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

Quality-Preserving Imperceptible Adversarial Attack on Skeleton-based Human Action Recognition

Adversarial attacks on skeletal human action recognition have received significant attention. However, existing methods typically introduce noise-like perturbations that degrade motion quality post-attack, and thereby are inherently perceptible with recent advancements in S-HAR systems. We discover that this degradation stems from the gap between empirical and true risks during the optimization process of previous adversarial attacks. To address this issue, we propose an attack where adversarial motions are obtained without compromising their motion quality. To minimize the risk gap and preserve motion quality, we propose a distribution-based adversarial attack method without introducing noise-like perturbations. To faithfully evaluate the motion quality, we propose a new metric that aligns with human perception on real-world naturalness. Experiments have been conducted on the state-of-the-art S-HAR methods across two datasets, demonstrating the superiority of our method in both the attack success rate and the post-attack motion quality through qualitative and quantitative analyses. The success of our quality-preserving attack application and distribution-based method raises serious concerns about the robustness of action recognizers, highlighting the need for further enhancements in this domain.

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

Physics-informed generative AI for semiconductor manufacturing: Enforcing hard physical constraints in generative models by construction

arXiv:2606.11247v1 Announce Type: cross Abstract: Generative models are increasingly used to propose designs, data, and control actions for physical systems, yet many such systems are governed by hard physical constraints rather than by perceptual plausibility. Semiconductor manufacturing provides a demanding test case: generated masks, layouts, synthetic defect data, and process recipes must obey lithography, transport, reaction, and device-physics constraints, because physically invalid samples are not merely low quality but unusable. This Perspective argues that semiconductor manufacturing exposes a broader computational-science challenge, namely that generative AI for constrained physical domains must be physics-informed by construction, not corrected only through post-hoc filtering. We survey the emerging architectural toolkit, including physics-informed diffusion, PDE-constrained variational models, neural-operator priors, and conservation-law-respecting generative networks, and show how it connects to differentiable lithography, TCAD, process simulation, and autonomous experimentation. We identify four integration patterns between generative models and physics-based simulators, and we propose a research agenda centered on physics-fidelity benchmarks, differentiable simulator infrastructure, and multimodal foundation models for physical design and manufacturing. The central claim is analytical rather than rhetorical: where physical validity is the binding criterion of success, architectures that enforce it by construction should be expected to outperform those that filter for it after the fact, and the fab is the setting where this distinction is sharpest.

03.
arXiv (quant-ph) 2026-06-17

Unclonable Encryption in the Haar Random Oracle Model

arXiv:2603.11437v2 Announce Type: replace-cross Abstract: We construct unclonable encryption (UE) in the Haar random oracle model, where all parties have query access to $U,U^\dagger,U^*,U^T$ for a Haar random unitary $U$. Our scheme satisfies the standard notion of unclonable indistinguishability security, supports reuse of the secret key, and can encrypt arbitrary-length messages. That is, we give the first evidence that (reusable) UE, which requires computational assumptions, exists in "microcrypt", a world where one-way functions may not exist. As one of our central technical contributions, we build on the recently introduced path recording framework to prove a natural ``unitary reprogramming lemma'', which may be of independent interest.

04.
medRxiv (Medicine) 2026-06-11

Beyond External Load: Integrative Immune Monitoring Reveals Injury-Predictive Signals in the Athlete's Internal State

Abstract (already in the PDF; paste if a box is required): Injury risk prediction in elite football relies almost exclusively on external load metrics derived from GPS tracking, overlooking the molecular state of the athlete. We monitored 26 male players from FC Barcelona's first team across the 2025 calendar year, integrating GPS-derived training load with longitudinal blood-based immune monitoring (systemic inflammation and TCR-derived immune age). Immune age acceleration and inflammation were elevated in the 14 days preceding musculoskeletal injuries. A logistic regression model combining external load, inflammation, immune age acceleration, and career injury history reached an overall AUC of 0.678 and a mean per-player AUC of 0.754 (SD 0.146), improving on a GPS-only baseline of 0.541. Applied to 2026 data, the frozen model ranked players who later sustained non-contact musculoskeletal injuries high in the risk distribution. Together, our data suggest multimodal immune monitoring in elite football to reveal the athlete's internal physiological state, which carries injury-relevant information that external load alone does not capture.

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

Evaluation Sovereignty in Metadata-Driven Classification: A Multi-Track Framework for Weakly Supervised Information Systems

arXiv:2606.13436v1 Announce Type: new Abstract: Evaluation in machine learning is typically treated as a neutral measurement process. However, in operational information systems, evaluation outcomes are often conditioned by the processes used to generate labels. This paper does not seek to improve classification performance. Instead, it examines the validity of performance measurement under differing label-authority regimes. This issue is particularly relevant in large-scale metadata-driven systems, where labels are often incomplete, inconsistent, or weakly supervised. We introduce evaluation sovereignty, defined as the degree to which performance metrics are independent of label authority and supervision regime, and propose a multi-track evaluation framework that systematically varies training and evaluation label sources. Using hierarchical multi-label classification on large-scale scientific metadata, we demonstrate that models exhibiting strong performance under operational ("silver") evaluation degrade substantially under independent ("gold") evaluation, particularly for fine-grained classification. For example, Micro-F1 decreases from approximately 0.54 to 0.03. Notably, ranking-based metrics remain above baseline, revealing a divergence between latent model signal and classification validity. These findings suggest that commonly reported performance metrics may reflect alignment with labeling processes rather than true predictive capability. We therefore reconceptualize evaluation validity as a system-level property shaped by label governance and provide a practical methodology for auditing intelligent systems operating under weak supervision.

06.
medRxiv (Medicine) 2026-06-10

A risk-of-contagion index using a Bayesian based model for the COVID-19 epidemic in Mexico

During the COVID-19 pandemic, limited testing capacity and reporting delays complicated epidemic surveillance and decision-making in Mexico. We calibrated textit{covidestim}, a Bayesian nowcasting model, to estimate the total SARS-CoV-2 infections from reported cases and deaths using Mexican surveillance data. Disease-progression distribution priors were calibrated using Mexico City records and validated through comparisons with national seroprevalence surveys, hospitalization data, and annual reported severe-case rates across all states. Using the reconstructed estimates of active infections, we implemented an event-based risk framework that quantifies the probability of encountering at least one infectious individual in gatherings of different sizes. This probability was subsequently translated into a four-level epidemiological traffic-light indicator and computed at both state and municipality levels. The resulting estimates revealed substantial spatial heterogeneity that is obscured by state-level aggregation, particularly in states with marked differences between urban and rural municipalities. To evaluate consistency with public-health indicators, we compared the proposed risk classification with the official Mexican epidemiological traffic-light system, considering interpretable gathering sizes relevant to public-health decision making. Weekly reports derived from this framework were delivered to policymakers in the State of Queretaro in Mexico, as an anticipation tool for school reopening and public-space management. This demonstrates that this Bayesian reconstruction of infections combined with event-based risk metrics can provide an interpretable and generalizable municipality-level complement to routine surveillance systems, particularly in regions with limited testing capacity and heterogeneous local transmission dynamics.

07.
arXiv (CS.CV) 2026-06-16

MVOFormer: Flow-Semantic Transformer for Robust Monocular Visual Odometry

Monocular visual odometry (MVO) is foundational to autonomous navigation and robotic localization. However, existing learning-based MVO approaches often struggle with either a lack of interpretable, complementary features or overly complex multi-stage architectures. These limitations inherently restrict their robustness and cross-domain generalization. In this work, we propose MVOFormer, a novel transformer framework for robust monocular visual odometry. Our architecture features a Flow-Semantic Dual Branch Encoder that synergizes dense geometric motion cues with object-centric semantic priors, explicitly distinguishing static structures from dynamic distractors. These representations are then fused by an Iterative Multimodal Decoder, enabling coarse-to-fine pose refinement while dynamically suppressing attention on unreliable regions. Extensive evaluations demonstrate that, without any target-domain fine-tuning, MVOFormer achieves superior zero-shot generalization and robustness, significantly outperforming prior learning-based frame-to-frame methods across diverse benchmarks including TartanAir, KITTI, TUM-RGBD, and ETH3D-SLAM.

08.
arXiv (CS.LG) 2026-06-16

Can Neural Networks Achieve Optimal Computational-statistical Tradeoff? An Analysis on Single-Index Model

arXiv:2606.15219v1 Announce Type: new Abstract: In this work, we tackle the following question: Can neural networks trained with gradient-based methods achieve the optimal computational-statistical tradeoff in learning Gaussian single-index models? Prior research has shown that any polynomial-time algorithm under the statistical query (SQ) framework requires $\Omega(d^{s^\star/2}\lor d)$ samples, where $s^\star$ is the generative exponent representing the intrinsic difficulty of learning the underlying model. However, it remains unknown whether neural networks can achieve this sample complexity. Inspired by prior techniques such as label transformation and landscape smoothing for learning single-index models, we propose a unified gradient-based algorithm for training a two-layer neural network in polynomial time. Our method is adaptable to a variety of loss and activation functions, covering a broad class of existing approaches. We show that our algorithm learns a feature representation that strongly aligns with the unknown signal $\theta^\star$, with sample complexity $\widetilde{O} (d^{s^\star/2} \lor d)$, matching the SQ lower bound up to a polylogarithmic factor for all generative exponents $s^\star\geq 1$. Furthermore, we extend our approach to the setting where $\theta^\star$ is $k$-sparse for $k = o(\sqrt{d})$ by introducing a novel weight perturbation technique that leverages the sparsity structure. We derive a corresponding SQ lower bound of order $\widetilde{\Omega}(k^{s^\star})$, matched by our method up to a polylogarithmic factor. Our framework, especially the weight perturbation technique, is of independent interest, and suggests potential gradient-based solutions to other problems such as sparse tensor PCA.

09.
arXiv (CS.CV) 2026-06-16

An Extensive Benchmark for Single-round and Multi-round Instruction-based Image Editing

In recent years, there have been notable advancements in the area of instruction-based image editing (IIE), which focuses on the automatic alteration of input images using a model. Nevertheless, assessing the effectiveness of these editing models poses a considerable challenge due to the intricate nature of instructions and the wide variety of edits. To tackle this problem, one urgent task in this domain is the development of a robust evaluation framework that can precisely gauge the quality of editing outcomes and offer valuable benchmarks to guide future improvements. To address this challenge, we present a comprehensive evaluation benchmark named I2EBench2.0, designed for single-round and multi-round assessment of IIE models. I2EBench2.0 has four key features: 1) Evaluation Across Single and Multi-rounds: I2EBench2.0 simultaneously evaluates both single-round and multi-round instruction-based edits, assessing the precision and consistency of the edits. 2) Extensive Evaluation Criteria: I2EBench2.0 encompasses a broad range of criteria, evaluating both high-level and low-level aspects of each IIE model. Specifically, it incorporates 16 dimensions for single-round evaluations and 7 for multi-round evaluations. 3) Alignment with Human Judgment: To ensure our benchmark aligns with human evaluation, we conducted a comprehensive user study for each criterion. 4) Research-driven Insights: By analyzing the strengths and weaknesses of current IIE models across all 16 single-round and 7 multi-round dimensions, we provide critical insights aimed at directing future research in this area. We tested eight recently developed IIE models using I2EBench2.0 and derived academic insights through meticulous comparison and analysis. The related code, dataset, and images generated by all IIE models are available on GitHub: https://github.com/cocoshe/I2EBench.

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

Unlocking Diffusion Hierarchies: Adaptive Timestep Selection for Zero-Shot Segmentation

Zero-shot segmentation has recently shown notable improvement by leveraging the rich visual priors in large-scale text-to-image diffusion models, such as Stable Diffusion. However, current diffusion-based methods often face limitations due to the trade-off between spatial resolution and contextual information, as well as their reliance on a single static timestep for feature extraction. To overcome these challenges, our work introduces two key advancements. First, our Contextual Similarity Maps fuse high-resolution attention maps with rich U-Net encoder features, providing both fine-grained and robust per-pixel representations. Second, we identify an emergent hierarchical semantic progression within the denoising process of various diffusion models: representations transition from part-level abstractions at earlier timesteps to object-level abstractions at later stages. Leveraging this insight, we introduce a mechanism to adaptively select the optimal timestep for each pixel. Extensive experiments demonstrate that our method consistently outperforms existing zero-shot segmentation baselines, validating the efficacy of combining contextual features with dynamic, hierarchical timestep selection.

12.
medRxiv (Medicine) 2026-06-23

Timing of S. aureus-related mortality in a large randomized clinical trial: Implications for future study design

Background: Longer follow-up periods in clinical trials for S. aureus bacteremia (SAB) may capture unrelated deaths, adding random noise that risks biasing trial results towards the null. Objective: To evaluate the timing and infection-relatedness of deaths within a large SAB clinical trial platform. Design: Blinded duplicate adjudication of trial deaths using a modified 7-point Likert-Scale. A third reviewer settled disagreements. Setting: 37 Canadian hospitals participating in the S. aureus Network Adaptive Platform (SNAP) Trial. Participants: 1515 adult patients recruited to SNAP between February 2022 and May 2026. Measurements: Timing and relatedness of 90-day deaths categorized as at least possibly SAB-related not likely to be SAB-related. Optimal follow-up cut-off was determined using Youden's index and graphically. Results: 247 deaths occurred; 97 (39.3%) were adjudicated as at least possibly SAB-related and 150 (60.7%) as not likely related. For probably/definitely related deaths, interrater agreement was 85.0% (Gwet's AC 0.73, substantial); for at least possibly related, it was 77.3% (Gwet's AC 0.55, moderate). Median survival was significantly shorter for SAB-related deaths (12 vs. 30.5 days; difference: 19 days earlier, 95% CI: 12-26, p

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

Bridging data-driven priors via the score function for posterior sampling – Comparative review and experimental study

arXiv:2606.14800v1 Announce Type: cross Abstract: This paper reviews how a diverse set of popular data-driven priors commonly used in Bayesian inverse problems can be unified through their respective score functions. By framing these priors under this common perspective, we show that they can benefit from their straightfoward and effective integration into a recently proposed sampling algorithm. The applicability of this common framework is illustrated by considering several data-driven priors, namely regularization-by-denoising, normalizing flow-based priors, score-based generative models, and convex-ridge regularizers. For these four particular priors, the performance of the method is evaluated when conducting image inpainting and single image super-resolution. These results, as well as those obtained when restoring real images acquired in a geological context, demonstrate the efficiency of the method. This unified framework proves versatile enough to handle any posterior distribution defined by a broad class of score function-based priors, beyond the specific cases considered in this paper.

14.
arXiv (CS.AI) 2026-06-12

Modern analog computing for solving differential and matrix equations

arXiv:2606.13179v1 Announce Type: cross Abstract: In recent years, driven by the computational demands of data-intensive applications such as artificial intelligence and scientific computing, analog computing has gained renewed interest. Given the diversity of computational tasks and recent advancements in analog CMOS circuits and resistive memory technologies, we refer to the evolving landscape as modern analog computing. In this context, we identify three core computational primitives: solving differential equations, solving matrix equations, and performing matrix-vector multiplications, and we explore the connections among them. We also examine various hardware implementations of these analog computing operators, including those built with discrete components, integrated circuits, and resistive memory devices. Among these, resistive memory arrays emerge as particularly promising due to their implementation efficiency. The paper then surveys recent progress in leveraging modern analog computing to solve differential and matrix equations using both advanced analog CMOS circuits and resistive memory arrays. Finally, we discuss the applications of these circuits, the precision and scalability issues and their potential solutions, the relationship with in-memory computing, and the unique computational complexity of analog computing. This paper provides a unified perspective on analog computing, highlighting its strengths, current developments, and challenges, and positioning it as a pivotal enabler of next-generation computational frontiers.

15.
bioRxiv (Bioinfo) 2026-06-11

Calibrated Uncertainty Quantification for Patient-Level AML Drug Sensitivity Prediction Using Split Conformal Prediction

Accurate prediction of ex vivo drug sensitivity in acute myeloid leukemia (AML) patients from transcriptomic data is a critical challenge for precision oncology. Existing computational approaches have explored uncertainty quantification in cancer drug response prediction primarily using cell line data, while patient-level AML models typically rely on heuristic confidence measures rather than statistically calibrated uncertainty estimates. Here, we present a framework applying split conformal prediction to patient-level AML drug response modeling using the BeatAML 2.0 cohort. We trained Elastic Net and XGBoost regressors on bulk RNA-seq gene expression profiles from 318 AML patients, analyzing 34,764 patient-drug observations across 122 compounds. Baseline models achieved median Pearson R values of 0.291 (Elastic Net) and 0.281 (XGBoost) across 122 drugs. Wrapping these models with split conformal prediction yielded well-calibrated prediction intervals across three confidence levels: empirical coverages of 81.4%, 90.7%, and 95.5% against nominal targets of 80%, 90%, and 95%, respectively. Analysis of prediction interval widths revealed substantial drug-class-specific uncertainty patterns, with HDAC and BCL-2 inhibitors exhibiting markedly higher uncertainty than MDM2 inhibitors, suggesting a potential association between transcriptomic predictability and drug mechanism of action, although several drug classes were represented by only a small number of compounds. Predictive uncertainty was not significantly associated with ELN2017 molecular risk classification (Kruskal-Wallis p=0.395) or NPM1 mutation status (p=0.788). These results demonstrate that statistically valid uncertainty quantification can be achieved for patient-level AML drug response prediction despite substantial biological heterogeneity. to the best of our knowledge, no published study has applied split conformal prediction to patient-level ex vivo drug sensitivity prediction in the BeatAML cohort, providing a principled alternative to heuristic confidence scoring approaches. Keywords: Acute myeloid leukemia (AML); Ex vivo drug sensitivity; Conformal prediction; Uncertainty quantification; Precision oncology; BeatAML; Transcriptomic biomarkers; Machine learning.

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

Sentinel: Decoding Context Utilization via Attention Probing for Efficient LLM Context Compression

Retrieval-augmented generation (RAG) often suffers from long and noisy retrieved contexts. Existing context compression methods typically rely on heuristic relevance estimation or supervised compression models rather than on how LLMs utilize retrieved context during inference. We propose Sentinel, a lightweight sentence-level compression framework that decodes inference-time contextual utilization behaviors from head-wise attention patterns of frozen LLMs. To ground supervision in retrieval-dependent answering behavior, Sentinel trains a lightweight probe using QA examples where the model succeeds only when retrieved context is available. Sentinel performs compression using only a single non-autoregressive forward pass without dedicated compression training or autoregressive scoring. Empirically, we find that effective contextual utilization signals remain accessible even in compact proxy models. On LongBench, Sentinel with a 0.5B proxy model achieves up to 5$\times$ compression while attaining question-answering performance competitive with compression methods built on 7B-scale models. Despite being trained only on English QA data, Sentinel also generalizes effectively to Chinese and out-of-domain settings.

17.
arXiv (CS.AI) 2026-06-12

Understanding the Rejection of Fixes Generated by Agentic Pull Requests – Insights from the AIDev Dataset

arXiv:2606.13468v1 Announce Type: cross Abstract: AI coding agents are increasingly used to generate pull requests (PRs) that propose code fixes in software projects. From a first exploration of the AIDev dataset, we find that 46.41\% of the fixes proposed by the agents Copilot, Devin, Cursor, and Claude are rejected. This represents a significant amount of wasted resources that require human reviews, verifications, and running tests and validations for fixes that are merely discarded. Our goal in this paper is to understand the failure modes of AI-agents, an understanding that is crucial for better integrating AI-agents as efficient teammates. In this paper, we conduct a qualitative study on a representative sample of 306 non-merged pull requests created or co-authored by the agents mentioned earlier, followed by a quantitative analysis of the reasons for rejection. Our qualitative findings identify 14 reasons divided into four high-level categories for rejecting AI-agent fixes. We observe that developers can reject fixes due to fixes whose implementation is incorrect (e.g., incomplete, wrong approach), fixes that do not pass the continuous integration (CI) pipelines and fail tests, fixes for which the agent is unable to perform the implementation (e.g., no code generated, sessions lost), and fixes whose priority is low. Our results shed light on the importance of better guiding the model at these levels: (1) proposing hints about the approach to follow for fixing an issue, (2) outlining constraints or limitations regarding the approaches that should not be taken, and (3) instructing the agent on how to validate the implementation through CI pipelines and without introducing a breaking change. Our results suggest the need for good prioritization of tasks so that generated fixes do not lead to wasted human review efforts or wasted agent resources (e.g., tokens, compute, or allowed number of requests).

18.
arXiv (quant-ph) 2026-06-19

Recursive perturbation approach to time-convolutionless master equations: Explicit construction of generalized Lindblad generators for arbitrary open systems

arXiv:2506.04095v2 Announce Type: replace Abstract: We develop a recursive perturbative expansion for the time-convolutionless (TCL) generator of an open quantum system in a generalized Lindblad form. This formulation provides a systematic approach to derive the generator at arbitrary order while preserving a Lindblad-like structure, without imposing assumptions on the system or environment beyond an initially uncorrelated state. The generator is written, at all orders, in a canonical form, which also corresponds to the minimal dissipation condition, which uniquely specifies the decomposition of the generator into Hamiltonian and dissipative contributions. To validate the method and show its effectiveness in addressing non-Markovian dynamics and strong-coupling effects, we compute the generator explicitly up to fourth order.

19.
arXiv (CS.LG) 2026-06-18

A Human-in-the-Loop Bayesian Optimization Framework for Constraint-Aware Bioprocess Development

arXiv:2606.19230v1 Announce Type: new Abstract: This work presents an extension to Pareto Front Guided Sampling (PFGS), a Human-in-the-Loop (HitL) Bayesian Optimization (BO) framework in which Gaussian process (GP) surrogate-derived quantities are reformulated as objectives of a multi-objective optimization problem, and the resulting Pareto front is exposed to a domain expert for interactive candidate selection rather than returning a single automated recommendation. The framework is extended in two directions: constrained optimization is addressed by incorporating the posterior probability of satisfying output specification limits as an explicit Pareto objective, computed analytically from the GP posterior distribution; robust optimization is addressed by a Monte Carlo sampling strategy that estimates expected lower-confidence performance over a user-defined variability of input perturbations, capturing performance degradation under likely implementation deviations. The resulting multi-dimensional Pareto representation renders trade-offs between predicted performance, model uncertainty, probabilistic constraint satisfaction, and input robustness simultaneously visible through pairwise two-dimensional projections on an interactive dashboard, enabling selection criteria to be iteratively refined as the surrogate model improves and development objectives evolve. The framework is showcased on an eight-dimensional fed-batch Chinese Hamster Ovary (CHO) cell culture simulator demonstrating systematic identification of high-performing, feasibility-compliant, and perturbation-resilient operating conditions, and illustrating how expert-defined requirements provide a principled stopping criterion and support informed allocation of experimental resources.

20.
PLOS Medicine 2026-05-22

Differences in tuberculosis prevalence by sex in low- and middle-income countries over 1993–2025: A systematic review and meta-analysis

by Nicole A. Swartwood, Nanki Singh, Seyed Alireza Mortazavi, Melike Hazal Can, Hening Cui, Do Kyung Ryuk, Peter MacPherson, Katherine C. Horton, Nicolas A. Menzies Background Global and national initiatives to combat tuberculosis (TB) have expanded over recent years. Despite this, the TB burden remains high in some population groups, with men recognized as having elevated TB risks. Summary measures of sex differences in TB prevalence were last estimated in 2016. Since then, many additional prevalence surveys have been conducted, including in the highest TB burden countries. We conducted a systematic review of sex-stratified TB prevalence survey data published over 1993–2025, to provide updated estimates of male-to-female (M:F) TB prevalence ratios and determine whether sex-related disparities in TB burden have closed over time. Methods and findings We identified surveys reporting community-representative, sex-stratified estimates of pulmonary TB prevalence in low- and middle-income countries (LMICs), including surveys from an earlier review (covering January 1993–March 2016) and a new systematic review (covering 1st December 2015–13th October 2025). This review was prospectively registered with PROSPERO (CRD42024503853) and included searches of PubMed, Embase, Global Health, the Cochrane Library, Africa Index Medicus, LILACS, and SciELO. We extracted data on bacteriologically confirmed and smear-positive TB prevalence among adults (aged ≥ 15 years), stratified by sex. Risk of bias was evaluated using eight criteria specific to prevalence surveys. We fit multi-level Bayesian regression models with study- and country-level random effects to estimate the M:F ratio of TB prevalence (male prevalence divided by female prevalence), overall and for key subgroups. In meta-regression analyses, we estimated how prevalence ratios varied over time and according to known TB risk factors and TB case definitions.We identified 10,124 publications and extracted data from 100 eligible studies representing 102 unique prevalence surveys and 4,658,310 participants (45.6% male) in 33 LMICs. TB prevalence was higher in men than women in 90/102 of the included surveys, with a pooled M:F prevalence ratio of 2.02 (95% credible interval (CrI): 1.71, 2.34) for bacteriologically confirmed TB and 2.38 (95% CrI: 1.91, 2.90) for smear-positive TB. Time trend analyses showed a 2.0% (95% CrI: −0.2, 4.5%) average annual change in the M:F ratio of bacteriologically confirmed TB over the study period. The M:F prevalence ratio was estimated to be higher for countries with greater excess HIV prevalence among men, and countries with greater gender equity (as measured by the United Nation’s Gender Development Index). The estimated M:F prevalence ratio was also higher for surveys that did not restrict testing to individuals reporting TB symptoms. Study limitations include heterogeneity in survey methods and definitions, as well as limited data from the Americas, Eastern Mediterranean, and Europe WHO world regions and post-COVID-19 period. Conclusions Men in LMICs consistently experience TB at a higher prevalence than women. Time trend estimates are uncertain, but consistent with widening sex differences in TB prevalence over the last three decades, despite efforts to address the risk factors underlying this excess TB burden.

21.
arXiv (CS.CL) 2026-06-16

Does Traversal Order Matter? A Systematic Study of Tree Traversal Methods in Transformer Grammars

Transformer Grammars (TGs) enhance language modeling by incorporating syntactic tree structures. Despite the potentially significant impact on model performance of how syntactic trees are linearized in TGs, existing studies rely solely on Depth-First Traversal (DFT) for linearization. In this paper, we expand the traversal design space by exploring Breadth-First Traversal (BFT) and a novel hybrid traversal strategy, Production-Rule Traversal (PRT), which combines the structural lookahead of BFT with the early lexical generation of DFT. We integrate these traversal methods with varying tree configurations and masking strategies, and empirically evaluate their performance on language modeling, syntactic generalization and summarization. We reveal the inherent trade-offs between nested composition and global lookahead, providing actionable recommendations for designing task-aware Transformer Grammars.

22.
arXiv (CS.CL) 2026-06-11

Geometry of Reason: Spectral Signatures of Valid Mathematical Reasoning

Verifying whether a language model is genuinely reasoning or pattern-matching remains an open problem: learned verifiers are expensive, and output-based heuristics are brittle. We show that valid mathematical reasoning induces a measurable, training-free spectral signature in transformer attention. By treating each attention matrix as a weighted token graph, we extract four diagnostics: Fiedler value, High-Frequency Energy Ratio (HFER), spectral entropy, and smoothness, that require no learned parameters. Experiments across seven models from four architectural families yield effect sizes up to Cohen's $d = 3.30$ ($p < 10^{-116}$), enabling $85$–$96\%$ single-threshold classification accuracy. Two findings sharpen the interpretation. First, Platonic validity: the spectral signal tracks logical coherence rather than compiler acceptance, proofs rejected for timeouts or missing imports are correctly classified as valid, a distinction confirmed by a manual audit ($\kappa = 0.82$, $n = 51$). Second, architectural determinism: Sliding Window Attention shifts the discriminative feature from HFER to smoothness ($d = 2.09$, $p < 10^{-48}$), showing that attention design governs which spectral channel encodes reasoning quality. Causal ablation confirms the signature traces induction-head circuits. The method generalises to informal chain-of-thought ($d = 0.78$, $p < 10^{-3}$), and in proof search, HFER reranking improves Best-of-16 Pass@1 by $+4.4$–$6.6$\%, matching $98\%$ of the AUC of fully supervised probes with zero labels. Spectral graph analysis is a principled, architecture-aware primitive for reasoning verification.

23.
arXiv (CS.LG) 2026-06-16

Asymptotically Optimal Sequential Testing with Markovian Data

arXiv:2602.17587v3 Announce Type: replace-cross Abstract: We study one-sided and $\alpha$-correct sequential hypothesis testing for data generated by an ergodic, finite-state Markov chain. The null hypothesis is that the unknown transition matrix belongs to a prescribed set $P$ of stochastic matrices, and the alternative corresponds to a disjoint set $Q$. We establish a non-asymptotic instance-dependent lower bound on the expected stopping time of any valid sequential test under the alternative, which is asymptotically tight. Our novel analysis improves the existing lower bounds, which are either asymptotic or provably sub-optimal in this setting. Our lower bound incorporates both the stationary distribution and the transition structure induced by the unknown Markov chain. We further propose an optimal test whose expected stopping time matches this lower bound asymptotically as $\alpha \to 0$. We illustrate the usefulness of our framework through applications to sequential detection of model misspecification in Markov Chain Monte Carlo and to testing structural properties, such as the linearity of transition dynamics, in Markov decision processes. Our findings yield a sharp and general characterization of optimal sequential testing procedures under Markovian dependence.

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

Optimizing Rank for High-Fidelity Implicit Neural Representations

Implicit Neural Representations (INRs) based on vanilla Multi-Layer Perceptrons (MLPs) are widely believed to be incapable of representing high-frequency content. This has directed research efforts towards architectural interventions, such as coordinate embeddings or specialized activation functions, to represent high-frequency signals. In this paper, we challenge the notion that the low-frequency bias of vanilla MLPs is an intrinsic, architectural limitation to learn high-frequency content, but instead a symptom of stable rank degradation during training. We empirically demonstrate that regulating the network's rank during training substantially improves the fidelity of the learned signal, rendering even simple MLP architectures expressive. Extensive experiments show that using optimizers like Muon, with high-rank, near-orthogonal updates, consistently enhances INR architectures even beyond simple ReLU MLPs. These substantial improvements hold across a diverse range of domains, including natural and medical images and novel view synthesis, with up to +9 dB PSNR over the same architecture. Code is available at (https://rank-inrs.github.io).

25.
bioRxiv (Bioinfo) 2026-06-16

FlowBench: separating planning, fault recovery and interpretation in agentic bioinformatics

Agentic large language model (LLM) systems are being deployed in bioinformatics faster than they are understood, and single-metric evaluations conflate capabilities that fail independently. We introduce FlowBench, a benchmark that decomposes agentic bioinformatics performance into planning, fault recovery, biological interpretation, and end-to-end output-fidelity. Existing systems achieve high plan completeness, but their closed, single-provider designs prevent attribution of performance to scaffolding versus the underlying model. We therefore built FlowAgent, a modular, provider-agnostic framework whose components can be selectively disabled and whose backbone model can be swapped across providers on a shared harness, and used it to evaluate 23 models from three main providers. Three findings emerge. First, generating a valid workflow plan from a named toolchain is largely solved, whereas inferring an appropriate toolchain from biological intent alone is uniformly difficult regardless of model tier, compressing all models into a narrow 44-57% pass-rate band. Second, ablation shows that the dependency-structured plan and a completeness-reflection step drive performance, while adding a same-context validator-driven retry makes structural quality worse. Third, fault recovery and data-grounded interpretation remain unsolved. Models frequently propose fixes that force a clean exit while leaving the underlying data invalid, and data-grounded interpretation lags internal-knowledge recall by a consistent margin. Safety does not emerge from capability, and reasoning-tier models were among the least reliable at recognising unrecoverable faults. Once planning saturates, agent architecture and refusal calibration, not model scale, are the productive frontier.