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

Focus When Necessary: Adaptive Routing and Collaborative Grounding for Training-Free Visual Grounding

While Multimodal Large Language Models (MLLMs) excel in cross-modal reasoning, they often struggle to perceive fine-grained details in complex high-resolution images. Recent training-free methods address this through image scaling and localized cropping. However, applying these manipulations indiscriminately introduces computational redundancy for simple queries and can degrade accuracy by truncating essential global context or introducing irrelevant background noise. To this end, we propose LazyMCoT, a dynamic and training-free framework that adaptively allocates visual grounding efforts based on sample difficulty. The framework features an Adaptive Routing mechanism that evaluates predictive uncertainty using first-token statistics from a single forward pass. This efficiently bypasses confident cases while ensuring the recall of difficult samples via conformal calibration. For these challenging cases, a Collaborative Grounding module integrates the inherent cross-modal attention of the model with an external visual expert through a two-stage refinement process. This refinement process generates a precise localized display to recover small or occluded targets. Extensive experiments across diverse benchmarks demonstrate that LazyMCoT rivals training-based approaches by simultaneously improving reasoning accuracy and reducing average inference latency. Our code is availble at https://github.com/TencentBAC/LazyMCoT.

02.
arXiv (CS.AI) 2026-06-15

EvoTrainer: Co-Evolving LLM Policies and Training Harnesses for Autonomous Agentic Reinforcement Learning

arXiv:2606.03108v2 Announce Type: replace Abstract: Autonomous LLM training is often framed as recipe search, which leaves the training harness largely static. This limitation sharpens in agentic RL, where shifting bottlenecks and scalar rewards mask diverse failure modes. We introduce EvoTrainer, an autonomous training framework that co-evolves LLM policies and training-side harnesses through empirical feedback: it diagnoses rollout-level evidence, revises diagnostics, backtests interventions, and accumulates reusable skills. Evaluated on mathematical reasoning, competitive-programming code generation, and repository-level software engineering, EvoTrainer matches or exceeds the human-engineered RL references under the same data, codebase, and evaluation protocol, with the largest gain on long-horizon agentic SWE. Trajectory analyses show that retained strategies diverge across domains, evolving diagnostics prevent invalid high-scoring branches from being promoted, and reusable skills shape later search. Autonomous LLM RL should move beyond recipe search toward joint evolution of policies and the training harnesses that interpret them.

03.
arXiv (CS.LG) 2026-06-16

Learning the generating functional for variance reduction in lattice QCD

arXiv:2606.15986v1 Announce Type: cross Abstract: The generating functional in quantum field theory provides the natural framework for constructing correlation functions as derivatives with respect to source operators. We present a methodology that leverages machine-learned normalizing flows to reduce the variance of arbitrary $N$-point correlation functions of bosonic operators in lattice gauge field theory calculations by encoding a representation of the generating functional. We show that it is possible to systematically approach noiseless estimators of correlation functions in this framework. We demonstrate this methodology with applications to calculations of glueball correlation functions and Wilson loops in Quantum Chromodynamics and Yang-Mills theory. The results show up to three orders of magnitude variance reduction.

04.
arXiv (CS.CV) 2026-06-16

OmniTraffic: A Controllable Generation Pipeline and Benchmark for Spatio-Temporal Traffic Reasoning

Traffic scene understanding requires models to reason beyond object recognition, including lane topology, multi-view geometry, temporal evolution, and signal-phase semantics. However, existing traffic-oriented multimodal benchmarks largely emphasize passive visual recognition or isolated video understanding, offering limited support for evaluating structure-aware traffic reasoning under controlled conditions. We introduce OmniTraffic, a controllable generation pipeline and benchmark for spatio-temporal traffic reasoning. Built around 12 real-world intersections reconstructed into editable 3D traffic environments and complemented by surveillance footage from two countries, OmniTraffic supports both controlled and natural-condition evaluation. It defines a three-level task hierarchy spanning scene perception, multi-view and temporal reasoning, and decision support. Using structured traffic metadata, OmniTraffic generates synchronized multi-view VQA samples covering vehicle states, lane functions, view–BEV correspondence, temporal dynamics, and signal-phase analysis, resulting in 8M VQA samples and a 3K human-verified test set. Evaluation of eleven frontier MLLMs reveals a large human–model gap, with the most pronounced failures in topology-grounded and spatio-temporal reasoning tasks. Fine-tuning a lightweight MLLM on simulated OmniTraffic data further improves performance on real-world traffic scenes, demonstrating the value of simulation-generated supervision for traffic-specific multimodal reasoning. Beyond a fixed dataset, OmniTraffic provides an extensible pipeline with configurable intersections, camera views, traffic demands, signal phases, visual conditions, and rare events.

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

Adaptive generative moment matching networks for improved learning of dependence structures

arXiv:2508.21531v2 Announce Type: replace-cross Abstract: An adaptive bandwidth selection procedure for the mixture kernel in the maximum mean discrepancy (MMD) for fitting generative moment matching networks (GMMNs) is introduced, and improved learning of copula random number generators is demonstrated. Based on the relative error of the training loss, the number of kernels is increased during training; additionally, the relative error of the validation loss is used as an early stopping criterion. While training time remains similar, adaptively training GMMNs (AGMMNs) significantly increases training performance, which is shown based on validation MMD trajectories, samples and validation MMD values. Superiority of AGMMNs over GMMNs and parametric copula models is also demonstrated in terms of three applications. First, convergence rates of estimators based on quasi-random versus pseudo-random samples from copulas are investigated in dimensions as large as 100 for the first time. Second, replicated validation MMDs, as well as Monte Carlo and quasi-Monte Carlo applications demonstrate the improved training of AGMMNs for a copula model implied by the 50 constituents of the S&P 500 index after deGARCHing. Last, both the latter dataset and 50 constituents of the FTSE 100 are used to demonstrate that the improved training of AGMMNs indeed translates to an improved model prediction.

06.
PLOS Medicine 2026-06-12

Placenta accreta spectrum in the 21st century: Challenging dogma and redefining disorder

by Eric Jauniaux, Helena C. Bartels, Yalda Afshar Placenta accreta spectrum (PAS) is a serious pregnancy complication caused by abnormal placental attachment to the uterus. In this Perspective, Eric Jauniaux and colleagues discuss emerging evidence that challenges our long-held pathophysiological understanding of PAS, and argue that a critical reassessment of definition, diagnosis, and management is overdue. In this Perspective, Jonathan Evans and colleagues discuss why restricting access to joint replacement surgery based on BMI alone is not supported by evidence, and highlight how such rest rictions risk exacerbating stigma, inequity and avoidable harm to those who would benefit from surgery.

07.
arXiv (CS.CV) 2026-06-11

DrivingAgent: Design and Scheduling Agents for Autonomous Driving Systems

Many autonomous driving systems are increasingly incorporating foundation models to improve generalization and handle long-tail scenarios. However, this trend introduces two key challenges: (i) the manual and labor-intensive process of designing and integrating new models, and (ii) the lack of intelligent, dynamic scheduling mechanisms to meet strict real-time constraints. While Large Language Model (LLM)-based agents offer a promising avenue for automation, existing frameworks are ill-suited for autonomous driving. Specifically, they fail to distinguish between the fundamentally different requirements of system design and real-time scheduling, treat modules as opaque black boxes, and are not designed for continuous operation. To address these limitations, we propose DrivingAgent, a novel agent framework tailored to the dual challenges of autonomous driving system design and scheduling. In the design phase, DrivingAgent automates module development by interpreting system architecture, generating code, and validating modules via super-network training. In the scheduling phase, it employs a lightweight LLM trained with reinforcement learning to dynamically orchestrate system modules in real time, supported by a structured memory that integrates long-term storage with timestamped short-term context. Experimental results demonstrate that DrivingAgent achieves a superior speed–accuracy trade-off on both the nuScenes and Bench2Drive benchmarks.

08.
arXiv (CS.CV) 2026-06-15

A Robust Point Cloud Analysis Framework Inspired By Primary Visual Cortex

Despite significant advancements in point cloud analysis, reducing energy consumption and improving robustness remain understudied, largely due to the inherent limitations of Convolutional Neural Networks (CNNs). To address this issue, we draw inspiration from the primary visual cortex and propose a Dendritic-Connected Continuous-Coupled Neural Network (DC-CCNN), a novel Brain-Inspired Neural Network (BINN) architecture for point cloud analysis. By combining discrete and continuous encoding, our design replaces traditional Multilayer Perceptrons (MLPs) with more efficient and robust BINNs. Building upon this framework, we further propose an extended model, DC-CCNN++, to improve robustness under complex corruption conditions. Specifically, we introduce a Neuro-Inspired Robust Modulation-and-Readout Module (NRMR) to enhance feature stability and decision robustness through global-context gain modulation and dual-code evidence integration. We also design a Cortically Inspired Progressive Variability Training (CPVT) strategy, which progressively exposes the model to structured environmental variability while preserving stable clean-sample anchors during training. Experimental results show that DC-CCNN++ improves the performance of brain-inspired networks on point cloud analysis while maintaining performance comparable to state-of-the-art methods. Compared with the original DC-CCNN, it achieves stronger results on both classification and part segmentation, and exhibits enhanced robustness against sparsity, occlusion, Gaussian noise, salt-and-pepper noise, and spatial transformations. With its efficiency, robustness, and biologically grounded design, DC-CCNN++ provides a promising alternative to traditional deep learning methods for point cloud analysis. Code is available at https://anonymous.4open.science/r/DC-CCNNpp-44E3.

09.
arXiv (CS.LG) 2026-06-16

Information Leakage Detection through Approximate Bayes-optimal Prediction

arXiv:2401.14283v4 Announce Type: replace-cross Abstract: In today's data-driven world, the proliferation of publicly available information raises security concerns due to the information leakage (IL) problem. IL involves unintentionally exposing sensitive information to unauthorized parties via observable system information. Conventional statistical approaches rely on estimating mutual information (MI) between observable and secret information for detecting ILs, face challenges of the curse of dimensionality, convergence, computational complexity, and MI misestimation. Though effective, emerging supervised machine learning based approaches to detect ILs are limited to binary system sensitive information and lack a comprehensive framework. To address these limitations, we establish a theoretical framework using statistical learning theory and information theory to quantify and detect IL accurately. Using automated machine learning, we demonstrate that MI can be accurately estimated by approximating the typically unknown Bayes predictor's log-loss and accuracy. Based on this, we show how MI can effectively be estimated to detect ILs. Our method performs superior to state-of-the-art baselines in an empirical study considering synthetic and real-world OpenSSL TLS server datasets.

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

Inference-time Policy Steering via Vision and Touch

arXiv:2606.14981v1 Announce Type: cross Abstract: Inference-time steering adapts pre-trained generative robot policies during deployment by verifying candidate actions before execution. While prior methods typically perform this verification only with visual observations, vision alone is often insufficient for contact-rich manipulation, where success depends on both global task progress and subtle local interactions such as contact force. We introduce ViTaL, a visuo-tactile inference-time steering framework that formulates multimodal guidance as a bi-level optimization problem. At the high level, visual sampling-and-verification performs long-horizon mode selection, deciding what behavior the robot should execute. At the low level, tactile-guided diffusion editing refines the selected action sequence over a shorter horizon to satisfy local contact requirements. To support outcome-based steering, ViTaL learns a visuo-tactile latent world model and employs semantically aligned visual and tactile verifiers, including a novel text-conditioned tactile reward that scores predicted tactile futures directly in latent space. Across three real-world contact-rich manipulation tasks, ViTaL improves overall success by 51% over the base policy, outperforms unimodal steering by at least 33%, and exceeds naive multimodal fusion by at least 20%. Website: https://yilin-wu98.github.io/vital_website.

11.
arXiv (quant-ph) 2026-06-16

Morphology-resolved scrambling in a chaotic quantum billiard

arXiv:2606.16865v1 Announce Type: new Abstract: Chaotic quantum systems can retain spatial memory through scarred eigenstates, but whether these static structures control scrambling remains unclear. This work establishes a morphology-resolved connection between scarred eigenstates and eigenstate-resolved OTOCs in a peanut-shaped quantum billiard. Scalar localisation diagnostics, including differential entropy and continuum participation ratios, detect anomalous concentration but discard spatial architecture. A scale-normalised density overlap, in contrast, directly compares probability density profiles, revealing families of orthogonal eigenstates with nearly identical spatial morphology. Comparing the complete OTOC time traces of these orthogonal eigenstates reveals that morphological recurrence has dynamical content: moderate density overlap yields no universal prediction, whereas strongly recurring morphologies exhibit nearly identical OTOC growth and saturation. Thus, scarred structures act as spatial templates for operator growth, not merely static violations of ergodicity. This morphology-resolved framework turns eigenstate shape into a quantitative predictor of scrambling and provides a scale-controlled diagnostic of weak ergodicity breaking in quantum chaos.

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

Closing the Approximation Gap in Simulation-free Latent SDEs

arXiv:2606.16138v1 Announce Type: cross Abstract: Recovering dynamical systems from noisy observations is a recurring challenge across scientific domains, including neuroscience and physics. Latent stochastic differential equations (SDEs) address this by modeling the system as an unobserved state that evolves according to a learnable SDE and generates the observations. Variational inference (VI) provides a tractable objective for fitting latent SDEs. Traditional VI algorithms evaluate this objective by numerical simulation over a time discretization, trading fidelity for computational cost. A recent class of algorithms, simulation-free VI, sidesteps this tradeoff by parameterizing the posterior through its instantaneous marginals rather than its drift. In this work, we show that the efficiency of existing simulation-free VI algorithms comes at a price: their parameterizations restrict the approximate posterior to a subset of the SDEs available to simulation-based methods, degrading posterior inference and parameter learning. We propose Helmholtz-SDE, a simulation-free VI algorithm that closes this gap by optimizing over path laws compatible with a prescribed collection of marginals. Helmholtz-SDE recovers dynamics more faithfully than prior simulation-free methods, with the largest gains under high posterior uncertainty. It further matches the performance of simulation-based VI at a fraction of the runtime.

13.
arXiv (quant-ph) 2026-06-16

High-Order Hermite Optimization: Fast and Exact Gradient Computation in Open-Loop Quantum Optimal Control using a Discrete Adjoint Approach

arXiv:2505.09857v5 Announce Type: replace-cross Abstract: This work introduces the High-Order Hermite Optimization (HOHO) method, an open-loop discrete adjoint method for quantum optimal control. Our method is the first of its kind to efficiently compute exact (discrete) gradients when using continuous, parameterized control pulses while solving the forward equations (e.g. Schrodinger's equation or the Linblad master equation) with an arbitrarily high-order Hermite Runge-Kutta method. The HOHO method is implemented in QuantumGateDesign$.$jl (https://github.com/leespen1/QuantumGateDesign.jl), an open-source software package for the Julia programming language, which we use to perform numerical experiments comparing the method to Juqbox$.$jl (https://github.com/LLNL/Juqbox.jl). For realistic model problems we observe speedups up to 775x.

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

The Emergence of Autonomous Penetration Capabilities in Large Language Model-Powered AI Systems

arXiv:2606.13079v1 Announce Type: cross Abstract: Nowadays, the autonomous execution of cyberattacks capable of causing substantial real-world harm is widely regarded as one of the critical red lines that frontier AI systems must not cross. Within this broader red-line scenario, autonomous penetration represents a core enabling capability and subtask: the ability of LLM-powered AI systems to independently conduct adversarial operations against a target server without human intervention, identify and exploit vulnerabilities, and obtain unauthorized access or control. A growing body of work has sought to assess the autonomous penetration capabilities of AI systems. However, existing evaluations often employ opaque methodologies, rely on unrealistic or overly simplified penetration-testing scenarios, or provide LLMs with excessive prior knowledge and task-specific guidance, and cannot accurately capture the extent to which modern AI systems can autonomously perform this core capability within broader high-impact cyberattack scenarios. To address these limitations, we construct a new autonomous penetration evaluation framework consisting of two components: target servers and agent scaffolding. Specifically, on the target-server side, we design two levels of target environments based on the number of secure services without known vulnerabilities deployed alongside a vulnerable service: Tier~1 (one secure service) and Tier~2 (three secure services), resulting in a total of 300 target servers. Meanwhile, the agent scaffolding adopts a general-purpose agent architecture equipped with a set of general-purpose cybersecurity tools, without any target-specific prior knowledge. We evaluate 19 open-weight and proprietary LLMs, and find that current models achieve penetration success rates ranging from 10.7% to 69.3%. Moreover, we observe that autonomous penetration capability continues to improve alongside advances in overall model capability.

15.
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.

16.
arXiv (quant-ph) 2026-06-15

Link-Free Multi-Node Timing Synchronization for Scalable Quantum Networking

arXiv:2606.14077v1 Announce Type: new Abstract: Precise timing synchronization is essential for distributed quantum networking, enabling entanglement distribution, quantum teleportation, and entanglement swapping across remote nodes. Existing synchronization architectures rely on dedicated timing-distribution infrastructure, most notably White Rabbit networks, which constrain topology, scalability, and deployment in free-space and satellite environments. Here we demonstrate link-free synchronization of quantum network nodes using independently operating miniature rubidium atomic clocks and computational post-processing. We validate the approach on a deployed metropolitan-scale telecom fiber network spanning three geographically separated nodes. Following drift correction, atomic-clock-based synchronization achieves timing performance approaching that of a White Rabbit benchmark and remains stable over continuous 8-hour operation. As a stringent test of quantum-network functionality, we observe Hong-Ou-Mandel interference across spatially separated nodes with visibility exceeding 70%, statistically equivalent to that obtained using dedicated White Rabbit timing links. To the best of our knowledge, this represents the first observation of quantum interference across a deployed metropolitan-scale telecom fiber network synchronized entirely without dedicated timing-transfer infrastructure. These results establish atomic-clock-based synchronization as a scalable, topology-independent alternative to conventional timing-distribution architectures and a practical pathway toward terrestrial, airborne, and space-based quantum networks where dedicated timing links are unavailable.

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

ResAware: Cross-Environment Website Fingerprinting via Resource-Privileged Distillation

arXiv:2606.17462v1 Announce Type: new Abstract: While Website Fingerprinting (WF) attacks achieve high accuracy in controlled laboratory settings, they often degrade substantially in real-world environments due to spatio-temporal drift, browser heterogeneity, proxy obfuscation and etc. This limitation stems from their sole reliance on low-level traffic features that are noisy and highly sensitive to environmental perturbations. To address this problem, we propose ResAware, a cross-environment resource-aware distillation framework under a training-rich/inference-poor asymmetric setting. Specifically, ResAware trains a teacher model on resource-level features, and then distills the resulting privileged knowledge into a student model through heterogeneous knowledge distillation. At deployment time, the student model performs inference using only encrypted traffic, incurring zero additional cost. We evaluate ResAware on a large-scale dataset collected over five months from six globally distributed vantage points, comprising more than $160{,}000$ paired samples. The results show that ResAware significantly enhances the cross-environment robustness of diverse WF baselines. Under a 150-day temporal drift, for example, ResAware improves the F1-score of Var-CNN from $72.77\%$ to $81.49\%$ and the open-world $TPR@1\%FPR$ from $22.40\%$ to $27.20\%$. Our results demonstrate that resource-level supervision improves WF robustness without expanding online observation capabilities.

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

Learning Fine-Grained Correspondence with Cross-Perspective Perception for Open-Vocabulary 6D Object Pose Estimation

Open-vocabulary 6D object pose estimation empowers robots to manipulate arbitrary unseen objects guided solely by natural language. However, a critical limitation of existing approaches is their reliance on unconstrained global matching strategies. In open-world scenarios, trying to match anchor features against the entire query image space introduces excessive ambiguity, as target features are easily confused with background distractors. To resolve this, we propose Fine-grained Correspondence Pose Estimation (FiCoP), a framework that transitions from noise-prone global matching to spatially-constrained patch-level correspondence. To systematically eliminate background interference, FiCoP first employs an object-centric disentanglement step to isolate the target from macro-level environmental noise. Building upon this localized region, our core methodological innovations are twofold. Firstly, a Cross-Perspective Global Perception (CPGP) module is proposed to fuse dual-view features, establishing structural consensus through explicit context reasoning and text-guided semantic injection. Secondly, we design a Patch Correlation Predictor (PCP) that leverages a patch-to-patch correlation matrix as a structural prior. This generates a precise block-wise association map, acting as a spatial filter to enforce fine-grained, noise-resilient matching. Experiments on the REAL275 and Toyota-Light datasets demonstrate that FiCoP improves Average Recall by 8.0% and 6.1%, respectively, compared to the state-of-the-art method, highlighting its capability to deliver robust and generalized perception for robotic agents operating in complex, unconstrained open-world environments. The source code will be made publicly available at https://github.com/zjjqinyu/FiCoP.

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

On the Stability of Nonlinear Dynamics in GD and SGD: Beyond Quadratic Potentials

arXiv:2602.14789v2 Announce Type: replace Abstract: The dynamical stability of the iterates during training plays a key role in determining the minima obtained by optimization algorithms. For example, stable solutions of gradient descent (GD) correspond to flat minima, which have been associated with favorable features. While prior work often relies on linearization to determine stability, it remains unclear whether linearized dynamics faithfully capture the full nonlinear behavior. Recent work has shown that GD may stably oscillate near a linearly unstable minimum and still converge once the step size decays, indicating that linear analysis can be misleading. In this work, we explicitly study the effect of nonlinear terms. Specifically, we derive an exact criterion for stable oscillations of GD near minima in the multivariate setting. Our condition depends on high-order derivatives, generalizing existing results. Extending the analysis to stochastic gradient descent (SGD), we show that nonlinear dynamics can diverge in expectation even if a single batch is unstable. This implies that stability can be dictated by a single batch that oscillates unstably, rather than an average effect, as linear analysis suggests. Finally, we prove that if all batches are linearly stable, the nonlinear dynamics of SGD are stable in expectation.

20.
arXiv (quant-ph) 2026-06-19

String dynamics of a (2+1)D U(1) quantum link model on a digital quantum computer

arXiv:2606.19601v1 Announce Type: new Abstract: The (2+1)D U(1) pure gauge theory always exists in the confining phase, with strings of non-zero string tension giving a characteristic linear potential between static charges. This makes it a useful testing ground for quantum computing methods designed to study string dynamics of confining gauge theories. Here we implement a minimal U(1) quantum link model on a quantum computer with qubit degrees of freedom representing the dual height variables of the model. This facilitates an efficient realization of plaquette interactions and enables effective calculations of real-time dynamics that are inaccessible to traditional quantum Monte Carlo. A specifically tailored lattice geometry is chosen to match the heavy-hexagonal geometry of the IBM quantum hardware used here, minimizing non-adjacent qubit interactions. By performing quantum quenches from a simple initial string state, we probe the transverse quantum fluctuations of the string before it thermalizes. Our experimental results from digital quantum simulations, with up to 112 qubits, show good agreement with reference tensor-network calculations at short times and with thermal averages at long times. Near the phase transition, the quench dynamics exhibit large fluctuations of the initial string that extend across both spatial dimensions of the lattice. Nonetheless, our error-mitigated estimators from the quantum hardware also give accurate predictions in that regime, with noise-induced violations of local gauge symmetries comparable to finite-bond-dimension tensor-network results.

21.
arXiv (CS.LG) 2026-06-15

XRDiff: Crystal Structure Prediction from Powder X-Ray Diffraction Data Using Diffusion Models

arXiv:2606.14003v1 Announce Type: cross Abstract: Determining the crystal structure of a material from its powder X-ray diffraction (PXRD) pattern is a central challenge in materials science. PXRD is an accessible and widely used characterization technique, yet recovering the atomic structure from diffraction data requires solving an underdetermined inverse problem due to the loss of phase information. Generative modeling can provide a prior over atomic structure and learn the mapping from PXRD patterns to crystal structures via simulated structure-spectrum pairs. We present XRDiff, a diffusion model that recovers crystal structures from PXRD given either the stoichiometry or, in a more challenging setting, the elemental constituents and total number of atoms in the unit cell. We evaluate on datasets where each stoichiometry has multiple polymorphs and all polymorphs of a given composition are held out together, ensuring that high performance reflects genuine use of the diffraction signal. XRDiff achieves strong structure recovery rates on simulated benchmarks, indicating that the model learns a spectrum-to-structure mapping precise enough to differentiate between polymorphs. To address generalization to experimental data, we compare a full-spectrum encoding against an encoding based on peak descriptors. The peak-based encoding generalizes substantially better, outperforming even a model trained on full spectra with augmentations fitted to the experimental noise distribution. These results demonstrate that representations robust to the noise and artifacts present in real-world PXRD offer a practical and scalable path toward closing the simulation-to-experiment gap, enabling zero-shot crystal structure solution from experimental PXRD with full or partial chemical composition input.

22.
medRxiv (Medicine) 2026-06-16

Preventing postpartum depression through mitigating breastfeeding grief: A convergent parallel mixed methods study

Background: Women who did not meet their breastfeeding goals often experience breastfeeding grief (BG) and may be likely to have postpartum depression (PD). Furthermore, PD is nearly twice as common in African American (AA) women as in Non-Hispanic White women. No research exists on BG and its role in PD. This study examined the BG experiences of AA women and its possible contributions to PD symptoms. Methods: A convergent parallel mixed methods design was used. A purposive sample of 16 AA women with children aged 6 months to 2 years with BG participated in individual semi-structured interviews about their experiences of BG and completed an online survey including the Edinburgh Postnatal Depression Scale (EPDS). Qualitative and quantitative data were analyzed using reflexive thematic analysis and descriptive statistics, respectively. Both data were integrated using joint display of data and side-by-side comparison. Results: The mean age of participants was 29.5 years. Four meaning-based themes about BG were generated including: We looked forward to breastfeeding, But it did not go as expected, So we grieve, and These would have helped. From quantitative results, 87.5% of participants reported a history of PD symptoms and almost 44% had EPDS scores >11. All participants reported that experiencing BG contributed to their PD symptoms. Findings suggest that BG influenced PD symptoms in AA women without prior diagnosis of depression. Conclusions: Qualitative and quantitative findings from this novel exploratory study revealed an overlap that AA women with BG report PD symptoms. Clinicians should support women to achieve their breastfeeding goals to prevent BG and PD. Keywords: African American; Breastfeeding grief; Mental health; Mixed methods; Postpartum depression

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

AURA: Adaptive Uncertainty-aware Refinement for LLM-as-a-Judge Auditing

arXiv:2606.19714v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used as judges for open-ended generation, as large-scale human evaluation is often expensive and difficult to scale, yet their preferences remain imperfect proxies for human judgment. Existing auditing pipelines often assume that a reliable subset of examples or clean supervision signals are available beforehand, for example from human annotation, heuristic filtering, or the outputs of strong judges. In LLM evaluation, this assumption is fragile: the initial split may inherit judge bias, while human verification is typically too scarce to define stable groups at scale. We propose AURA, an adaptive uncertainty–aware refinement framework for auditing pairwise LLM–as–a–judge decisions under selected human verification. AURA iteratively learns a human-consistency signal, propagates reliable evidence, and prioritizes uncertain comparisons for human review. The key idea is to treat trust in a judge as a latent quantity that is progressively refined as evidence accumulates. We provide a compact formulation, a stable refinement procedure, and a comprehensive evaluation on both synthetic and real pairwise LLM-answer data.

24.
medRxiv (Medicine) 2026-06-18

AlphaGenome identifies a deep intronic variant in a family with PLA2G6-associated neurodegeneration: Closing the diagnostic gap in rare genetic diseases

A molecular diagnosis remains out of reach for a substantial subset of patients with clinically recognizable Mendelian disorders, even after comprehensive next-generation sequencing. Causal variants in non-coding regions are difficult to detect and interpret using standard pipelines. Deep intronic variants that disrupt splicing are a known but underexplored source of pathogenic alleles, and systematic tools to evaluate them at scale have only recently emerged. We aimed to resolve an incomplete genetic diagnosis in two siblings with early-onset parkinsonism, prominent neuropsychiatric features, and autonomic dysfunction consistent with PLA2G6-associated neurodegeneration (PLAN), an autosomal recessive condition. Prior clinical exome sequencing, genome sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and long-read sequencing had identified only a single heterozygous PLA2G6 missense variant, c.2132C>G (p.Pro711Arg). We used AlphaGenome to score 91 non-coding variants shared among the affected siblings and their father within 1 megabase of the PLA2G6 locus. The deep-learning model identified an intronic variant (c.2034+355G>A) that was predicted to create a cryptic splice acceptor site that could result in inclusion of a 160-bp cryptic exon. Tissue-specific predictions indicated the aberrant splicing would be detectable in blood, confirmed by junction-spanning RNA-seq reads from an unrelated carrier. This analysis completed a compound heterozygous PLAN diagnosis nearly two decades after symptom onset and demonstrates the utility of sequence-to-function models. Systematic integration of tools like AlphaGenome into rare disease workflows offers a practical, low-barrier route to closing the diagnostic gap for patients with compelling Mendelian phenotypes and incomplete genetic diagnoses.

25.
bioRxiv (Bioinfo) 2026-06-12

The Geometry of Allostery: A Laplacian Minor Hierarchy for Many-Body Protein Communication

Quantifying how cooperative, many-body relationships drive allostery in protein networks remains a major challenge. To address this, we develop the Laplacian minor hierarchy, a mathematical framework that characterizes the geometric invariants of a protein network. Lower-order minors yield standard metrics including the partition function and effective distances, whereas higher-order minors define novel topological measures: cooperation indices, each bounded between zero and one, that characterize pathway correlations at increasing levels of complexity, the third-order minor determines whether allosteric pathways are correlated or uncorrelated, and the fourth-order minor quantifies how distinct pathways communicate through intermediary residues. We apply this framework to analyze the evolutionary adaptation of the PSD95pdz3 domain from Class I to Class II ligand specificity via mutations G330T and H372A. The cooperation index demonstrates a distinct evolutionary hierarchy: the G330T mutation establishes distributed pathway couplings that the H372A mutation subsequently exploits, whereas H372A alone produces minimal global changes. Furthermore, the fourth-order analysis identifies His317 as a critical intermediary node bridging the class-switching (330-372) and class-bridging (330-400) allosteric pathways. These results demonstrate that allosteric dependencies emerge only when mutations accumulate in specific combinations, with a hierarchical organization of pathways structured around position 330 and intermediary nodes His317 and Phe400. Rather than predicting allosteric mechanisms, this framework provides a mechanistic explanation for why and how allostery emerges during protein evolution.