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01.
arXiv (CS.CL) 2026-06-15

Does the Judge Prefer English? Evaluating Language-Switching Invariance in LLM-as-a-Judge

Authors:

Large language models (LLMs) are now widely used as automatic judges for open-ended instruction-following evaluation. This practice is convenient, scalable, and often more semantically aware than reference-based metrics, but it also introduces a new reliability question: does a judge evaluate the quality of an answer, or does it also react to the language in which the comparison is presented? We propose Judge-LS, a lightweight meta-evaluation protocol that transforms LLMBar response-pair items into English, Chinese, and Chinese-English language-switched variants. A reliable judge should preserve its preference under label-preserving language transformations and should not prefer a language when two answers are translation-equivalent. We evaluate four API-accessible judges on the full 419-item LLMBar benchmark, producing 13,408 successful pairwise judgments. Across models, Chinese and language-switched presentations induce 10.7–14.4% preference flips relative to English, and all judges achieve their highest accuracy in English. However, translation-equivalent tie probes do not reveal a systematic English preference: most probes are judged as ties, and non-tie decisions more often favor Chinese. We add confidence intervals, paired significance tests, and an automatic transformation audit with a sensitivity analysis that excludes mechanically flagged high-risk variants. The experiment requires no model training, uses only API calls, and is feasible on modest local hardware.

02.
arXiv (CS.LG) 2026-06-24

Forget Without Compromise: Nexus Sampling for Streaming KV-Cache Eviction Under Fixed Budgets

arXiv:2606.23961v1 Announce Type: new Abstract: Long-context and agentic LLM workloads push the KV cache past any fixed memory budget, forcing the inference stack to permanently evict tokens at every step of a continuous-inference stream. Existing methods all share the same template, a per-step direct-attention score followed by deterministic top-$K$ selection, which converts a single below-cutoff step into an irreversible verdict and permanently erases any subtly important token that direct attention cannot single out from noise. To address this challenge, we propose Nexus Sampling, a training-free eviction method that pairs Nexus scoring, an iterative walk over direct attention that surfaces bridge tokens, with weighted reservoir sampling, which retains tokens with inclusion probability in place of deterministic top-$K$. Theoretically, we show that Nexus Sampling dominates deterministic top-$K$ in long-run survival of subtly important tokens. Empirically, at 80% KV cache eviction, Nexus Sampling matches dense attention within 1% on LongBench while outperforming top-$K$ baselines on retrieval-heavy tasks, with up to 10x smaller per-sequence cache memory.

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

MMDiff: Extending Diffusion Transformers for Multi-Modal Generation

Diffusion transformers have demonstrated remarkable generative capabilities, yet the rich perceptual representations computed across their denoising trajectory are discarded once the content is rendered. We present MMDiff, a framework that transforms a frozen diffusion transformer into a multi-modal generative system that jointly produces images alongside any combination of dense perceptual modalities using lightweight decoder heads. Our central finding is that perceptual information is temporally distributed along the denoising trajectory, and that multi-timestep feature fusion with spatially varying aggregation weights is essential, improving semantic segmentation results by up to 28.7% mIoU over single-timestep extraction. We further adopt concept-driven attention extraction for interpretable spatial guidance, and show that frozen diffusion features are competitive with and complementary to state-of-the-art encoders such as DINOv3. By training only lightweight decoder heads on a frozen backbone, we achieve strong performance in semantic segmentation, salient object detection, and depth estimation, and demonstrate that this framework enables effective synthetic data generation at scale.

04.
arXiv (CS.LG) 2026-06-15

A theoretical model for task routing in mixture-of-expert transformers

arXiv:2606.14398v1 Announce Type: new Abstract: Mixture-of-experts (MoE) layers enable the scaling of transformer models while keeping the inference compute fixed. While task-expert specialization has been observed in empirical studies of frontier MoE transformer models, existing theoretical work analyzes this using continuous mixture models that cannot be used to model natural language effectively. An important open question is to theoretically explain task-expert specialization in transformer MoE models using discrete models of language. To address this, we represent structured knowledge via syntactic templates and finite key-value dictionaries, and prove formally that a single-layer MoE transformer can encode knowledge by using experts that specialize in the corresponding tasks. Our construction shows how queries are routed to unique, task-specific experts whose size depends solely on the intrinsic complexity of the given task (i.e. the combined size of its syntactic templates and factual dictionary). Our construction provides a theoretical support for empirical results on localized knowledge circuits in MoE models. We support our theoretical findings with experiments evaluating model performance under varying MoE loss functions.

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

A Multi-level Analysis of Factors Associated with Student Performance: A Machine Learning Approach to the SAEB Microdata

arXiv:2510.22266v3 Announce Type: replace-cross Abstract: Identifying the factors that influence student performance in basic education is a central challenge for formulating effective public policies in Brazil. This study introduces a multi-level machine learning approach to classify the proficiency of 9th-grade and high school students using microdata from the System of Assessment of Basic Education (SAEB). Our model uniquely integrates four data sources: student socioeconomic characteristics, teacher professional profiles, school indicators, and principal management profiles. A comparative analysis of four ensemble algorithms confirmed the superiority of a Random Forest model, which achieved 90.2% accuracy and an Area Under the Curve (AUC) of 96.7%. To move beyond prediction, we applied Explainable AI (XAI) using SHAP, which revealed that the school's average socioeconomic level is the most dominant predictor, demonstrating that systemic factors have a greater impact than individual characteristics in isolation. The primary conclusion is that academic performance is a systemic phenomenon deeply tied to the school's ecosystem. This study provides a data-driven, interpretable tool to inform policies aimed at promoting educational equity by addressing disparities between schools.

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

Data-Driven Dynamic Assortment in Online Platforms: Learning about Two Sides

arXiv:2606.11118v2 Announce Type: replace Abstract: We study a dynamic assortment problem on a two-sided service platform with incomplete information and heterogeneous customers in a discrete-time setting. In each period, a customer arrives seeking service, and the platform chooses an assortment of sellers to display. The customer then proposes a transaction to at most one seller in the assortment according to a multinomial logit choice model. After a fixed number of periods, sellers review the proposals they have received and each chooses at most one customer according to another multinomial logit choice model, after which the cycle repeats. A key challenge is that the platform does not know the choice-model parameters of either customers or sellers in advance. To our knowledge, this is the first study of a dynamic assortment problem in which both sides' choice parameters are unknown. We develop a data-driven algorithm that learns these parameters while optimizing the platform's objective over time. We evaluate performance using regret, which measures revenue loss relative to a clairvoyant benchmark that knows all parameters and customer arrivals in advance. We show that the algorithm's worst-case regret grows polylogarithmically over time, and we derive a matching lower bound, establishing its rate optimality.

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

OnDeFog: Online Decision Transformer under Frame Dropping

arXiv:2606.19721v1 Announce Type: cross Abstract: In challenging real-world reinforcement learning applications, communication delays or sensor failures often cause frame dropping, in which the agent cannot receive the dropped states and associated rewards. To address the performance degradation caused by frame dropping, the Decision Transformer under Random Frame Dropping (DeFog) was developed by incorporating additional mechanisms into the decision transformer to tackle frame dropping. Although DeFog can mitigate performance degradation in frame-dropping environments, since DeFog is an offline learning method, it struggles to effectively generalize to novel states not adequately represented in the training dataset. In this study, we propose OnDeFog, which integrates the mechanisms in DeFog with the online decision transformer (ODT), an online reinforcement learning method that learns policies through direct environmental interaction. Comprehensive experimental evaluation demonstrates that our proposed OnDeFog achieves superior performance compared to ODT in environments characterized by high dropping frame rate and outperforms DeFog on datasets containing a large amount of low-reward data.

08.
Nature Biotechnology 2026-06-19

Optimized R2 retroelement complexes for DNA insertion into plant genomes

Traditional approaches for DNA insertion into plant genomes using Agrobacterium tumefaciens result in random integration. Newer genetic engineering methods based on nucleases, prime editors, transposases and recombinases extend capabilities but remain constrained with low efficiencies, off-target integration or limited payload size. Here we adapt the avian Taeniopygia guttata R2 protein (R2Tg) for targeted DNA insertion into plant genomes by engineering R2Tg expression cassettes and RNA payloads carrying intron-disrupted reporters, with optimized ribosomal DNA homology arms and untranslated regions. In Arabidopsis thaliana protoplasts, Nicotiana benthamiana leaves and Solanum lycopersicum seedlings, our R2Tg editor system achieves targeted insertion of full-length payloads ranging from 2.2 kb to 5 kb. In Nicotiana benthamiana leaves, integration occurs, on average, at 1 copy per genome, which is 30 times more efficient than that achieved by Cas9 homology-directed repair. This work establishes an R2Tg ribonucleoprotein platform for targeted DNA insertion into plant genomes, using a multicopy genomic safe-harbor site to enable efficient addition of multikilobase genes. R2 retrotransposons are used to integrate DNA into plant and crop 25S ribosomal DNA sites.

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

Sustainability assessment using multimodal AI agents

arXiv:2507.17012v2 Announce Type: replace Abstract: Reducing the rapidly growing environmental impact of the computing industry requires assessing the emissions of electronics at scale. However, a traditional life cycle assessment (LCA) of an electronic device, which maps materials and processes to environmental impacts, often requires proprietary or unavailable data. Here, we reimagine conventional sustainability assessment by introducing a multimodal multi-agent AI system that emulates the collaborative process between LCA professionals and stakeholders (such as product managers and engineers) to automatically estimate the carbon footprint of electronic devices. The agents iteratively construct a complete life-cycle inventory by leveraging a structured data abstraction and software tools that mine information from the public internet, including repair communities and government regulatory databases. This reduces data gaps and data collection from weeks or months of expert time to under one minute. The system can calculate carbon footprint within 19% of expert LCAs with zero proprietary data (typical of the variation between human LCAs). We also show that by encoding domain-specific knowledge, environmental impact estimation can be reframed as a data-driven prediction task, in which both unknown products and emission factors are represented as weighted combinations of similar ones with known emissions.

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

Smoothness Errors in Dynamics Models and How to Avoid Them

arXiv:2602.05352v3 Announce Type: replace Abstract: Modern neural networks have shown promise for solving partial differential equations over surfaces, often by discretizing the surface as a mesh and learning with a mesh-aware graph neural network. However, graph neural networks suffer from oversmoothing, where a node's features become increasingly similar to those of its neighbors. Unitary graph convolutions, which are mathematically constrained to preserve smoothness, have been proposed to address this issue. Despite this, in many physical systems, such as diffusion processes, smoothness naturally increases and unitarity may be overconstraining. In this paper, we systematically study the smoothing effects of different GNNs for dynamics modeling and prove that unitary convolutions hurt performance for such tasks. We propose relaxed unitary convolutions that balance smoothness preservation with the natural smoothing required for physical systems. We also generalize unitary and relaxed unitary convolutions from graphs to meshes. In experiments on PDEs such as the heat and wave equations over complex meshes and on weather forecasting, we find that our method outperforms several strong baselines, including mesh-aware transformers and equivariant neural networks.

11.
arXiv (CS.AI) 2026-06-16

HCP-MAD:Heterogeneous Consensus-Progressive Reasoning for Efficient Multi-Agent Debate

arXiv:2604.09679v2 Announce Type: replace-cross Abstract: Multi-Agent Debate (MAD) is a collaborative framework in which multiple agents iteratively refine solutions through the generation of reasoning and alternating critique cycles. Current work primarily optimizes intra-round topologies and inter-round interactions separately, limiting the adaptation of token costs to task complexity. This work introduces Heterogeneous Consensus-Progressive Reasoning for Efficient Multi-Agent Debate (HCP-MAD), leveraging consensus as a dynamic signal to facilitate progressive reasoning. The core motivation is that a majority of straightforward tasks can be effectively resolved via lightweight pair-agent debates, while complex tasks require expanded collaboration. Firstly, Heterogeneous Consensus Verification conducts rapid consensus verification using a pair of heterogeneous agents for early stopping. Next, Heterogeneous Pair-Agent Debate applies an adaptive stopping criterion to terminate mutual critique of reasoning traces. Finally, the unresolved tasks are addressed through Escalated Collective Voting by aggregating diverse perspectives from additional agents. Experiments across six benchmarks show that HCP-MAD enhances accuracy while substantially reducing token costs. Code is https://github.com/fuyu66/HCP-MAD.

12.
arXiv (CS.CV) 2026-06-11

PIGEON: VLM-Driven Object Navigation via Points of Interest Selection

Object navigation in unseen indoor environments requires agents to perform semantic search under partial observability. Vision-language models (VLMs) provide strong semantic-spatial priors for this task, but how to interface them with robot navigation remains challenging: dense VLM inference is expensive, while abstracting environments into symbolic memories often separates high-level reasoning from the raw visual evidence that supports it. We propose we propose PIGEON (Point of Interest Guided Exploration for Object Navigation), a VLM-driven framework that formulates object navigation as raw-observation-grounded sparse decision problem. PIGEON introduces Points of Interest (PoIs) as sparse visual decision units that couple geometrically executable waypoints with raw egocentric observations. Rather than using VLMs as dense controllers or restricting them to frontier ranking, PIGEON enables VLMs to select among task-critical PoIs, including exploration frontiers, suspected target objects, traversable stairs, and floor-level summaries, while low-level planners execute continuous motion between them. This PoI interface further makes high-level navigation decisions verifiable, allowing us to develop an RLVR pipeline that improves local VLMs without manual Chain-of-Thought annotations. Extensive experiments on Habitat ObjectNav benchmarks show that PIGEON achieves state-of-the-art zero-shot performance, scales consistently with foundation model capacity, and transfers to Active Embodied Question Answering with only prompt modifications. Real-world deployments on physical robots further demonstrate its robustness and efficiency.

13.
arXiv (quant-ph) 2026-06-19

Universality in Ionic Three-body Systems Near an Ion-atom Feshbach Resonance

arXiv:2511.00325v3 Announce Type: replace-cross Abstract: We calculate bound and scattering properties of a system of two neutral atoms and an ion near an atom-ion Feshbach resonance. Our results indicate that long-range atom-ion interactions lead to significant deviations from universal behavior derived from contact or van der Waals potentials. We find that ionic systems display an overall suppression of inelastic transitions leading to recombination rates and lifetimes of Efimov state orders of magnitude smaller with respect to those for neutral atoms. We further characterize the dense spectra of triatomic molecular ions with extended lifetimes. Our results provide a deeper insight on the universality and structure of three-body ionic systems and establishing them as a promising platform for exploring novel few- and many-body phenomena with long-range interactions.

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

SCR-Guided Difficulty-Aware Optimization for Infrared Small Target Detection

Infrared small target detection remains challenging due to severe background clutter, low contrast, and weak spatial responses where geometric overlap alone is insufficient to characterize detection quality. In this work, we propose REEM (Reweighted Explicit-visibility Enhanced Modulation), a lightweight SCR-guided difficulty-aware optimization framework that incorporates Signal-to-Clutter Ratio (SCR) as a physically meaningful visibility prior during training. Instead of modifying the network architecture or directly optimizing SCR, REEM computes a ground-truth local SCR from the input image and applies a differentiable modulation to the soft-IoU learning signal, emphasizing low-visibility targets while preserving stable optimization and identical inference behavior. REEM is integrated into a U-Net-based MSHNet without introducing additional parameters, architectural modifications, or inference-time overhead. Extensive experiments demonstrate consistent improvements over the baseline, achieving higher IoU and detection probability (Pd) together with substantially reduced false alarms (FA), particularly under challenging low-visibility conditions. These results suggest that SCR-guided difficulty-aware optimization provides an effective and physically grounded complement to conventional overlap-based objectives for infrared small target detection. The code is available at https://github. com/yall-in-one/Reemm.

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

Dual-Granularity Orthogonal Disentanglement for Generalizable Audio Deepfake Detection

arXiv:2606.16532v1 Announce Type: cross Abstract: Audio deepfake detectors often fail to generalize across speakers, as they learn speaker-identity features rather than synthesis artifacts, known as implicit identity leakage. Existing methods address this but incur architectural complexity or training instability. This paper proposes a dual-granularity orthogonal disentanglement framework enforcing feature independence at two levels: sample-level cosine orthogonality captures directional decorrelation, while batch-level cross-covariance regularization eliminates linear correlations across embedding dimensions. A curriculum disentanglement schedule progressively strengthens the orthogonality constraint without auxiliary networks or adversarial dynamics. Experiments on ASVspoof 2019 LA, ASVspoof 2021 DF, and In-the-Wild datasets demonstrate that the proposed method achieves 1.35%, 7.88%, and 21.58% equal error rates (EER), respectively, surpassing gradient reversal disentanglement by 2.60% absolute on cross-dataset transfer.

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

Multi-entropy in heavy local quenches

arXiv:2606.12526v1 Announce Type: cross Abstract: We study the time evolution of tripartite entanglement in heavy local quenches in two-dimensional holographic conformal field theories. Our diagnostic is the genuine multi-entropy of adjacent intervals, computed from both bulk and boundary perspectives. A perturbative bulk analysis shows that the first-order small-mass perturbation around the vacuum geodesic network cancels identically at any time after the quench. In the fully back-reacted geometry, a vacuum-subtracted genuine multi-entropy arises from a mismatch between the winding selected by the trivalent geodesic network and the windings selected independently by the pairwise geodesics. In the sharp quench limit, the time dependence of genuine multi-entropy is kinematically fixed to logarithms of rational functions of time and is independent of the heavy operator dimension. The CFT calculation reproduces the same formula within the heavy-light vacuum block approximation, where the branch choice in the heavy-background uniformization map corresponds to the winding selection in the bulk. These results indicate that, in this setup, the genuine multi-entropy is controlled by global saddle selection, rather than by a local energy response or quasiparticle propagation.

17.
arXiv (CS.CL) 2026-06-18

Beyond Tokenization: Direct Timestep Embedding and Contrastive Alignment for Time-Series Question Answering

Recent advances in large language models (LLMs) have given rise to time-series question answering (TSQA), which formulates time-series analysis as natural-language question answering. However, directly feeding raw numerical series into LLMs suffers from a tokenization bottleneck: Byte Pair Encoding fragments continuous values into unstable tokens whose embeddings lack meaningful metric structure, resulting in the loss of magnitude, scale, and trend information. Prior methods use patch-based encoders that split the series into fixed windows, locking in one granularity that breaks patterns and hides exact timesteps, through a separate module that rarely transfers across datasets with different lengths or sampling rates. To address this challenge, we propose CADE (Contrastive Alignment with Direct Embedding), a novel framework for TSQA built upon two key components: direct timestep embedding and semantic alignment. The proposed framework maps each timestep directly into the LLM embedding space through a point-wise linear encoder and MLP projector, preserving exact index-level access while eliminating the need for patching and padding. To further bridge the semantic gap between time-series and language representations, we introduce a novel one-directional supervised contrastive loss that aligns time-series embeddings with frozen class-name text anchors. Experimental results on the public Time-MQA benchmark demonstrate that our framework consistently improves performance across six TSQA tasks, outperforming both open-source and proprietary LLM baselines.

18.
arXiv (CS.AI) 2026-06-24

Synergizing Physically Constrained MCMC and Chemical-Informed Gaussian Processes for Reaction Network Discovery

arXiv:2606.23757v1 Announce Type: cross Abstract: Extracting interpretable governing equations from sparse, noisy chemical time-series data remains difficult because discrete reaction topology and continuous kinetic parameters are tightly coupled. We present PC-MCMC-CIGP, a reproducible gray-box workflow that combines spike-and-slab topology sampling, hard conservation and thermodynamic screening, and a Chemical-Informed Gaussian Process (CIGP) residual model for parameter calibration and experimental design. The methodological contribution is not a new MCMC or GP family in isolation; rather, it is the integration of these components into a physically constrained workflow with explicit uncertainty-aware acquisition choices. On the H2 + Br2 benchmark, the constrained sampler distinguishes elementary radical pathways from deceptive phenomenological fits in our experiments. On styrene epoxidation, the CIGP optimization loop improves final yield by 12.5% over the reported GP-BO baseline. A new 10-seed acquisition study shows that EI, GWU, PC-EI, uncertainty sampling, discrepancy hunting, and random search have different trade-offs: PC-EI substantially reduces low-yield BO suggestions, while EI-style criteria give the strongest final-yield performance.

19.
arXiv (CS.LG) 2026-06-16

A Comparative Study of Graph Neural Network Layer Selection for Interaction Modelling in Driving Trajectory Prediction

arXiv:2606.14956v1 Announce Type: new Abstract: Autonomous driving systems rely on precise trajectory prediction to plan safe and efficient movement. Graph Neural Networks (GNNs) have become a promising approach for modelling spatiotemporal interactions among road agents. However, designing GNN architectures for trajectory prediction remains non-standardized, with little guidance on which graph layers effectively capture spatial interactions and temporal dynamics. This paper offers a detailed comparative study of 19 graph layer types, focusing on their spatial and temporal processing capabilities to discover the most effective architectures for trajectory prediction. Within the explored hyperparameter setting, we highlight five standout layer combinations, with ARMA, Chebyshev, and topology-aware layers consistently performing better than others. Beyond performance metrics, our findings yield practical design principles: sum-based aggregation is more effective than mean-based methods, multi-head attention mechanisms enable richer interactions, and assigning different weights to different hop distances significantly improves prediction accuracy. These findings offer useful guidance for designing more interpretable and effective trajectory prediction models.

20.
arXiv (CS.CV) 2026-06-19

VisDom: Sparse Novel View Synthesis with Visible Domain Constraint

Sparse novel view synthesis (NVS) remains challenging due to the ambiguity of recovering 3D geometry from few input views. While NeRF- and Gaussian Splatting (GS)-based methods perform well with dense supervision, they often overfit in sparse settings, producing floating artifacts and inconsistent geometry. Silhouette consistency is commonly used as a regularizer, but it remains insufficient, as silhouette-consistent regions can extend beyond the true object geometry. We introduce VisDom, a learning-free geometric constraint that augments classical carving-based visual hull reconstruction by enforcing a minimum multi-view visibility requirement. Specifically, we define a visible domain as the subset of 3D space observed by at least $K$ views and use it as an additional filtering criterion on top of standard silhouette-based reconstruction. This provides a stronger spatial prior in sparse-view settings. We integrate VisDom into both implicit (NeRF) and explicit (GS) pipelines by restricting volumetric sampling and guiding Gaussian placement during optimization. Experiments on three challenging datasets show consistent improvements in sparse-view NVS, enabling high-quality object-centric reconstruction from as few as four input images. Our method is domain-agnostic, requires only silhouettes, and introduces no learned parameters, making it a simple complement to existing approaches. Applying VisDom on top of GaussianObject further improves performance on Omni3D and MipNeRF360, while matching or surpassing it at 22 $\times$ lower training cost.

21.
arXiv (CS.LG) 2026-06-24

The Cost Geometry of Belief: finite-resource inference under noisy observation

arXiv:2606.21585v2 Announce Type: replace Abstract: A finite machine's digital twin of a system observes the territory through finite, noisy sensors; we model its coherent output as a belief, a probability density over states, the Bayes posterior, never a point. Certainty, the perfect twin, is denied twice, by observation and by physics, both read off the Fisher information. To make this finiteness geometric, we model what it costs to change a belief: a belief-cost geometry, optimal transport in Wasserstein space reweighted conformally by Fisher information. The framework rests on two posed commitments: that revision cost is a scalar price on transport (the arena), and that the price is honest: one nat costs the same length everywhere. Honesty selects the Fisher reweighting because transport demotes the Fisher information from the metric ruler of distinguishability to the slope of entropy, the move that sets transport apart from Fisher-Rao. From these two postulates, three results follow on the conformal class (essentially location-scale), all invariants of one change of cost unit. A wall: a well-posed inference rejects certainty to infinite distance as soon as the cost dominates the Fisher information (necessity conjectured beyond power laws). An honest family: the eikonal price where each nat the same length everywhere, is equivalent to proportionality U=cJ, the Fisher family. A rigidity: these geometries are hyperbolic, and the Stam bound crowns the Gaussian, the most hyperbolic location-scale belief; -1/4 is one image of a relativity of cost. The cost of reaching a given precision then has a geometric cost floor diverging at certainty. Thermodynamics fixes the cost unit and motivates the framework; the results are geometric, in nats.

22.
medRxiv (Medicine) 2026-06-23

Systemic and Mucosal Antibody Correlates of Protection Against Bordetella pertussis in a Controlled Human Infection Model

Abstract Background Despite high vaccination coverage, pertussis has resurged globally. Whole-cell (wP) and acellular (aP) pertussis vaccines induce distinct immune profiles, yet immune correlates of protection against infection and symptomatic disease remain incompletely defined. We leveraged a controlled human infection model (CHIM) to identify systemic and mucosal humoral signatures associated with resistance to Bordetella pertussis. Methods Adults with documented history of vaccination had previously been enrolled in a CHIM study and challenged intranasally with B. pertussis D420. For the present work, longitudinal serum and nasal wash samples were analyzed using systems serology to comprehensively profile antibody features. Multivariate modeling and network analyses were performed to define discriminatory immune features. Findings Baseline aP vaccine antigen-specific antibodies did not distinguish infection outcomes. In wP-primed individuals, protection from B. pertussis infection was associated with broad, high-magnitude, polyfunctional antibody responses targeting non-canonical antigens, including BrkA, TcfA, OmpP, OmlA, FauA, and Pal. Protective signatures associated with resistance to symptomatic disease in both vaccine groups were characterized by enhanced Fc-receptor-engaging antibody profiles with distinct antigenic patterns shaped by vaccine history. Importantly, while conventional aP vaccine antigens failed to reliably distinguish individuals susceptible to infection or symptom development, correlates generated by integrated serum and mucosal models based on select non-canonical antigens achieved near-perfect discrimination of infection and symptom outcomes, outperforming models restricted to aP-vaccine. antigens only. Interpretation Resistance to infection was largely restricted to wP-primed individuals and was associated with integrated systemic and mucosal antibody responses directed against antigens beyond those included in acellular vaccines. Protection from symptomatic disease in both vaccine groups was linked to distinct antibody response signatures, shaped by prior vaccination history. These findings indicate that immune mechanisms preventing infection differ from those limiting clinical disease and provide a framework for redesign of next-generation pertussis vaccines aimed at blocking infection and symptomatic disease.

23.
arXiv (quant-ph) 2026-06-19

Generating function and Bloch representation for quantum Fisher tensor

arXiv:2511.05260v2 Announce Type: replace Abstract: The Uhlmann relative amplitude between two density matrices is shown to be a generating function, through which the quantum Fisher tensor that contains both the quantum Fisher information matrix and the mean Uhlmann curvature can be obtained via differentiation over system parameters. In the pure state limit, our generating function recovers that of the quantum geometric tensor proposed by Het\'{e}nyi and L\'{e}vay, and also clarifies the fidelity and phase between two quantum states as the generating functions of the quantum metric and Berry curvature, respectively. A generic expression for the quantum Fisher tensor in terms of the Bloch representation of density matrices is derived, which facilitates the calculation of the tensor, mean Uhlmann curvature, and geometric properties derived from the quantum Fisher information matrix. Canonical ensembles of spins are adopted to demonstrate our formalism, which reveals a constant Ricci scalar, a vacuum Einstein equation, and a cosmological constant on the 3D Euclidean manifold of the magnetic field

24.
Science (Express) 2026-04-16

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase | Science

Authors: Unknown Author

Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo–electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.

25.
arXiv (CS.CV) 2026-06-16

An Adaptive Data cleaning Framework for Noisy Label Detection

Deep neural networks (DNNs) excel in computer vision tasks given large annotated datasets. In real-world applications, however, labels are often corrupted by ambiguity, human error, or dynamic environments. Over-parameterized DNNs easily memorize these noisy labels during training, degrading model accuracy and generalization. Existing data-cleaning and sample-selection strategies often rely on manually specified thresholds, prior knowledge of the noise ratio, or a single metric (either learning dynamics or geometric structure), making them unstable in complex data regimes. This paper proposes a self-adaptive data-cleaning framework that integrates local, global, and learning dynamics cues for robust noisy-label detection. Samples are mapped into a unified low-dimensional feature space through a modular feature concatenation paradigm. We provide two instantiations: a 2D metric integrating class-adaptive KNN-based local disagreement with k-means-based global centroid distance, and a 3D multi-metric that additionally incorporates a z-normalized score. Unlike conventional 1D Gaussian Mixture Models applied to a single scalar metric, our framework performs multi-metric clustering on the feature space to adaptively partition samples into clean-dominant and noise-dominant components without requiring manual thresholds or noise priors. Experiments on CIFAR-10, MNIST, and ImageNet-100 with 5% to 40% symmetric label noise show high recall across settings, including near-perfect recall (>=98%) on ImageNet-100 at 40% noise. Subsequent training yields accuracy gains across evaluated settings, especially under severe corruption on ImageNet-100. These findings suggest that multi-metric integration provides a threshold-free, practical, and low-tuning strategy for noisy label detection.