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01.
arXiv (CS.AI) 2026-06-19

SARLO-80: Worldwide Slant SAR Language Optic Dataset 80cm

arXiv:2606.20523v1 Announce Type: cross Abstract: Multimodal foundation models have advanced rapidly thanks to large optical benchmarks, but comparable resources for synthetic aperture radar (SAR) remain limited. Existing SAR–optical datasets largely rely on low-resolution, intensity-only Ground Range Detected~(GRD) products and do not preserve complex-valued SAR measurements or native acquisition geometry, which restricts physically grounded multimodal learning. In particular, large-scale public datasets combining very-high-resolution (VHR) SAR SLC, aligned optical imagery, and natural-language descriptions are still lacking. We present a VHR SAR–optical–text dataset built from open-access Umbra spotlight acquisitions distributed as Sensor Independent Complex Data (SICD). From around 2,500 worldwide scenes (VV/HH, 20cm–2m native resolution), we standardize all SAR data to an 80cm slant-range grid via band-limited FFT resampling and tile the imagery into 1024 by 1024 patches. For each SAR patch, we retrieve a high-resolution optical tile and warp it into the SAR grid using local coordinate correspondences for local pixel-level alignment. We further generate three caption variants (SHORT/MID/LONG) per sample to support vision–language training and evaluation. Our dataset contains 119,566 triplets (complex and amplitude slant-range SAR patch, aligned optical patch, natural-language description) covering 257 locations across 72 countries and a broad range of land types and infrastructures. We release fixed train/validation/test splits and the full preprocessing and baseline code to enable reproducible benchmarks for multimodal alignment on cross-modal retrieval and conditional generation in native SAR geometry. The dataset is publicly available on the Hugging Face Hub at https://huggingface.co/datasets/ONERA/SARLO-80.

02.
arXiv (CS.CL) 2026-06-11

FOCUS: DLLMs Know How to Tame Their Compute Bound

Diffusion Large Language Models (DLLMs) offer a compelling alternative to Auto-Regressive models, but their deployment is constrained by high decoding cost. In this work, we identify a key inefficiency in DLLM decoding: while computation is parallelized over token blocks, only a small subset of tokens is decodable at each diffusion step, causing most compute to be wasted on non-decodable tokens. We further observe a strong correlation between attention-derived token importance and token-wise decoding probability. Based on this insight, we propose FOCUS, an inference system designed for DLLMs. By dynamically focusing computation on decodable tokens and evicting non-decodable ones on-the-fly, FOCUS increases the effective batch size, alleviating compute limitations and enabling scalable throughput. Empirical evaluations demonstrate that FOCUS achieves up to 3.52$\times$ throughput improvement over the production-grade engine LMDeploy in large-batch settings, while preserving or improving generation quality across multiple benchmarks.

03.
medRxiv (Medicine) 2026-06-15

Population-scale genomics reveals divergent pathogenicity of variant classes across paralogous collagen IV genes

Monoallelic pathogenic or likely pathogenic variants in COL4A3 and COL4A4 occur in approximately 1 in 106 individuals, yet whether these paralogous genes confer equivalent pathogenicity for the same variant classes has not been tested at population scale. Using whole-genome sequencing data from the UK Biobank (UKB; n = 500,000), with replication in the All of Us Research Program (n = 414,000), we performed per-variant association testing, gene-based collapsing analyses and phenome-wide association studies (PheWAS) across haematuria, proteinuria and chronic kidney disease. We identified 64 COL4A3 and 92 COL4A4 rare variants significantly associated with haematuria or proteinuria, generating a quantitative allelic series for clinical variant interpretation. Glycine substitutions within collagenous domains conferred similar risks in both genes. In contrast, truncating and non-collagenous domain (NC1) missense variants were strongly associated with haematuria and proteinuria in COL4A4 carriers but showed substantially attenuated or absent associations in COL4A3 carriers despite comparable carrier frequencies and predicted pathogenicity scores. These findings were independently replicated in All of Us. Genome-wide association analysis identified the COL4A3/COL4A4 locus as the dominant genetic determinant of haematuria, with the signal attributable to the aggregate effects of rare coding variants and no evidence of independent common variant or trans-acting modifier effects. These findings demonstrate substantial gene-specific differences in tolerance to truncating and NC1 variants between COL4A3 and COL4A4, challenging assumptions of equivalent pathogenicity across paralogous collagen IV genes. Gene identity and not variant class alone, should inform risk stratification, variant interpretation and genetic counselling in individuals carrying collagen IV risk genotypes.

04.
arXiv (CS.AI) 2026-06-17

Extracting Semantics: LLM-Guided Automatic Population of Robot Ontology from URDF

arXiv:2606.17073v1 Announce Type: cross Abstract: While commonsense knowledge may suffice for virtual agents, embodied robots interacting with humans require grounded and semantically rich representations of both their environment and their own physical embodiment. In cognitive robotics, ontologies are effective for integrating such heterogeneous knowledge to enable explainable reasoning, even during continuous knowledge updates. Yet, their manual construction remains a bottleneck. We present a preliminary approach for the automatic generation of robot semantic abstractions by transforming Unified Robot Description Format (URDF) models into populated ontologies. Although URDF files provide structural and kinematic descriptions, their identifiers often require commonsense interpretation to recover meaningful semantics, a task at which Large Language Models (LLMs) excel. Our pipeline leverages LLMs to infer semantic relationships by prompting them with concepts from an existing ontology, ensuring the final classification remains aligned with the formal model. To improve reliability, the pipeline combines majority voting across multiple LLM queries along with syntactic and schema-level validation to ensure that generated outputs conform to the expected representation format and ontology constraints. We evaluate the approach on multiple robot descriptions and discuss the generated abstractions. Initial results indicate that the proposed method can effectively bridge the gap between low-level robot descriptions and the structured, grounded knowledge representations required for human-robot interaction.

05.
Nature (Science) 2026-06-08

Fifty years since a simple equation described the chaos of biology

An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics. An exploration of chaos theory in population dynamics showed that unpredictable systems can often be modelled using surprisingly simple mathematics.

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

Systematic Study of Dysarthric Speech Recognition: Spectral Features and Acoustic Models

arXiv:2606.19793v1 Announce Type: cross Abstract: The challenge associated with recognizing dysarthric speech primarily arises from pronounced acoustic variability attributed to impaired articulatory precision. Past research has demonstrated improved recognition through the use of hybrid DNN/HMM sequence discriminative training. This paper presents a comprehensive investigation of various combinations of acoustic features tailored to different Acoustic Models, offering suitable feature selections for each. The incorporation of Pitch features notably improved recognition performance, especially for sentence recognition tasks involving dysarthric speech. Through a systematic examination of the TORGO database, we have demonstrated the potential to enhance the performance of the state-of-the-art Factorized Time Delay Neural Network (F-TDNN) model for recognizing dysarthric speech. Our methods, implemented with the F-TDNN model, resulted in a 4.65\% relative improvement in isolated word recognition and a 4.63\% relative improvement in sentence recognition for dysarthric speech, compared to previous research. This improvement effectively compensates for speech variability, attributable to our deliberate selection of the number of overlapping frames between consecutive training example chunks.

07.
arXiv (CS.LG) 2026-06-19

PU-UNet: Stable Multiplicative Interactions for Medical Image Segmentation

arXiv:2606.20035v1 Announce Type: cross Abstract: Many dense prediction networks rely on additive feature transformations and model higher-order feature interactions only implicitly. Product units provide an explicit mechanism for multiplicative feature modeling, but their logarithmic–exponential formulation can cause numerical instability, which has limited their use in deep dense prediction networks. In this work, we propose Product-Unit U-Net (PU-UNet), a residual U-Net that integrates stable product-unit residual blocks into rich low-resolution stages for medical image segmentation. The proposed formulation combines smooth positivity mapping with log-domain clipping, enabling stable multiplicative feature learning with negligible computational overhead. On ISIC 2018, Kvasir-SEG, and BUSI, PU-UNet achieves Dice scores of 0.942, 0.959, and up to 0.925, respectively. Compared with a matched Residual U-Net baseline, PU-UNet consistently improves Dice and IoU while keeping parameters, FLOPs, and inference latency nearly unchanged, and reduces the image-level false-positive rate on normal BUSI cases from 0.077 to zero. Ablation studies suggest that the gains are associated with product-unit interactions, are strongest under low-resolution placement, and benefit from the proposed stabilization design. These results suggest that stable product-unit residual learning can be an effective way to enhance U-Net-style segmentation networks with explicit multiplicative interactions.

08.
arXiv (CS.AI) 2026-06-19

eCNNTO: A Highly Generalizable ConvNet for Accelerating Topology Optimization

arXiv:2606.19921v1 Announce Type: new Abstract: This work proposes an element-based Convolutional Neural Network (CNN) to accelerate density-based Topology Optimization (TO), termed eCNNTO. TO generally undergoes a large number of iterations, where finite element analysis is performed in every iteration, leading to the efficiency bottleneck especially when dense meshes are used to achieve high-resolution designs. To address this limitation, eCNNTO is proposed to build upon Kallioras et al. (2020), where a Deep Belief Network (DBN) was trained for every element to predict its near-optimal density from its early history, thereby skipping the great majority of iterations and significantly accelerating the TO procedure. However, the method lacks spatial correlations among neighboring elements and may lead to disconnected features in the final structure. The proposed method employs CNN with residual connections to address this issue. On top of it, a novel training strategy is introduced to further enhance the optimization efficiency, where the training dataset consists of the final stage density histories rather than early ones. This change can also help reduce the required training data size. eCNNTO requires only a small dataset to train and yet it can be generalized to problems with largely different boundary conditions, loading cases, design domain geometries, mesh resolutions, as well as non-design domains. In the end, the generalization capabilities and efficiency of eCNNTO are demonstrated through a variety of examples in two and three dimensions, achieving up to 90% and 97% reduction of iterations, respectively.

09.
arXiv (CS.AI) 2026-06-24

A Survey on Federated Causal Discovery and Inference

arXiv:2606.23741v1 Announce Type: cross Abstract: Causal reasoning, which encompasses the discovery of causal structures and the inference of causal effects, is fundamental to data-driven decision making. In practice, data for reliable causal analysis are often distributed across institutions and cannot be centralized due to privacy regulations or communication constraints. Federated learning (FL) addresses this by enabling collaborative analysis without raw data sharing, giving rise to the rapidly growing field of federated causal discovery (FCD) and inference (FCI). However, the interdisciplinary nature of this field and the absence of a comprehensive survey present barriers to entry for researchers. This paper bridges that gap by providing a systematic review through multi-dimensional taxonomies. Grounded in the three core design decisions underlying any FCD solution, namely how structures are learned, how data are partitioned, and what structural knowledge each party obtains, we organize FCD along three axes: methodological paradigm, federation topology, and structural scope. We further examine key practical dimensions, including temporal dynamics, data heterogeneity, missing data, and non-identical variable sets. For FCI, we categorize methods by target estimand (average versus individualized/conditional treatment effects) and by estimation strategy, from classical weighting methods to modern deep generative architectures. Unlike prior works that treat FCD and FCI separately, we formalize their connection as complementary stages of a unified federated causal reasoning pipeline, where FCD supplies the structural knowledge required for valid effect estimation in FCI. Finally, we highlight their shared concerns regarding privacy, communication efficiency, theoretical guarantees, and application domains, and conclude by identifying open challenges for future research.

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

Your "Pro" LLM Subscription May Actually Be "Free": Exposing Fingerprint Spoofing Risks in LLM Inference Services

As Large Language Model (LLM) APIs become ubiquitous, users increasingly rely on black-box fingerprinting to verify that providers are serving the advertised premium models. However, these methods may overlook adversarial providers who manipulate model weights to cheat the fingerprint process. We introduce a novel threat termed fingerprint spoofing, where a malicious provider stealthily serves a weaker model that has been parameter-efficiently fine-tuned to mimic a stronger model, thereby evading user-side fingerprinting. We first formally prove that user-side resource constraints (i.e., finite query budgets and weak fingerprinting classifiers) make current fingerprinting vulnerable to fingerprint spoofing. Guided by this theoretical analysis, we propose GhostPrint, a cost-effective attack framework leveraging surrogate modeling, reward-ranked fine-tuning, and knowledge distillation. Extensive evaluations in both static and continual fingerprinting settings demonstrate that GhostPrint allows weak models to consistently bypass representative fingerprint methods while maintaining utility at a low fine-tuning cost, exposing a critical vulnerability in current LLM fingerprinting pipelines.

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

MemToolAgent: Leveraging Memory for Tool Using Agents Based on Environment and User Feedback

Modern large language model (LLM) agents can use external tools to help users solve complex tasks. However, for problems that require learning from long-term historical events or from previous agent-environment interactions, LLM agents are required to use memory mechanisms to store and retrieve experiences. While sophisticated memory systems exist for dialogue agents, few studies have empirically examined how to improve agents' tool-using capabilities through past user-agent conversations. We propose MemToolAgent, a framework that improves tool use through memory management. Our approach contains a memory extraction module that processes past experiences into structured memory entries, and a retrieval module that dynamically selects a subset of the stored memory entries. This enables more personalized and accurate responses aligned with user preferences and feedback without requiring LLM fine-tuning. In summary, this work has three main contributions: (1) a unified memory entry format that improves both general-purpose and personalized tool use without LLM fine-tuning, (2) a reflection-based memory extraction that uses environment and user feedback to distill wrong executions into critiques to store, and (3) a retrieval module that chooses how many past experiences to use based on the memory similarity distribution. MemToolAgent achieves 29%, 80%, and 17% relative improvements compared to strong baselines on the WorkBench, NESTFUL, and PEToolBench benchmarks, respectively.

12.
arXiv (quant-ph) 2026-06-16

Phase controlled spectral topology, dynamic stability and sensitivity in Non-Hermitian Cavity Magnonics

arXiv:2606.16522v1 Announce Type: new Abstract: We theoretically investigate a non-Hermitian cavity-magnon platform in which coherent photonmagnon interactions and reservoir-mediated dissipative coupling interfere through a single externally tunable phase. We show that this interference phase provides a universal control parameter that continuously rotates the effective coupling between Hermitian and anti-Hermitian regimes, enabling dynamic transitions between level repulsion and level attraction without modifying intrinsic system parameters. The resulting phase-controlled non-Hermitian topology gives rise to exceptional points, linewidth engineering, and zero-damping conditions. Owing to the propagation-direction dependence of the dissipative interaction, the system further exhibits strong nonreciprocal transport and phase-tunable isolation arising from asymmetric hybridization of the cavity and magnon modes. Beyond its spectral and transport properties, we establish a direct connection between nonHermitian spectral topology and nonequilibrium population dynamics. The interference phase governs the stability of the hybrid modes, driving transitions between stable relaxation, critical slowing down near exceptional points, oscillatory energy exchange, and exponentially amplified dynamics. We further demonstrate that the same phase-controlled exceptional topology can be exploited for enhanced sensing, where the eigenvalue response exhibits the characteristic square-root scaling associated with exceptional-point physics. Our results provide a unified framework linking spectral topology, directional transport, dynamical stability, and sensing functionality through reservoirengineered interference in cavity magnonic systems.

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

HK-LegiCoST: Leveraging Non-Verbatim Transcripts for Speech Translation

We introduce HK-LegiCoST, a new three-way parallel corpus of Cantonese-English translations, containing 600+ hours of Cantonese audio, its standard traditional Chinese transcript, and English translation, segmented and aligned at the sentence level. We describe the notable challenges in corpus preparation: segmentation, alignment of long audio recordings, and sentence-level alignment with non-verbatim transcripts. Such transcripts make the corpus suitable for speech translation research when there are significant differences between the spoken and written forms of the source language. Due to its large size, we are able to demonstrate competitive speech translation baselines on HK-LegiCoST and extend them to promising cross-corpus results on the FLEURS Cantonese subset. These results deliver insights into speech recognition and translation research in languages for which non-verbatim or ``noisy'' transcription is common due to various factors, including vernacular and dialectal speech.

14.
arXiv (quant-ph) 2026-06-11

Nonlocal continuous-variable gates by amplified optical connections

arXiv:2603.12866v2 Announce Type: replace Abstract: Nonlocal quantum gates, coupling quantum systems located at a distance, are crucial for distributed quantum computing. To this aim, high-capacity optical noiseless connections between different processing units are essential for transmitting large amounts of information per mode. Simultaneously, optical quantum computing offers future high-speed multimode quantum processors. We propose a library of feasible protocols to implement a necessary nonlocal continuous-variable (CV) quantum nondemolition (QND) gate between two distant users sharing a quantum channel and exploiting classical communication. The users are endowed with a newly achieved high-fidelity and large-bandwith element - single-pass phase-sensitive optical parametric amplifier (OPA), that allows for both online squeezing and channel-loss compensation. The use of OPAs enhances quality of the resulting gate in terms of both excess noise and entangling capability. The proposed schemes are also applicable to CV cluster state fusion, providing a first step towards development of distributed CV measurement-based quantum computation.

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

SURGELLM: Rethinking Multi-Task Evaluation through Task-Aware Feature Gating with Class-Balanced Normalization

Fine-tuned encoders deployed across heterogeneous NLP tasks face three compounding problems: mismatched inductive biases, class-imbalance corruption of feature statistics, and no mechanism to condition attention on external lexical knowledge. We introduce \surgellm, a unified transformer framework that addresses each with a dedicated lightweight module: a surgical feature gate (learned per-dimension sigmoid over curated lexical indicators and \texttt{[CLS]}; provably degenerates to identity when features are uninformative), task-conditioned prefix tokens (quantized feature values and task identity prepended to every input), and Instance-Weighted Normalization (IWN; removes class-prior bias from gate statistics). We prove an excess-risk bound linking gate benefit to surgical feature alignment. Across four tasks, SST-2, multi-hop retrieval, LLM-prompt attribution, and authorship detection, covering 17,830 examples and eleven model variants over three seeds, the IWN variant achieves macro-F1 0.940 ($+0.036$ over the strongest non-IWN baseline; $+0.130$ on authorship detection). A random-vocabulary control ($-0.028$ avg.\ F1) confirms gains are lexical, not parametric. Code, vocabularies, and a $99.5\%$-recovery auto-extraction recipe are released.

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

LatentLens: Revealing Highly Interpretable Visual Tokens in LLMs

Transforming a large language model (LLM) into a vision-language model (VLM) can be achieved by mapping the visual tokens from a vision encoder into the embedding space of an LLM. Intriguingly, this mapping can be as simple as a shallow MLP transformation. To understand why LLMs can so readily process visual tokens, we need interpretability methods that reveal what is encoded in the visual token representations at every layer of LLM processing. In this work, we introduce LatentLens, a novel approach for mapping latent representations to descriptions in natural language. LatentLens encodes a large text corpus and stores contextualized token representations for each token in that corpus. Visual token representations are then compared to these contextualized representations and the top-nearest neighbor representations serve as descriptions of the visual token. We evaluate this method on 15 different VLMs, showing that commonly used methods, such as LogitLens, substantially underestimate the interpretability of visual tokens. With LatentLens instead, the majority of visual tokens are interpretable across all studied models and all layers. Qualitatively, we show that the descriptions produced by LatentLens are semantically meaningful and provide more fine-grained interpretations for humans compared to individual tokens. More broadly, our findings contribute new evidence on the alignment between vision and language representations and open up new directions for analyzing the latent representations of LLMs.

17.
arXiv (CS.LG) 2026-06-25

From Uncertain to Safe: Conformal Adaptation of Diffusion Models for Safe PDE Control

arXiv:2502.02205v4 Announce Type: replace Abstract: The application of deep learning for partial differential equation (PDE)-constrained control is gaining increasing attention. However, existing methods rarely consider safety requirements crucial in real-world applications. To address this limitation, we propose Safe Diffusion Models for PDE Control (SafeDiffCon), which introduce the uncertainty quantile as model uncertainty quantification to achieve optimal control under safety constraints through both post-training and inference phases. Firstly, our approach post-trains a pre-trained diffusion model to generate control sequences that better satisfy safety constraints while achieving improved control objectives via a reweighted diffusion loss, which incorporates the uncertainty quantile estimated using conformal prediction. Secondly, during inference, the diffusion model dynamically adjusts both its generation process and parameters through iterative guidance and fine-tuning, conditioned on control targets while simultaneously integrating the estimated uncertainty quantile. We evaluate SafeDiffCon on three control tasks: 1D Burgers' equation, 2D incompressible fluid, and controlled nuclear fusion problem. Results demonstrate that SafeDiffCon is the only method that satisfies all safety constraints, whereas other classical and deep learning baselines fail. Furthermore, while adhering to safety constraints, SafeDiffCon achieves the best control performance. The code can be found at https://github.com/AI4Science-WestlakeU/safediffcon.

18.
arXiv (CS.CV) 2026-06-15

HARBOR: Heading Analysis and Reconstruction from Behavioral Observation and Radar

Maritime situational awareness often relies on Automatic Identification System (AIS) transmissions to track vessel movements. However, in operational or conflict scenarios, these data may be unavailable due to signal loss, deliberate deactivation, or intentional spoofing. In such conditions, synthetic aperture radar (SAR) imagery becomes a critical sensing alternative for wide-area maritime monitoring, despite providing only static scene snapshots. This work introduces HARBOR (Heading Analysis and Reconstruction from Behavioral Observation and Radar), a complete pipeline for transforming a single SAR image into predictive motion information without requiring any auxiliary data source at inference time. The method begins with SAR image preprocessing to enhance and segment vessel candidates, followed by automatic detection, size-based classification, and heading estimation using skeleton geometry and local intensity patterns. AIS data are used exclusively during an offline calibration phase to derive vessel-type-dependent motion parameters, which are then applied to generate probabilistic heatmaps of candidate future vessel positions. A case study using real COSMO-SkyMed SAR imagery demonstrates the pipeline on a maritime scene in southern Brazil, showing its ability to extract motion tendencies and generate probabilistic projections of vessel positions in data-denied environments.

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

A homotopy-type-theoretic generalization of neurosymbolic inference

arXiv:2606.17851v1 Announce Type: new Abstract: A wide range of neurosymbolic (NeSy) systems compute one functional: a belief-weighted sum of a logical quantity over a space of $\sigma$-structures, of which weighted model counting, fuzzy logic, and probabilistic logic are special cases. This account is built on sets, and a set deliberately forgets two things that are important for NeSy: when two $\sigma$-structures are the same up to a symmetry of the theory, and how many distinct proofs witness a query. Replacing the underlying sets by types, in the sense of homotopy type theory, preserves this information, and turns this functional into a belief-weighted homotopy cardinality, a notion of size that counts each object in inverse proportion to its symmetries. We develop the framework from scratch for NeSy systems, prove a conservativity theorem that recovers the classical functional when symmetries are trivial, and show that the symmetry our framework exposes is exactly the one behind reasoning shortcuts. The payoff is concrete: the shortcut-aware concept posterior that recent methods reach by ensembling or expressive density estimation is the only symmetry-invariant point of the confusion-set simplex, computable in closed form by averaging a single model over the symmetry group. On MNIST reasoning-shortcut benchmarks this single-model wrapper is better calibrated than a diversity-trained ensemble, while leaving label accuracy and identifiable concepts untouched. Code is freely available at https://github.com/bio-ontology-research-group/hott-nesy.

20.
medRxiv (Medicine) 2026-06-18

Avidity of anti-pertussis toxin antibodies is associated with symptomatic Bordetella pertussis infection in a novel controlled human infection model

Background The association between functional antibody responses following Bordetella pertussis infection and symptomatic disease remains unclear. We characterized the maturation of anti-pertussis toxin (PT) IgG avidity after human challenge with B. pertussis and determined its association with symptomatic infection. Methods Healthy adults were intranasally inoculated with live B. pertussis organisms in a controlled human infection model and monitored for development of pertussis symptoms (NCT05136599). Serum samples were collected one day before inoculation and at 14, 28, 56, 180, and 365 days post challenge. Anti PT IgG avidity was tested using a titration of ammonium isothiocyanate (the bond breaking agent) to quantify a wide range of antibody avidities from low to very-high. Associations between covariates and avidity were examined using linear regression models, and high dimensional analyses were used to integrate all data. Findings Anti PT IgG avidity increased in both symptomatic (n=20) and asymptomatic (n=10) participants after the challenge, reached maximum levels at day 56, and then declined through day 365. Symptomatic participants developed significantly higher levels of high- and very high-avidity anti-PT antibodies at 28, 56, 180, and 365 days post-challenge compared with those who remained asymptomatic. In multivariate analyses, symptomatic infection was associated with higher levels of high and very high avidity anti-PT IgG at day180 and365 after challenge. Distinct avidity profiles in symptomatic vs asymptomatic participants emerged at day28 onwards, with the former group having higher levels of antibodies with higher avidities. However, levels of medium-high, high and very high avidity antibodies in symptomatic participants were lower at day 365 after challenge compared to their peak levels. Interpretation Anti-PT IgG avidity was associated with symptomatic B. pertussis infection and thus may serve as a surrogate of clinical disease outcome. These results highlight that antibody avidity provides an additional functional assay besides antibody quantitation to dissect immune responses to pertussis. Further investigation of anti PT IgG avidity should be pursued in natural pertussis outbreaks to determine whether it might be used to differentiate symptomatic from asymptomatic infections for epidemiologic purposes.

21.
arXiv (CS.AI) 2026-06-11

The Art of Interrogation: Consistency Amplifies Factuality in Spatial Reasoning

arXiv:2606.11918v1 Announce Type: new Abstract: Current Large Reasoning Models (LRMs) exhibit remarkable general capabilities but significantly underperform in spatial reasoning tasks. Existing approaches treat this gap as a knowledge deficit, relying on supervised fine-tuning (SFT) to ingest labeled spatial data from external vision sources or synthetic engines. In contrast, we argue that for many tasks, spatial reasoning capabilities are already present in pre-trained LRMs but require alignment through logical coherence under geometric 2D and 3D constraints. In this work, we propose a self-supervised reinforcement learning (RL) framework that targets the internal reasoning process without requiring ground-truth annotations. By formalizing the notion of consistency verifiers – reward functions that check for geometric and semantic consistency under transformations – we demonstrate that models can improve their spatial reasoning abilities. We use both image transformations, like flipping, and textual transformations, like swapping the order of objects in the question, and propose a new optimal transport-based RL strategy, OT-GRPO, which is a minimal-matching variant of group relative policy optimization tailored to pairwise verifiers. We show that this label-free consistency training approaches the accuracy of models trained with ground-truth supervision and achieves similar generalization across diverse tasks and data domains.

22.
arXiv (CS.CL) 2026-06-12

Does AI Reviewer See the Full Picture? Attacking and Defending Multimodal Peer Review

The integration of Large Language Models (LLMs) and Multimodal LLMs (MLLMs) into scientific peer-review workflows introduces novel and significant risks for adversarial manipulation, especially given the multimodal nature of scientific papers where figures, not just text, convey core evidence. This creates a significant gap: current robustness studies on AI peer-review are overwhelmingly text-only. Moreover, the problem is distinct from standard jailbreaking, as a peer-review attack seeks to induce a domain-specific, targeted failure (e.g., "inflate this score") rather than a general safety policy violation, for which no practical defenses exist. To address this, we introduce PaperGuard, the first comprehensive benchmark designed to systematically evaluate and defend AI-generated peer-review against these domain-specific, cross-modal attacks. Our framework is built on three pillars: (1) a new multimodal peer-review dataset spanning multiple scientific domains; (2) a unified suite of attacks, including black-box prompt injections and white-box perturbations, specifically designed to target both text (GCG) and figures (PGD); and (3) a practical defense, motivated by the long-context challenge of academic papers, that uses chunk-based embedding search to efficiently localize and mitigate harmful instructions. Our extensive experiments, conducted across state-of-the-art models, confirm that AI reviewers are pervasively vulnerable. PaperGuard establishes the foundational benchmark, protocols, and actionable defense necessary to pioneer trustworthy, attack-resilient AI-assisted scholarly reviewing.

23.
bioRxiv (Bioinfo) 2026-06-24

RNabel-A Standalone Software Tool for Annotating Tandem Mass Spectra of Modified Ribonucleic Acids

Ribonucleic acid (RNA) modifications, with over 170 identified types, play diverse roles in cellular processes. The past decade has witnessed surging demand for accurate identification and localization of RNA modifications in both endogenous and synthetic therapeutic RNAs. With accurate spectral annotation for RNA, tandem mass spectrometry (MS/MS) can meet this demand. Here we present RNabel, a user-friendly software tool for in-depth annotation of MS/MS spectra of RNA oligonucleotides. RNabel considers a full set of backbone-cleavage ions (a, b, c, d, a-B, w, x, y, z) in which the ribonucleotide unit could be A, U, C, G, Y (pseudouridine), or I (Inosine). Additionally, RNabel considers 196 modifications on the base, the phosphoribose linkage, the 5' or the 3' terminus, or detachment of a sub-nucleotide fragment as a neutral or charged group. Users can create new components if needed, including ribonucleotides, modifications, neutral or charged groups that could detach from a ribonucleotide. RNabel efficiently processes large datasets in four acceptable formats including .mgf, .raw, .txt from msConvert, and RNabel batch files. Multiple statistical metrics are provided for quality assessment of spectral annotation. To accelerate RNA modification analysis, RNabel is made freely available for Mac and Windows users at https://github.com/songge1111/RNabel/releases.

24.
Nature (Science) 2026-06-19

Daily briefing: Human detritus remakes geology

Authors:

What, exactly, is a rock? Plus, a stem-cell success for a severe autoimmune disease and evidence that ‘AI deskilling’ is real. Researchers have tracked the electrical activity of individual brain cells during conversation in real time. Plus, the history of GPS and a cross-species transplant that could reveal clues about the origin of animals.

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

Consistent Evaluation of Operators Involving the Position Operator in the Bloch Representation: Application to the Orbital Moment

arXiv:2606.11679v1 Announce Type: cross Abstract: The position operator plays a central role in condensed-matter observables such as velocity, orbital moment, and electric polarization. In solid-state physics, the evaluation of operators incorporating the position operator has not reached a consensus, as observed in the operator-level discrepancy between the local circulation of Wannier functions and the self-rotation of wave packets. Here, to achieve a consistent evaluation of such operators, we propose three rules for evaluating operators involving the position operator in the Bloch representation. The rules are devised to satisfy physical conditions: independence from the choice of unit cell, preservation of Hermitian conjugacy for the product of operators, and recovery of the correct intraband velocity. We further address the gauge dependence of the position operator and introduce a scheme termed gauge filtration, which systematically removes gauge-dependent contributions from the operators containing the position operator. This methodology ensures that the quantities obtained from the operator evaluation correspond to observable physical phenomena. By applying our framework, we reconcile the results concerning the self-rotation of the wave packet and the local circulation of the Wannier function. We expect our proposal to establish a consistent framework for evaluating operators involving the position operator.