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01.

Nature Medicine 2026-06-11 DOI: HASH:d41e362c735a27b9725317334cebb886

Clinical Profile and Genomic Characterization of the 2026 Bundibugyo Virus Index Case in Uganda

作者:

Bundibugyo virus disease (BVD) remains a high-consequence threat in Eastern and Central Africa, where cross-border mobility, nonspecific early symptoms, and delayed recognition can obscure transmission. In this case report, we describe Uganda’s 2026 BVD index case: a male patient who traveled from the Democratic Republic of the Congo to Uganda and was admitted to a private hospital in Kampala on 11 May 2026 after more than two weeks of vomiting and diarrhea, with epigastric pain, weakness, and hiccups. He deteriorated rapidly, developing acute kidney injury, pulmonary edema, hepatic dysfunction, hypoxemia, delirium, atrial flutter, possible disseminated intravascular coagulation, and multiorgan failure, and died on 14 May. A posthumous EDTA whole-blood specimen tested at the Central Emergency Response and Surveillance Laboratory was positive for orthoebolavirus RNA and confirmed as Bundibugyo virus (BDBV) by RT-qPCR. Sequencing achieved 99% genome coverage at ≥100× depth. The 2026 BDBV genome formed a distinct lineage approximately equidistant from the 2007–2008 Butalya and 2012 Isiro variants, differing by 216–227 nucleotides (~1.2% sequence divergence). Here, we demonstrate the value of fatality surveillance, private-sector surveillance, diagnostic optimization through national specimen referral, and rapid molecular-genomic diagnostics for early detection, transmission chain interruption, and public health response coordination.

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02.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2606.15841

Heteroskedastic Signals in Budgeted LLM Verification: Structural Heterogeneity Limits Optimization Gains

作者:

Jinlong Yang ↗

arXiv:2606.15841v1 Announce Type: new Abstract: Large language model (LLM) systems increasingly use uncertainty signals to allocate limited computation across verification, test-time scaling, tool execution, and other selective-compute decisions. Such policies rely on a global signal comparability assumption: equal scores should carry comparable decision value across inputs. Using budgeted verification as a controlled diagnostic setting, we identify a failure mode of this assumption: uncertainty quality is heteroskedastic across cost strata, with some regions exhibiting near-random discriminability despite concentrating many errors. Under an explicit local model, we characterize the resulting distortion of global allocation and show that its upper bound scales with cross-stratum signal-quality dispersion. We separate weak signals, optimization instability, and structural heterogeneity through a controlled intervention hierarchy: Threshold, MP-Adapt, MP-Strat, and a deliberately simple cost-stratified thresholding intervention (CST). Across MBPP and MATH using Qwen3-8B, LLaMA3-8B, and GPT-4o-mini, global online adaptation yields inconsistent gains over static thresholding; MP-Strat partially recovers performance, while CST improves hit rate by up to 17 percentage points in strongly heterogeneous settings without gradient updates. These results identify structural heterogeneity, rather than optimizer weakness alone, as the primary bottleneck in the observed settings. More broadly, misaligned feedback structure cannot always be repaired by stronger optimization.

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03.

arXiv (CS.CL) 2026-06-16 DOI: arXiv:2606.16527

DoubtProbe: Black-Box Jailbreak Defense via Structural Verification and Semantic Auditing

作者:

Xuanyu Yin ↗Yilin Jiang ↗Jun Zhou ↗Kai Chen ↗Zhengfu Cao ↗Xiaolei Dong ↗

As large language models (LLMs) are increasingly deployed in user-facing systems, black-box jailbreak defense has become an important practical problem. Existing defenses often rely on known-attack coverage, prompt-level semantic judgment, or local runtime control, yet these paths can become unstable under evolving prompt packaging, expression rewriting, and structure manipulation. We observe that many black-box jailbreaks do not remove the harmful goal, but reorganize the information needed to express and execute it, thereby evading safety alignment while remaining recoverable during generation. Motivated by this observation, we propose DoubtProbe, a dual-branch inference-time defense framework that combines structural verification with semantic auditing and formulates black-box jailbreak defense as consistency checking under controlled transformation. The structural branch extracts a structured representation from the original request, reconstructs the request under representation constraints, and detects information-preservation failures between the original and reconstructed requests; the semantic branch audits the original prompt directly. We evaluate DoubtProbe against representative black-box defenses on jailbreak and benign-request benchmarks, and further test backbone transfer from Qwen2.5-72B to Llama-3.1-70B. Results show that DoubtProbe achieves a stronger and more stable defense-utility trade-off: on Qwen2.5-72B, it reduces the JBB attack success rate from 0.293 to 0.100 and the CodeAttack attack success rate from 0.152 to 0.001, while maintaining false positive rates of 0.022 and 0.016 on AlpacaEval and OR-Bench; the same pattern remains stable on Llama-3.1-70B. These findings show that structural inconsistency signals provide a practical and generalizable basis for black-box jailbreak defense, especially when combined with semantic auditing.

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04.

arXiv (CS.CL) 2026-06-16 DOI: arXiv:2606.16825

Tying the Loop – Tied Expert Layers in Mixture-of-Experts Language Models

作者:

Martin Jaggi ↗

Mixture-of-Experts (MoE) architectures efficiently scale Large Language Models (LLMs) by activating only a small fraction of their experts per token, yet the full parameter count - dominated by the expert parameters - must be held in training and inference memory. To address this, we introduce Expert Tying, an architectural modification that shares expert parameters across consecutive transformer layers while preserving independent, layer-wise routing and attention. We evaluate this approach across common, state-of-the-art architectures, including OLMoE, Qwen3, and DeepSeek-style MoEs. Our pretraining experiments demonstrate that tying experts can reduce memory footprint by almost 2x at virtually no degradation in perplexity or downstream quality. By exploiting the parameter redundancy inherent in MoE pathways, our method provides a highly favorable compute-to-memory trade-off, advancing efficient training and scaling of next-generation LLMs.

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05.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2606.19292

Risk Stratification for ICU Delirium using Pervasive Ambient Sensing Information

作者:

arXiv:2606.19292v1 Announce Type: new Abstract: Delirium is a common and serious complication in the Intensive Care Unit (ICU), associated with increased morbidity, prolonged hospital stays, and higher healthcare costs. Despite its prevalence, early prediction and prevention remain challenging. Environmental factors such as ambient sound and light may influence the onset of delirium, yet they are often overlooked in risk assessments. In this study, we examined whether light intensity and sound pressure levels can independently predict delirium across multiple prediction horizons. We evaluated four efficient sequential neural network models on data collected from 9 ICUs across 309 patients to predict delirium for 10 prediction-window sizes. We reported feature importance and direction of influence using Shapley Additive Explanations analysis. The convolutional model achieved the strongest discrimination, with AUC = 0.80 on sound data and on combined data. Sound features were the dominant predictors overall. Integrating sound with light improved short-term ($

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06.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2606.15762

Snyk VulnBench JS 1.0: Can LLMs Find the Same Bugs Twice?

作者:

Liran Tal ↗Johannes Kloos ↗Arsenii Rudich ↗Stephen Thoemmes ↗Manoj Nair ↗

arXiv:2606.15762v1 Announce Type: cross Abstract: We ran 300 repeated vulnerability-finding scans to measure how repeatable agentic large language model (LLM) security review is on the same JavaScript code, prompt, and benchmark harness. The headline result is that LLM security findings were unevenly repeatable: reference-matched findings were stable, but extra model reports varied heavily from run to run. Across 250 model runs, 80 of 161 unique unmatched findings appeared in only one of five identical repetitions, while only 22 appeared in all five. By contrast, when Claude matched a Snyk Code reference finding, the behavior was much more stable: 134 of 158 unique reference-matched findings appeared in all five repetitions. The benchmark also shows complementarity. Models consistently found familiar, high-signal exploit shapes, and in one case surfaced a likely Snyk Code product gap. Snyk Code static application security testing (SAST) was deterministic and better at systematically enumerating repeated data-flow sinks. The results support combining agentic LLM review with deterministic SAST rather than treating either technique as a replacement for the other.

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07.

arXiv (CS.CL) 2026-06-16 DOI: arXiv:2606.16753

P3B3: A Multi-Turn Conversational Benchmark for Measuring European and Brazilian Portuguese Variety Bias in LLMs

作者:

Rafael Ferreira ↗In\^es Vieira ↗In\^es Calvo ↗James Furtado ↗Iago Paulo ↗Diogo Tavares ↗Diogo Gl\'oria-Silva ↗David Semedo ↗Jo\~ao Magalh\~aes ↗

As Large Language Models (LLMs) become embedded in everyday communication, capturing regional linguistic variation is essential for reliable and equitable language use. In Portuguese, European (pt-PT) and Brazilian (pt-BR) varieties remain unevenly represented, with pt-BR dominating in data quantity, while LLM preference for Portuguese variants remains underexplored. To address this gap, we introduce P3B3, an expert-curated language variety agnostic benchmark of conversational prompts, along with an evaluation framework for measuring variety bias and controllability. Experiments on several models show that most LLMs exhibit a strong bias toward pt-BR, with variation in controllability across models. These results highlight the need for more balanced multilingual representation across language varieties.

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08.

arXiv (CS.CV) 2026-06-19 DOI: arXiv:2606.19495

LooseControlVideo: Directorial Video Control using Spatial Blocking

作者:

Shariq Farooq Bhat ↗Niloy J. Mitra ↗Kalyan Sunkavalli ↗

Precise 3D spatial orchestration in text-to-video generation remains a significant challenge, particularly for multi-object scenes where semantic layout and temporal dynamics are often entangled. While existing depth-conditioned models achieve good structural fidelity, they necessitate dense, frame-accurate guidance that is labor-intensive to author for dynamic events involving deformable objects. We present LooseControlVideo, a framework that enables intuitive and expressive control by using sparse, oriented 3D boxes as a "blocking" proxy. This allows users to author high-level layout and trajectory while leveraging a video generative model to generate realistic occlusions, dynamics and interactions. We achieve this by fine-tuning a Wan 2.2 backbone on a video dataset annotated with DNOCS, a novel encoding for 3D size, orientation and depth-ordered occlusions. Furthermore, our method allows for localized refinement, such as adjusting a jump trajectory or adding an interaction, with minimal disruption to the global scene context. Extensive evaluations on the nuScenes, HO-3D, and BEHAVE benchmarks demonstrate that LooseControlVideo significantly outperforms existing 2D-box and flow-based baselines. Our findings indicate a 1.2x to 3x improvement in Trajectory Error; 2x improvement in Rigid Motion Consistency; and a 1.5x to 2x increase in Occlusion Accuracy over current state-of-the-art layout-conditioned models, demonstrating that oriented 3D primitives provide good geometric prior for complex, multi-agent video authoring.

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09.

arXiv (quant-ph) 2026-06-17 DOI: arXiv:2604.20912

Quantum-HPC Software Stacks and the openQSE Reference Architecture: A Survey

作者:

arXiv:2604.20912v2 Announce Type: replace Abstract: Quantum resources are increasingly integrated into high-performance computing (HPC) and cloud environments, but quantum high-performance computing (QHPC) software stacks remain isolated, often proprietary, full-stack solutions lacking common interfaces across runtime, resource management, orchestration, and execution layers. This paper analyzes nine production QHPC stacks and identifies common design patterns and emerging requirements, covering deployment models, application interaction patterns, SDK support, and readiness for fault-tolerant operation. The survey exposes consistent needs in runtime abstraction, resource management, interconnect semantics, and observability. Based on these findings, we propose the open quantum-HPC software ecosystem ( openQSE) reference architecture as a first step toward unifying the state-of-the-practice. openQSE defines a set of layer boundaries that allow different implementations to interoperate while preserving deployment flexibility, and is structured to support both current noisy intermediate-scale quantum (NISQ) workloads and future fault-tolerant quantum computing (FTQC) systems without changes to upper-layer application interfaces.

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10.

arXiv (CS.CV) 2026-06-17 DOI: arXiv:2606.18063

When LLMs Analyze Scars: From Images to Clinically-Meaningful Features

作者:

Ruman Wang ↗Hangting Ye ↗

Medical image classification faces a fundamental dilemma: while deep learning models achieve remarkable performance at scale, real-world clinical scenarios often suffer from severe data scarcity due to annotation costs, privacy constraints, and disease rarity. This challenge is particularly pronounced in pathological scar classification, where differentiating keloids from hypertrophic scars requires subtle expert knowledge and labeled images are extremely limited. We propose a novel paradigm that repositions large language models (LLMs) as knowledge-driven feature engineers rather than end-to-end classifiers. We call this framework ScaFE (Scar Feature Engineering). Our key insight is that LLMs encode rich medical knowledge that can be externalized as executable feature extraction code, enabling the transformation of high-dimensional images into low-dimensional, clinically interpretable representations. Specifically, we prompt an LLM with established scar assessment criteria to generate deterministic Python code that extracts features aligned with clinical scoring systems such as the Vancouver Scar Scale. Our approach offers three key advantages: (1) data efficiency, achieving robust performance with limited training samples by decoupling knowledge acquisition from statistical learning; (2) privacy preservation, as raw images are processed locally without exposure to external LLMs; and (3) interpretability, through explicit features grounded in clinical reasoning. Extensive experiments on scar classification demonstrate that our method consistently outperforms end-to-end deep learning baselines or using LLMs as black-box classifiers under limited data conditions, establishing a promising direction for integrating LLMs into data-efficient and clinically transparent medical AI systems.

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11.

arXiv (CS.LG) 2026-06-11 DOI: arXiv:2602.14913

Coverage Guarantees for Pseudo-Calibrated Conformal Prediction under Distribution Shift

作者:

Farbod Siahkali ↗Ashwin Verma ↗Vijay Gupta ↗

arXiv:2602.14913v2 Announce Type: replace Abstract: Conformal prediction (CP) offers distribution-free marginal coverage guarantees under an exchangeability assumption, but these guarantees can fail if the data distribution shifts. We analyze the use of pseudo-calibration as a tool to counter this performance loss under a bounded label-conditional covariate shift model. Using tools from domain adaptation, we derive a lower bound on target coverage in terms of the source-domain loss of the classifier and a Wasserstein measure of the shift. Using this result, we provide a method to design pseudo-calibrated sets that inflate the conformal threshold by a slack parameter to keep target coverage above a prescribed level. Finally, we propose a source-tuned pseudo-calibration algorithm that interpolates between hard pseudo-labels and randomized labels as a function of classifier uncertainty. Numerical experiments show that our bounds qualitatively track pseudo-calibration behavior and that the source-tuned scheme mitigates coverage degradation under distribution shift while maintaining nontrivial prediction set sizes.

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12.

arXiv (CS.AI) 2026-06-17 DOI: arXiv:2606.17317

Transformer-Based Warm-Starting for Feasible and Optimal Terminal Approach to Tumbling Objects with Space Manipulators

作者:

Yuji Takubo ↗Maximilian Adang ↗Mac Schwager ↗Simone D'Amico ↗

arXiv:2606.17317v1 Announce Type: cross Abstract: Real-time trajectory generation for on-orbit robotic servicing is challenging due to the nonlinear coupling between spacecraft bus motion, manipulator dynamics, visibility cone, and trajectory-level safety constraints. This paper studies learning-based warm-starting for sequential convex programming (SCP) in the terminal approach of a space manipulator toward a tumbling target. The proposed framework decomposes the problem into a system center-of-mass translational planning stage and a coupled attitude–manipulator torque-allocation stage, and applies a causal transformer warm-start to the latter, which constitutes the dominant computational bottleneck. Linear and flow matching action decoders are compared under different action-chunking and training dataset sizes, and the resulting warm-starts are evaluated under both cost-optimal and feasibility projection using SCP. Across 300 held-out scenarios, the learned warm-start reduces the second-stage SCP iteration count by up to 28% and the runtime by 23% while preserving the final control-cost distribution. When the learned warm-starts are used for nonconvex feasibility projection, they nearly halve the runtime relative to cost-optimal SCP, while avoiding the catastrophic high-cost tail behavior observed when initialized heuristically. These results indicate that sequence-model warm-starts can improve both the computational efficiency and trajectory robustness of optimization-based terminal guidance for space manipulation.

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13.

arXiv (CS.AI) 2026-06-11 DOI: arXiv:2606.11632

Sovereign Assurance Boundary: Certificate-Bound Admission for Agentic Infrastructure

作者:

Jun He ↗Deying Yu ↗

arXiv:2606.11632v1 Announce Type: cross Abstract: Agentic infrastructure introduces a critical control-plane authorization problem: non-deterministic reasoning systems can propose high-stakes mutations to production resources, yet existing security mechanisms – such as identity and access management (IAM), policy engines, consensus protocols, and audit logs – either enforce static, context-unaware permissions or merely record actions post-execution. This paper introduces the Sovereign Assurance Boundary (SAB), a certificate-bound runtime admission layer for autonomous execution authority. SAB intercepts agent proposals at an assurance airlock, compiles them into typed execution contracts $C$, and binds these contracts to cryptographic evidence digests $H(E)$ and policy versions. The contracts are then routed through consequence-aware certification paths. Upon successful admission, the system emits a signed Sovereign Assurance Certificate ($\Omega$) that is strictly scoped to a specific execution identity, revocation epoch, and validity window. Finally, a sovereign execution broker verifies $\Omega$ and performs fresh pre-execution revocation and drift checks before invoking infrastructure APIs. We detail the airlock-broker architecture, formalize its admission and revocation invariants, and report preliminary feasibility measurements from a Go prototype evaluated over 2,500 admission attempts. Ultimately, this broker-enforced model prevents autonomous reasoning from directly mutating state, transforming delegated execution authority into a cryptographically verifiable, evidence-bound, revocable, and replayable runtime artifact.

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14.

arXiv (CS.CV) 2026-06-15 DOI: arXiv:2606.14096

A New Multi-Domain Benchmark for Micro-Action Recognition and Detection

作者:

Yanbin Hao ↗Pengyu Liu ↗Xing Wei ↗Xun Yang ↗Dan Gu ↗Meng Wang ↗

Micro-actions are short-duration, low-amplitude subtle body movements at the whole-body level that can reveal latent intentions, involuntary reactions, and fine-grained affective changes. Our previous MA-52 benchmark has provided an important foundation for micro-action recognition, but it remains limited in scale, scene diversity, task coverage, and evaluation protocols. To advance micro-action analysis toward more realistic and comprehensive settings, we introduce MMA-82, a large-scale multi-domain extension of MA-52. MMA-82 expands the label space from 52 to 82 fine-grained micro-action categories and covers four distinct domains, including laboratory interviews, street interviews, psychiatric patient interviews, and emotion-rich television videos, resulting in 77,856 annotated instances from 454 subjects. Built upon MMA-82, we establish two core tasks: Micro-Action Recognition and Multi-label Micro-Action Detection. For recognition, we further define in-domain and cross-domain protocols, including few-shot and zero-shot settings, to evaluate model robustness, transferability, and generalization. Extensive experiments show that current methods still struggle with realistic micro-action understanding, especially under domain shift, long-tailed category distributions, and complex temporal localization. Beyond benchmarking, we investigate the relationship between micro-actions and emotion, showing that micro-actions are strongly associated with emotional states and provide complementary cues to facial micro-expressions for improved emotion recognition. These results demonstrate that MMA-82 serves as a comprehensive and challenging benchmark for realistic micro-action analysis and a valuable resource for human-centered AI. MMA-82 is available at https://github.com/LpyNow/MMA-82.

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15.

arXiv (CS.CL) 2026-06-15 DOI: arXiv:2606.14113

Simulating Students' Java Programming Errors with Large Language Models

作者:

Ali Keramati ↗Jie Cao ↗Iman Mohammadi ↗Mark Warschauer ↗Yang Shi ↗

Understanding student errors in the programming is a cornerstone of programming education, yet obtaining a representative set of student errors for any newly designed task remains slow and costly, since authentic submissions only accumulate after extensive classroom deployment. This paper explores whether large language models (LLMs) can serve as scalable proxies for students by simulating realistic logical errors in code submissions. Using the CodeWorkout dataset of 74,000+ unique student Java submissions across 37 problems, we evaluate five LLMs under three mainstream prompting strategies: Input-Output (IO), Chain-of-Thought (CoT), and iterative Self-Refine. We assess performance along two key dimensions: diversity (the range of distinct error patterns) and alignment (alignment with authentic student mistakes), and examine how these vary by struggling level of programming tasks. Our quantitative findings reveal that while all models generate diverse errors, their alignment to human submissions diverges: Claude Sonnet 4 achieves the most balanced performance. In addition, we conducted a blinded expert annotation study (N = 401) comparing synthetic and authentic errors. This qualitative analysis confirms that the generated errors are functionally indistinguishable from authentic student errors. Moreover, higher-struggling-level problems elicit more diverse but less student-like errors. These results highlight trade-offs in using LLMs to simulate human learners and suggest design considerations for integrating synthetic errors into teachable agents, intelligent tutoring systems, and large-scale learning analytics.

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16.

arXiv (CS.CV) 2026-06-15 DOI: arXiv:2606.14534

A Lightweight Fiducial-Based Pipeline for 3D Hyperspectral Mapping of ex-vivo Lumpectomy Specimens

作者:

Anna Bicchi ↗Alberto Rota ↗Leonardo Passoni ↗Nicola Ancellotti ↗Andrea Peroni ↗Lorenzo Vinco ↗Dario Polli ↗Elena De Momi ↗

Hyperspectral Imaging (HSI) is a promising modality for intraoperative assessment of resection margins in Breast-Conserving Surgery (BCS), but its clinical translation requires aligning the inherently 2D spectral information onto the 3D shape of the excised tissue so that suspicious regions can be precisely localized for targeted follow-up. We present a fully automated, calibration-free pipeline that produces a 3D hyperspectral point cloud of an ex-vivo lumpectomy specimen from a set of consumer-camera RGB images and a single top-down HSI acquisition. The 3D geometry is reconstructed with a deep-learning Structure-from-Motion backbone, stabilized in a metric reference frame by a custom bundle adjustment that enforces consistency on the corners of four ArUco markers placed around the specimen. The HSI cube is then registered to the reconstruction without recovering the HSI camera pose: the markers, visible in both modalities, define 16 corner correspondences that drive a planar homography, and 3D coordinates are recovered by lookup on an orthographically rendered depth map. Evaluated on two ex-vivo lumpectomy specimens, the pipeline achieves a median 3D registration error below 1~mm and a 2D reprojection error below 0.02 mm, with a total per-specimen processing time under 4 minutes on accelerated hardware. These results support the feasibility of integrating HSI-guided spatial localization into intraoperative margin assessment workflows for breast-conserving surgery.

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17.

arXiv (quant-ph) 2026-06-17 DOI: arXiv:2602.23773

Entanglement dynamics for atoms near a reflecting boundary: Enhancement and suppression by environment-induced interactions

作者:

Ying Chen ↗Hongwei Yu ↗Jiawei Hu ↗

arXiv:2602.23773v2 Announce Type: replace Abstract: We investigate how environment-induced interactions influence the entanglement dynamics of two atoms held at fixed positions near a perfectly reflecting boundary. Within the framework of open quantum systems, we explicitly incorporate the environment-induced energy shifts, including both atom-boundary contributions and an environment-induced atom-atom interaction, which are often neglected in previous studies. We show that, for any initial two-atom state, these energy-shift effects qualitatively and quantitatively modify the entanglement dynamics relative to treatments that omit them. Depending on the geometry and parameter regime, the environment-induced interactions can either enhance entanglement generation – yielding a larger maximum concurrence and a longer entanglement lifetime – or suppress it, reducing both the peak concurrence and the survival time. This behavior contrasts sharply with the free-space case, where the environment-induced atom-atom interaction affects entanglement generation only for a restricted class of initial states and does so in an exclusively assisting manner.

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18.

arXiv (CS.AI) 2026-06-19 DOI: arXiv:2606.19934

Speeding up the annotation process in semantic segmentation industrial applications

作者:

Marta Fernandez-Moreno ↗Margarita Guerrero ↗Rosalia Rementeria ↗Pablo Mesejo ↗Raul Moreno ↗

arXiv:2606.19934v1 Announce Type: cross Abstract: Current machine learning models commonly require large and well-annotated datasets. However, the annotation process often becomes a bottleneck, with increased complexity leading to higher chances of human errors. Within this context, our goal in this paper is to leverage unsupervised algorithms to improve data annotation efficiency for complex semantic segmentation problems in industrial materials science. Previous research has quantified labeling time and others explored unsupervised methods. However, to the best of our knowledge, this is the first study to quantify how much unsupervised algorithms accelerate the labeling process. We aim to validate the extent to which this laborious process can be accelerated, focusing on semantic segmentation tasks that involve annotating each pixel of high-resolution images, such as the microstructure characterization challenge in materials science. Specifically, we demonstrate that by using unsupervised computer vision algorithms, the time required for the labeling process can be reduced from 170 hours to 37 hours, achieving an approximate reduction of 78\%. The dataset we work with includes large images of dimensions 1280x959 and 960x703, which further increases the complexity of the annotation task. Despite these challenges, we create and share the largest public steel microstructure segmentation dataset to date, available under MIT License with permanent DOI, contributing a fully annotated, high-resolution dataset to the field. Additionally, this is the first work to compare the labeling time from scratch (a common approach in previous studies) to the labeling time when using these unsupervised algorithms as a pre-annotation step. Furthermore, we provide a Deep Learning model trained on this dataset, validated by field experts, and deployed in an industrial setting, serving as an initial benchmark for this public dataset.

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19.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2603.02274

Contextual Invertible World Models: A Neuro-Symbolic Agentic Framework for Colorectal Cancer Drug Response

作者:

Christopher Baker ↗Tianyu Ren ↗Karen Rafferty ↗Hui Wang ↗

arXiv:2603.02274v3 Announce Type: replace-cross Abstract: Precision oncology is currently limited by the small-N, large-P paradox, where high-dimensional genomic data is abundant but pharmacological response samples are sparse. While deep learning achieves predictive accuracy, it frequently fails to provide the mechanistic clarity required for clinical adoption. We present the Contextual Invertible World Model (CIWM), a Neuro-Symbolic Agentic Framework that bridges this gap by integrating a quantitative machine learning emulator with a Large Language Model reasoning layer. Utilising a stringently curated, high-fidelity data engineering pipeline on the Sanger GDSC dataset ($ N=83 $), we isolate true biological signals from in vitro artifacts to establish a rigorous baseline predictive correlation for complex transcriptomics ($ r=0.268 $). Through Inverse Reasoning, we perform in silico CRISPR perturbations across the colorectal landscape. The framework autonomously overturns classical mechanistic assumptions, identifying a hierarchical dominance of mutant KRAS over the APC/Wnt-axis in driving 5-fluorouracil resistance ($ \Delta=-0.0469 $) via a "KRAS Shield" mapped to MAPK/PI3K networks. Furthermore, the agentic layer identified a "PIK3CA Paradox", revealing that repairing PIK3CA inadvertently increases chemoresistance ($ \Delta=+0.0085 $) by triggering a compensatory feedback loop that hyperactivates the dominant MAPK survival pathway.

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20.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2601.20361

TINNs: Time-Induced Neural Networks for Solving Time-Dependent PDEs

作者:

Chen-Yang Dai ↗Che-Chia Chang ↗Te-Sheng Lin ↗Ming-Chih Lai ↗Chieh-Hsin Lai ↗

arXiv:2601.20361v2 Announce Type: replace Abstract: Physics-informed neural networks (PINNs) solve time-dependent partial differential equations (PDEs) by learning a mesh-free, differentiable solution that can be evaluated anywhere in space and time. However, standard space-time PINNs take time as an input but reuse a single network with shared weights across all times, forcing the same features to represent markedly different dynamics. This coupling degrades error performance and can destabilize training when enforcing PDE, boundary, and initial constraints jointly. We propose Time-Induced Neural Networks (TINNs), a novel architecture that parameterizes the network weights as a learned function of time, allowing the effective spatial representation to evolve over time while maintaining shared structure. The resulting formulation naturally yields a nonlinear least-squares problem, which we optimize efficiently using a Levenberg-Marquardt method. Experiments on various time-dependent PDEs show up to 4 times improved relative error and 10 times faster convergence compared to PINNs and strong baselines.

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21.

arXiv (CS.AI) 2026-06-17 DOI: arXiv:2604.24357

DPRM: A Plug-in Doob h transform-induced Token-Ordering Module for Diffusion Language Models

作者:

Dake Bu ↗Wei Huang ↗Andi Han ↗Hau-San Wong ↗Qingfu Zhang ↗Taiji Suzuki ↗Atsushi Nitanda ↗

arXiv:2604.24357v2 Announce Type: replace-cross Abstract: Diffusion language models generate without a fixed left-to-right order, leaving token ordering as a central algorithmic choice. Existing systems mainly use random masking or confidence-driven ordering, which respectively suffer from train–test mismatch and myopic exploration. We introduce DPRM (Doob -transform Process Reward Model), a plug-in token-ordering module that keeps the host architecture, denoising objective and supervision unchanged, and modifies only the ordering policy. DPRM starts from confidence-driven ordering and gradually shifts to process-reward-guided ordering through online estimates. We characterize the exact DPRM policy as a reward-tilted Gibbs reveal law, prove convergence of its stagewise Soft-BoN approximation, show that the online bucketized controller tracks the exact DPRM score at empirical-Bernstein rates, and establish a sample-complexity advantage under tractable optimization assumptions. Across nine hosts covering language reasoning, test-time scaling, protein, single-cell, molecular, DNA, text-to-image generation, and VQA, DPRM order variants improve several language, DNA, and multimodal settings while also identifying boundary cases where confidence-only ordering or task-specific utilities are preferable. Code is available at: https://github.com/DakeBU/DPRM-DLLM

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22.

arXiv (CS.AI) 2026-06-15 DOI: arXiv:2606.08881

Benchmarking Vision-Language-Action Models on SO-101: Failure and Recovery Analysis

作者:

Yi Yu ↗Xinchuan Qiu ↗

arXiv:2606.08881v2 Announce Type: replace-cross Abstract: Vision-Language-Action (VLA) models have demonstrated strong generalization in robotic manipulation, yet existing evaluations are primarily conducted in simulation or on expensive robotic platforms, leaving their robustness on affordable real-world robots largely unexplored. We present a standardized real-world benchmark for evaluating representative VLA and imitation learning policies on the low-cost SO-101 robotic platform. The benchmark comprises four representative manipulation tasks together with unified evaluation protocols, enabling systematic comparison under embodiment uncertainty. Using real-world teleoperated demonstrations, we fine-tune and evaluate $\pi_{0.5}$, SmolVLA, Wall-X, and ACT directly on the physical platform. Beyond conventional task success rates, the benchmark incorporates a structured failure taxonomy, semantic- and execution-level failure decomposition, and recovery-aware evaluation metrics to characterize policy robustness. Experimental results show that stronger pretrained VLA policies generally outperform the imitation learning baseline, although performance remains highly task-dependent under low-cost robotic deployment conditions. Execution instability emerges as the dominant failure source, while recovery capability varies substantially across architectures. These results highlight the importance of failure and recovery analysis beyond binary task success and establish SO-101 as a practical benchmark for evaluating embodied AI systems under realistic low-cost robotic deployment conditions.

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23.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2606.18496

Neural Phase Correlation

作者:

Cole Reynolds ↗

Correspondence is fundamentally relational: it seeks the unknown transformation between two observations of a common scene, not the content of either. Yet the dominant learning-based methods do not represent the transformation as a first-class object in the architecture. They encode each image independently and let a learned similarity function or a deep decoder discover the mapping implicitly. Phase correlation is the canonical exception, measuring the inter-image relationship directly in the Fourier domain, but the rigidity of its fixed basis confines it to global translation. We introduce a learned generalization of phase correlation that lifts this restriction by learning the basis on which the transformation decomposes. The same algebraic primitive extends to dense non-rigid deformations and to unitary dynamics. On the ACDC cardiac-MRI benchmark the framework matches or exceeds prior published baselines on both registration directions. On CAMUS echocardiography it matches state-of-the-art without auxiliary scoring or adaptive-smoothness mechanisms. Applied to time-evolved wavefunction pairs of the 1-D quantum harmonic oscillator, the same framework recovers the Hermite-function eigenstates and the quantized energy levels of the unknown Hamiltonian from observation pairs alone.

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24.

bioRxiv (Bioinfo) 2026-06-18 DOI: HASH:7fcefcd040c1145a35d06e6a4578f1ed

Benchmarking attention-based methods for vision transformers' interpretability in retinal fundus imaging

作者:

Bors ↗Beyeler ↗Trofimova ↗VascX Consortium ↗Presby ↗Bontempi ↗Bergmann ↗

Deep learning models based on Vision Transformers (ViTs) have shown strong performance in retinal fundus imaging, but their interpretability remains poorly understood. In particular, attention-based attribution methods are widely used to explain ViT predictions, despite limited evaluation of their faithfulness and biological relevance in medical imaging. Here, we systematically benchmark four attention-based interpretability methods for RETFound, a retinal ViT-based foundation model, that we previously fine-tuned to predict 17 retinal vascular phenotypes from UK Biobank fundus images1. We compare raw attention, attention rollout, gradient-weighted attention rollout, and Chefer's hybrid relevance-based method using both qualitative visualisation and quantitative evaluation frameworks. To assess attribution faithfulness, we perform perturbation-based deletion and insertion experiments, quantifying changes in model predictions as highly attended image regions are progressively removed or restored. To evaluate biological specificity, we run structure-aware analyses combining attribution maps with vessel segmentation and artery-vein labels through the Relative ratio of Attention Intensity (RAI) metric. Across models, attribution maps differed substantially depending on the selected interpretability method, highlighting the need for rigorous quantitative evaluation. Among the evaluated approaches, gradient-weighted attention rollout consistently achieved the strongest perturbation performance and produced attribution maps most closely aligned with the anatomical definition of the predicted retinal traits. Furthermore, vessel-type specific models systematically concentrate attention on the corresponding vascular structures despite being trained using only a single scalar value per image as supervision. These findings demonstrate that attention-based attribution methods capture biologically meaningful vascular representations, while also revealing method-dependent variability in attribution behaviour. This work provides a quantitative framework for evaluating interpretability methods in medical imaging with annotated segmentation and contributes toward more transparent and biologically grounded medical AI systems.

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25.

arXiv (CS.CV) 2026-06-11 DOI: arXiv:2510.06596

SDQM: Synthetic Data Quality Metric for Object Detection Dataset Evaluation

作者:

Ayush Zenith ↗Arnold Zumbrun ↗Neel Raut ↗Jing Lin ↗

The performance of machine learning models depends heavily on training data. The scarcity of large-scale, well-annotated datasets poses significant challenges in creating robust models. To address this, synthetic data generated through simulations and generative models has emerged as a promising solution, enhancing dataset diversity and improving the performance, reliability, and resilience of models. However, evaluating the quality of this generated data requires an effective metric. We introduce the Synthetic Dataset Quality Metric (SDQM) to assess data quality for object detection tasks without requiring model training to converge. This metric enables more efficient generation and selection of synthetic datasets, addressing a key challenge in resource-constrained object detection tasks. In our experiments, SDQM demonstrated a strong correlation with the mean average precision (mAP) scores of YOLO11, a leading object detection model, whereas previous metrics only exhibited moderate or weak correlations. In addition, it provides actionable insights into improving dataset quality, minimizing the need for costly iterative training. This scalable and efficient metric sets a new standard for evaluating synthetic data. The code for SDQM is available at https://github.com/ayushzenith/SDQM

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