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

CMI-RewardBench: Evaluating Music Reward Models with Compositional Multimodal Instruction

arXiv:2603.00610v3 Announce Type: replace-cross Abstract: While music generation models have evolved to handle complex multimodal inputs mixing text, lyrics, and reference audio, evaluation mechanisms have lagged behind. In this paper, we bridge this critical gap by establishing a comprehensive ecosystem for music reward modeling under Compositional Multimodal Instruction (CMI), where the generated music may be conditioned on text descriptions, lyrics, and audio prompts. We first introduce CMI-Pref-Pseudo, a large-scale preference dataset comprising 110k pseudo-labeled samples, and CMI-Pref, a high-quality, human-annotated corpus tailored for fine-grained alignment tasks. To unify the evaluation landscape, we propose CMI-RewardBench, a unified benchmark that evaluates music reward models on heterogeneous samples across musicality, text-music alignment, and compositional instruction alignment. Leveraging these resources, we develop CMI reward models (CMI-RMs), a parameter-efficient reward model family capable of processing heterogeneous inputs. We evaluate their correlation with human judgment scores on musicality and alignment on CMI-Pref along with previous datasets. Further experiments demonstrate that CMI-RM not only correlates strongly with human judgments, but also enables effective inference-time scaling via top-k filtering. Code is available at GitHub (https://github.com/Haiwen-Xia/CMI-RewardBench). Model weights: CMI-RM (https://huggingface.co/HaiwenXia/CMI-RM). Datasets: CMI-Pref-Pseudo (https://huggingface.co/datasets/HaiwenXia/cmi-pref-pseudo) and CMI-Pref (https://huggingface.co/datasets/HaiwenXia/cmi-pref)

02.
arXiv (quant-ph) 2026-06-19

Progress on the Kretschmann-Schlingemann-Werner Conjecture

arXiv:2308.15389v4 Announce Type: replace Abstract: Given any pair of quantum channels $\Phi_1,\Phi_2$ such that at least one of them has Kraus rank one, as well as any respective Stinespring isometries $V_1,V_2$, we prove that there exists a unitary $U$ on the environment such that $\|V_1-({\bf1}\otimes U)V_2\|_\infty\leq\sqrt{2\|\Phi_1-\Phi_2\|_\diamond}$. Moreover, we provide a simple example which shows that the factor $\sqrt2$ on the right-hand side is optimal, and we conjecture that this inequality holds for every pair of channels.

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

MacrOData: New Benchmarks of Thousands of Datasets for Tabular Outlier Detection

arXiv:2602.09329v3 Announce Type: replace Abstract: Quality benchmarks are essential for fairly and accurately tracking scientific progress and enabling practitioners to make informed methodological choices. Outlier detection (OD) on tabular data underpins numerous real-world applications, yet existing OD benchmarks remain limited. The prominent OD benchmark AdBench is the de facto standard in the literature, yet comprises only 57 datasets. In addition to other shortcomings discussed in this work, its small scale severely restricts diversity and statistical power. We introduce MacrOData, a large-scale benchmark suite for tabular OD comprising three carefully curated components: OddBench, with 790 datasets containing real-world semantic anomalies; OvrBench, with 856 datasets featuring real-world statistical outliers; and SynBench, with 800 synthetically generated datasets spanning diverse data priors and outlier archetypes. Owing to its scale and diversity, MacrOData enables comprehensive and statistically robust evaluation of tabular OD methods. Our benchmarks further satisfy several key desiderata: We provide standardized train/test splits for all datasets, public/private benchmark partitions with held-out test labels for the latter reserved toward an online leaderboard, and annotate our datasets with semantic metadata. We conduct extensive experiments across all benchmarks, evaluating a broad range of OD methods comprising classical, deep, and foundation models, over diverse hyperparameter configurations. We report detailed empirical findings, practical guidelines, as well as individual performances as references for future research. All benchmarks containing 2,446 datasets combined are open-sourced, along with a publicly accessible leaderboard hosted at https://huggingface.co/MacrOData-CMU.

04.
arXiv (CS.LG) 2026-06-19

Optimal Ansatz-free Hamiltonian Learning In Situ

arXiv:2606.19486v1 Announce Type: cross Abstract: Characterizing the features of a Hamiltonian that governs a quantum system serves as a fundamental subroutine of quantum device calibration, signal sensing, and error correction. Recent works proposed protocols have achieved the optimal Heisenberg-limited scaling learning ansatz-free Hamiltonians from their real-time evolutions without fully specifying interaction structures. However, these protocols rely on both deep circuits with interleaving probes and control, and extremely short time resolution, making them difficult to implement on near- and intermediate-term in situ quantum experiments. In this work, we propose a computationally efficient, control-free, and ancilla-free algorithm that uses only Pauli product state preparation and measurement, and learns an ansatz-free Hamiltonian $H$ with $||H||\leq\Lambda$ in total evolution time of $\Theta(\frac{\Lambda}{\epsilon^2}\log(\frac{\Lambda}{\epsilon}))$. The evolution time cost of our algorithm is optimal for any control-free protocols as we further prove a lower bound of $\Omega(\frac{\Lambda}{\epsilon^2}\log(\frac{\Lambda}{\epsilon}))$. Technically, our method introduces a randomized-sampling framework that combines band-limited kernel-based time sampling with a displacement sieve for Hamiltonian structure learning. The characteristic probe time resolution depends only on $\Lambda$ instead of $\varepsilon$, which makes our protocol especially appealing in the high-precision regime for sensing and calibration applications. We also show that the algorithm maintains the same asymptotic total evolution time in the presence of state-preparation-and-measurement (SPAM) noise when the Hamiltonian is local after calibration. Our results demonstrate the fundamental cost of experimentally friendly Hamiltonian learning and provide a practical route to rigorous in situ characterization of near-term quantum platforms.

05.
arXiv (CS.CV) 2026-06-11

AVIS: Adaptive Test-Time Scaling for Vision-Language Models

Modern Vision-Language Models (VLMs) benefit from chain-of-thought prompting and test-time scaling, but these gains often come with prohibitive inference cost due to large visual contexts and long decoding chains. We view this cost through two coupled axes: Visual Context Scaling (VCS), which controls how much visual evidence is passed to the language model, and Visual Reasoning Scaling (VRS), which controls how much inference-time reasoning search is performed. Existing methods typically optimize one axis at a time, leaving the joint allocation of compute across these axes underexplored. We introduce Adaptive Visual Inference Scaling (AVIS), a lightweight policy that adapts both VCS and VRS per query. AVIS realizes VCS through Key Diversity Visual (KDV) pruning, a training-free $O(N)$ key-based rule for removing redundant visual tokens before prefilling, and realizes VRS through adaptive self-consistency, using a learned difficulty predictor to select the number of reasoning rollouts. AVIS is deployment-friendly and compatible with shared-prefill inference, where all rollouts reuse a single prefilling pass and KV cache. Across diverse image and video reasoning benchmarks, AVIS improves the accuracy–compute trade-off relative to VCS-only and VRS-only baselines, and remains effective on top of RL post-trained VLMs while keeping compute and latency low.

06.
medRxiv (Medicine) 2026-06-18

Cost analysis of overseas versus domestic vaccination of US-bound refugees

Context: To ensure healthy resettlement and protect US health security, the Vaccination Program for US-bound Refugees (VPR) offers some recommended vaccines to refugees overseas before resettlement to the United States. The selected vaccines and number of doses vary by country of departure. VPR was found to be cost-saving in 2018 but had since expanded to more sites. Objective: Assess VPR's current costs and impact on post-arrival domestic vaccination needs and costs. Setting and Participants: A model-based analysis of the Federal government costs for VPR and post-arrival (US) vaccination of resettled refugees separated across five regions: Africa, Asia, the Middle East and North Africa/Republic of Turkiye and Middle East, Europe, and the Americas using fiscal year 2024 data. Design: We quantified and compared full vaccination costs for refugees under two scenarios: (1) 'No VPR' and (2) 'VPR'. Refugees would receive no vaccines overseas and be fully vaccinated after US arrival under 'No VPR'. Under 'VPR', refugees receive one or two doses of selected vaccines overseas before completing vaccination schedules after arrival. Main Outcomes: Costs were reported in 2023 US dollars for 'VPR' and 'No VPR' scenarios and further subdivided by grouping countries/sites depending on whether the International Organization for Migration (IOM) provides vaccination services for refugees (IOM sites) versus non-IOM providers (non-IOM sites). Results: 'VPR' resulted in average net cost savings of $147 per person or $14.7 million per 100,000-refugee cohort compared to providing all vaccines after US arrival ('No VPR'). 'VPR' was cost-saving across most regions, except for IOM sites in Europe, where a net cost of $44 per person was observed. Net cost savings per person were highest for IOM sites in Africa ($333). Conclusions: VPR remains a cost-saving strategy, while protecting US-bound refugees' health and US health security by preventing disease outbreaks during resettlement.

07.
bioRxiv (Bioinfo) 2026-06-08

DDI_single: Single-Sequence-Based Protein Domain Assembly

作者:

Domains are the basic units of protein structure and function. Appropriate inter-domain organization is critical to enable cooperative execution of multiple related functions. It is thus a crucial step to determine the full-length structure of multi-domain proteins for the purpose of elucidating their functions and designing new drugs to regulate these functions. Existing structure prediction algorithms are generally better at solving the internal conformation of domains, rather than modeling the relative positions between domains. To address the challenge of accurately determining multi-domain protein conformations, we develop a single-sequence-based domain assembly algorithm called DDI_single. DDI_single directly extracts features from the amino acid sequence using the protein language model ESM-1b, and accurately predicts the interactions between residue pairs of structural domains through a novel gated cross-attention module, thus achieving the correct assembly of structural domains. With the knowledge of domain definition, DDI_single achieves more than 20% higher accuracy in the task of predicting the relative distances of residue pairs between domains than that of the single-sequence-based structure prediction algorithm trRosettaX_single. When assembling domains with known spatial conformations, DDI_single correctly assembles 74.4% of the samples in the test set (TM-score>0.5). When assembling domains with unknown spatial conformations, in cases where the internal spatial conformations of domains are correctly modeled, DDI_single correctly assembles 73.9% of the samples.

08.
arXiv (CS.CL) 2026-06-12

Beyond the Commitment Boundary: Probing Epiphenomenal Chain-of-Thought in Large Reasoning Models

Chain-of-thought (CoT) reasoning is the dominant paradigm for inference-time scaling in language models, yet the causal influence of individual steps on the final answer poorly understood. We estimate each step's causal importance via early exit and use this measure to study how answers form across the reasoning traces of several model families. Across diverse tasks, we find that reasoning typically crosses a commitment boundary – a sharp transition from transient intermediate guesses to a stable, high-confidence answer. This transition often happens in a single step, well before the model's reasoning block ends, and is followed by epiphenomenal CoT steps that leave the final answer probability unaltered. Using attention probes, we show that answer-formation stages can be linearly decoded from intermediate reasoning steps with high accuracy and generalize robustly to unseen reasoning tasks. We exploit this signal to early-exit reasoning blocks at the commitment boundary, reducing the length of CoTs up to 55\% on average with negligible impact on model performance.

09.
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.

10.
arXiv (CS.CV) 2026-06-12

SmartFont: Dynamic Condition Allocation for Few-Shot Font Generation

Few-shot font generation simultaneously requires global structural completeness and fine-grained local style fidelity. Existing methods usually either rely on global content-style modeling, which is robust but imperfectly disentangled, or emphasize component/local modeling, which captures fine details but relies heavily on local priors and reference coverage. We argue that the key challenge is not merely to learn purer conditions, but to organize complementary yet biased global and local conditions through multi-level allocation during generation. To this end, we propose SmartFont, a diffusion-based few-shot font generation framework that combines global content-style generation with weakly supervised local corrective experts. The local branch performs semantic-spatial allocation by learning expert-wise local concepts and semantically meaningful spatial maps under weak component supervision, enabling fine-grained correction without requiring explicit component-conditioned inference. On top of this, a denoising-state condition allocation module adaptively weights global content, global style, and local corrective feature across timesteps and injection blocks. Extensive experiments show that SmartFont achieves better global-local balance, improves glyph quality and local detail fidelity.

11.
arXiv (math.PR) 2026-06-17

How long does it take to train an Elephant Random Walk

作者:

arXiv:2509.15049v2 Announce Type: replace Abstract: We study how conditioning on the first $k$ steps, which we think of as training, affects the long-term behavior of the Elephant Random Walk. When the elephant is conditioned to be at position $k$ at time $k$, the first return time to the origin scales as $k^{(4-4p)/(3-4p)}$ in the diffusive regime, and grows exponentially in the critical regime. We loosely interpret this as a measurement of the rate at which the elephant forgets its training.

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

Modality-Aware Feature Matching in Visual and Vision-Language Applications: A Comprehensive Survey

Feature matching is a cornerstone task in computer vision, essential for applications such as image retrieval, stereo matching, 3D reconstruction, and SLAM. This survey comprehensively reviews modality-based feature matching, exploring traditional handcrafted methods and emphasizing contemporary deep learning approaches across various modalities, including RGB images, depth images, 3D point clouds, LiDAR scans, medical images, and vision-language interactions. Traditional methods, leveraging detectors like Harris corners and descriptors such as SIFT and ORB, demonstrate robustness under moderate intra-modality variations but struggle with significant modality gaps. Contemporary deep learning-based methods, exemplified by detector-free strategies like CNN-based SuperPoint and transformer-based LoFTR, substantially improve robustness and adaptability across modalities. We highlight modality-aware advancements, such as geometric and depth-specific descriptors for depth images, sparse and dense learning methods for 3D point clouds, attention-enhanced neural networks for LiDAR scans, and specialized solutions like the MIND descriptor for complex medical image matching. Cross-modal applications, particularly in medical image registration and vision-language tasks, underscore the evolution of feature matching to handle increasingly diverse data interactions.

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

Entity Labels Are Not Entity Signals: A Framework for Observable Relevance in Document Re-Ranking

Entity-aware document retrieval uses query-associated entities as ranking signals, assuming that semantically relevant entities are also useful retrieval signals. We show this assumption is insufficient- and explain why. Unlike terms, which are ground-truth observations, entity links are hypotheses produced by an imperfect linker: an entity can be topically central yet provide no discriminative signal if the linker fires indiscriminately across relevant and non-relevant documents. We formalize this as a distinction between Conceptual Entity Relevance (CER)- whether an entity is topically related to a query- and Observable Entity Relevance (OER)- whether its observed presence in a collection discriminates relevant from non-relevant documents. Across four collections and annotation sources including human entity judgments, CER and OER exhibit near-chance agreement ($\kappa \approx 0$), while OER operationalizations agree substantially ($\kappa \approx 0.5$), confirming CER as the systematic outlier. CER-based supervision selects topically plausible but weakly discriminative entities, pruning fewer than 4% of non-relevant documents on some collections. Aligning supervision with OER improves non-relevant pruning by up to 10x and open-world MAP by 0.051 over BM25. Our findings motivate a shift from conceptual to observable notions of entity relevance in entity-aware retrieval.

14.
arXiv (CS.CV) 2026-06-18

Posterior Continuation with Noise-Conditioned Frequency Exposure for Diffusion Inverse Problems

Diffusion posterior sampling solves inverse problems by combining a pretrained diffusion prior with measurement-consistency guidance. However, full-band guidance can be unreliable at high noise levels, where clean estimates contain score-induced errors and high-frequency measurement directions are weakly identifiable. We argue that posterior guidance should expose measurement frequencies according to the instantaneous diffusion noise level. Based on this principle, we propose a posterior continuation framework that constructs a family of intermediate posteriors whose likelihood emphasizes currently reliable frequency bands and gradually returns to full-band consistency. We instantiate this framework with a stabilized sampler that combines a diffusion predictor, frequency-limited likelihood refinement, and a Haar-domain commitment rule that commits reliable coarse corrections while deferring weakly identifiable details. Across super-resolution, inpainting, and deblurring, our method achieves competitive-to-state-of-the-art restoration performance, including up to 5 dB PSNR improvement on motion deblurring over strong baselines in evaluations on FFHQ and ImageNet.

15.
bioRxiv (Bioinfo) 2026-06-11

DyMoTree decodes early cell state transitions and drivers from single-cell transcriptomes using a tree-structured neural network

Inferring early cell fate from single-cell RNA-sequencing data is essential for identifying cellular origins and fate plasticity in development and disease. However, existing methods often fail to exploit tree-structured lineage trajectories, limiting the accuracy and interpretability of fate mapping. Here we present DyMoTree, a computational framework that models cell fate decisions as nonlinear mappings between progenitor and terminal cell states under explicit lineage constraints. By integrating lineage graphs with a tree-structured neural architecture, DyMoTree learns lineage-resolved cell-state transition maps from single-cell transcriptomes, enabling robust inference of early fate bias and identification of fate-specific progenitor substates and driver genes. Across simulations, lineage-tracing experiments, and in vivo systems, DyMoTree outperformed existing methods in resolving early fate biases. Applications to mouse embryogenesis, lung adenocarcinoma progression, and CAR-T immunotherapy revealed regulatory programs underlying developmental and disease-associated transitions. DyMoTree provides a general framework for modeling lineage-resolved cell-state dynamics underlying development and disease progression.

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

Cognitive Debt: AI as Intellectual Leverage and the Dynamics of Systemic Fragility

作者:

arXiv:2606.15078v1 Announce Type: new Abstract: We develop a formal theory of cognitive debt: the stock of unverified reasoning obligations that accumulates when individuals use AI as a substitute rather than a complement for first-principles cognition. The model features two state variables per agent, cognitive capital and cognitive debt, and a multiplicative production technology in which cognitive capital functions as collateral that determines the return to AI adoption. We establish six propositions. Rational agents incur positive cognitive debt because the costs are deferred, partially external, and masked by short-run productivity gains. Tranquil periods lower subjective risk assessments, raise AI substitution intensity, and compound leverage, generating a cognitive Minsky moment in which subjective risk falls while true systemic fragility rises. Expected crisis losses are convex in aggregate leverage. Post-crisis, output-target pressure can produce a false-correction loop in which agents patch AI failures with more AI. The decentralised equilibrium over-adopts substitutive AI relative to the social optimum because of systemic risk, cognitive public goods, and arms-race externalities. In a two-type heterogeneous-agent economy, high-cognitive-capital agents adopt AI more intensively and may eventually erode their unaided cognitive capital below that of initially lower-skilled agents.

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

A Gradient-based Causal Discovery Framework with Applications to Complex Industrial Processes

arXiv:2507.11178v3 Announce Type: replace-cross Abstract: With the advancement of deep learning technologies, various neural network-based Granger causality models have been proposed. Although these models have demonstrated notable improvements, several limitations remain. Most existing approaches adopt the component-wise architecture, necessitating the construction of a separate model for each time series, which results in substantial computational costs. In addition, imposing the sparsity-inducing penalty on the first-layer weights of the neural network to extract causal relationships weakens the model's ability to capture complex interactions. To address these limitations, we propose Gradient Regularization-based Neural Granger Causality (GRNGC), which requires only one time series prediction model and applies $L_{1}$ regularization to the gradient between model's input and output to infer Granger causality. Moreover, GRNGC is not tied to a specific time series forecasting model and can be implemented with diverse architectures such as KAN, MLP, and LSTM, offering enhanced flexibility. Numerical simulations on DREAM, Lorenz-96, fMRI BOLD, and CausalTime show that GRNGC outperforms existing baselines and significantly reduces computational overhead. Meanwhile, experiments on real-world DNA, Yeast, HeLa, and bladder urothelial carcinoma datasets further validate the model's effectiveness in reconstructing gene regulatory networks.

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

HOLO-MPPI: Multi-Scenario Motion Planning via Hierarchical Policy Optimization

arXiv:2606.16480v1 Announce Type: cross Abstract: Robots deployed in the real world must plan motions across diverse scenarios without per-scenario retuning. End-to-end reinforcement learning (RL) can generalize across scenarios but often becomes brittle under distribution shift, reward misspecification, and stochastic interactions. Model predictive path integral (MPPI) control enables strong real-time refinement without gradients, but its performance depends on a well-shaped sampling prior, while manually designing the priors does not scale to multi-scenario deployment. We present HOLO-MPPI (High-level Offline, Low-level Online MPPI), a multi-scenario motion planning framework that combines high-level policy learning with low-level stochastic optimal control. Offline, we learn a high-level policy that proposes scenario-robust plans in an abstract action space, with a learned world model for online rollout. Online, the policy serves as a data-driven prior generator that parameterizes MPPI's sampling distribution conditioned on the current observation and goal. MPPI then optimizes low-level control sequences around this prior in real time to adapt to local disturbances. We instantiate HOLO-MPPI in autonomous driving by designing an effective high-level action space and tailored model architectures. Our evaluation across diverse driving scenarios shows that HOLO-MPPI improves upon MPPI and end-to-end RL baselines while maintaining real-time control.

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

Bi-Anchor Interpolation Solver for Accelerating Generative Modeling

arXiv:2601.21542v3 Announce Type: replace-cross Abstract: Flow Matching (FM) models have emerged as a leading paradigm for high-fidelity synthesis. However, their reliance on iterative Ordinary Differential Equation (ODE) solving creates a significant latency bottleneck. Existing solutions face a dichotomy: training-free solvers suffer from significant performance degradation at low Neural Function Evaluations (NFEs), while training-based one- or few-steps generation methods incur prohibitive training costs and lack plug-and-play versatility. To bridge this gap, we propose the Bi-Anchor Interpolation Solver (BA-solver). BA-solver retains the versatility of standard training-free solvers while achieving significant acceleration by introducing a lightweight SideNet (1-2% backbone size) alongside the frozen backbone. Specifically, our method is founded on two synergistic components: 1) Bidirectional Temporal Perception, where the SideNet learns to approximate both future and historical velocities without retraining the heavy backbone; and 2) Bi-Anchor Velocity Integration, which utilizes the SideNet with two anchor velocities to efficiently approximate intermediate velocities for batched high-order integration. By utilizing the backbone to establish high-precision ``anchors'' and the SideNet to densify the trajectory, BA-solver enables large interval sizes with minimized error. Empirical results on ImageNet-256^2 demonstrate that BA-solver achieves generation quality comparable to 100+ NFEs Euler solver in just 10 NFEs and maintains high fidelity in as few as 5 NFEs, incurring negligible training costs. Furthermore, BA-solver ensures seamless integration with existing generative pipelines, facilitating downstream tasks such as image editing.

20.
bioRxiv (Bioinfo) 2026-06-17

In silico characterization of lysis and host-recognition modules in Staphylococcus aureus bacteriophage genomes

Background/aim: Antimicrobial resistance in methicillin-resistant Staphylococcus aureus (MRSA) requires precision non-antibiotic therapeutics, yet phage lytic efficacy is poorly predicted by phenotypic assays, as shown by paradoxical biofilm responses. This study characterized the genomic architecture of lytic S. aureus bacteriophages, focusing on the conservation of the lysis module and the variability of host-recognition modules, to provide a rational basis for phage candidate selection. Materials and methods: Twenty-two complete S. aureus phage genomes were retrieved from NCBI GenBank. Genomic features were extracted with custom Biopython scripts. Lysis (endolysin, holin) and host-recognition (tail fiber/receptor-binding protein) modules were annotated and validated by InterPro domain analysis, with disrupted endolysins resolved by tBLASTn. Phylogeny was reconstructed from large terminase subunit (TerL) sequences using maximum likelihood. Results: Genome size spanned three classes, from 17.5 to 148.6 kb. The LysK-type endolysin (CHAP, Amidase, SH3b) was highly conserved, whereas tail fiber/RBP genes were detected in only 14 of 22 phages. Domain analysis reclassified two proteins annotated as endolysins as virion-associated peptidoglycan hydrolases, and identified two independent mechanisms, HNH endonuclease insertion and intron splitting, that interrupt lysis-module genes and confound automated annotation. Maximum likelihood analysis recovered a strongly supported, highly conserved core clade with EW and SA13 as divergent lineages. Conclusion: Lysis modules are conserved whereas host-recognition modules are variable, indicating that host recognition rather than the lytic enzyme is the principal determinant of host range and the more rational target for phage selection and engineering.

21.
Nature (Science) 2026-06-09

People are turning to AI chatbots to plug gaps in health information

A systematic assessment of health-related queries to a chatbot powered by artificial intelligence highlights shortfalls in health-care provision and the responsibilities of AI companies. A systematic assessment of health-related queries to a chatbot powered by artificial intelligence highlights shortfalls in health-care provision and the responsibilities of AI companies.

22.
bioRxiv (Bioinfo) 2026-06-14

FENNEC: Fine-Tuned Ensemble Neural Networks Accelerate Chemically Modified siRNA Design and Screening

Small interfering RNAs (siRNAs) are a clinically validated therapeutic modality, yet designing potent chemically modified siRNAs remains a costly and iterative process, limited by scarce public data. Computational prediction of siRNA efficacy is therefore essential for rational design and accelerated preclinical development. However, despite the critical role of chemical modifications in therapeutic performance, current state-of-the-art machine learning methods either are not designed to model the chemical diversity of therapeutic siRNAs, or exhibit poor generalization performance. Here, we present FENNEC (Fine-Tuned Ensemble of Neural Networks for siRNA Efficiency Characterization), a machine-learning framework for predicting siRNA activity across chemically diverse design spaces. To support this effort, we curated the largest patent-derived dataset to date of chemically modified siRNAs from 42 patents using OCR-based table extraction and stringent filtering. FENNEC combines temporal convolutional networks with thermodynamic descriptors, experimental covariates, and embeddings from RNA foundation models to capture both local chemical determinants and broader target-context information. Importantly, we show that language-model-derived embeddings provide meaningful higher-order representations of target transcripts, particularly in data-scarce settings. FENNEC achieved robust predictive performance across both gene-level and scaffold-level validation settings, with additional experimental validation on a novel AHSA1-targeting dataset further supporting its generalizability across chemically modified siRNAs. In benchmarking, FENNEC outperformed classical machine-learning and state-of-the-art deep learning models, demonstrating generalization to unseen chemistry. Model interpretation recovered established design principles, including position-specific effects of glycol nucleic acid, 2'-fluoro modifications, and phosphorothioate backbones. Furthermore, in silico perturbation analyses suggest that FENNEC can serve not only as a predictive model, but also as an oracle for the design and optimization of chemically modified siRNAs. Together, our work addresses a key gap in the field by enabling chemically aware deep learning for siRNA design, supported by a large and diverse collection of chemically modified siRNA measurements.

23.
arXiv (CS.CV) 2026-06-17

Reinforcing Dual-Path Reasoning in Spatial Vision Language Models

Spatial VLMs have made substantial progress in geometric perception, yet complex spatial reasoning requiring multi-step inference over depth, distance, and scene relations remains challenging. Moreover, different spatial queries call for fundamentally different strategies: some are best addressed through purely linguistic, step-by-step deduction, while others require explicit 3D grounding before quantitative inference. We present Dual-Path Spatial Reasoning via Reinforcement Learning for Spatial VLMs (SR-REAL), a unified framework that equips a spatial VLM with two complementary reasoning paths: Language-Only Reasoning (LOR), which performs step-by-step linguistic deduction, and Detect-Then-Reason (DTR), which detects 3D geometric cues (e.g., centers or bounding boxes) via region tokens before explicit geometric inference. SR-REAL begins with a cold-start supervised fine-tuning stage that constructs LOR and DTR chain-of-thought supervision and exposes a region-to-3D interface, followed by RL that optimizes the policy model with accuracy and format rewards; for DTR, a discrete center-based detection reward further refines geometric alignment. Across diverse spatial benchmarks, SR-REAL significantly outperforms spatial VLM baselines: (i) a single RL-trained model supports both reasoning paths, with DTR excelling in region-aware tasks through precise 3D localization and LOR enhancing general spatial reasoning; (ii) jointly training both paths fosters mutual reinforcement; (iii) high-quality, blended cold-start data is crucial for stable RL optimization; and (iv) the model generalizes across datasets and domains without per-task tuning, demonstrating positive transfer between LOR and DTR.

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

UltraSketchLLM: Sub-1-Bit LLM Compression via Sketch and Hardware-Friendly Operators

arXiv:2506.17255v2 Announce Type: replace-cross Abstract: Large language models (LLMs) require larger GPU memory size these days, necessitating efficient and extreme weight compression methods. Existing compression methods are either theoretically limited by 1 bit per weight or face severe performance degradation and inefficiency. To deploy LLMs in resource-constrained scenarios, we introduce UltraSketchLLM, compressing LLMs with data sketch. It reduces peak GPU memory footprint with a high compression rate down to 0.5 bit per weight. Combined with hardware-friendly implementation, UltraSketchLLM keeps tolerable performance degradation and extremely low latency overhead with 14.9x speedup compared to naive sketch solution.

25.
arXiv (math.PR) 2026-06-18

Very large cliques in a scale-free random graph

arXiv:2606.18722v1 Announce Type: new Abstract: In this short article we consider a preferential attachment random graph model with edge steps, studied by Alves, Ribeiro and Sanchis. Starting with an initial graph $\mathbb{G}_1$ formed by a vertex with a self-loop attached to it, the model evolves as follows. At every subsequent (discrete) time step, either with probability $p$ we add a vertex to the graph and connect it to exactly one of the older vertices selected with probability proportional to its degree, or with probability $1-p$ we add one edge between two existing vertices, both selected (independently) with probability proportional to their degrees. Let $\omega(\mathbb{G})$ be the clique number of a graph $\mathbb{G}$, i.e.\ the number of vertices in a largest complete subgraph of $\mathbb{G}_{}$. Alves, Ribeiro and Sanchis showed that, for any given $\varepsilon>0$, we have $\omega(\mathbb{G}_{2t})\geq t^{\frac{1-p}{2-p}(1-\varepsilon)}$ with high probability (i.e.\ with probability tending to $1$ as $t\rightarrow \infty$). Here we strengthen this bound by showing that, for any function $f:\mathbb{N}\mapsto \mathbb{N}$ that satisfies $f(t)\rightarrow \infty$ as $t\rightarrow \infty$, with high probability \[\omega(\mathbb{G}_{2t}) = \Omega\left(t^{\frac{1-p}{2-p}}\Big(\log^{\frac{1}{2-p}}(t)f(t)\Big)^{-1}\right).\]