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

A Decision-Theoretic View of Test-Time Training: When, How Far, and Which Directions to Adapt

arXiv:2606.15569v1 Announce Type: new Abstract: Test-time training (TTT) adapts a pretrained model to each prompt via parameter updates, improving accuracy under pretraining-to-test distribution shifts. Yet, its performance often suffers from instability and sensitivity to hyperparameters such as update steps and subspace. We explain this behavior through a decision-theoretic lens, treating TTT as implicit Bayesian inference in the kernel regime. Under a Gaussian process benchmark, we show that TTT reduces prediction error when updates are spectrally matched to the prompt's signal-to-noise ratio and aligned with query-relevant eigen-directions. This perspective underpins the following results: (1) we show when fixed update steps and subspaces fail under distribution shifts, motivating adaptive strategies; (2) we prove that selecting update steps via prompt evidence admits a PAC-Bayes guarantee against overfitting; and (3) we characterize the Bayes-optimal update subspace under a linear-Gaussian correction model, yielding a scoring rule for selecting Transformer blocks and heads. Our theory helps explain the empirical instability of TTT, taking a step toward principled guidance for when, how far, and which directions to adapt.

02.
arXiv (CS.AI) 2026-06-19

SPOT-E: Test-Time Entropy Shaping with Visual Spotlights for Frozen VLMs

arXiv:2606.20244v1 Announce Type: cross Abstract: Vision-language models (VLMs) often underperform on evidence intensive tasks because decisive visual evidence are small, localized, and easy to overlook, leading to failures in evidence readout even when high-level reasoning is intact. Prior inference-time visual interventions can improve grounding without retraining, but they are largely open-loop and lack a mechanism to verify whether highlighted evidence is actually used. We study answer-span prediction entropy as a model-internal feedback signal and show that naive entropy minimization is ambiguous, since low entropy may arise from evidence-grounded confidence or shortcut collapse. To resolve this ambiguity, we introduce low-entropy anchors and an entropy-shaping objective that reduces answer uncertainty while preserving baseline high-confidence tokens. We instantiate this principle in SPOT-E, a plug-and-play test-time method that produces question-conditioned spotlights, optimized per instance via light-weight tuning based on Group Relative Policy Optimization (GRPO). Across all benchmarks and different VLM families, SPOT-E yields consistent gains and improved robustness under visual corruptions. Code is publicly available at: \url{https://github.com/YinBo0927/SPOT-E}

03.
arXiv (CS.CL) 2026-06-24

MorfFlex: Handling Rich Morphology

We present MorfFlex, a morphological dictionary architecture suitable for languages with extensive regularity in both inflection and derivation. As the primary example of MorfFlex in use we introduce MorfFlex CZ, a morphological dictionary of Czech. It is distributed as a simple, unstructured list of triplets, however, its manually maintained, unpublished source files and conversion scripts encode a sophisticated system of inflectional and derivational patterns. These patterns dramatically reduce the otherwise enormous size of the dictionary, which currently contains over 100 million wordforms and more than 1 million lemmas. The MorfFlex CZ dictionary serves as an essential resource for ensuring the consistency of manual morphological annotation in the Prague Dependency Treebanks and underpins state-of-the-art automatic tools such as MorphoDiTa. In this paper, we focus on: (i) presenting an effective method for managing the rich morphological system within the dictionary, and (ii) demonstrating the utility of such a language resource for maintaining annotation consistency in corpora and supporting the development of advanced NLP applications.

04.
Nature (Science) 2026-06-10

Diverse binding poses of agonistic neurotoxins on human Na<sub>v</sub>1.6

作者:

Voltage-gated sodium (Nav) channels are key targets of various venomous toxins. Deciphering the binding poses and mechanisms of action of representative toxins will help to dissect the functional mechanism of the channels and facilitate therapeutic development targeting Nav channels1,2. Here we present cryo-electron microscopy&nbsp;(cryo-EM) structures of distinct binding poses of three agonistic peptide toxins on the human Nav1.6–β1 channel complex. The globular β-scorpion toxin Cn2 nestles between the extracellular segment of voltage-sensing domain (VSD)&nbsp;in the second repeat of the Nav1.6 core α-unit (VSDII) and the pore extracellular loops in the third repeat of the Nav1.6 core α-unit (ECLIII), where it is stabilized by interactions with both protein regions and the branched N1372-glycan. Cone&nbsp;snail ι-conotoxin RXIA adopts an elongated conformation, spanning VSDI and VSDIV to wrap around the shoulder of the pore domain (PD). The bullet&nbsp;ant-derived toxin δ-paraponeritoxin-Pc1a exists as a transmembrane helix that stands between VSDII and PDIII. Our findings, corroborated by functional characterizations, illustrate the diversity in peptide toxin binding poses and mechanisms of action, link stabilization of the up state of VSDI or VSDII to channel activation, and provide clues to the rational design of selective Nav channel modulators. Structures of the distinct binding poses of three agonistic peptide toxins—bullet-ant-derived toxin δ-paraponeritoxin-Pc1a, cone&nbsp;snail ι-conotoxin RXIA and the globular β-scorpion toxin Cn2—on the human Nav1.6–β1 channel complex illustrate a diversity in binding poses and mechanisms of action.

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

NTS-CoT: Mitigating Hallucinations in LLM-based News Timeline Summarization with Chain-of-Thought Reasoning

The rapid updates of online news make tracking event developments challenging, highlighting the need for timeline summarization (TLS). Hallucinations, where LLM-generated content deviates from source news, still remain a critical issue in LLM-based TLS and are not well studied in existing works. To bridge this gap, we identify two primary types of hallucinations: unfaithful content during news summarization and information omission in date-event summarization. Then, we propose NTS-CoT, a novel framework that leverages Chain-of-Thought (CoT) reasoning to mitigate hallucinations in TLS. The framework consists of three key modules: i) Element-CoT to capture essential news elements for faithful summarization, ii) Date Selection to combine temporal saliency and event prominence for timestamp selection, and iii) Causal-CoT to infer causal relationships and reduce omissions in date-event summarization. Extensive experiments, including quantitative analysis on three TLS benchmarks and human evaluation, demonstrate that NTS-CoT outperforms state-of-the-art baselines, effectively mitigating hallucinations and improving LLM-based TLS performance. Our source code is available at https://anonymous.4open.science/r/NTS-CoT .

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

VoidPadding: Let [VOID] Handle Padding in Masked Diffusion Language Models so that [EOS] Can Focus on Semantic Termination

MDLMs generate text by denoising a preallocated masked response canvas, making response-length modeling central to instruction tuning. Existing MDLMs often inherit the autoregressive convention of using repeated \texttt{[EOS]} tokens for padding during instruction tuning, giving \texttt{[EOS]} a dual role as both a semantic terminator and a padding token. We show that this dual role is a root cause of \texttt{[EOS]} overflow under large-block decoding. To decouple these roles, we propose VoidPadding, which introduces \texttt{[VOID]} for padding and reserves \texttt{[EOS]} for termination. During inference, the learned \texttt{[EOS]} signal enables early stopping, while the learned \texttt{[VOID]} signal guides adaptive response canvas expansion. On Dream-7B-Instruct, VoidPadding improves the block-size-averaged four-task mean across mathematical reasoning and code generation benchmarks by \(+17.84\) points over the original model and \(+6.95\) points over RainbowPadding, while reducing decoding NFE by 55.7\% on average. Code is available at https://github.com/Haru-LCY/VoidPadding.

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

Navigating Gigapixel Pathology Images with Large Multimodal Models

Recent advances in large multimodal models have allowed for the development of interactive chat models that can converse and reason about pathology whole-slide images (WSIs). However, existing slide-level chat systems are often highly specialized, typically compressing WSIs into fixed slide-level embeddings or relying on multi-component pipelines, which can lose multi-scale detail and limit generalizability beyond the target task. We present GIANT (Gigapixel Image Agent for Navigating Tissue), a simple, training-free approach that lets general-purpose multimodal models navigate WSIs on their own, iteratively selecting multi-magnification crops and aggregating evidence over time. To evaluate generalizability in WSI question answering and to promote reproducibility, we introduce MultiPathQA, a benchmark suite spanning five clinical challenges and 934 questions over 868 unique WSIs. This includes a new set of 128 pathologist-authored multiple-choice questions designed to mirror real diagnostic search and multi-scale reasoning. Using GPT-5, GIANT outperforms models specialized for pathology question answering, achieving state-of-the-art performance on four out of five benchmarks.

08.
arXiv (quant-ph) 2026-06-16

Non-perturbative CPMG scaling and qutrit-driven breakdown under compiled superconducting-qubit control: a single-qubit study

作者:

arXiv:2603.29525v3 Announce Type: replace Abstract: Decoherence in superconducting qubits arises from both multilevel dynamics and structured environmental noise, yet perturbative models cannot capture all resulting signatures. Here, EmuPlat couples instruction-set-architecture-level waveform generation to the hierarchical equations of motion HEOM under $1/f$ non-Markovian pure dephasing. In the resulting non-perturbative regime – where filter-function predictions become quantitatively uninformative – CPMG scaling of a three-level superconducting transmon yields one calibration result, two physical findings, and one structural null. Y-CPMG exhibits axis-dependent scaling-law breakdown – non-monotonic decoherence, partial coherence revival, and pronounced X–Y population asymmetry ($0.204$ vs ${

09.
medRxiv (Medicine) 2026-06-22

An integrated AI-microfluidic platform reveals the broad persistence and developmental potential of rare sperm in non-obstructive azoospermia

Non-obstructive azoospermia (NOA) represents the most severe form of male infertility, severely limiting a patient's prospects for biological fatherhood when surgical retrieval fails. However, the true biological limits of NOA remain obscured by the inherent limitations of conventional gamete recovery protocols: standard centrifugation frequently causes substantial cell loss, masking extremely rare sperm, while surgical interventions are constrained by spatial sampling biases. Here we report SpermSeek, an integrated AI-guided microfluidic platform for real-time, non-destructive isolation of single sperm directly from semen. Operating at scalable throughput (0.36 mL/h), the system achieves 98.3% detection precision and a 95.5% target encapsulation efficiency, suppressing background debris. In a 59-patient NOA cohort, SpermSeek detected morphologically identifiable sperm in 64.4% (38/59) of cases, spanning diverse genetic etiologies, including AZFb/c microdeletions, and severe histopathological phenotypes, such as Sertoli-cell-only syndrome (SCOS). Notably, among a sub-cohort of 41 patients who remained consistently sperm-negative despite prior medical or micro-TESE interventions, our platform identified gametes in 53.7% (22/41) of these cases. Comprehensive safety profiling in healthy human donors and wild-type mice confirmed that processed sperm retain high DNA integrity and epigenomic concordance (r=0.98), supporting transgenerational developmental stability in mice. Furthermore, in a 26-patient validation cohort, SpermSeek recovered rare sperm in 11 cases. Utilizing gametes from a subset (n=5), we demonstrated their capacity to support early human embryogenesis, yielding high-quality cleavage-stage embryos with confirmed genomic euploidy. This work establishes a highly sensitive framework for re-examining the biological limits of human spermatogenesis, laying the foundation to expand autologous reproductive options for patients refractory to conventional retrieval protocols.

10.
medRxiv (Medicine) 2026-06-15

Filum Terminale Diameter on Routine Pediatric MRI: A Large-Cohort Clinical Reference in 3,406 Children and the Age-Dependent Meaning of the 2-mm Thickened-Filum Threshold

Background. A filum diameter >2 mm is the conventional MRI threshold for a thickened filum, but it derives from small, mostly adult series showing no age dependence; whether one cutoff suits all of childhood is untested. Objective. To build an age-specific filum-diameter reference on routine pediatric MRI and test, adjusting for image resolution, whether the 2-mm threshold is age-stationary. Materials and methods. In this retrospective study an nnU-Net tracer measured the maximal filum diameter on consecutive lumbosacral MRI; versus manual tracing it showed negligible bias but moderate single-measure agreement. After excluding report-confirmed fatty filum, lipoma, or tethered cord, the proportion >2 mm was analysed within one acquisition protocol and by logistic regression adjusting for voxel size and slice thickness. Results. Of 7,245 examinations, 3,869 (53%) were traceable; untraced ones were younger (median 0.75 vs 2.0 years). The presumed-normal cohort had median diameter 1.48 mm. At matched resolution, 2 mm marked the 94th percentile in infants (5.6% exceeded it) but the 83rd by 3-6 years (17.4%); the age effect persisted after adjusting for voxel size and slice thickness (3-6 years vs infants, adjusted OR 4.7; P < .001). Conclusion. Filum diameter clusters near 1.5 mm, and the fixed 2-mm cutoff flags ~5% of infants but ~17% of preschoolers. Caliber should be judged against an age-specific clinical reference, not one fixed cutoff; a thick filum is not itself a diagnosis of tethered cord.

11.
arXiv (CS.CL) 2026-06-15

Reward-SQL: Boosting Text-to-SQL via Stepwise Execution-Aware Reasoning and Process-Supervised Rewards

Recent advances in large language models (LLMs) trained with reinforcement learning (RL) have improved Text-to-SQL performance. However, RL-based approaches still struggle with complex queries due to two key limitations: insufficient stepwise execution-aware reasoning grounded in database feedback, and the lack of process-level rewards for guiding reasoning optimization. To address these issues, we propose CoCTE, a divide-and-conquer and execution-aware reasoning framework that progressively composes SQL queries through intermediate view validation and structured Common Table Expressions (CTEs), improving both accuracy and interpretability. To realize a CoCTE reasoning process, we develop Reward-SQL, a unified approach with three stages: (1) model initialization, which equips LLMs with structured CoCTE reasoning capabilities; (2) process reward design, which delivers fine-grained, execution-aware supervision; and (3) process-supervised RL and inference, which integrates process rewards into training and guides the inference stage by process rewards. This paper addresses the core challenges in Reward-SQL and makes the following contributions. We introduce a process reward model (PRM) that combines execution-aware trajectory scoring with entropy-based step weighting, providing dense and interpretable supervision across reasoning steps. We integrate PRM into both RL training and inference stages, stabilizing optimization and improving trajectory exploration with process-level signals. Experiments show that Reward-SQL significantly outperforms baselines with comparable model sizes, and exhibits strong cross-domain generalization.

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

WeGenBench: A Multidimensional Diagnostic Benchmark towards Text-to-Image Model Optimization

Recent text-to-image generation models have demonstrated remarkable capabilities in synthesizing highly realistic images from text inputs alone. Although existing benchmarks can evaluate the generation capabilities of various models to some extent, they struggle to comprehensively and accurately measure performance across multiple dimensions, often failing to reveal the inherent deficiencies of models in specific categories. To address these limitations, we propose WeGenBench, a novel benchmark designed for the comprehensive, multi-perspective evaluation of text-to-image generation capabilities. Our benchmark comprises a total of 4,000 test prompts across two primary categories, meticulously balanced between Chinese and English to evaluate bilingual and cross-cultural generation capabilities. Beyond macroscopic scene classification, we annotate each prompt with multi-dimensional tags tailored to the distinct content and challenges of each language, thereby refining the generation tasks into more specific sub-categories. Through a cross-dimensional evaluation mechanism leveraging both scene classifications and multi-dimensional tags, WeGenBench can precisely pinpoint model shortcomings in specific generation categories. Furthermore, to measure generation quality more accurately, we design and validate several novel evaluation metrics by integrating Vision-Language Models (VLMs), which assess model performance on domain-specific tasks from three core aspects. Crucially, our approach yields both the assessment outcomes and the detailed reasoning trajectories, facilitating a rigorous verification of the accuracy and soundness of the evaluation results. Finally, we conduct systematic benchmarking on current state-of-the-art methods and provide an in-depth analysis of the limitations present in existing models.

13.
arXiv (CS.LG) 2026-06-17

Beyond IGO-Flow: Toward Convergence Analysis of IGO in Continuous Spaces

arXiv:2606.17523v1 Announce Type: cross Abstract: Information-Geometric Optimization (IGO) provides a unified framework for black-box optimization by interpreting the adaptation of a search distribution as a natural gradient update. Despite its conceptual importance, the convergence theory of IGO remains limited: most existing results concern continuous-time idealizations such as the IGO flow, rather than discrete-time updates with non-infinitesimal learning rates. In this paper, we study discrete-time IGO in continuous spaces, formulated as natural gradient updates in the expectation-parameter coordinates of an exponential family. In particular, we analyze IGO over the multivariate Gaussian family on strongly convex quadratic objective functions. Our analysis covers a setting that simultaneously incorporates full covariance adaptation, a fixed positive learning rate, and quantile-based weights. In this setting, we prove that the covariance matrix converges to the zero matrix. We further show that the mean vector converges to the global optimum, provided that the condition number of the appropriately scaled covariance matrix is bounded at sufficiently frequent iterations. These results advance the convergence theory of IGO and help bridge the gap between the mathematical theory of IGO and practical covariance-adaptive search methods such as CMA-ES.

14.
bioRxiv (Bioinfo) 2026-06-18

Accounting for allelic diversity and multicopy gene detection improves the accuracy of antibiotic resistance genotypic determination

Background Genomic prediction of antimicrobial resistance (AMR) relies on the accurate detection of resistance genes or allelic variants of core genes from raw or assembled genomes sequences. For several bacterial species and antibiotics, AMR genotype-phenotype discrepancies are common, indicating that important sources of error remain unresolved. For Enterococcus faecium, we focused on identifying the sources of discrepancies for tetracycline resistance, for which genotypic detection had shown particularly low accuracy. We investigated the effect of structural variation in antibiotic resistance genes (ARGs), including gene duplications, truncations, interruptions, and mixed configurations of complete and partial gene copies, as a source of genotype-phenotype discrepancies from short-read data. We conduct further extended investigations to other antibiotic families and into another bacterial species: Escherichia coli. Methods We analyzed collections of E. faecium and E. coli genomes, integrating high-quality complete assemblies, simulated Illumina short reads, and matched AMR phenotypic data. The integrity, copy number, and allelic diversity of ARGs were examined for multiple antibiotic classes, and their impact on ARG detection and accuracy of AMR determination was assessed using several commonly used bioinformatic tools (SRST2, ARIBA and AMRFinderPlus). Results For E. faecium, after ruling out the effect of specific tet allelic variants on tetracycline susceptibility, we found that the integrity and copy number of tet(M) had a major effect on detection accuracy. Duplicated and incomplete ARGs are also common in E. faecium genomes, particularly for macrolides (erm(B)) and aminoglycosides (ant(6)-Ia and aph(3')-IIIa). In E. coli, similar patterns were observed for tet(A), erm(B) and aminoglycoside-associated genes (aph(3')-IIIa and ant(6)-Ia). Across ARGs in both species, short-read mapping methods wrongly reported interrupted genes as complete in some instances, while assembly-based methods often failed to resolve complete copies of duplicated genes. Detection accuracy improved when tools were adapted to account for gene integrity and when extended AMR databases incorporating species-specific alleles were included. Conclusions Our findings reveal that bioinformatic limitations in dealing with ARG copy number and completeness, and in accounting for allelic variation, underly a substantial source of genotype-phenotype errors, highlighting the need for improved AMR databases and bioinformatic tools that consider these factors to achieve reliable genomic prediction of AMR.

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

PhysGuard: Fisher-Guided Gradient Projection for Sim-to-Real Neural PDE Surrogates

arXiv:2606.16602v1 Announce Type: new Abstract: Neural operator models trained on simulation data often lose accuracy when applied to experimental measurements due to the sim-to-real gap. Standard fine-tuning with limited real data can reduce this gap, but it may also damage the core physics-relevant representations learned during pretraining. Although knowledge-preserving adaptation has been widely investigated in vision or language tasks, it remains unclear whether these methods are suitable for neural operators whose architectures and protected knowledge are fundamentally different. Neural operators need to preserve core-scale physical structures rather than semantic or visual features. We propose PhysGuard, a physics-preserving framework for accurate sim-to-real adaptation of neural operators. Specifically, PhysGuard uses the empirical Fisher Information Matrix computed on simulation data to identify physics-critical parameter directions, then restricts fine-tuning updates to directions that do not interfere with them. A layer-wise Gram-matrix formulation makes this efficient for models with millions of parameters, while an adaptive threshold automatically determines the protected subspace size. A spectral probe experiment shows that the dominant Fisher directions are strongly associated with low-frequency output structures. Experiments on benchmark across four neural operator architectures and different physical systems show that PhysGuard performs strongly on most evaluation metrics compared to baselines. The benefits are most evident under severe domain shift, where it reduces low-frequency error by up to 32\% compared to standard fine-tuning while maintaining adaptability. Our code is available at https://github.com/ZhouChaunge/PhysGuard.

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

Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction

arXiv:2606.14217v1 Announce Type: new Abstract: Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery. Recent geometric deep learning methods have achieved promising performance by representing protein-ligand complexes as three-dimensional graphs. However, most existing approaches mainly rely on static interaction geometry from a single bound conformation, while neglecting molecular flexibility and binding-induced conformational changes. To address this limitation, we propose a curvature-informed potential energy surface (CPES) graph neural network for protein-ligand binding affinity prediction, which incorporates physics-informed curvature representations to model conformational flexibility. CPES first derives curvature spectral descriptors from the Hessian of the potential energy surface evaluated at equilibrium configurations, whose eigenvalues define the local principal curvatures of the potential energy surface. It then uses spectral cross-attention to compare the unbound ligand and protein with the bound complex, thereby capturing binding-induced changes in conformational dynamics. In parallel, hierarchical protein-ligand interaction representations are learned from static structural features through geometry-aware message passing, soft clustering, and bidirectional cross-attention. Finally, CPES fuses the curvature-informed dynamic representations with static interaction representations for affinity regression. Extensive evaluations on multiple benchmark datasets demonstrate that CPES achieves improved predictive performance and offers physical interpretability.

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

MARIC: Multi-Agent Reasoning for Image Classification

Image classification has traditionally relied on parameter-intensive model training, requiring large-scale annotated datasets and extensive fine tuning to achieve competitive performance. While recent vision language models (VLMs) alleviate some of these constraints, they remain limited by their reliance on single pass representations, often failing to capture complementary aspects of visual content. In this paper, we introduce Multi Agent based Reasoning for Image Classification (MARIC), a multi agent framework that reformulates image classification as a collaborative reasoning process. MARIC first utilizes an Outliner Agent to analyze the global theme of the image and generate targeted prompts. Based on these prompts, three Aspect Agents extract fine grained descriptions along distinct visual dimensions. Finally, a Reasoning Agent synthesizes these complementary outputs through integrated reflection step, producing a unified representation for classification. By explicitly decomposing the task into multiple perspectives and encouraging reflective synthesis, MARIC mitigates the shortcomings of both parameter-heavy training and monolithic VLM reasoning. Experiments on 4 diverse image classification benchmark datasets demonstrate that MARIC significantly outperforms baselines, highlighting the effectiveness of multi-agent visual reasoning for robust and interpretable image classification.

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

PhononBench:A Large-Scale Phonon-Based Benchmark for Dynamical Stability in Crystal Generation

arXiv:2512.21227v3 Announce Type: replace-cross Abstract: In recent years, generative artificial intelligence has made significant advances in the design of crystalline materials, giving rise to approaches based on graph neural networks, diffusion models, and large language models. Existing evaluations commonly follow the stability-uniqueness-novelty (S.U.N.) framework, where stability is primarily assessed using thermodynamic criteria, which do not fully capture the dynamical stability essential for a material's practical existence. Dynamical stability is a key determinant of whether a material can be synthesized and persist, with phonon spectrum calculations serving as the standard for its evaluation. However, the high computational cost of such calculations has prevented large-scale assessment of dynamical stability in generated crystals. In this work, we introduce PhononBench, the first large-scale benchmark for dynamical stability in AI-generated crystals. Leveraging the recently developed MatterSim interatomic potential, which achieves density-functional-theory (DFT)-level accuracy in phonon predictions across more than 10,000 materials, PhononBench enables efficient phonon calculations and dynamical-stability analysis for 133,838 crystal structures generated by 7 leading crystal generation models. PhononBench reveals a widespread limitation of current generative models: unless otherwise specified, all reported dynamical-stability metrics are evaluated at a phonon-frequency threshold of -0.1 THz, with the average dynamical-stability rate across all generated structures being only 32.15%, and the top-performing model, MatterGen, reaching just 45.05%.In addition, we identify 32,995 crystal structures that are phonon-stable across the entire Brillouin zone under a strict threshold of -0.001 THz. In addition, a web-based service is accessible at http://phononbench.cn/, enabling minute-level ultra-fast phonon predictions.

19.
bioRxiv (Bioinfo) 2026-06-11

DLDN-Bench: A Benchmark Framework for Deep Learning de Novo Peptide Sequencing in Proteomics

De novo peptide sequencing is an essential approach for analyzing mass spectrometry data because it enables the identification of novel peptides without relying on protein sequence databases. Recent advances in deep learning have substantially improved the performance of de novo sequencing methods, but the rapid emergence of new models has led to heterogeneous evaluation practices and limited comparability. To address this, we introduce DLDN-Bench, a benchmark framework including a set of benchmark datasets derived from human muscle biopsy mass spectrometry data retrieved from PRIDE and annotated through consensus across multiple widely used database search engines. Using these datasets, we systematically benchmark recent deep learning-based de novo sequencing tools alongside traditional approaches. Performance is assessed using established metrics, including precision and coverage relative to a pseudo-ground truth defined by cross-engine agreement. To demonstrate the utility of DLDN-Bench, we benchmark four recent deep learning models and make all results publicly available. This benchmark framework provides a standardized basis for comparing state-of-the-art methods and offers an extensible resource for evaluating future tools in de novo peptide sequencing.

20.
arXiv (CS.CL) 2026-06-12

Agent-based models for the evolution of morphological alternation patterns

Why is the past of English "go" the apparently unrelated "went"? Such alternations are frequent in languages. They neither aid communication nor learnability, yet they can be persistent, surviving over centuries or millennia. We present a multi-agent simulation of the emergence of morphological stem and inflection alternations. Alternate forms arise by phonological changes or, as with "go/went", from lexical alternatives associated with a subset of the population. When an agent 'hears' another agent use a novel form for a slot in the paradigm of a word (say, the past tense of go), they will with some probability adopt that form, possibly spreading its use to other slots in the paradigm that shared the same original form. Thus alternative forms can spread through the population and become entrenched as stem or inflectional marker alternants. Unlike many previous computational studies, our system allows for naturalistic lexical forms, realistic phonological rules, lexicons with hundreds or thousands of entries, and agent populations in the tens or hundreds. It supports several network topologies, diffusion patterns and agent adoption policies. One issue with such simulations is evaluation: how realistic is the resulting morphology compared to those of real languages? We introduce the AI Historical Linguist, a novel Large Language Model-driven system that models a debate between two historical linguists. We use this to compare a set of real language morphologies, disguised morphologies, and experimentally evolved morphologies. The results suggest that among the factors that favor more plausible morphologies are scale-free social networks and random Bernoulli adoption of forms. We also present three case studies modeling attested historical changes, allowing us to test what might have happened if history had been different. All code and data are released.

21.
arXiv (math.PR) 2026-06-17

The Erdős-Hajnal High-Girth Subgraph Conjecture Holds in the Polynomial Chromatic-Sparsity Regime

作者:

arXiv:2606.17901v1 Announce Type: cross Abstract: For a graph $G$ put $h_r(G)=\max{\chi(H):H\subseteq G,\operatorname{girth}(H)\ge r}.$ Erdős and Hajnal asked whether $h_r(G)\to\infty$ as $\chi(G)\to\infty$, for every fixed $r\ge4$. We prove this in every fixed polynomial edge-density regime: for all $r\ge4$, $k\ge2$, $P,C>0$, there is $M=M_{r,k}(P,C)$ such that $\chi(G)\ge M,\ e(G)\le C\chi(G)^P\Longrightarrow h_r(G)\ge k.$ Quantitatively, after replacing $P$ by $P\vee2$ and $C$ by $C\vee2$, $M_{r,k}(P,C)\le \exp!\left(O_{r,k}\bigl((P+2+\log(C\vee2))^2\bigr)\right),$ and consequently the same conclusion holds throughout the quasi-polynomial range $e(G)\le \exp\bigl(C_0(\log\chi(G))^a\bigr),\ 1 < a < 3/2,$ for all sufficiently large $\chi(G)$. In each fixed polynomial-density regime we also obtain $f_{P,C}(k,r)\le k^{O_{r,P,C}(1)}.$ The proof combines a chromatic-defect random extraction lemma, compact and near-quadratic sparse-core bases, and a peeling/thinning bootstrap increasing the admissible edge exponent by $1/(r-1)$. We also prove structural saturation results for possible counterexamples, including Moore-strength exact-cycle packings and quadratic saturation in projected colour-pair space. Finally, writing $h_r^{\mathrm f}(G)=\max{\chi_{\mathrm f}(H):H\subseteq G,\operatorname{girth}(H)\ge r},$ we develop a fractional random-extraction framework based on Mohar-Wu preservation. We prove sufficient cheap-cycle-killing criteria and verify them for several structured families, including clique-organised families, line graphs of incidence graphs of equal-order generalized quadrangles and generalized hexagons, and the Bohman-Keevash tracking-time triangle-free-process graph. We also isolate a density-free obstruction that any proof using this fractional surgery route must overcome.

22.
arXiv (CS.CV) 2026-06-24

UniRED: Unified RGB-D Video Frame Interpolation with Event Guidance

High frame-rate RGB-D videos are crucial for a variety of downstream tasks, including motion analysis, dynamic scene understanding, and 3D reconstruction. However, due to hardware and sensing constraints, practical RGB-D cameras are typically limited to low frame rates, making it difficult to capture rapid scene dynamics. Existing video interpolation methods have achieved strong performance on RGB data, but they are not readily applicable to RGB-D scenarios, where they often yield blurry boundaries, visible artifacts, and degraded geometric consistency. Furthermore, motion estimation from only two boundary frames is inherently under-constrained in complex dynamic scenes. Event cameras, by contrast, provide asynchronous measurements with ultra-high temporal resolution, offering dense motion cues. In this paper, we propose a unified multimodal framework for RGB-D video interpolation that jointly exploits RGB appearance, depth geometry, and event-based temporal cues. Specifically, it first extracts and fuses RGB, depth and event cues, then estimates bidirectional flow with motion basis refinement for RGB and Z-axial refinement for depth, and finally synthesizes the target RGB-D frame via bidirectional warping and soft blending. In addition, we construct a new RGB-D-Event dataset to alleviate the scarcity of tri-modal training data. Extensive experiments on a public benchmark and the proposed dataset demonstrate that our method achieves superior photometric fidelity for RGB interpolation and stronger geometric accuracy for depth interpolation than existing approaches.

23.
arXiv (quant-ph) 2026-06-24

Reinforcement Learning to Disentangle Multiqubit Quantum States from Partial Observations

arXiv:2406.07884v3 Announce Type: replace Abstract: Using partial knowledge of a quantum state to control multiqubit entanglement is a largely unexplored paradigm in the emerging field of quantum interactive dynamics with the potential to address outstanding challenges in quantum state preparation and compression, quantum control, and quantum complexity. We present a deep reinforcement learning (RL) approach using an actor-critic algorithm for constructing short disentangling circuits for states with up to 16 qubits. With access to only two-qubit reduced density matrices, our agent decides which pairs of qubits to apply two-qubit gates on; requiring only local information makes it directly applicable on modern NISQ devices, as we demonstrated experimentally on a trapped-ion quantum computer. Utilizing a permutation-equivariant transformer architecture, the agent can autonomously identify qubit permutations within the state, and adjusts the disentangling protocol accordingly. Once trained, it provides circuits from different initial states without further optimization. We demonstrate the agent's ability to identify and exploit the entanglement structure of multi-qubit states. We analyze the disentangling circuits constructed by the agent for 4- and 5-qubit Haar-random states, and observe strong correlations between consecutive gates and among the qubits involved. Through extensive benchmarking, we show the efficacy of the RL approach to find disentangling protocols with minimal gate resources. We explore the resilience of our trained agents to noise, highlighting their potential for real-world quantum computing applications. Analyzing optimal disentangling protocols, we report a general circuit to prepare an arbitrary 4-qubit state using at most 5 two-qubit (10 CNOT) gates.

24.
arXiv (CS.AI) 2026-06-15

No Accidental Software Agent First Canonical Code for Human Code Entropy Reduction and 30 to 500 times Lower Frontier Model Requirements

arXiv:2606.14357v1 Announce Type: cross Abstract: Frontier coding models may spend substantial capacity learning not only program behavior, but also accidental entropy in human repositories. Such repositories contain valuable signals: tests, incidents, migrations, edge cases, product judgment, and operational history. These signals are entangled with framework churn, naming drift, generated-source ambiguity, dependency rituals, CI dialects, weak proof routes, and human-oriented review customs. We propose agent-first canonical code, a proof-carrying substrate that rewrites routine product software into canonical behavior profiles, typed change algebra, proof lanes, constrained edit grammars, semantic patch cells, runtime negative memory, and proof-carrying change objects. The core hypothesis is that quotienting software by behavior equivalence under a declared oracle can collapse equivalent encodings into governed representatives with explicit evidence and proof obligations. The endpoint is amortized cost per verified correct change, including source, context, reasoning, tools, verification, security, provenance, review, failed loops, defects, and foundry cost under a common oracle. Reported reduction bands are hypotheses, not measured frontier results. The proposed limit is a No-Accident Horizon: removable accident decreases until residual novelty, evidence, governance, risk, and future optionality dominate. For supported routine-product distributions, this gives a defensible planning target near 100-fold all-in cost reduction, not a guarantee for all software. Preliminary QLoRA experiments on Qwen2.5-Coder-14B show that 64,088 canonical trajectories are learnable and suppress tested forbidden-language markers, but do not establish behavior preservation, scaling economics, or verified-change cost. The contribution is a falsifiable program centered on minimum functional description length and verified-change cost.

25.
arXiv (CS.AI) 2026-06-19

Lagrange: An Open-Vocabulary, Energy-Based Sparse Framework for Generalized End-to-End Driving

arXiv:2606.20274v1 Announce Type: new Abstract: Scaling end-to-end autonomous driving to complex, open-world environments requires perceptual models that generalize to anomalous scenarios and planners that produce kinematically valid trajectories. Existing paradigms face a distinct dichotomy between representational efficiency and generalization capacity. Dense models (e.g., occupancy networks), while geometrically robust, incur critical computational bottlenecks and struggle with high-level semantic reasoning. Conversely, sparse, query-based planners are efficient but reliant on closed-set definitions, rendering them vulnerable to out-of-distribution (OOD) events. Although recent Vision-Language-Action (VLA) models offer open-vocabulary reasoning, their autoregressive, discrete token generation fundamentally conflicts with the continuous, high-frequency control requirements of vehicle dynamics. To address this, we propose Lagrange, an open-vocabulary, computationally sparse driving framework based on Masked Latent Fields (MLF). Rather than relying on dense volumetric reconstructions or closed-set query mechanisms, Lagrange exploits Vision-Language Models (VLMs) to encode class-agnostic object proposals into continuous semantic visual tokens. We introduce an intent-driven masked cross-attention module that temporally filters irrelevant entities, decoding the attended tokens into an implicit continuous energy field defined over spatial coordinates. By framing decision-making as a Lagrangian action minimization problem spanning this energy field, we enforce strict compliance with vehicle kinematics while executing collision avoidance. Extensive offline evaluations on both standard (nuScenes) and long-tail (CODA) benchmarks demonstrate that Lagrange establishes a promising framework for robust, interpretable, and kinematically feasible open-world autonomy.