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01.
Nature (Science) 2026-06-17

Structure of the pre-initiation complex explains CMGE biogenesis

When cells enter S phase, bidirectional DNA replication is initiated through the kinase-regulated recruitment of three activators (Cdc45, GINS and Pol ε) to a duplex-DNA-loaded double hexamer of minichromosome maintenance (MCM) ATPases. Together, these proteins form two CMGE helicases that establish divergent replication forks as they become separated1. Here, to gain an understanding of CMGE biogenesis, we reconstituted the pre-initiation complex with purified yeast proteins. The cryo-electron-microscopy structure shows a set of firing factors caught in the act of assembling two symmetrical CMGEs. We show how stepwise complex formation reshapes MCM in preparation for DNA opening, and we explain how ATP promotes firing-factor ejection and CMGE maturation. We find that although Sld2 facilitates the recruitment of GINS to MCM, as expected, it also aids the efficient separation of the CMGE dimer, and is essential for the ejection of the lagging strand from MCM. These findings have direct implications for our understanding of the metazoan Sld2 orthologue, RECQL4, and point to a replication-fork establishment mechanism that is conserved across eukaryotes. Cryo-electron microscopy and biochemical reconstitution experiments in yeast provide insight into the assembly of the CMGE complex, a helicase that establishes bidirectional DNA replication in eukaryotic cells, and elucidate the role of the firing factor Sld2.

02.
medRxiv (Medicine) 2026-06-22

Modelling the decadal expansion of West Nile virus in Italy: the role of climatic, anthropogenic, and macroecological drivers

Abstract BACKGROUND West Nile virus (WNV) is a growing health burden in Italy. Anticipating human infection risk is hampered by the pathogen's complex ecology, highlighting the need for comprehensive early-warning tools. AIM We aimed to model municipal-level WNV risk in Italy and characterize its decadal expansion in Italy, providing a comprehensive ecological understanding of viral emergence. METHODS We applied a machine learning framework to annual human WNV case data from 2014 to 2024. The model integrated a suite of environmental, socio-economic, and macroecological predictors to generate risk projections. We evaluated the model's performance through multiple validation settings. We also performed an anticipation test for the 2025 epidemic season, using 2024 environmental data to assess the model's predictive accuracy against observed 2025 human cases. RESULTS Our model achieved robust performance (True Skill Statistic > 0.4) and captured WNV progressive expansion from 184 predicted positive municipalities in 2014 to 2,012 in 2024 (an 11-fold increase in 11 years). Seasonal minimum temperature was the primary risk driver, followed by monitoring year and population density, indicating active spatial spread. Environmental suitability consistently preceded clinical detection. Municipalities with cases in 2023-2024 exhibited significantly higher predicted suitability during 2018-2022 than those without cases (average risk 0.58 vs 0.20). Our model successfully identified emerging risk hotspots along the Adriatic coast and southern Italy before the official human spillover of 2025. CONCLUSION Embedding macroecological drivers into WNV risk modelling provides an improved understanding of drivers of rapid WNV expansion. Our model enables proactive risk mapping, surveillance efforts, and targeted public health measures.

03.
arXiv (CS.CV) 2026-06-19

CARE: Competence-Aware Reward Shaping for Adaptive Reasoning Length in Video-MLLMs

In multimodal video reasoning, reinforcement learning-based methods typically rely on simplistic and inflexible reasoning-length control strategies that fail to adapt to the model's evolving competence. This mismatch may suppress necessary exploration at early stages, while encouraging redundant reasoning and inefficient decoding once the model becomes more competent. In this paper, we propose CARE, a competence-aware reward shaping framework for adaptive reasoning length optimization in multimodal reasoning. Specifically, CARE maintains a smoothed competence estimate via an exponential moving average of pass rates, and uses it to route training into progressive stages that shift the reward preference from exploration-oriented long-form reasoning to efficiency-oriented concise reasoning. To avoid conflating verbosity with intrinsic task complexity, CARE further normalizes reasoning effort with batch-level statistics, and introduces a posterior amplifier to strengthen reward signals for unexpectedly strong performance on historically difficult samples. The proposed mechanism is seamlessly integrated into the GRPO training pipeline and incurs no additional inference-time overhead. Extensive experiments on multiple video reasoning and general video understanding benchmarks demonstrate that CARE consistently improves reasoning accuracy, stabilizes reinforcement learning, and significantly enhances token efficiency. Moreover, CARE exhibits a characteristic inverted-U trajectory of reasoning length during training, and yields shorter yet more informative reasoning traces at convergence, indicating effective adaptive allocation of reasoning budget. We provide the source code for our proposed CARE framework and experiments at https://github.com/1Pansy/Video-CARE.

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

A Generalizable Light Transport 3D Embedding for Global Illumination

Global illumination (GI) is essential for realistic rendering but remains computationally expensive due to the complexity of simulating indirect light transport. Recent neural methods have mainly relied on per-scene optimization, sometimes extended to handle changes in camera or geometry. Efforts toward cross-scene generalization have largely stayed in 2D screen space, such as neural denoising or G-buffer based GI prediction, which often suffer from view inconsistency and limited spatial understanding. We propose a generalizable 3D light transport embedding that approximates global illumination directly from 3D scene configurations, without using rasterized or path-traced cues. Each scene is represented as a point cloud with geometric and material features. A scalable transformer models global point-to-point interactions to encode these features into neural primitives. At render time, each query point retrieves nearby primitives via nearest-neighbor search and aggregates their latent features through cross-attention to predict the desired rendering quantity. We demonstrate results on diffuse global illumination prediction across diverse indoor scenes with varying layouts, geometry, and materials. The embedding trained for irradiance estimation can be quickly adapted to new rendering tasks with limited fine-tuning. We also present preliminary results for spatial-directional radiance field estimation for glossy materials and show how the normalized field can accelerate unbiased path guiding. This approach highlights a path toward integrating learned priors into rendering pipelines without explicit ray-traced illumination cues.

05.
arXiv (CS.CV) 2026-06-16

Decoupled Object-Centric Video Understanding for Generating Robotic Manipulation Commands

Translating video demonstrations into executable robot commands remains challenging because existing methods often fail to identify which objects are functionally involved in the demonstrated action. As a result, they may generate commands that are linguistically plausible but operationally ambiguous. We propose an object-centric video understanding framework that decouples action recognition from object identification to generate precise, grammar-free manipulation commands. Our approach integrates Temporal Shift Modules (TSM) for efficient spatio-temporal action classification with a novel Object Selection algorithm that identifies task-relevant objects through trajectory-based role classification, blur detection, and overlap minimization. The selected objects are then processed by Vision-Language Models (VLMs) for robust category recognition and zero-shot generalization. Evaluated on a modified Something-Something V2 dataset, our method achieves 86.79\% action classification accuracy and BLEU-4 scores of 0.337 on standard objects and 0.261 on novel objects. These results improve over the strongest task-specific baseline by 80.2\% and 143.9\%, respectively. Larger gains are observed in METEOR and CIDEr, reaching 157.9\% and 171.7\% on novel objects. Across all semantic metrics, our approach consistently outperforms task-specific methods and remains competitive with, or surpasses, large general-purpose VLMs while retaining a modular, object-centric design.

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

Rethinking Cross-Layer Information Routing in Diffusion Transformers

Diffusion Transformers (DiTs) have become a de facto backbone of modern visual generation, and nearly every major axis of their design – tokenization, attention, conditioning, objectives, and latent autoencoders – has been extensively revisited. The residual stream that governs how information accumulates across layers, however, has been directly inherited from the original Transformer. In this paper, we present a systematic empirical analysis of cross-layer information flow in DiTs, jointly along depth and denoising timestep, and identify three concrete symptoms of traditional residual addition, namely monotonic forward magnitude inflation, sharp backward gradient decay, and pronounced block-wise redundancy. Motivated by this diagnosis, we propose Diffusion-Adaptive Routing (\textsc{DAR}), a drop-in residual replacement that performs learnable, timestep-adaptive, and non-incremental aggregation over the history of sublayer outputs. Moreover, the proposed \textsc{DAR} is compatible with many modern Transformer enhancement methods, such as REPA. On ImageNet $256\times256$, \textsc{DAR} improves SiT-XL/2 by $2.11$ FID ($7.56$ vs.\ $9.67$) and matches the baseline's converged quality with $8.75\times$ fewer training iterations. Stacked on top of REPA, it yields a $2\times$ training acceleration in the early stage, suggesting cross-layer information routing as an underexplored design axis in diffusion modeling, one that operates orthogonally to existing representation-alignment objectives. Beyond pretraining, \textsc{DAR} can also be applied during the fine-tuning stage of large-scale T2I models and preserves high-frequency details during Distribution Matching Distillation.

07.
arXiv (quant-ph) 2026-06-15

Who can compete with quantum computers? Lecture notes on quantum inspired tensor networks computational techniques

arXiv:2601.03035v2 Announce Type: replace Abstract: This is a set of lectures on tensor networks with a strong emphasis on the core algorithms involving Matrix Product States (MPS) and Matrix Product Operators (MPO). Compared to other presentations, particular care has been given to disentangle aspects of tensor networks from the quantum many-body problem: MPO/MPS algorithms are presented as a way to deal with linear algebra on extremely (exponentially) large matrices and vectors, regardless of any particular application. The lectures include well-known algorithms to find eigenvectors of MPOs (the celebrated DMRG), solve linear problems, and recent learning algorithms that allow one to map a known function into an MPS (the Tensor Cross Interpolation, or TCI, algorithm). The lectures end with a discussion of how to represent functions and perform calculus with tensor networks using the "quantics" representation. They include the detailed analytical construction of important MPOs such as those for differentiation, indefinite integration, convolution, and the quantum Fourier transform. Three concrete applications are discussed in detail: the simulation of a quantum computer (either exactly or with compression), the simulation of a quantum annealer, and techniques to solve partial differential equations (e.g. Poisson, diffusion, or Gross-Pitaevskii) within the "quantics" representation. The lectures have been designed to be accessible to a first-year PhD student and include detailed proofs of all statements.

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

Unstable Features, Reproducible Subspaces: Understanding Seed Dependence in Sparse Autoencoders

Sparse autoencoders (SAEs) are widely used to interpret neural network representations, but their utility depends on whether the learned features are reproducible across training runs. We study this question through feature stability: for each SAE feature, we estimate the probability that a similar feature reappears in an independently trained SAE. This yields a scalable per-feature signal that separates stable from unstable features. In a large-scale study across seeds, models, layers, dictionary sizes, and SAE variants, we find a pronounced functional asymmetry: stable features carry most of the reconstruction- and prediction-relevant signal, while unstable features have weak marginal impact and are dominated by low-frequency surface-form triggers in both activation statistics and automatic explanations. Geometrically, unstable features are individually non-reproducible but concentrate in reproducible lower-rank subspaces, suggesting that seed dependence often reflects basis ambiguity within a shared region of activation space rather than pure noise. A controlled synthetic model makes this mechanism explicit, showing that low-rank ground-truth features can be recovered at the subspace level while remaining non-identifiable as individual SAE latents across seeds. Finally, by pooling unique cross-seed features, we construct more stable SAEs while preserving explained variance in this setting. Together, these results show that unstable features are not merely failed or noisy latents: they have weak individual functional impact, but reflect reproducible low-dimensional structure that standard SAEs resolve differently across seeds.

09.
arXiv (CS.AI) 2026-06-11

EvalStop: Using World Feedback to Detect and Correct Reward Overoptimization in Multi-Tenant RLHF Platforms

arXiv:2606.04145v2 Announce Type: replace-cross Abstract: Cloud LLM fine-tuning platforms increasingly serve RLHF workloads, where a learned reward model is optimized as a proxy for human quality. As Gao et al. (2023) showed, this proxy diverges from world feedback (downstream eval metrics) under sustained optimization pressure, a phenomenon known as reward overoptimization. Existing platform schedulers ignore this divergence: non-clairvoyant schedulers optimize JCT without any quality signal, SLAQ-style quality-aware schedulers use training loss (a weaker proxy that drops monotonically through hacking), and classical per-job early stopping requires human monitoring and does not free shared GPUs. We propose EvalStop, a composable scheduling primitive that terminates jobs on k consecutive eval-score declines, releases GPUs, preserves the best checkpoint, and delegates to any base scheduler. We frame scheduler-level early stopping as a detection problem and evaluate it in a discrete-event simulator whose RLHF workload mixes reward-hacking and structurally healthy runs, with ground-truth labels hidden from schedulers. On RLHF-heavy workloads (80% RLHF, 64 GPUs), EvalStop achieves precision 98% / recall 99% / FPR 1.5% while improving JCT by 9% and cutting wasted compute by 22% over SRTF-Est (p

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

The Algebra of Units: From Buckingham's Pi-grec Theorem to Latent-Variable Learning

arXiv:2606.16737v1 Announce Type: cross Abstract: Engineers often measure many quantities-speed, pressure, temperature, length-expressed in different physical units. The Buckingham Pi-grec theorem states that these variables can always be combined into a smaller set of dimensionless numbers whose values fully determine the system's behaviour. Identifying the appropriate dimensionless groups has traditionally required expert knowledge and physical insight. This paper shows that they can instead be discovered automatically from data, without prior knowledge of the governing physics. The key observation is that, after logarithmic transformation, measurements collected under different scalings of the same system lie on a low-dimensional manifold whose geometry is determined by the underlying dimensionless groups. Singular value decomposition (SVD) identifies this manifold directly from data. A subsequent search over integer-exponent combinations recovers candidate dimensionless quantities, while a repeating-variable filter retains only those constructed from the machine's characteristic scales. This procedure recovers familiar engineering groups, including the flow coefficient, head coefficient, and Mach number, while excluding equivalent but less interpretable alternatives. The method is demonstrated on a synthetic compressor dataset containing 16,000 measurements. Starting from raw dimensional variables and no physics input, it recovers the correct dimensionless groups to numerical precision and reproduces the compressor performance map with an error below 0.01%. More broadly, the work reveals a close connection between classical dimensional analysis and modern data-driven learning. Both rely on the same underlying algebraic structure, suggesting new approaches for building physical models that are simultaneously interpretable, scalable, and data-efficient.

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

Minimum Distance Summaries for Robust Neural Posterior Estimation

arXiv:2602.09161v2 Announce Type: replace-cross Abstract: Simulation-based inference (SBI) enables amortized Bayesian inference by first training a neural posterior estimator (NPE) on prior-simulator pairs, typically through low-dimensional summary statistics, which can then be cheaply reused for fast inference by querying it on new test observations. Because NPE is estimated under the training data distribution, it is susceptible to misspecification when observations deviate from the training distribution. Many robust SBI approaches address this by modifying NPE training or introducing error models, coupling robustness to the inference network and compromising amortization and modularity. We introduce minimum-distance summaries, a plug-in robust NPE method that adapts queried test-time summaries independently of the pretrained NPE. Leveraging the maximum mean discrepancy (MMD) as a distance between observed data and a summary-conditional predictive distribution, the adapted summary inherits strong robustness properties from the MMD. We demonstrate that the algorithm can be implemented efficiently with random Fourier feature approximations, yielding a lightweight, model-free test-time adaptation procedure. We provide theoretical guarantees for the robustness of our algorithm and empirically evaluate it on a range of synthetic and real-world tasks, demonstrating substantial robustness gains with minimal additional overhead.

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

Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment

arXiv:2606.18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation. Yet these distributions are learned from broad unlabeled corpora and are not naturally conditioned on task-specific biological contexts such as interaction partners, cellular environments, or therapeutic interventions. Existing contextual matching methods often distort this interface through pooled embeddings, contrastive latent spaces, or task-specific prediction heads. We introduce LOGICA (Logit-space Contrastive Alignment), a framework for context-conditioned prediction that performs contrastive learning directly in output-logit space. Using gated cross-modal adapters compatible with each model's native token head, LOGICA preserves the pretrained likelihood interface and converts contextualized token log-likelihoods into matching scores. Alignment is defined through context-sensitive token probabilities rather than proximity in a shared embedding space, enabling learning from sparse paired data across models with distinct vocabularies, without a shared tokenizer or decoder. LOGICA is particularly effective for mutation-local variant ranking, where comparisons reduce to context-conditioned likelihoods of mutant tokens at perturbed sites. Across protein–ligand binding, TCR–peptide activity, and drug-conditioned resistance prediction, LOGICA improves over prior state-of-the-art methods, including matched latent-contrastive and conditional MLM baselines, while retaining a token-level interface for interpretation and generation. On held-out-gene single-mutation drug-resistance prediction, LOGICA improves AUC from near-random latent-space baselines of $\sim$0.55 to $\sim$0.65.

13.
medRxiv (Medicine) 2026-06-18

Rare Coding Variants Reveal Distinct Genetic Architectures Across Multidimensional Sleep Phenotypes

Sleep and circadian traits have been widely studied using common variants, but the contribution of rare coding variation remains unclear. We analyzed rare coding variants in 397,065 whole-exome sequenced UK Biobank participants across 36 sleep phenotypes from self-report, diagnoses, sleep medication use and accelerometry, and meta-analyzed results with 171,536 whole-genome sequenced All of Us participants of diverse ancestries, with replication in the Mass General Brigham Biobank (N = 31,275). We identified 260 genes associated with sleep phenotypes, including novel associations with sleep medication use in 29 genes and 24 out of 29 have not previously been reported with any sleep phenotypes. We observed modest but significant rare variant heritability and strong genetic correlations between sleep medication use, insomnia and fatigue. Temporal gene expression trajectory analyses indicate that genes associated with self-reported sleep traits show constant high prenatal expression, whereas genes linked to sleep medication phenotypes exhibit peak expression in the late prenatal period. These findings highlight distinct biological mechanisms captured by different measurement sources of sleep phenotypes and reveal rare-variant-informed targets for therapeutic discovery.

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

PISA: A Pragmatic Psych-Inspired Unified Memory System for Enhanced AI Agency

arXiv:2510.15966v2 Announce Type: replace Abstract: Memory systems are fundamental to AI agents, yet existing work often lacks adaptability to diverse tasks and overlooks the constructive and task-oriented role of AI agent memory. Drawing from Piaget's theory of cognitive development, we propose PISA, a pragmatic, psych-inspired unified memory system that addresses these limitations by treating memory as a constructive and adaptive process. To enable continuous learning and adaptability, PISA introduces a trimodal adaptation mechanism (i.e., schema updation, schema evolution, and schema creation) that preserves coherent organization while supporting flexible memory updates. Building on these schema-grounded structures, we further design a hybrid memory access architecture that seamlessly integrates symbolic reasoning with neural retrieval, significantly improving retrieval accuracy and efficiency. Our empirical evaluation, conducted on the existing LOCOMO benchmark and our newly proposed AggQA benchmark for data analysis tasks, confirms that PISA sets a new state-of-the-art by significantly enhancing adaptability and long-term knowledge retention.

15.
arXiv (CS.LG) 2026-06-12

A green solvent screening tool for emerging materials via uncertainty aware, transformer enhanced transfer learning

arXiv:2606.13060v1 Announce Type: new Abstract: Accurate prediction of solubility remains a central challenge across materials science and sustainable chemistry. In particular due to emerging technologies like organic and hybrid photovoltaics, batteries, and catalysis, solvent usage is expected to increase significantly within the coming years. Therefore, substituting solvents with greener alternatives is vital. This is where machine learning can have substantial impact. However, the limited data on critical parameters of solubility significantly constraints machine learning efficacy. In this work, we transfer a pre-trained foundational model on QM9 targets to our application with minimal data requirements. Additionally, the pipeline integrates uncertainty quantification, allowing the user to gauge the confidence of the predictions. As baseline, we succeed in predicting the Hansen solubility parameters and Dielectric Constant for which extensive databases exist. Importantly, we achieve high model performance on additional targets, such as Gutmann Donor and Acceptor numbers, where the available data is extremely limited. Overall, we augment data on solubility descriptors by orders of magnitude with high quality predictions. For effective dissemination, we deploy easy-to-use, easily integrateable with high throughput labs, customizable tool for ranking and screening possible solvent substitutes. Finally, we rediscovered known green solvent alternatives and proposed new candidates proving its relevance for finding eco-friendly solvents.

16.
medRxiv (Medicine) 2026-06-22

Body composition subphenotypes, cardiometabolic risk and incident outcomes: validation in the population-based NAKO and UK Biobank imaging cohorts

Background Anthropometric measures do not adequately capture heterogeneity in body fat distribution and corresponding cardiometabolic risk, whereas magnetic resonance imaging (MRI) enables precise differentiation and quantification of adipose tissue compartments and ectopic fat. We aimed to validate previously derived MRI-based body composition subphenotypes and their cardiometabolic risk profiles in two independent European cohorts. Methods Using deep learning-based image analysis, we quantified bone marrow, visceral, subcutaneous, cardiac, renal sinus, hepatic, skeletal muscle, and pancreatic fat in the imaging substudies of two population-based cohorts: the German National Cohort (NAKO, N=29,314, age range 19-74 years) and the UK Biobank (N=36,109, age range 40-69 years). Body composition subphenotypes, previously identified by k-means clustering, were evaluated using a rigorous statistical cluster validation framework with method-based and results-based approaches. In NAKO, cross-sectional associations between subphenotypes and estimated cardiovascular disease risk scores were examined using linear regression. In UK Biobank, longitudinal associations between subphenotypes and incident cardiometabolic outcomes, ascertained through hospital record linkage, were analysed using Cox regression. Findings All five body composition subphenotypes were robustly validated across both cohorts, and showed distinct fat distribution patterns and cardiometabolic risk profiles: I "lean", II "average adiposity", III "bone and muscle adiposity", IV "hepato-abdominal adiposity", and V "general and pancreatic adiposity". Subphenotypes I-III showed progressive adipose tissue remodelling patterns likely reflecting ageing trajectories. The "hepato-abdominal adiposity" subphenotype showed highest risk of incident diabetes, whereas the "general and pancreatic adiposity" subphenotype showed highest overall cardiovascular disease burden and metabolic impairment. Interpretation MRI-derived body composition subphenotypes represent distinct fat distribution patterns that reflect ageing- and disease-related processes, which supports the potential of body composition phenotyping for improved cardiometabolic risk stratification and targeted prevention.

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

CogGuard: Cognitive and Operational Profiling for Proactive Warning in Edge Intelligent Services

arXiv:2606.15199v1 Announce Type: new Abstract: Proactive warning is an important capability for edge intelligent services, where the system predicts whether a subject will successfully complete an incoming task under strict latency and privacy constraints. Such prediction depends on both long-term static attributes and short-term dynamic states derived from historical interaction logs. Recent Large Language Models (LLMs) offer strong long-context reasoning for constructing structured profiles from these logs, but existing solutions face two challenges for edge deployment: (1) profiling methods are typically domain-specific and lack a reusable abstraction across service scenarios, and (2) fine-tuning alignment models on heterogeneous edge clusters incurs high synchronization overhead due to the variance in input sequence lengths. To address these challenges, we propose CogGuard, a proactive-warning framework for edge intelligent services. CogGuard decouples offline LLM-based profile construction from online Small Language Model (SLM)-based score prediction through a shared static-dynamic profile-to-score pipeline, and instantiates it in two representative scenarios: educational performance warning and operational task outcome warning. For efficient profile construction, we design scenario-specific profiling methods with prefix-aligned KV-cache reuse to reduce repeated encoding overhead. For edge-side model alignment, we propose a length-aware distributed fine-tuning strategy with contrastive regularization to mitigate workload imbalance on heterogeneous clusters. Experiments on education and operation datasets show that CogGuard reduces profile construction time by up to 48% and distributed fine-tuning time by 19%, while achieving MAEs of 13.4 and 5.9, respectively, on 100-point-scale warning tasks. In the largest educational setting, CogGuard reduces prediction error by 15.4% compared with the strongest baseline.

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

Ontology Memory-Augmented ASR Correction for Long Text-Speech Interleaved Conversations

Automatic speech recognition (ASR) correction has traditionally focused on isolated utterances or short local contexts. However, as text and speech become increasingly interleaved in long interactions, ASR correction requires conversation-level contextual evidence. Existing ASR correction methods often rely on the current hypothesis or concatenate raw dialogue history. In such contexts, sparse correction evidence can be difficult to locate amid redundancy and noise. Addressing these challenges, we propose an ontology memory-augmented ASR correction framework for long text-speech interleaved conversations. The framework organizes preceding interaction history into a dynamically updatable ontology memory, where entities, terminology, surface variants, potential ASR confusions, and semantic relations are stored as retrievable nodes for context-grounded correction. To evaluate this setting, we construct RAMC-Corr, a dataset derived from MAGIC-RAMC for long-range ASR correction with grounded context. Experiments on RAMC-Corr show that our method improves over direct correction in 9 out of 10 paired backbone-setting combinations and encourages more selective and evidence-grounded corrections for context-dependent ASR errors.

20.
arXiv (math.PR) 2026-06-12

Data-driven subsampling rates for diffusion parameter estimation of SDEs

arXiv:2606.13615v1 Announce Type: new Abstract: We study the problem of diffusion parameter estimation for stochastic differential equation (SDE) models in scenarios where data and model are compatible only on specific scales that have yet to be determined. We introduce a simple and efficient method for selecting suitable rates at which given time series data should be subsampled in order to ensure that the statistical structure of the subsampled data is consistent with the behavior of the SDE model on an infinitesimal scale. Our approach is based on analyzing the statistics of the lengths of monotonically increasing or decreasing segments in the subsampled data sequence, which we refer to as monotone runs. As an analytical foundation, we prove for a large class of SDEs with additive noise that the lengths of monotone runs at an infinitesimal scale are approximately geometrically distributed with success probability $1/2$. This universal characterization is employed to derive an automated method for selecting appropriate subsampling rates for given time series data that is directly applicable in real-world scenarios and does not rely on an asymptotic framework of multiscale diffusions. The approach is demonstrated using an application from industrial mathematics concerning surrogate models for fiber lay-down curves in production processes of nonwoven textiles.

21.
arXiv (CS.AI) 2026-06-18

Spotlight: Synergizing Seed Exploration and Spot GPUs for DiT RL Post-Training

arXiv:2606.19004v1 Announce Type: cross Abstract: Reinforcement learning (RL) post-training of Diffusion Transformers (DiTs) is prohibitively expensive, requiring thousands of high-end GPUs. Existing works explore two directions to reduce cost: seed exploration improves training convergence by selecting high-contrast samples, yet adds compute to the critical path; spot GPUs offer 69–77\% lower cost, yet sit idle during training because DiT rollouts finish nearly simultaneously, which prevents LLM-style pipelining of rollout with training. Spot preemptions further break Sequence Parallelism (SP) groups, fragmenting GPU topology. We present Spotlight, the first system that harvests spot GPUs for DiT RL post-training. Spotlight rests on two key insights we devise: (1)~we show that exploration can tolerate stale model weights because exploration that uses the model weights from the previous iteration preserves the relative ranking of random seeds, allowing exploration to run on idle spot GPUs during training. (2)~SP reconfiguration can reuse on-node state, reducing group recovery from minutes to sub-second launches. Built on these insights, Spotlight introduces three techniques: a bandit-based exploration planner that maximizes reward variance within the training time budget, elastic sequence parallelism that reconfigures SP groups on the fly via persistent schedulers and intra-node weight copying, and a preemption-aware pull-based request scheduler that balances load and commits in-flight state upon preemption. We implement Spotlight on the open-source RL platform ROLL and evaluate it on Qwen-Image post-training. Spotlight reaches the same target validation score $4\times$ faster than baselines, reducing total cost by $1.4$-$6.4\times$ while achieving superior image quality on DeepSeek-OCR and Geneval datasets with resolution $512\times512$ and $1280\times1280$.

22.
bioRxiv (Bioinfo) 2026-06-15

VrySure: A Multi-Task AI Scientific Fraud Detection Platform for Identifying Manipulated and AI-Generated Biomedical Research Images

Integrity of scientific data is critical in biomedical research, where images often serve as primary evidence for experimental observations and conclusions. Advances in image-editing technologies and generative artificial intelligence (AI) have increased the accessibility and realism of visual manipulation, making detection through manual review increasingly challenging. To empower our laboratory researchers to continuously monitor and uphold scientific rigor and data integrity, and serve the global scientific community, we developed VrySure, an easy-to-deploy, AI-driven multi-task platform for automated image-integrity screening in biomedical research. VrySure integrates four detection modules: cross-image transformation detection, within-image copy-move detection, splicing detection in blot and gel images, and AI-generated image detection. The system identifies potentially manipulated images and, when possible, localizes suspicious regions using bounding-box outputs to support downstream verification. To support development and evaluation, we constructed task-specific datasets by combining public biomedical image resources, curated manipulated examples, and synthetic images generated by multiple generative AI systems. We evaluated VrySure using region-level F1 score, recall, precision, false negative rate (FNR), and false discovery rate (FDR) across multiple manipulation categories and compared its performance with two commonly used commercial image-integrity screening platforms under a predefined benchmark protocol. Under the tested conditions, VrySure achieved a higher F1 score and recall, lower FNR, and maintained a low FDR for within-image copy-move detection, splicing detection, and AI-generated image detection, while showing comparable performance in transformation detection. Beyond automated screening, VrySure is designed to support source-data comparison and evidence-based assessment in scientific integrity investigations. By integrating multiple detection capabilities into a unified and scalable workflow, VrySure provides a practical framework to improve the efficiency and consistency of image-integrity screening in biomedical research.

23.
arXiv (CS.CL) 2026-06-15

Graph-based Target Back-Propagation for Context Adaptation in Multi-LLM Agentic Systems

Context adaptation automates prompt engineering in LLM-based systems by iteratively revising tunable prompts from task feedback, without modifying model weights. Extending this paradigm to multi-LLM agentic systems is crucial: existing methods suffer from inaccurate credit assignment and lack convergence guarantees. We propose Graph-based Target Back-Propagation (GTBP), a context adaptation framework for agentic workflows modeled as directed acyclic graphs. GTBP propagates local target outputs backward through the workflow graph and uses target–output discrepancies to guide a stage-wise prompt update mechanism. Theoretically, we show that GTBP's stage-wise prompt updates become stable over iterations, and that a sufficiently capable LLM optimizer can decrease the overall objective. Empirically, GTBP consistently outperforms strong baselines across three benchmarks while maintaining comparable computational cost.

24.
bioRxiv (Bioinfo) 2026-06-10

Is level-1 blob reconstruction under the network multispecies coalescent easy?

作者:

Hybridization is an important evolutionary process, commonly modeled by the network multispecies coalescent. Reconstructing evolutionary histories under this model is notoriously costly, even for level-1 networks where hybridization events are isolated from each other. The widely used methods that combine speed with statistical guarantees rely on quartet concordance factors computed for all subsets of four species, resulting in an o(n^4k) bottleneck that severely limits scalability to large numbers of species (n) and genes (k). Among quartet-based methods, NANUQ+ is notable because it decomposes the problem into two steps: first reconstructing a tree of blobs, which compresses each non-treelike part of the network, called a blob, into a single vertex, and second reconstructing the internal structure of each level-1 blob, specifically its circular order and hybrid vertex. Here, we investigate whether level-1 blob reconstruction is difficult once the tree of blobs is known. We present a fast and statistically consistent algorithm, called NetCS, based on two simple primitives: majority voting and merge sort, circumventing the bottleneck of computing all quartet concordance factors. In simulations, NetCS achieved comparable accuracy to NANUQ+ and was dramatically faster, enabling analyses of 200 taxa and 1000 genes in only a few minutes. Both methods attained near-perfect accuracy when given the true tree of blobs; however, their performance degraded in end-to-end pipelines due to errors in tree of blobs reconstruction. Strikingly, even methods that reconstruct level-1 networks directly struggled to accurately predict hybrid ancestry. Our results suggest that reconstructing level-1 blobs is unexpectedly easy once the tree of blobs is known, and that a major challenge for phylogenetic network inference lies in accurate tree of blobs reconstruction.

25.
arXiv (quant-ph) 2026-06-12

First-order and interior-point methods for entanglement detection

arXiv:2508.05854v3 Announce Type: replace Abstract: Quantum entanglement lies at the heart of quantum information science, yet its reliable detection in high-dimensional or noisy systems remains a fundamental computational challenge. Semidefinite programming (SDP) hierarchies, such as the Doherty-Parrilo-Spedalieri (DPS) and Extension (EXT) hierarchies, offer complete methods for entanglement detection, but it is well known that their practical use is limited by exponential growth in problem size if implemented naively. We make three contributions. First, we introduce a new SDP hierarchy, PST, that is sandwiched between EXT and DP – offering a tighter approximation to the set of separable states than EXT, while incurring significantly lower computational overhead than DPS. Second, we explicitly construct compact, polynomially-scalable descriptions of EXT and PST using partition mappings and operators. These descriptions in turn yield formulations that satisfy desirable properties such as the Slater condition and are well-suited to both first-order methods (FOMs) and interior-point methods (IPMs). Third, we design a suite of entanglement detection algorithms: three FOMs (Frank-Wolfe, projected gradient, and fast projected gradient) based on a least-squares formulation, and a custom primal-dual IPM based on a conic programming formulation. These methods are numerically stable and capable of producing entanglement witnesses or proximity measures, even in cases where states lie near the boundary of separability. Numerical experiments on benchmark quantum states demonstrate that our algorithms improve the ability to solve deeper levels of the SDP hierarchy.