy. Together they expose, across a wide range of VLMs (and LLMs via OCR), three patterns: (i) low-budget accuracy collapses on the high-human-error tail at every model size; (ii) test-time scaling (TTS) raises token use roughly linearly with cohort error rate, while accuracy gains follow a non-monotonic curve; (iii) within a single family, TTS flips between anti-scaling on the hardest items and overthinking on easier ones – two faces of the same alignment failure. On DRG, models with near-identical accuracy can sit at near-opposite values: one model gets wrong what humans also find hard, while another solves the hardest items yet fails on items humans find easy – a contrast that aggregate accuracy hides. Our code and dataset builder will be open-sourced at https://github.com/naver-ai/KCSAT-ML.

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06.
medRxiv (Medicine) 2026-06-11

Computer Vision for Real-Time Anatomical Navigation in Neurosurgery: First-in-Human Clinical Evaluation and Iterative Development (IDEAL Stage 1)

Authors:
Khan↗D. Z↗Mao↗Wijekoon↗Das↗Williams↗S. C↗Blandford↗Jain↗Harris↗Borg↗Dorward↗…

Introduction: Precise anatomical navigation is fundamental to safe endoscopic pituitary surgery, a high-stakes procedure characterised by a challenging learning curve. While traditional navigation systems often rely on workflow-disrupting probes or static preoperative imaging, advancements in computer vision AI (CVAI) now enable dynamic, real-time anatomical segmentation directly from live surgical video1-3. Our group has previously conducted a series of preclinical human-computer interaction studies to refine the system's design, alongside digital and high-fidelity physical simulations demonstrating the benefit of AI assistance in improving overall performance, training, and safety4-8. Building on this foundation, the current study represents a first-in-human application of real-time CVAI assistance in the neurosurgical operating room, serving to assess feasibility and safety, and to iteratively improve the system. Method: Guided by DECIDE-AI and IDEAL frameworks, this single-centre evaluation comprises an initial proof-of-concept phase (n=6) for endoscopic transsphenoidal pituitary surgeries. The AI model utilised a DINOv3-derived vision transformer architecture, deployed via a high-performance edge computing unit to achieve low-latency, real-time inference without reliance on cloud infrastructure2. Given the high-risk nature of the procedure and the early stage of clinical AI integration, the system was initially deployed as an educational adjunct on a secondary monitor, ensuring the primary surgical feed remains uncompromised. Functionality and safety were assessed via structured questionnaire, prospective observation, and blinded retrospective review of the recordings of the endoscopic surgical video feed and wider operating room environment. Continuous multi-stakeholder feedback through validated human factors surveys drove iterative technical refinements between cases. Results: Six patients with pituitary adenomas were enrolled. The CVAI system was successfully deployed in four cases, demonstrating acceptable real-time sella segmentation accuracy. Deployment failed pre-operatively in two cases owing to a single recurring system reboot bug. Iterative refinement between cases were driven by our experience and surgical team feedback. This resulted in the integration of additional anatomical structure segmentations (e.g., carotid arteries), enhanced model accuracy via training dataset expansion, and hardware firmware upgrades. Multi-stakeholder surveys demonstrated satisfactory system feasibility, usability, and acceptability among the surgical team. Both prospective observation and retrospective video review confirmed the absence of adverse events, including no significant distraction to the primary surgeon, and there were no AI-related clinical complications. Conclusion: This first-in-human early clinical evaluation demonstrates the feasibility, safety and iterative development of real-time, CVAI-based anatomical navigation during high-stakes neurosurgery. Future work will include a larger single-centre case series (IDEAL Stage 2a) with more surgical teams to further iterate the system and explore its impact on training and workflow. As the underpinning technology improves, deployment will transition to direct intra-operative decision support and integration with other intra-operative navigational technologies.

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

Exploring Extrinsic and Intrinsic Properties for Effective Reasoning with Code Interpreter

Authors:
Patomporn Payoungkhamdee↗Napat Laosaengpha↗Jenta Wonglertsakul↗Pittawat Taveekitworachai↗Pume Tuchinda↗Panjapong Poobanchuen↗Ekapol Chuangsuwanich↗Can Udomcharoenchaikit↗Samuel Cahyawijaya↗Peerat Limkonchotiwat↗Sarana Nutanong↗

Reasoning with a Code Interpreter (CI) has emerged as an effective paradigm for enhancing the reasoning capabilities of large language models (LLMs) through executable computation and iterative verification. Despite its growing adoption, the behavioral properties underlying effective code reasoning remain largely underexplored. In this work, we investigate code reasoning from two distinct perspectives inspired by prior studies of natural language reasoning: extrinsic properties, represented by crucial tokens, and intrinsic properties, represented by code-specific cognitive behaviors. Across multiple LLMs, we find that stronger CI reasoning models consistently exhibit a higher prevalence of crucial tokens and cognitive behaviors, particularly verification, backtracking, and backward chaining. Building on these observations, we examine how these properties can be leveraged during both inference and training. At inference time, appending code-specific crucial tokens improves performance on several reasoning capabilities, including mathematical, ordering, and optimization, while yielding limited benefits elsewhere. At training time, augmenting a state-of-the-art framework with code-specific cognitive behaviors improves supervised fine-tuning and reinforcement learning performance in two of three evaluated models. Further analysis shows that these behaviors reduce overthinking in incorrect responses and improve token efficiency, while also revealing factors that limit gains in a certain model. Our findings provide the first systematic characterization of effective reasoning with CI and demonstrate both the potential and limitations of leveraging key properties to improve CI-based reasoning.

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

Knowing When to Ask: Self-Gated Clarification for Hierarchical Language Agents

Authors:
Aijing Gao↗Yiming Kang↗Mengdie Flora Wang↗Jae Oh Woo↗

arXiv:2606.11349v1 Announce Type: new Abstract: In hierarchical reasoning, failures often originate at intermediate decision points where the agent commits to a wrong branch without recognizing that it lacks critical information. Rather than treating clarification as an external uncertainty trigger, we propose ACTION-RATING, a formulation that places it inside the agent's action space on a shared ordinal scale with navigation, so that asking competes directly with acting at every decision point and help-seeking becomes observable at intermediate states. Two structurally distinct information-seeking modes emerge from the agent's own ratings: mandatory (no viable branch) and opportunistic (residual uncertainty despite a leading candidate). On Harmonized Tariff Schedule classification (30,000-node taxonomy, three benchmarks, 9~LLMs across 4 families), we observe a regime shift from mandatory to opportunistic clarification, with Information-Seeking Effectiveness (ISE), a local diagnostic defined as the fraction of help interactions followed by a correct next navigation step (not a final-task metric), rising from 50% to 74%. Three diagnostic contrasts fail to reproduce this structure. A separability test shows that the information-seeking pattern (mode split, ISE ranking) persists when answer quality is degraded (-18.8% accuracy), supporting an empirical separation between where an agent seeks help and the quality of the help it receives. Under the controlled answer channel, accuracy gains reach +16.2% at 10-digit; we read this as an upper bound on what better localization could unlock, not a deployment estimate.

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09.
arXiv (quant-ph) 2026-06-17

Fermionic Hamiltonian engineering with local control

Authors:
\"Ozg\"un Kum↗Matthias Zipper↗Ludwig Mathey↗Martin Kliesch↗

arXiv:2606.17158v1 Announce Type: new Abstract: Quantum simulators enable the exploration of complex quantum phenomena in condensed-matter systems by reproducing their dynamics on controllable quantum devices. However, experimental constraints often restrict the class of Hamiltonians that can be realized natively. Hamiltonian engineering addresses this limitation by expanding the set of accessible target Hamiltonians from a fixed system Hamiltonian defined by the hardware. We introduce a new framework for fermionic Hamiltonian engineering based on conjugating free evolution under the system Hamiltonian with sequences of experimentally feasible local fermionic unitaries. The required sequences and free-evolution times are obtained efficiently via a linear program. By interleaving system evolution with these local unitaries, our method realizes effective time evolution under a broad class of target Hamiltonians, with intrinsic robustness to finite-pulse-time errors. In particular, we demonstrate that arbitrary complex tunnelling coefficients can be realized, constrained only by the connectivity of the underlying system Hamiltonian. We illustrate this capability by engineering the dynamics of the non-interacting Harper-Hofstadter model on a 1088-mode lattice and an interacting Fermi-Hubbard chain with complex tunnelling coefficients. By construction, our approach avoids the continuous energy absorption inherent to Floquet engineering.

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10.
arXiv (quant-ph) 2026-06-16

Long-range nonstabilizerness of topologically encoded states from mutual information

Authors:
David Aram Korbany↗Tyler D. Ellison↗David T. Stephen↗Lorenzo Piroli↗

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.

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

Learning Cardiac Electrophysiology Digital Twins Through Agentic Discovery of Hybrid Structure

Authors:
Ziqi Zhou↗Yubo Ye↗Sumeet Atul Vadhavka↗Linwei Wang↗Zhiqiang Tao↗

arXiv:2606.18154v1 Announce Type: new Abstract: Building personalized cardiac electrophysiology (EP) digital twins requires identifying the appropriate model structure for each patient, not merely fitting parameters. Traditional methods rely on experts to manually prescribe hybrid physics-neural architectures, which requires deep domain expertise and does not transfer across patients. Recent works have applied large language models (LLMs) to generate or act as hybrid models. However, despite their promising generalization capacity, these LLM-based methods lack the structural priors needed for stable cardiac simulations. Hence, we propose LEADS, a framework that formulates cardiac EP domain knowledge as a structured action space and utilizes an LLM agent to discover hybrid models. The agent follows an iterative reasoning-and-action loop to select, combine, and refine hybrid models, whilst gradient descent handles parameter fitting. The proposed LEADS designs every candidate model towards physically grounded, interpretable, and numerically stable, while allowing open-ended architectural discovery. We validate LEADS on synthetic data with three ground-truth reaction models and on real cardiac EP data, demonstrating that it outperforms both human-designed hybrid models and other LLM-based hybrid modeling.

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12.
Nature (Science) 2026-06-17

Cortical development dynamics across autism spectrum disorder mouse models

Authors:
Lena A. Schwarz↗

Despite the functional diversity of over 100 causal genes1–3, phenotypic convergence across models may reveal common neurobiological processes in autism spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse models of ASD using single-nucleus multi-omic sequencing across three developmental stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. These alterations reflect a transient developmental delay rather than lasting lineage misspecification and resolve by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis showed molecular convergence across models within each developmental stage, suggesting that diverse mutations linked to ASD impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with female mice often displaying larger effect sizes than male mice. Together, our findings provide a comprehensive view of developmental cellular and molecular dynamics across models of ASD. Using single-nucleus multi-omic sequencing, diverse autism spectrum disorder-linked gene mutations converge on transient, stage-specific disruptions in early brain development, and highlight sex-specific gene expression alterations.

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13.
medRxiv (Medicine) 2026-06-15

Instrumental Activities of Daily Living in Older Adults with Epilepsy: A Cross-Sectional and Longitudinal Multicenter Study

Authors:
Zawar↗Reyes↗Arrotta↗Hermann↗B. P↗Busch↗R. M↗Quigg↗Kapur↗Struck↗A. F↗Punia↗…

Objective: Instrumental activities of daily living (IADLs) represent a critical but understudied measure of day-to-day function in persons with epilepsy(PWE). In the multicenter Brain Aging and Cognition in Epilepsy (BrACE) study of PWE aged greater than or equal to 55 years, we examined the proportion, clinical correlates, epilepsy-related predictors, and longitudinal trajectory of IADL impairment. Methods: IADLs were assessed using the Functional Activities Questionnaire (FAQ; range=0 to 30; higher=more impaired); a FAQ greater than or equal to 2 defines MCI-level impairment, and a FAQ greater than or equal to 5 defines dementia-level functional impairment. Multivariable logistic regression identified predictors of baseline function. Global cognition (Montreal Cognitive Assessment [MoCA]), individual cognitive measures, and quality of life (QOL) were compared between the impaired and unimpaired groups. Linear regression evaluated predictors of longitudinal functional decline. Results: Of 57 participants (mean age=66.6 years; female=52.6%), 38.6% (n=22) had MCI-level functional impairment and 17.5% (n=10) had dementia-level functional impairment. In univariate analyses, worse FAQ scores were associated with lower education, higher area deprivation index, early-onset epilepsy (EOE less than 60 years), antiseizure medication polytherapy, and epilepsy localization. In multivariable analysis, temporal lobe epilepsy (OR=4.46, 95% CI=1.09, 21.83,p=0.047), EOE(OR=7.14, 95% CI=1.16, 59.97, p=0.046), and lower education(OR=0.70,95% CI=0.49, 0.93, p=0.025) remained independently associated with baseline MCI-level functional-impairment. Lower education (OR=0.55,95% CI=0.29, 0.84, p=0.021) was the only factor associated with dementia-level IADL-impairment. IADL-impaired participants demonstrated lower verbal memory scores (adjusted p=0.041) and MoCA scores (adjusted p

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14.
arXiv (CS.LG) 2026-06-16

InfoNCE Induces Gaussian Distribution

Authors:
Roy Betser↗Eyal Gofer↗Meir Yossef Levi↗Guy Gilboa↗

arXiv:2602.24012v2 Announce Type: replace Abstract: Contrastive learning has become a cornerstone of modern representation learning, allowing training with massive unlabeled data for both task-specific and general (foundation) models. A prototypical loss in contrastive training is InfoNCE and its variants. In this work, we show that the InfoNCE objective induces Gaussian structure in representations that emerge from contrastive training. We establish this result in two complementary regimes. First, we show that under certain alignment and concentration assumptions, projections of the high-dimensional representation asymptotically approach a multivariate Gaussian distribution. Next, under less strict assumptions, we show that adding a small asymptotically vanishing regularization term that promotes low feature norm and high feature entropy leads to similar asymptotic results. We support our analysis with experiments on synthetic and CIFAR-10 datasets across multiple encoder architectures and sizes, demonstrating consistent Gaussian behavior. This perspective provides a principled explanation for commonly observed Gaussianity in contrastive representations. The resulting Gaussian model enables principled analytical treatment of learned representations and is expected to support a wide range of applications in contrastive learning.

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

StyleShield: Exposing the Fragility of AIGC Detectors through Continuous Controllable Style Transfer

Authors:
Guantian Zheng↗

arXiv:2605.00924v2 Announce Type: replace-cross Abstract: AI-generated content (AIGC) detectors are increasingly deployed in high-stakes settings such as academic integrity screening, yet their reliability rests on a fundamental paradox: as language models are trained on human-written corpora, the statistical boundary between AI and human writing will inevitably dissolve as models improve. Commercial incentives have further distorted this landscape – detection services and "de-AIification" tools often operate within the same supply chain, replacing evaluation of content quality with judgment of content origin. We present StyleShield, the first flow matching framework for conditional text style transfer, operating directly in continuous token embedding space via a DiT backbone with zero-initialized cross-attention adapters conditioned on frozen Qwen-7B representations. At inference, we adapt the SDEdit paradigm from image synthesis to text embeddings, with a single parameter gamma providing smooth continuous control over the evasion-preservation trade-off. On a multi-domain Chinese benchmark, StyleShield achieves 94.6% evasion against the training detector and >=99% against three unseen detectors, maintaining 0.928 semantic similarity. We further introduce RateAudit, a document-level scheduling algorithm that demonstrates detection-rate verdicts can be set to arbitrary values, directly questioning the reliability of score-based evaluation.

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17.
arXiv (CS.AI) 2026-06-12

Is It You or Your Environment? A Bayesian Inference Framework for Genomically-Anchored Personalized Physiological Interpretation

Authors:
Aruna Dey↗Suraj Biswas↗

arXiv:2606.13556v1 Announce Type: new Abstract: Personalized health AI systems face a fundamental cold-start problem: machine learning models for physiological interpretation require weeks of individual behavioral data before they can distinguish constitutional variation from environmentally driven deviation. We propose a solution grounded in causal inference and Bayesian prior design. An individual's genomic profile serves as an exogenous genetic anchor – a domain-informed, personalized prior that is fixed at conception, immune to reverse causation, and available before a single behavioral observation is collected. The anchor initializes a Bayesian belief state over an individual's physiological set point G-hat = mu + sum(beta_i * g_i), where beta_i are GWAS-derived effect sizes and g_i are risk-allele counts. Each incoming physiological measurement P produces a non-constitutional deviation delta = P - G-hat that separates the signal attributable to environment and state from the constitutionally fixed baseline. As behavioral data accrue, the prior decays according to G-hat_t = w(t)*G-hat_genomic + [1-w(t)]*P-bar_t, transitioning from genome-dominated to empirical-baseline-dominated inference. The same observed HRV of 55 ms generates a suppression hypothesis for a person whose prior predicts 80 ms, and an enhancement hypothesis for a person whose prior predicts 30 ms – a reversal impossible without a personalized anchor. We develop this architecture across six physiological domains, grading genomic priors by evidence strength, distinguishing robustly replicated anchors (FTO, FADS1/2, FKBP5) from contested candidate genes (SLC6A4, MAOA, DRD2). We address the inference boundary between association, Mendelian randomization, and individual token causation, and define four constraints for deployment: evidence-graded priors, dynamic decay, ancestry-matched effect sizes, and attribution rather than deterministic output.

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18.
arXiv (CS.AI) 2026-06-19

Hidden Anchors in Multi-Agent LLM Deliberation

Authors:
Apurba Pokharel↗Ram Dantu↗

arXiv:2606.19494v1 Announce Type: new Abstract: Multi-agent LLM deliberation, where agents exchange and revise answers over several rounds, is increasingly used to improve reasoning and accuracy, yet how and why it works is rarely modelled. Such deliberation mirrors how humans reach decisions. As social animals we are pulled both by the group, the herd effect that classical opinion-dynamics models such as DeGroot and Friedkin–Johnsen capture, and by our own internal belief, which they do not. We model multi-agent deliberation as a closed-loop dynamical system in which each agent carries a hidden internal belief, its anchor, that continually pulls its opinion regardless of its neighbours. We show this anchor can be recovered from the deliberation alone, and that it explains a behaviour classical consensus rules forbid: an agent's confidence in the correct answer can climb past where any agent started, escaping the space (convexhull) formed by the initial beliefs. Checking whether the recovered anchor also predicts held-out runs (generalizes) gives a simple test for when a model is truly driven bysuch an anchor. Across three open-weight model families this is a spectrum, not all-or-nothing. All anchors' influence are about equally strongly, but they differ in where the anchor sits, and only when it sits far from the initial opinions does deliberation escape the hull and need the full closed-loop model.

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19.
arXiv (CS.AI) 2026-06-17

PowerOPD: Stabilizing On-Policy Distillation with Bounded Power Transformation

Authors:
Anhao Zhao↗Junlong Tong↗Yingqi Fan↗Ping Nie↗Wenjie Li↗Xiaoyu Shen↗

arXiv:2606.17199v1 Announce Type: cross Abstract: Standard on-policy distillation (OPD) for large language models estimates the reverse-KL objective using student-sampled tokens, yielding an unbiased single-sample Monte Carlo estimator that avoids vocabulary-wide computation. However, we show that this estimator suffers from severe training pathologies in practice: sample inefficiency, unstable generation dynamics, and a substantial performance gap compared to exact full-vocabulary OPD. Reward-level diagnosis traces these pathologies to the log-ratio reward, which is unbounded by construction, producing extremely high-variance gradients concentrated at early positions and persisting throughout training; standard post-hoc scaling fail as they operate only after this distortion occurs. To solve this problem, we propose PowerOPD: a family of natively bounded, sign-consistent rewards from the Box-Cox power transformation, parameterized by alpha > 0, of which the log-ratio is the degenerate alpha -> 0 limit. Across six mathematical reasoning benchmarks and four Qwen3 teacher-student pairs, PowerOPD achieves benchmark-averaged Avg@8/Pass@8 gains of up to +6.37/+5.71 over vanilla OPD, +3.01/+3.54 over post-hoc stabilization, and +2.59/+8.90 over full-vocabulary OPD, while reducing wall-clock time by 59.2% and peak GPU memory by 23.1%. Larger alpha generally improves accuracy, consistently shortens responses, and keeps gradient norms more than 3,000x smaller than vanilla OPD.

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20.
medRxiv (Medicine) 2026-06-16

Adherence to Red Reflex and Vision Screening Recommendations: A Deep Dive into Primary Care Implementation Gaps

Authors:
Asare↗A. O↗Robles↗Hartmann↗E. E↗Stipelman↗Calder↗Omotowa↗Montgomery↗Baugh↗B. T↗Stagg↗…

Introduction: Early childhood vision screening is critical for detecting amblyopia and other vision-threatening conditions. Despite screening recommendations during well-child visits, rates remain low. Red reflex assessment is recommended to identify serious ocular pathology, yet its use in primary care is not well described. We examined rates and drivers of vision screening in pediatric primary care. Methods: We conducted a retrospective review of electronic health records for children 3 to 5 years attending well-child visits in 2022 in one of three representative primary care clinics within a university health system. Outcomes were documented red reflex and functional vision tests. We evaluated associations with patient demographics and clinic site using multivariable logistic regression Results: Among 1,003 visits, 21.1% (n=212) had a documented red reflex assessment, and 60.8% (n=610) a functional vision test. Younger children (ages 3 and 4 vs. 5 years) had higher odds of red reflex assessment [adjusted odds ratio (aOR) 9.00 and 8.64], and lower odds of a functional vision (aOR 0.47 and 0.59) test. Females had higher odds of red reflex assessment (aOR 1.53). Other/Multiracial children had lower odds of red reflex assessment than Non-Hispanic White children (aOR 0.48). Screening rates varied significantly by clinic site Conclusions: Visual function and red reflex assessment are inconsistently performed in pediatric primary care, with particularly low rates of red reflex documentation. Screening rates varied between clinics and were affected by age. These findings highlight missed opportunities for early detection of vision-threatening conditions and identify targets for improving adherence to pediatric vision screening recommendations

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21.
Nature (Science) 2026-06-15

Nanocrystal-tailored recombination for all-perovskite tandem solar modules

Authors:
Ke Xiao↗

The commercialization of all-perovskite tandem solar modules is hindered by the reliance on the conventional gold-based tunnel recombination junction (TRJ)1,2. Specifically, this TRJ introduces substantial near-infrared parasitic absorption3 and suffers from interfacial instability4, limiting both photocurrent generation and operational durability. Here, we develop a solution-processed interconnecting layer based on surface-engineered indium oxide (In2O3) nanocrystals featuring high optical transparency, wherein controlled nanocrystal morphology and tailored ligand chemistry enable smooth interfacial contact and favorable energy level alignment. Critically, we introduce a phosphonic acid additive into the lead–tin (Pb–Sn) perovskite precursor, which synergistically improves the electronic contact with the In2O3 recombination layer, thereby enhancing hole extraction. In addition, the additive regulates perovskite crystallization to mitigate residual strain during film formation, ensuring high-quality large-area deposits. This coordinated interfacial and crystallization engineering strategy simultaneously enhances carrier recombination efficiency at the interconnection layer, improves carrier extraction, and promotes large-area film uniformity in all-perovskite tandems. As a result, a 65-cm2 all-perovskite tandem solar module achieves a certified power conversion efficiency of 26.2%5, with an open-circuit voltage of 2.182 V, a fill factor of 77.4%, and a short-circuit current density of 15.6 mA cm-2 in terms of averaged subcell performance, measured by Japan Electrical Safety and Environment Technology Laboratories (JET). This marks a significant advance toward scalable perovskite tandem photovoltaics.

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22.
arXiv (CS.CV) 2026-06-19

MMD-SLAM: Structure-Enhanced Multi-Meta Gaussian Distribution-Guided Visual SLAM

Authors:
Fan Zhu↗Ziyu Chen↗Peichen Liu↗Yifan Zhao↗Zhisong Xu↗Hui Zhu↗Hongxing Zhou↗Sixun Liu↗Chunmao Jiang↗

3D Gaussian Splatting (3DGS) has significantly boosted novel view synthesis and high-fidelity scene reconstruction, expanding the potential of 3DGS-based Visual Simultaneous Localization and Mapping (SLAM) methods. However, most existing systems fail to fully exploit the underlying structural information, which limits rendering quality and often leads to inconsistent maps. To address these limitations, we propose MMD-SLAM, a structure-enhanced Visual SLAM framework that leverages the Atlanta World (AW) assumption to guide a Multi-Meta Gaussian representation for photorealistic mapping. First, we introduce a point-line fusion strategy for pose optimization, where 3D line segments are incorporated to improve tracking robustness and provide additional constraints for mapping. Second, we design a Multi-Meta Gaussian representation with dominant directions, explicitly encoding structural priors from the AW hypothesis. Finally, we propose a Gaussian evolution strategy that adapts to scene geometry and incorporates structural cues into global optimization. Extensive experiments demonstrate that these innovations enable MMD-SLAM to achieve state-of-the-art performance in both tracking accuracy and mapping quality. e.g., our method achieves a 48.56% reduction in ATE RMSE on ScanNet and a 5.71% improvement in PSNR on Replica, compared with MonoGS.

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23.
bioRxiv (Bioinfo) 2026-06-22

Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states

Authors:
Zhu↗Hu↗Xie↗M. B↗Qin↗Szul↗Z. J↗Young↗D. M↗Yuan↗Wang↗Liu↗…

Spatial transcriptomics enables the quantification of gene expression within its native tissue context, providing unprecedented insight into tissue architecture, cellular ecosystems, and local cell-cell interactions at regional and single-cell resolution. Accurate cell type annotation is a critical prerequisite for interpreting these data and is often the first and most essential step in downstream analysis. Despite rapid advances in computational methods, cell type annotation remains challenging and frequently requires extensive expert-driven manual curation based on marker-gene expression, spatial context, and prior biological knowledge. While early approaches relied primarily on transcriptional similarity, newer methods increasingly incorporate spatial information, histological features, and multimodal data to improve annotation accuracy. Nevertheless, reliable annotation remains difficult when biological interpretation requires fine-grained subtype resolution, particularly for platforms with limited gene panels, tissues undergoing dynamic cellular state transitions, and studies in which reference and query datasets differ substantially in biological context or technical modality. Here, we present a systematic benchmark of 20 state-of-the-art cell type annotation methods across four spatial transcriptomics datasets spanning diverse technologies, experimental conditions, cell numbers, and gene panel sizes. Importantly, all benchmark datasets contain expert-curated cell type labels, including well-resolved cell populations and subtype annotations, providing high-quality biological ground truth for evaluation. The benchmark encompasses both reference-based and reference-free methods representing a broad range of computational frameworks. Performance was assessed using conventional classification metrics, including accuracy and F1-based measures, together with structure-aware metrics that evaluate both cell-level annotation accuracy and preservation of higher-order biological organization. Across datasets, annotation performance varied substantially according to tissue context, reference-query similarity, and annotation granularity. Fine-grained subtype annotation and recovery of rare cell populations remained challenging for many methods, particularly in datasets capturing injury, repair, developmental, and regenerative processes characterized by continuous cellular state transitions. Notably, high classification accuracy did not necessarily correspond to preservation of global cellular relationships or biologically coherent downstream pathway and gene-set enrichment analyses. Overall, scANVI, Seurat, and TACCO consistently ranked among the top-performing methods, although their relative advantages were context dependent. Together, our results provide a comprehensive assessment of current annotation strategies for spatial transcriptomics and offer practical guidance for selecting methods that best align with specific biological questions, dataset characteristics, and analytical priorities.

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

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

Authors:
Shridhar Vashishtha↗Krishna Prasath Logakannan↗Jacob Hochhalter↗Shandian Zhe↗Robert M. Kirby↗

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.

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25.
arXiv (quant-ph) 2026-06-11

Superspace Concentration and Adversarial Robustness in Quantum Algorithms

Authors:
Eric Yocam↗Christian Yocam↗Varghese Vaidyan↗Yong Wang↗Mahesh Kalappattil↗Anthony Rizi↗

arXiv:2606.11580v1 Announce Type: new Abstract: We study superspace concentration as a quantum resource, formalized through the focus measure F(\r{ho}) = {\lambda}_max(\r{ho}_super) - the largest eigenvalue of the reduced superspace state - which quantifies the capacity of a quantum system to concentrate informational weight into a preferred subspace of an extended degree-of-freedom space. We develop a complete resource-theoretic framework around this measure and validate its properties through GPU-accelerated numerical simulation. Analytic decoherence predictions are confirmed to machine precision (1.11 x 10^{-16}) for superspace dimensions dS in {2,4,8,16,32}. Focus monotonicity holds across 10,000 random states with zero violations under four focus-non-generating channels across six system configurations. Focused quantum states resist coherent unitary attacks with significantly greater resilience than standard fidelity predicts, with focus remaining above 0.9 at attack strength {\epsilon} = 0.302 versus {\epsilon} = 0.174 for fidelity. We further demonstrate that the focus measure and the U(dS)-asymmetry measure are operationally distinct: asymmetry remains near zero and provides no robustness signal under coherent and targeted attacks while focus tracks spectral concentration and remains robust until {\epsilon} > 0.3. The connection between Grover's algorithm and superspace concentration is made explicit via the identity F(|{\psi}_k>

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