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01.
arXiv (math.PR) 2026-06-11

Persistent Homology of the Planar Wiener Sausage: Brownian Scaling and a Logarithmic Expectation Law

arXiv:2606.11248v1 Announce Type: new Abstract: We study degree-one persistent homology of the planar Wiener-sausage filtration generated by standard Brownian motion without drift. In the drifted case, regeneration along the drift direction leads to linear-in-time laws for persistent-homological observables. In the recurrent zero-drift case, this renewal structure disappears. The organizing mechanism is instead Brownian self-similarity: the persistence diagram at time $T$ is equal in law to the image of the unit-time diagram under spatial dilation by $\sqrt T$. Consequently, large-time questions on fixed radius windows are transformed into small-radius questions for the unit-time Brownian trace. Let $B$ be standard planar Brownian motion, let $K_T=B\left(\left[0,T\right]\right)$, and let $K_T^{\left(r\right)}$ be the radius-$r$ Wiener sausage. Since $K_T^{\left(r\right)}$ is connected, its first Betti number $\beta_1^T\left(r\right)$ is the number of bounded complementary components of $K_T^{\left(r\right)}$. For a bounded nonnegative Borel function $\psi$ supported in a compact interval $\left[a,b\right]\subset\left(0,\infty\right)$, we consider the smoothed Betti-curve observable $\left[r_0,r_1\right] \mathrm{\Phi}_\psi \left(T\right) = \int_{r_0}^{r_1} \beta_1^T \left( r \right) \psi \left( r \right) dr$. We prove that there exist absolute constants 0

02.
bioRxiv (Bioinfo) 2026-06-11

GermRL: Alleviating The Germline Bias In Autoregressive Antibody Language Models Through Reinforcement Learning

Antibodies are powerful therapeutics whose antigen specificity arises from sequence diversity shaped during development. Recently, language models trained on large antibody repertoire datasets have enabled the generation and screening of novel candidates, but these models retain a strong germline bias. As AI adoption increases in therapeutic workflows, it is crucial to develop models that harness the diversity of antibodies necessary for the discovery of mutations that encode desirable properties. Previous work explored the germline bias in masked antibody language models, yet the bias in generative autoregressive language models has not yet been addressed. Here, we present GermRL, a lightweight and modular reinforcement learning (RL) framework capable of alleviating the germline bias in pre-trained antibody autoregressive language models through group relative policy optimization (GRPO). GermRL achieves consistent one-shot generation of antibodies that satisfy specified mutation thresholds from germline while maintaining structural plausibility. Under the lowest and highest mutation thresholds tested (5 and 35 mutations from germline), GermRL scores 0.992 and 0.950 pass@1, respectively, compared to 0.398 and 0.034 for the pre-trained language model. Within GermRL, we introduce a key pair of modifications to GRPO that increase training efficiency by discouraging reward hacking under our antibody application. Furthermore, comparison of RL generated and natural antibody sequences reveals how RL based optimization can explore alternative evolutionary mutational patterns and residue compositional strategies while preserving key global properties of natural antibodies, including identifiable germline assignments, embedding-level similarity and comparable developability profiles. Thus, RL-trained generative models optimized to promote antibody mutations through diversity from germline provide a promising framework for navigating the antibody sequence landscape, enabling exploration of novel yet biologically plausible candidates for therapeutic design.

03.
arXiv (CS.CL) 2026-06-15

The Coin Flip Judge? Reliability and Bias in LLM-as-a-Judge Evaluation

LLM-as-a-Judge is now widely used to rank model outputs, train reward models, and populate public leaderboards, but its run-to-run reliability remains under-characterized. We study repeated identical evaluations on 29 tasks spanning 10 categories using two OpenAI judge models (GPT-4o-mini and GPT-4.1-mini), with 50 pairwise trials and 50 pointwise trials per question, supplemented by temperature and prompt-sensitivity ablations. Across judges, pairwise preferences flip on average 13.6% of the time, with 28% of questions exceeding a 20% flip rate and one question reaching 56%. GPT-4o-mini also exhibits a significant first-position bias (72% A-majority, p = 0.024). At the same time, mean pointwise score gaps are small (0.19–0.36 on a 10-point scale) and not statistically significant in aggregate, producing a pairwise–pointwise gap: judges frequently choose a winner even when their own scalar scores provide little evidence of a meaningful quality difference. Beyond within-judge instability, cross-judge agreement is only 76% ($\kappa = 0.51$), semantically equivalent prompt templates change majority outcomes in 25% of tested cases, and deterministic decoding reduces but does not eliminate inconsistency. A reliability curve analysis shows that, in our dataset, 11 repeated trials are needed for a majority vote to recover the 50-trial reference verdict with 95% probability on average, rising to 15 for high-variance questions. These findings suggest that single-trial LLM judging is often too noisy for high-stakes evaluation, and that multi-trial aggregation, position randomization, and explicit uncertainty reporting should be standard practice. Because both judges are from a single provider, cross-provider replication remains an important next step.

04.
arXiv (CS.CL) 2026-06-11

AI4SLT: Empirical Processes in Lean 4 for Formal Statistical Learning Theory

We present the first comprehensive Lean 4 formalization of statistical learning theory (SLT) grounded in empirical process theory. Our en-to-end formal infrastructure implement the missing contents in latest Lean library, including a complete development of Gaussian Lipschitz concentration, Dudley's entropy integral theorem for sub-Gaussian processes, and an application to least-squares (sparse) regression with a sharp rate. The project was carried out using a human-AI collaborative workflow, in which humans design proof strategies and AI agents execute tactical proof construction, leading to the human-verified Lean 4 toolbox for SLT. Beyond implementation, the formalization process exposes and resolves implicit assumptions and missing details in standard SLT textbooks, enforcing a granular, line-by-line understanding of the theory. This work establishes a reusable formal foundation and opens the door for future developments in machine learning theory. The code is provided in https://github.com/YuanheZ/lean-stat-learning-theory.

05.
PLOS Computational Biology 2026-05-29

A prototype-augmented graph representation learning framework for identifying brain disorder-associated genes and facilitating drug repurposing

作者:

by Jiafang Li, Yifei Li, Siying Lin, Jiahua Rao, Huiying Zhao Many genetic loci were identified as associated with neuropsychiatric disorders and neurodegenerative disorders by Genome-wide association studies (GWAS). How these loci impact these diseases is unclear. Advances in deep-learning approaches and multi-omics data have the potential to link GWAS findings with disease mechanisms. Here, we proposed the Multi-omics Graph Transformer Network (MOGT), a semi-supervised graph neural network that leverages graph representation learning to model biological networks derived from multi-omics data to predict disease-associated genes. MOGT outperforms the current approaches in disease gene prediction for two psychiatric disorders and three neurodegenerative/neurological diseases. High-risk genes (HRGs) for Parkinson’s disease (PD) predicted by MOGT were used to drug discovery by integrating with the CMAP database. Finally, 10 drugs were identified as potential candidates. Among them, the effect of drug UK-356618 was experimentally verified in a primary neuron model, showing that UK-356618 reversed the abnormal expression of PD-associated genes and improved the cell-level phenotypes of PD. Together, these results indicate that MOGT can be used to identify HRGs for brain disorders, and these predicted HRGs provide high-level insights into the mechanisms and treatments of brain disorders.

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

Canonical regularization of the stationary Coulomb problem and an Aufbau-like spectral ordering

arXiv:2606.17359v1 Announce Type: new Abstract: The stationary hydrogen atom has Coulomb degeneracy across orbital levels, whereas the Aufbau/Madelung ordering is an empirical, many-electron rule established in atomic physics. We examine the hydrogen atom through a regularized de Broglie–Bohm representation, in which stationary amplitude current constraints generate separable Sturm–Liouville branches. In this formulation, the radial, orbital, and magnetic sectors acquire canonical Langer-like inverse square corrections. The modified boundary value problems allow analytical solutions and produce a hydrogen-like spectrum with regularized radial and angular indices. Consequently, radial Coulomb quantization acquires an orbital dependent shift, lifting the Coulomb degeneracy and producing a spectral ordering that follows the Aufbau/Madelung sequence. On this basis, we construct the ordering of the regularized de Broglie–Bohm states and show that the spectral structure retains the standard degenerate Rydberg sequence in the l=0 sector. The separated amplitudes are represented by generalized special function branches, including the associated Laguerre, Legendre, and Bessel functions with non-integral parameters arising from regularized separation. Therefore, the treatment is intended as an analytical examination of spectral ordering in a regularized one center Coulomb problem rather than as a replacement for the many electron atomic structure theory. Keywords: de Broglie–Bohm representation; Coulomb spectrum; canonical regularization; Langer correction; Sturm–Liouville equations; Aufbau principle; Madelung ordering; associated Legendre functions; associated Laguerre functions; Bessel functions.

07.
arXiv (CS.CV) 2026-06-17

StereoFactory: A Unified Merging Framework for Robust Stereo Matching

Stereo matching has advanced through foundation models trained on large-scale datasets, yet this paradigm suffers from a scalability bottleneck: incorporating new data requires costly joint retraining. Model merging offers a scalable post-hoc alternative by integrating knowledge from specialized models after source checkpoints are available. However, existing merging methods typically retain all available models or rely on greedy inclusion, which can preserve harmful task-vector interference. We propose StereoFactory, a coarse-to-fine evolutionary framework for adaptive model merging. Stage~1 employs a genetic algorithm to search the combinatorial space of model subsets, determining which models should participate. Stage~2 addresses module-level knowledge specialization (different functional modules exhibit distinct preferences for knowledge sources) through CMA-ES optimization of architecture-adaptive routing over the selected task vectors, with optional module-level scaling. Experiments across two architectures and four benchmarks demonstrate that StereoFactory consistently achieves the best four-benchmark average under the same checkpoint pool, reducing the average error from 3.80 to 3.30 on NMRF and from 2.88 to 2.19 on FoundationStereo relative to the strongest controlled baseline. The post-hoc search requires only 2.7–3.7\% of the corresponding joint-retraining wall-clock time. Analysis reveals that knowledge contributions are inherently module-specific, and selected subsets can transfer across architectures with minimal degradation. Code will be publicly released upon acceptance at: https://github.com/XiandaGuo/StereoFactory.

08.
medRxiv (Medicine) 2026-06-22

Nutrient Composition of Foods Represented in the U.S. Food and Nutrient Database for Dietary Studies, 2013-2023

Background: The U.S. Food and Nutrient Database for Dietary Studies (FNDDS) is updated across NHANES dietary cycles and is central to U.S. nutrition surveillance. However, multi-cycle food-code-level changes in nutrient composition have not been comprehensively characterized across the full WWEIA nutrient panel. Objective: To characterize ten-year temporal patterns in nutrient composition across five FNDDS cycles, evaluate pandemic-period food-code compositional stability, and distinguish exploratory mean-level signals from distributional heterogeneity that may reflect reformulation, database coverage, or food-code definition changes. Methods: We analyzed five consecutive FNDDS biennial releases: 2013-14, 2015-16, 2017-18, 2019-20, and 2021-23. Nutrient values were extracted from the public FNDDS/FoodData Central release files and standardized to per-100-g food-code-level records. Cycle midpoints, 2013.5, 2015.5, 2017.5, 2019.5, and 2022.0, served as the independent variable in an exploratory ordinary least squares (OLS) regression. Mann-Kendall testing assessed monotonic rank trends, Welch's ANOVA assessed food-code-level distributional heterogeneity, and pairwise Welch comparisons with Cohen's d summarized pre-pandemic, pandemic-period, and post-pandemic differences. Equivalence testing using TOST with +/-10% bounds was restricted to the 2019-20 versus 2021-23 stability comparison. OLS sensitivity analyses were repeated after excluding the structurally atypical 2017-18 cycle. Results: Sixty-three nutrients were analyzed. Eight nutrients showed nominal OLS trends, p < 0.05, but none remained significant after Bonferroni correction. Mann-Kendall testing identified two nominal monotonic signals, and none after adjustment. Welch's ANOVA detected cycle-level distributional differences for 61 of 63 nutrients at nominal p < 0.05 and 57 of 63 after adjustment. Pairwise pandemic-period analyses showed many adjusted differences when the pre-pandemic baseline was compared with 2019-20 or 2021-23, but standardized effects were small, with all absolute Cohen's d values < 0.20. No nutrient differed after adjustment between 2019-20 and 2021-23, and 39 of 48 primary analytes met +/-10% TOST equivalence criteria for that comparison. Slope estimates were directionally stable after excluding 2017-18, but nominal significance status remained sensitive to the short time series. Conclusions: FNDDS food composition varied across cycles, but there was no clear decade-long linear trend for most nutrients. The main signal was a possible increase in total PUFA and linoleic acid, which may reflect changes in fat quality. The 2021-23 cycle was very similar to 2019-20, suggesting no major post-pandemic shift in the foods represented. These findings should be interpreted as food-database signals, not as direct estimates of what people consumed.

09.
arXiv (CS.LG) 2026-06-12

Design Criteria for SGD Preconditioners: Local Conditioning, Noise Floors, and Basin Stability

arXiv:2511.19716v2 Announce Type: replace-cross Abstract: Stochastic Gradient Descent (SGD) often slows in the late stage of training due to anisotropic curvature and gradient noise. We analyze preconditioned SGD in the geometry induced by a symmetric positive definite matrix $\mathbf{M}$, deriving bounds in which both the convergence rate and the stochastic noise floor are governed by $\mathbf{M}$-dependent quantities: the rate through an effective condition number in the $\mathbf{M}$-metric, and the floor through the product of that condition number and the preconditioned noise level. For nonconvex objectives, we establish a preconditioner-dependent basin-stability guarantee: when smoothness and basin size are measured in the $\mathbf{M}$-norm, the probability that the iterates remain in a well-behaved local region admits an explicit lower bound. This perspective is particularly relevant in Scientific Machine Learning (SciML), where achieving small training loss under stochastic updates is closely tied to physical fidelity, numerical stability, and constraint satisfaction. The framework applies to both diagonal/adaptive and curvature-aware preconditioners and yields a simple design principle: choose $\mathbf{M}$ to improve local conditioning while attenuating noise. Experiments on a quadratic diagnostic and three SciML benchmarks validate the predicted rate-floor behavior.

10.
arXiv (CS.CV) 2026-06-25

Efficient Remote Sensing Instance Segmentation with Linear-Time State Space Distilled Visual Foundation Models

The computational complexity of Transformers scales quadratically with the number of tokens, which significantly constrains the efficiency of vision models, particularly recent ViT-based foundation models in dense prediction tasks. Instance segmentation, a typical dense visual prediction task in the remote sensing field, faces similar challenges. In this paper, inspired by the recent advances of knowledge distillation in large language models, we introduce RS4D - a new remote sensing instance segmentation method with linear computational complexity, which addresses the inefficiency of long sequence modeling through distilled state space modeling (SSM). We propose an adaptive noise and masking knowledge distillation training method for pre-training lightweight SSM backbones, which effectively compresses knowledge from the vast self-attention space into a compact, dense linear state space. We also design a remote sensing image instance segmentation architecture based on this lightweight visual encoder, where we explore variants of three different backbones and two segmentation heads. Extensive experiments are conducted on multiple benchmark datasets, including SSDD, WHU, and NWPU. Compared to ViT-based approaches, our proposed SSM backbone achieves an 8x reduction in parameters and a 9x reduction in FLOPs while maintaining comparable or superior accuracy to both ViT- and CNN-based instance segmentation methods. The implementation codes have been publicly available at https://github.com/QinzheYang/RS4D.

11.
arXiv (math.PR) 2026-06-12

Counterintuitive problems in discrete probability

arXiv:2606.07516v2 Announce Type: replace Abstract: This manuscript contains a collection of counterintuitive problems in discrete probability, together with detailed solutions. The dataset was constructed as part of a broader research project investigating the capabilities of the latest-generation Large Language Models (LLMs) in solving discrete probability problems, in order to assess whether LLMs tend to make systematic reasoning errors associated with known cognitive biases. The problems collected here are specifically designed to challenge heuristic reasoning strategies that often lead to intuitively appealing but mathematically incorrect conclusions. The dataset combines several types of problems. Some are adapted from classical probabilistic paradoxes and cognitive-bias literature, while others originate from recreational mathematics sources or were developed by ourselves following similar principles. The primary purpose of this document is to provide a transparent and publicly accessible reference for the problems used in our experimental evaluation of language models, as well as providing detailed human-made solutions. At the same time, we believe that this collection may also prove useful for future research on probabilistic reasoning, cognitive biases, and the evaluation of reasoning capabilities in artificial intelligence systems.

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

Non-negative Matrix Factorisation with Topological Regularisation

arXiv:2606.17531v1 Announce Type: new Abstract: We investigate the learning of interpretable bases in non-negative matrix factorisation (NMF) by regularising the topology of the learned basis functions. Our approach is motivated by the observation that many data modalities can be viewed as non-negative functions on a structured domain, where the quality of a basis is intrinsically linked to its topology. However, naive methods for incorporating the topology of the support are often hindered by discreteness and threshold dependence, rendering them unsuitable for continuous optimisation. We address these challenges by employing persistent homology as a stable, threshold-free topological quantifier and by designing topological scores that integrate into the NMF objective as regularisers. The resulting framework encompasses spatially coherent image components, periodic time-series structures, and clique-like graph signals within a unified modelling language.

13.
arXiv (CS.AI) 2026-06-24

SemChunk-C: Semantic Segmentation for C Code

arXiv:2606.23697v1 Announce Type: cross Abstract: Semantic segmentation of code written in a C-family language remains a challenging problem, due to the language's complex syntax, macro expansion, and irregular structural patterns. Existing chunking methods, such as fixed-sized windows, heuristic splitting, and syntax-based tools, often fail to capture meaningful functional units, limiting the efficacy of retrieval and other downstream LLM driven tasks. In this paper, we address the problem of chunking in C-related languages. First, we define a set of code chunk categories. Second, we train an LLM-based classifier to a) identify chunk boundaries, and b) assign each chunk a descriptive functional attribute (a category), which can be useful for downstream tasks. By leveraging the LLM's ability to capture semantic context within the code, we assume flexible chunk boundaries, allowing to adapt to the specific structure and context of each instance. Third, we introduce SemChunk-C, a family of lightweight language models for semantic chunking of C-related files (.c, .cpp, .h, .cs, etc.). These models are based on the first four Ettin encoders [1] with 17M, 32M, 68M, and 150M parameters. Despite their relatively small size, they are capable of identifying cohesive code units, such as data structures, interface blocks, and other components. Furthermore, we demonstrate the robustness of our approach on real-world code, including challenging constructs such as nested definitions and macros. We test our approach on various datasets, and show that it achieves high boundary accuracy and semantic coherence, matching or outperforming chunkers that are based on much larger code-oriented LLMs. We also validate the improved performance of the downstream tasks on a few curated benchmarks.

14.
arXiv (quant-ph) 2026-06-16

Generalized Kerr-Cat Qubit Codes

arXiv:2606.14901v1 Announce Type: new Abstract: We present a systematic study of Schrödinger cat codes constructed from Kerr-type coherent states, including displaced Kerr coherent states and Barut–Girardello Kerr coherent states, each admitting two distinct families determined by the sign of the Kerr nonlinearity. By tuning the Kerr parameter and coherent-state amplitude, these states interpolate between $\mathfrak{su}(2)$, $\mathfrak{su}(1,1)$ coherent states, providing a unified and versatile foundation for this type of bosonic quantum error correction. Unlike standard two-component Schrödinger cat codes, where a single photon-loss event induces an uncorrectable bit-flip, the nonlinear phase-space structure of Kerr cat states enables simultaneous detection and correction of both photon-loss and dephasing errors within a unified recovery framework, with optimal recovery operations determined via convex optimization. We demonstrate that Kerr cat encodings significantly outperform conventional cat codes under combined loss and dephasing noise, and that judicious parameter optimization can suppress both error channels to a level that reduces the overhead of additional error correction layers. We further show that Kerr-deformed coherent-state manifolds under engineered two-photon driving emerge as effective steady states of driven-dissipative dynamics, with single-photon decoherence strongly suppressed and leakage outside the protected manifold appearing only as higher-order corrections in the deformation strength. Our extended formalism identifies generalized Kerr Schrödinger cat codes as promising candidates for fault-tolerant bosonic quantum computation in experimental platforms such as nonlinear photonics.

15.
arXiv (quant-ph) 2026-06-19

Thermodynamic Value of XOR-Game-Induced Side Information in a Szilard Engine

arXiv:2605.12044v3 Announce Type: replace Abstract: We introduce a Szilard-type thermodynamic valuation of side-information channels induced by Bell-type correlations. In each round, a two-level working system is thermalized with a degenerate Hamiltonian, so that its physical microstate is a uniform classical bit. A trusted referee embeds this bit into a finite two-player XOR game, and a correlation resource produces a compressed controller bit. The controller uses only this compressed bit as side information for feedback. The construction is formulated first for arbitrary finite XOR games. The referee encoding makes the game-winning event equivalent to correct prediction of the physical microstate. Consequently, the induced side-information channel is binary symmetric, with success probability equal to the XOR-game winning probability of the supplied behaviour. The reversible Szilard feedback value is therefore fixed by the mutual information between the microstate and the controller record. Optimizing over local, quantum, and nonsignalling behaviour sets turns the corresponding game values into local, quantum, and nonsignalling thermodynamic ceilings. The construction is an effective-channel valuation, not a claim that Bell nonlocality is thermodynamic fuel. The controller receives only the compressed prediction bit, not the auxiliary variables that define the game. The thermodynamic costs of the referee, the correlation resource, and the preprocessing are not included. When controller-memory reset is included in a full cycle, the net work is non-positive, consistently with the second law.

16.
arXiv (quant-ph) 2026-06-24

Biophysical EPR Using Superconducting Resonators

arXiv:2606.23952v1 Announce Type: new Abstract: We present innovations that enable the use of superconducting resonators for high sensitivity, high bandwidth pulsed electron paramagnetic resonance (EPR) measurements on biologically relevant samples with enhanced stability and throughput. A custom-built X-band pulsed EPR spectrometer with AWG and digital IF capability generated by an FPGA was used to control a novel patterned thin film planar superconducting microstrip resonator capable of generating Rabi fields sufficient to achieve 6 ns pi/2 Gaussian pulses using a 100 W solid-state HPA. The system allows automated sequential calibration, measurement, and analysis of five 3.5 uL samples contained in a sample cartridge. Performance was validated through measurements of double electron-electron resonance (DEER) distances in a variety of spin-labeled protein samples with biologically relevant concentrations, including measurements below 10 uM. The results enable broadening the scope of applications for both superconducting resonators and the use of EPR in biotechnology.

17.
arXiv (CS.CL) 2026-06-24

Faithful by Construction: Claim-Anchored Attribution for Multi-Document Summarization

作者:

End-to-end large language models (LLMs) produce fluent multi-document summaries but remain prone to hallucination, and the attributions they offer are typically coarse (whole documents or passages) and generated post hoc, leaving each summary statement hard to verify. We revisit the modular Extract–Select–Rewrite paradigm and recast its intermediate representation as the unit of attribution. We present CAMS, a Claim-Anchored Multi-document Summarization framework that (i) extracts atomic claims with token-level provenance from every source document, (ii) clusters equivalent claims across documents while flagging inter-source conflicts, (iii) selects a support-aware and salient subset, and (iv) rewrites the selection into a summary in which every sentence is anchored to a support-checked claim that links back to one or more source spans. Because content is localized before it is realized, the pipeline is attribution-oriented by construction and faithfulness-oriented by construction: it structurally preserves fine-grained, multi-source traceability while using support-aware selection, constrained rewriting, and verification to encourage, rather than guarantee, factual faithfulness. We evaluate quality, faithfulness, and localization on MultiNews, analyze conflict handling on DiverseSumm, and test zero-shot transfer on WCEP, using a two-regime protocol that separates reference-free citation quality from gold-aligned localization accuracy, and we add an evaluator-decoupled audit that tests citation precision with a support model never used for selection or verification. CAMS matches strong end-to-end and span-attribution baselines on summary quality while substantially improving faithfulness and citation precision, lifting multi-source attribution accuracy by roughly two-thirds, and exposing a controllable faithfulness–coverage trade-off that end-to-end models leave implicit.

18.
medRxiv (Medicine) 2026-06-24

MedGenesis: Toward a World Model for Autonomous Clinical and Translational Research

Clinical research advances slowly because its core tasks, from evidence synthesis to mechanistic validation, remain fragmented. We present MedGenesis, a clinical artificial intelligence (AI) scientist built on a world-model reasoning loop that jointly updates a Latent Hypothesis Space and a Latent Action Space under expected information gain (EIG), uncertainty reduction (UR), and a safety prior P(safe), and integrates longitudinal electronic health records (EHRs) via the Virtual Clinical Trajectory and Observation Representation (ViCTOR) for cohort retrieval, trajectory stratification, and time-to-event analysis. On two benchmarks - ClinicalResBench (1,697 expert-curated questions) and ClinicalRepBench (40 paper-reproduction tasks) - MedGenesis outperformed frontier language models and biomedical AI systems while reducing hallucination. Across 1 million patient observations spanning five clinical evidence formats, it generated traceable outputs across meta-analysis, randomized controlled trials, real-world trajectories, case-control studies, and case reports, with one wet-lab-coupled run nominating a 3-hydroxybutyrate - neutrophil axis modulating antitumor immunity. These results compress hypothesis-to-evidence cycles from years to hours, creating a continuous clinical discovery process.

19.
arXiv (CS.CV) 2026-06-24

ActiveScope: Actively Seeking and Correcting Perception for MLLMs

Multimodal Large Language Models (MLLMs) have demonstrated impressive vision-language understanding, yet still struggle with fine-grained perception in high-resolution images. While existing training-free methods typically rely on attention-based localization or coarse-to-fine search, they are often misled by distractors and fail to locate multiple targets. Our investigation attributes these failures to Contextual Dominance, where salient distractors overwhelm target attention and cause inaccurate localization, and Semantic Bias, where global semantics cause the model to fixate on the most salient concept, resulting in incomplete localization in multi-object scenarios. Built on these insights, we propose ActiveScope, a training-free framework that enhances MLLMs by actively seeking and correcting perception. ActiveScope features two modules. The Semantic Anchor Localization (SAL) utilizes fine-grained semantic anchors to independently localize key targets, thereby mitigating semantic bias. The Interference-Suppressed Refinement (ISR) refines localization by suppressing attention on salient distractions to overcome contextual dominance. Extensive experiments on high-resolution image understanding benchmarks demonstrate that ActiveScope outperforms existing training-free methods (e.g., 96.34 percent accuracy on $V^{*}$ Bench), validating the superiority of the active search and self-correction paradigm. Our code is available at https://github.com/jasmine-ww/ActiveScope.

20.
arXiv (CS.CL) 2026-06-16

Generative causal testing to bridge data-driven models and scientific theories in language neuroscience

Representations from large language models are highly effective at predicting BOLD fMRI responses to language stimuli. However, these representations are largely opaque: it is unclear what features of the language stimulus drive the response in each brain area. We present generative causal testing (GCT), a framework for generating concise explanations of language selectivity in the brain from predictive models and then testing those explanations in follow-up experiments using LLM-generated stimuli.This approach is successful at explaining selectivity both in individual voxels and cortical regions of interest (ROIs), including newly identified microROIs in prefrontal cortex. We show that explanatory accuracy is closely related to the predictive power and stability of the underlying predictive models. Finally, we show that GCT can dissect fine-grained differences between brain areas with similar functional selectivity. These results demonstrate that LLMs can be used to bridge the widening gap between data-driven models and formal scientific theories.

21.
arXiv (quant-ph) 2026-06-19

Optimal Shadow Estimation with Minimal Measurement Settings

arXiv:2606.20003v1 Announce Type: new Abstract: Shadow estimation is a powerful framework for predicting quantum properties from randomized measurements. While $3$-design protocols achieve optimal worst-case performance, the minimal number of measurement bases required for such optimality has remained open. Here we prove that $\Theta(d^2)$ measurement bases are both necessary and sufficient for worst-case optimal shadow estimation and construct an explicit basis family. In stark contrast, any state $2$-design already suffices for average-case optimality: the mean squared shadow norm of normalized observables is bounded by a universal constant, and we prove strong concentration for Haar-random states, yielding constant sample complexity for generic pure-state fidelity estimation. Easily implementable $2$-designs – from mutually unbiased bases, cyclic measurements, or shallow $\mathcal{O}(\log n)$-depth circuits – enable optimal average-case protocols with remarkably simple measurement strategies. Our results establish a fundamental complexity separation: worst-case estimation requires $\Theta(d^2)$ bases, whereas average-case performance requires only $\Theta(d)$ bases, with broad implications for quantum information theory and near-term experiments.

22.
arXiv (CS.CV) 2026-06-16

Lightweight Distillation of SAM 3 and DINOv3 for Edge-Deployable Individual-Level Livestock Monitoring and Longitudinal Visual Analytics

Foundation-model pipelines for individual-level livestock monitoring – combining open-vocabulary detection, promptable video segmentation, and self-supervised visual embeddings – have raised the accuracy ceiling of precision livestock farming (PLF), but their GPU memory budgets exceed the envelope of commodity edge accelerators. To close this gap, the 446M-parameter Perception Encoder (PE-ViT-L+) backbone of SAM 3 is distilled into a 40.66M-parameter multi-scale student through three mechanisms: a Feature Pyramid Network student encoder built on TinyViT-21M-512, a four-term direction-then-scale distillation loss, and backbone-substitution inference with sliding-window session pruning that bounds streaming GPU memory growth. The DINOv3 family includes a pre-distilled ViT-S/16 variant (21.6M parameters) released alongside a 6716M-parameter ViT-7B teacher; the ViT-S (21M) variant is adopted as the per-individual embedder. On the Edinburgh Pig dataset, the compressed pipeline reaches 92.29% MOTA and 96.15% IDF1 against the SAM 3 teacher (1.68- and 0.84-percentage-point losses), achieves a 7.77-fold reduction in system-level parameters and a 3.01-fold reduction in peak VRAM (19.52GB -> 6.49GB), and reaches 97.34% top-1 accuracy with 91.67% macro-F1 on nine-class pig behaviour classification. The pipeline fits inside an NVIDIA Jetson Orin NX 16GB envelope with 4.9GB of headroom, supporting a proposed – but not yet empirically validated – on-device embedding-pool re-identification mechanism whose per-individual footprint of approximately 94MB per animal per year produces a longitudinal visual record amenable to retrospective association with disease, lameness, reproductive, and growth outcome labels.

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

Quantifying the Impact of Lossy Compression on Neural Generative Surrogate Modeling

arXiv:2606.15959v1 Announce Type: cross Abstract: Neural networks are used as generative surrogate models for scientific discovery, which are trainable approximations of scientific simulations. These models enable users to replace time-consuming numerical simulations with learned alternatives, providing quick solutions. However, high-fidelity generative surrogate models require massive training datasets, which can create storage and I/O challenges. Lossy compression is a promising way to reduce this burden, but compression errors may affect the model quality in subtle ways, making it challenging to quantify their impact. In this work, we examine how lossy compression of training data impacts the quality of generative surrogate models. We begin by characterizing the uncertainty inherent in training neural networks, showing that identical training configurations can produce different models. By exploiting this variability, we propose a method to estimate how much compression-induced error a surrogate model can tolerate without affecting its accuracy. Evaluation of two application simulations demonstrates that our approach significantly reduces memory/storage requirements and speeds up training while producing high-quality surrogate models. These results show that lossy compression saves data storage up to 23.7x and 39x with negligible impact on the quality of the surrogate model. Meanwhile, reducing the size of the training data set also enhances the data loading speed and reduces the training time by up to 3x.

24.
arXiv (CS.CL) 2026-06-19

NEST: Narrative Event Structures in Time for Long Video Understanding

Recent progress in vision-language models has enabled the processing of increasingly long video sequences, but the ability to handle extended token streams does not translate to understanding of narrative structure in long videos. Existing long video benchmarks focus on needle-in-a-haystack retrieval rather than evaluating how low-level actions form events, how events interact across time, and how narratives progress, for example, whether a model can connect an early setback, such as a job loss to a later relationship breakup, despite long gaps, intervening scenes, or flashbacks that reframe what occurred. We introduce NEST (Narrative Event Structures in Time for Long Video Understanding), a dataset of 1005 full-length movies (avg. 98 minutes), each annotated with 102 multimodal narrative events grounded in visual content, dialogue, and audio. NEST captures multimodal narrative events with structured annotations grounded in visual content, dialogue, and audio, and links them through relations that reflect narrative structure, including temporal ordering, hierarchical composition, and long-range dependencies. We introduce baselines for event trigger detection (ETD), event localization (EL), event argument extraction (EAE), and event relation extraction (ERE). The benchmark is highly challenging for grounded event discovery, with ETD below 8%, EL under 6%, and EAE below 11%. In contrast, ERE is more tractable once events are given, reaching 35.45% F1 zero-shot and 44.42% F1 after fine-tuning.

25.
medRxiv (Medicine) 2026-06-22

Associations of Chemical Exposures with Psychological Distress and Depression Diagnosis among Waste Pickers in Brasilia, Brazil: A Cross-Sectional Study

Introduction: Waste pickers face chemical exposures. We evaluated whether chemical exposure is associated with psychological distress and depression. Methods: A 2017 cross-sectional survey included 1,141 waste pickers working in the Estrutural open dump in Brasilia, Brazil. Participants self-reported occupational exposure to 11 chemical categories, 17 psychological distress symptoms, and depression diagnoses. Associations of chemical exposure with mean psychological distress scores and depression prevalence were assessed, adjusted for age, sex, marital status, and income. Results: Mean psychological distress score was higher among those exposed to any chemical (mean of 8.1 vs 6.1; adjusted mean difference [aMD]: 1.8 [0.9, 2.7]) and higher among those exposed to each of 11 chemical categories, for example, smoke (aMD: 1.2 [0.6, 1.7]), batteries (aMD: 1.5 [1.0, 1.9], and oils (aMD: 1.3 [0.9, 1.8]). Depression was more prevalent among those exposed to oils (16.6% vs 10.6%; adjusted prevalence difference [aPD]: 6.3% [95% CI: 2.3, 10.2]), cleaning products (aPD: 5.4% [1.2, 9.5]), medications (aPD: 4.7% [0.6, 8.8]), and aerosols (aPD: 5.3% [1.3, 9.3]) but, not smoke, batteries, greases, insecticides, solvents, paints, chemical containers, or any chemical. Conclusion: These associations highlight the need to consider policy level protections for waste pickers to reduce chemical exposure and guard against psychological distress. Further research is necessary to explore which specific chemicals, within broad chemical categories, are associated with psychological distress and depression.