Paper Plaza - AcademicHub

01.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2605.02249

A Study of Belief Revision Postulates in Multi-Agent Systems (Extended Version)

Authors:

arXiv:2605.02249v2 Announce Type: replace Abstract: We investigate the belief revision problem in epistemic planning, i.e., what will be the beliefs of all agents in a multi-agent system after an agent gains the belief in some state property. Based on the standard representation in epistemic planning of agents' beliefs via a single multi-agent Kripke model, we generalize the classical AGM belief revision postulates to the multi-agent setting, with the aim to provide a formal framework for evaluating dynamic epistemic reasoning frameworks in which the beliefs of all agents as the result of actions are computed. As an example of a simple operator that satisfies all of the generalized AGM postulates, we present generalized full-meet multi-agent belief revision. We moreover define a generalization of the standard postulates for iterated revision, present a more sophisticated, event model based revision operator, and discuss the potential issues in defining an epistemic operator on Kripke models that can satisfy all of the generalized postulates for iterated multi-agent belief revision.

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02.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2606.18992

Show, Don't Ask: Generative Visual Disambiguation for Composed Image Retrieval with Turn-Valid Coverage

Authors:

Amsisan Tran ↗Baogh Le ↗Tuan Kiet Pham ↗Sui Yang Guang ↗

Composed image retrieval (CIR) uses a reference image and a text modification to search for a target image. However, such queries often describe several possible images rather than one exact target, making the user's intent ambiguous. Recent methods address this by using conformal prediction to estimate ambiguity and by asking users clarifying text questions. However, these methods have two limitations: their coverage guarantee only holds at the first interaction, and text questions are often insufficient for resolving fine-grained visual differences such as appearance, attributes, or viewpoint. We propose CLARA, a clarification framework that resolves ambiguity by showing users a small panel of visual alternatives. Instead of answering text questions, the user simply selects the prototype image closest to the intended target. This provides a direct visual signal and avoids relying on a model to predict the user's answer. To maintain valid conformal guarantees across multiple interaction rounds, CLARA reweights calibration using the likelihood ratio induced by the user's selection. The displayed prototypes are also constrained to represent the current candidate set and are snapped to real corpus images, ensuring that generated images cannot artificially improve coverage. Experiments on open-domain and fashion benchmarks show that CLARA matches single-turn state-of-the-art retrieval performance, maintains nominal coverage across interaction rounds, and finds the intended target in fewer rounds than strong text-question baselines. Its advantage is especially clear when ambiguity involves viewpoint or fine-grained attributes, where visual clarification is more effective than textual questioning.

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03.

arXiv (CS.CV) 2026-06-17 DOI: arXiv:2606.17432

Edit3DGS: Unified Framework for Dynamic Head Editing via 2D Instruction-Guided Diffusion and 3D Gaussian Splatting

Authors:

Duy-Dat Tran ↗Trung-Nghia Le ↗

We present Edit3DGS, a unified framework for dynamic 3D head editing that integrates 2D instruction-guided diffusion with 3D Gaussian splatting. Unlike prior approaches that separately address frame-based edits or static 3D reconstruction, our method couples semantic controllability in the image domain with photorealistic, temporally consistent 3D representations. Given an input video, editable facial regions are masked and modified using a text-conditioned diffusion model to support fine-grained operations such as expression transformation, attribute modification, and appearance refinement. The edited frames are then aggregated through 3D Gaussian splatting to produce a coherent, high-fidelity avatar that preserves both identity and motion dynamics. To enforce consistency, Edit3DGS incorporates multi-view batch editing and lightweight inpainting strategies that recover lost expressions across timesteps. Experimental results demonstrate that our framework enables controllable, artifact-free head editing with smooth temporal transitions, offering practical applications in virtual avatars, immersive communication, film production, and interactive media.

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04.

arXiv (CS.LG) 2026-06-11 DOI: arXiv:2606.11699

A Data-Centric Framework for Detecting and Correcting Corrupted Labels

Authors:

Ha-Linh Nguyen ↗Hong-Anh Nguyen ↗Minh-Duc La ↗Thu-Trang Nguyen ↗Son Nguyen ↗Hieu Dinh Vo ↗

arXiv:2606.11699v1 Announce Type: new Abstract: The performance of machine learning and deep learning models largely depends on the quality of the training data. However, the quality of the real-world datasets is often compromised by noisy labels, which can substantially degrade model accuracy and reliability. To address this challenge, we propose Relabeler, an end-to-end data-centric framework for detecting and correcting corrupted labels. For corrupted label detection, Relabeler jointly leverages both local and global relationships among data instances to identify potentially noisy samples. After detecting suspicious instances, Relabeler further performs label correction by estimating the most probable clean label for each instance based on both its input features and observed noisy label. Extensive experiments across multiple datasets, noise types, and noise rates demonstrate that Relabeler consistently outperforms state-of-the-art baselines, achieving up to 58% improvement in label correction precision and 6% improvement in downstream task performance.

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05.

medRxiv (Medicine) 2026-06-17 DOI: HASH:9094feaae8b047109735b0a011edba93

Clinical Study Protocol of the 'Biomarkers of Severity of COVID-19 Patients' (BIOMARCOVID) Project

Authors:

Dinh ↗T.-A ↗Leroy ↗Brandolini-Bunlon ↗Berthier ↗Trocme ↗Varoquaux ↗Plazy ↗Vilotitch ↗Terra ↗Toussaint ↗Bosson ↗…

Introduction The coronavirus disease 2019 (COVID-19) pandemic has challenged health care systems worldwide, in certain areas exceeding hospital capacities and human resources. This has underscored the importance of having better tools to predict the outcome of potentially severe respiratory infections such as SARS-CoV-2. Predicting COVID-19 severity may allow physicians to better manage ICU beds and increase the chances of patient survival through appropriate management. During the toughest months of the pandemic, most physicians tried to identify patients that might develop severe forms based primarily on clinical features on admission (e.g., BMI, age). In this context, significant research has focused on identifying comorbidities, clinical manifestations, and routine blood biomarkers to predict disease severity. However, despite the demonstrated value of untargeted metabolomics in assessing severity, limited data exist on its use for identifying novel metabolite biomarkers that could improve both the sensitivity and specificity of outcome prediction. Our goal is to identify metabolite biomarkers that could enhance the predictive accuracy of standard medical biology data and clinical parameters. Methods and analysis This is a retrospective, observational, monocentric cohort study conducted at the Centre Hospitalier Universitaire Grenoble Alpes (CHUGA). The maximum number of eligible patients admitted for PCR-confirmed COVID-19 between March and December 2020 will be included. Severity outcome is defined using the WHO 10-category ordinal scale (mild: categories 4-5; severe: >5). Blood samples were collected within 48 hours of admission and analyzed for 62 routine blood tests and untargeted multiplatform LC-MS/MS metabolomics across four national platforms. Statistical analysis will include logistic regression with variable selection for the primary aim, and multi-block chemometric integration of clinical, biological, and metabolomics data as a secondary aim. Ethics and dissemination A study steering committee has been formed to ensure the accuracy of the collected data by thoroughly reviewing it prior to the data lock. All aspects of the study comply with ethical standards, including approval by the CHUGA institutional review board and adherence to CNIL Reference Methodology MR004 for the protection of participants' rights, privacy, and confidentiality. This study is registered on the French Health Data Hub (number F20210218154851). Results will be disseminated through peer-reviewed publications, presentations at national and international scientific and clinical conferences, and reports shared with key healthcare system stakeholders.

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06.

arXiv (CS.CL) 2026-06-12 DOI: arXiv:2604.10389

BLUEmed: Retrieval-Augmented Multi-Agent Debate for Clinical Error Detection

Authors:

Saukun Thika You ↗Nguyen Anh Khoa Tran ↗Wesley K. Marizane ↗Hanshu Rao ↗Qiunan Zhang ↗Xiaolei Huang ↗

Terminology substitution errors in clinical notes, where one medical term is replaced by a linguistically valid but clinically different term, pose a persistent challenge for automated error detection in healthcare. We introduce BLUEmed, a multi-agent debate framework augmented with hybrid Retrieval-Augmented Generation (RAG) that combines evidence-grounded reasoning with multi-perspective verification for clinical error detection. BLUEmed decomposes each clinical note into focused sub-queries, retrieves source-partitioned evidence through dense, sparse, and online retrieval, and assigns two domain expert agents distinct knowledge bases to produce independent analyses; when the experts disagree, a structured counter-argumentation round and cross-source adjudication resolve the conflict, followed by a cascading safety layer that filters common false-positive patterns. We evaluate BLUEmed on a clinical terminology substitution detection benchmark under both zero-shot and few-shot prompting with multiple backbone models spanning proprietary and open-source families. Experimental results show that BLUEmed achieves the best accuracy (69.13%), ROC-AUC (74.45%), and PR-AUC (72.44%) under few-shot prompting, outperforming both single-agent RAG and debate-only baselines. Further analyses across six backbone models and two prompting strategies confirm that retrieval augmentation and structured debate are complementary, and that the framework benefits most from models with sufficient instruction-following and clinical language understanding.

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07.

arXiv (CS.CL) 2026-06-24 DOI: arXiv:2606.03867

A Training-Free Mixture-of-Agents Framework for Multi-Document Summarization using LLMs and Knowledge Graphs

Authors:

Cuong Vuong Tuan ↗Trang Mai Xuan ↗Tien-Cuong Nguyen ↗Vu-Duc Ngo ↗Thien Van Luong ↗

Multi-Document Summarization (MDS) plays a critical role in distilling essential information from collections of textual data. Existing approaches often struggle to capture complex inter-document relationships, rely heavily on large amounts of labeled data for supervised training, or exhibit limited generalization across domains and languages. To address these limitations, we present a training-free mixture-of-agents framework for MDS that leverages the complementary strengths of large language models (LLMs) and knowledge graphs. Our approach decomposes summarization into specialized agent tasks: extractive selection, knowledge-aware abstraction, and iterative refinement, each operating without task-specific fine-tuning. We unify their outputs using a multi-perspective consistency mechanism guided by LLMs. Experiments across four datasets in English and Vietnamese demonstrate state-of-the-art or competitive performance, validating the effectiveness and adaptability of our modular design.

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08.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2606.16996

ActiveSAM: Image-Conditional Class Pruning for Fast and Accurate Open-Vocabulary Segmentation

Authors:

Tran Dinh Tien ↗Zhiqiang Shen ↗

Segment Anything Model 3 (SAM 3) provides a strong frozen backbone for concept-prompted segmentation, but applying it directly to open-vocabulary semantic segmentation (OVSS) is inefficient: full-resolution decoding is typically run over the entire dataset vocabulary, whereas each image contains only a small active subset of classes. We introduce ActiveSAM, a training-free, zero-shot inference framework that turns SAM 3 into an active-vocabulary segmenter. ActiveSAM first canonicalizes and expands class prompts, then estimates an image-conditioned active set from a low-resolution presence preview. Only the retained classes are decoded at full resolution, using bucketed prompt multiplexing with the frozen SAM 3 decoder. The preview stage uses only class-presence evidence and skips unnecessary segmentation-head computation, while the final stage applies margin-aware background calibration to suppress low-confidence pixels. ActiveSAM requires no target-dataset training, no weight updates, and no oracle class-presence labels. Across eight OVSS benchmarks, ActiveSAM improves the speed-accuracy tradeoff of training-free open-vocabulary semantic segmentation, outperforming the current state-of-the-art SegEarth-OV3 by approximately +1.4 mIoU on average while running up to 5.5x faster on large-vocabulary datasets. ActiveSAM also demonstrates the strongest robustness under image corruption that simulates real-world distribution shift, making it well-suited for deployment in noisy-input domains such as autonomous driving and embodied AI. Code is available at https://github.com/VILA-Lab/ActiveSAM.

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09.

arXiv (CS.AI) 2026-06-11 DOI: arXiv:2606.11695

Noise-Aware Framework for Correcting Corrupted Labels

Authors:

Ha-Linh Nguyen ↗Hong-Anh Nguyen ↗Minh-Duc La ↗Phong Lam ↗Thu-Trang Nguyen ↗Son Nguyen ↗Hieu Dinh Vo ↗

arXiv:2606.11695v1 Announce Type: cross Abstract: High-quality labeled data is essential for training reliable ML/DL models. However, real-world datasets often contain a considerable proportion of corrupted labels, which can severely degrade model performance. To address this problem, we propose CANOLA, a novel framework for correcting corrupted labels through noise-aware learning and iterative label refinement. CANOLA explicitly estimates the underlying noise distribution of the dataset and incorporates this information into the training of a noise-aware Deep Neural Network. By incorporating noise characteristics during learning, CANOLA enables the model to down-weight unreliable supervision signals and focus on trustworthy patterns, thereby improving robustness and generalization. Label correction is performed via cautious, iterative soft label refinement, in which model predictions are blended with observed labels to prevent premature or erroneous updates. This progressive refinement allows the dataset to be repaired in a stable and controlled manner. We evaluate CANOLA on six widely used datasets under realistic noisy labeling scenarios. Experimental results show that CANOLA consistently outperforms SOTA label correction methods, achieving relative improvements ranging from 19% to 52% in error reduction. Moreover, models trained on datasets corrected by CANOLA obtain substantial downstream performance gains. Even simple classifiers trained on CANOLA's corrected data can outperform complex model-centric approaches by margins of up to 67%.

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10.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2606.15019

Towards Global AI-Driven Cervical Cancer Screening

Authors:

The global elimination of cervical cancer is a key public health goal set by the World Health Organization (WHO), with screening programs reducing mortality by up to 80%. However, access to experts and biopsy services is limited in low- to middle-income countries (LMICs). Deep learning (DL)-based algorithms offer promising support for screening, but most existing approaches have been developed and validated on private datasets from single countries. We present the first DL-based approach to cervical cancer screening validated on data from multiple countries. Technically, we phrase the problem of detecting and classifying lesions in colposcopy images as a multi-task learning problem, in which we simultaneously perform image-level classification and lesion segmentation. Our model was trained on a private data set of acid stain colposcopy images with manually generated lesion segmentation masks and corresponding histopathological results, employing extensive data augmentation to address image variability. In an in-distribution validation with pathology results serving as ground truth, our algorithm outperformed medical experts (Balanced Accuracy: 0.68 vs 0.64) in CIN1- (Cervical intraepithelial neoplasia grade 1 or lower) versus CIN2+ (grade 2 or higher) classification. External validation on four colposcopy data sets from four countries featuring radical differences in prevalence and patient characteristics yielded superior performance of our method compared to baseline methods. Performance variability across countries was high with AUC values ranging from 0.54 - 0.80. Overall, algorithm performance varied with age, transformation zone (cervical area most prone to lesion development), presence of comorbidities and pathognomonic signs, with comorbidities having by far the largest negative effect. Future work should focus on improving model robustness and generalizability.

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11.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2508.13313

Flow Matching for Efficient and Scalable Data Assimilation

Authors:

Taos Transue ↗Bohan Chen ↗So Takao ↗Bao Wang ↗

arXiv:2508.13313v4 Announce Type: replace-cross Abstract: Data assimilation (DA) estimates a dynamical system's state from noisy observations. Recent generative models like the ensemble score filter (EnSF) improve DA in high-dimensional nonlinear settings but are computationally expensive. We introduce the ensemble flow filter (EnFF), a training-free, flow matching (FM)-based framework that accelerates sampling and offers flexibility in flow design. EnFF uses Monte Carlo estimators for the marginal flow field, localized guidance for observation assimilation, and utilizes a novel flow path that exploits the Bayesian DA formulation. It generalizes classical filters such as the bootstrap particle filter and ensemble Kalman filter. Experiments on high-dimensional benchmarks demonstrate EnFF's improved cost-accuracy tradeoffs and scalability, highlighting FM's potential for efficient, scalable DA. Code is available at https://github.com/Utah-Math-Data-Science/Data-Assimilation-Flow-Matching.

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12.

arXiv (CS.CV) 2026-06-24 DOI: arXiv:2606.24058

VisChronos: Revolutionizing Image Captioning Through Real-Life Events

Authors:

Phuc-Tan Nguyen ↗Hieu Nguyen ↗Minh-Triet Tran ↗Trung-Nghia Le ↗

This paper aims to bridge the semantic gap between visual content and natural language understanding by leveraging historical events in the real world as a source of knowledge for caption generation. We propose VisChronos, a novel framework that utilizes large language models and dense captioning models to identify and describe real-life events from a single input image. Our framework can automatically generate detailed and context-aware event descriptions, enhancing the descriptive quality and contextual relevance of generated captions to address the limitations of traditional methods in capturing contextual narratives. Furthermore, we introduce a new dataset, EventCap (https://zenodo.org/records/14004909), specifically constructed using the proposed framework, designed to enhance the model's ability to identify and understand complex events. The user study demonstrates the efficacy of our solution in generating accurate, coherent, and event-focused descriptions, paving the way for future research in event-centric image understanding.

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13.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2606.18555

Rethinking Text-to-Image as Semantic-Aware Data Augmentation for Indoor Scene Recognition

Authors:

Trong-Vu Hoang ↗Quang-Binh Nguyen ↗Dinh-Khoi Vo ↗Hoai-Danh Vo ↗Minh-Triet Tran ↗Trung-Nghia Le ↗

In the realm of computer vision, indoor image recognition presents challenges due to the intricate interplay of lighting conditions, occlusions, and diverse object arrangements within confined spaces. To address the lacks of training indoor images, we introduce a novel approach leveraging Stable Diffusion (SD) for the generation of synthetic images, which serve as a powerful data augmentation tool. The utilization of SD offers a principled framework for synthesizing diverse and realistic indoor scenes, thereby enriching the training data pool for robust indoor image recognition models. Experimental findings on the MIT Indoor Scene dataset reveal the potential of our proposed approach in enhancing the training of deep models when authentic data is limited. Furthermore, to prevent the misuse of SD synthetic images, we introduce a counter measure based on DIffusion Reconstruction Error (DIRE). The powerful DIRE presentation enables training robust classifiers only using lightweight deep models. Experiments show that our approach can perfectly recognize SD generated images with the accuracy of 100% using MobilenetV3.

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14.

arXiv (CS.AI) 2026-06-24 DOI: arXiv:2606.23993

Learning to Trigger: Reinforcement Learning at the Large Hadron Collider

Authors:

Zixin Ding ↗Shaghayegh Emam ↗Giovanna Salvi ↗Cecilia Tosciri ↗Abhijith Gandrakota ↗Jennifer Ngadiuba ↗Nhan Tran ↗Christian Herwig ↗David W. Miller ↗Yuxin Chen ↗

arXiv:2606.23993v1 Announce Type: cross Abstract: High-throughput scientific facilities such as the Large Hadron Collider depend on real-time event filtering (triggering) under tight constraints on bandwidth, latency, and storage. In practice, trigger menus are largely static and hand-tuned and can become suboptimal as detector conditions, pileup, and background composition drift over time. We cast online threshold tuning as a sequential decision-making problem: a reinforcement learning agent ingests streaming summaries of recent rates and signal-sensitive features and updates trigger thresholds to maximize signal efficiency while tracking a target background rate within a tolerance band. We adapt Group-Filtered Policy Optimization (GFPO) to streaming control and introduce two variants (GFPO-F, GFPO-FR) that enforce background rate feasibility during training. On a benchmark that emulates realistic collider operation, we study two representative triggers: a total transverse energy ($H_{T}$) trigger sensitive to pileup variation, and an anomaly-detection (AD) trigger based on reconstruction loss for rare or non-standard signatures. On Monte Carlo streams, our agent increases the fraction of in-tolerance time intervals by 48\% ($H_T$) and 28\% (AD), with a cumulative gain of up to 2\% in signal efficiency on those in-tolerance intervals. Transferring from simulation to real collision data (CMS Run 283408), the same agent, without fine-tuning, achieves a 56\% ($H_T$) and 28\% (AD) in-tolerance improvement over baselines, with further signal-efficiency gain on both triggers. To our knowledge, this is the first demonstration of RL-based trigger control on real Large Hadron Collider collision data. Code is available at https://github.com/Zixind/GFPO\_LHC.

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15.

arXiv (CS.CV) 2026-06-17 DOI: arXiv:2605.23176

DRIVESPATIAL: A Benchmark for Spatiotemporal Intelligence in VLMs for Autonomous Driving

Authors:

Spatiotemporal intelligence in autonomous driving (AD) requires an agent to integrate multi-view observations into a coherent scene representation, maintain object continuity across viewpoints and time, and reason about spatial relations, interactions, and future dynamics. However, existing AD vision-language benchmarks largely focus on single-view, static, ego-centric, or single-source question answering, leaving it unclear whether current Vision-Language Models (VLMs) can truly construct and reason over dynamic driving scenes. We introduce DriveSpatial, a benchmark of 15.6K human-verified QA pairs across 20 tasks from five large-scale AD datasets. DriveSpatial evaluates four abilities: Cognitive Scene Construction, Multi-view Relational Understanding, Temporal Reasoning, and Generalization. Unlike prior benchmarks, DriveSpatial is generated from a dynamic multi-relational scene graph that encodes object states, spatial relations, interactions, camera visibility, and temporal correspondences, enabling QA pairs that enforce genuine cross-view and spatiotemporal reasoning. Evaluating 15 representative VLMs reveals a substantial human-model gap: the strongest model trails humans by 28.4 points, with Cognitive Scene Construction emerging as the key bottleneck. Further diagnostics show that language-only prompting is insufficient, while explicit BEV grounding consistently improves performance. These results suggest that current VLMs lack the scene-construction ability needed for reliable spatiotemporal driving intelligence. DriveSpatial and its construction pipeline will be released to support future research.

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16.

arXiv (CS.CV) 2026-06-25 DOI: arXiv:2606.25838

Edges Before Embeddings: A Confidence-Aware Blur Gate for Vision-Language Pipelines

Authors:

Duy Tran Thanh ↗

Production vision pipelines silently degrade on blurry input, wasting compute on downstream OCR, retrieval, and vision-language model (VLM) calls that cannot recover a usable output. We present MagikaDocumentFromPixel, a lightweight, CPU-friendly image quality gate that classifies a single image as sharp, blurred, or uncertain in roughly 7 ms on a single CPU core. The contributions are (i) a recipe selected from a 46-configuration, 8-sweep empirical search that isolates input resolution as the dominant lever and shows architecture capacity only pays off at >= 384 px; (ii) a confidence-aware routing formalism grounded in classical selective prediction; (iii) the Edge Prior Module (EPM), a Laplacian-magnitude auxiliary input channel that gives the network direct access to the spectral evidence that classical blur heuristics rely on and that lifts test F1 by +1.3 points in a matched-env comparison; and (iv) an observation that the gate is one instance of a recurring design pattern that appears independently in Magika content-type detection, risk-controlled OCR with VLMs, and DocVLM. The final recipe MobileNetV3-Large with the EPM trained at 384x384 on paired GoPro Large frames, evaluated with 5-scale test-time augmentation reaches F1 = 0.9803 (AUC 0.9989) with a 17 MB ONNX artifact, improving over our fixed-scale baseline on the same hardware (F1 = 0.9672) by +1.31 points. We are explicit about limitations: results are on a single motion-blur distribution, numbers are from a single seed, and calibration is qualitative rather than measured.

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17.

arXiv (CS.CV) 2026-06-25 DOI: arXiv:2606.25298

KidRisk: Benchmark Dataset for Children Dangerous Action Recognition

Authors:

Minh-Kha Nguyen ↗Trung-Hieu Do ↗Kim Anh Phung ↗Thao Thi Phuong Dao ↗Minh-Triet Tran ↗Trung-Nghia Le ↗

Children are naturally energetic, and during their spontaneous activities, they often encounter potentially dangerous situations, especially when lacking parental supervision. Identifying actions that pose risks plays a crucial role in ensuring their safety. This paper build a novel challenging dataset, namely KidRisk, including 2,500 short videos of children's actions and 10,000 images for dangerous action of children. We also introduce a benchmark on our newly constructs dataset and find that traditional deep learning models demonstrated limited effectiveness on these tasks. Therefore, we develop vision-language based baselines with exceptional context understanding of visual information. Our proposed methods achieved an accuracy of 83.53% in classifying children's actions and 96.14% in recognizing children's dangerous actions, significantly outperforming traditional approaches. These results confirm that vision-language models are not only feasible but also highly effective in detecting hazardous actions, contributing positively to safeguarding children's safety.

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18.

bioRxiv (Bioinfo) 2026-06-22 DOI: HASH:abce381337436d713ce675949b96bd4c

PhaseWY: A pipeline for haplotype phasing, sex chromosome identification and extraction of sex-limited sequences

Authors:

Ellerstrand ↗S. J ↗Churcher ↗A. M. J ↗Kutschera ↗V. E ↗Hansson ↗

Sex chromosomes are central to many ecological and evolutionary processes. Evidence has accumulated that sex chromosome systems vary extensively in age, turnover and transitions, motivating renewed efforts to study the diversity of sex chromosome systems across the tree of life. However, successful genomic detection of sex chromosomes depends on several factors, including the size and divergence time, background genetic diversity, and the number of sequenced females and males. In addition, technical challenges associated with sequencing and analysing the sex-limited Y/W chromosome remain. Here, we present PhaseWY, an automated Snakemake pipeline that uses whole-genome sequencing data from multiple female and male individuals to identify sex-chromosomal regions and extract the corresponding Y/W sequences. PhaseWY (i) detects sex differences in alignment depth, (ii) applies read-based and statistical haplotype phasing, (iii) identifies sex-linked regions using haplotype clustering, and (iv) subsets autosomal, X/Z- and Y/W-linked variants for downstream analyses. We applied PhaseWY to simulated data to benchmark factors influencing sex-linkage detection and successful extraction of Y/W-linked variants. To demonstrate its practical utility, we further applied PhaseWY to the neo-sex chromosome system in Alauda larks (Alaudidae) and performed a range of downstream analyses demonstrating the scope of applications of the PhaseWY output. We conclude that PhaseWY provides an easy-to-use and reproducible tool for population-genomic analyses in non-model organisms, with particular importance for advancing our understanding of sex-chromosome evolution.

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19.

arXiv (CS.AI) 2026-06-18 DOI: arXiv:2606.00729

AI Sovereignty as National Learning Capacity: A Human-Centered Learning Mechanics Viewpoint on France, the United States, and China

Authors:

Kim Phuc Tran ↗

arXiv:2606.00729v2 Announce Type: replace Abstract: Artificial intelligence in France is often discussed through separate dimensions such as investment, compute, regulation, employment, sovereignty, and education. This viewpoint paper proposes a unified interpretation: France can be analyzed as a national AI learning system. Building on Human-Centered Learning Mechanics (HCLM), we use HCLM not as a validated econometric model, but as a conceptual and diagnostic lens for interpreting national AI development as a balance between information injection, absorptive capacity, and institutional dissipation. Information injection includes compute, data, talent, research, capital, industrial deployment, and policy experimentation. Institutional dissipation refers to avoidable frictions such as administrative overload, coordination failures, energy constraints, regulatory uncertainty, talent mobility pressures, and weak industrial absorption. Regulation is not treated as mere friction: adaptive governance, trusted data spaces, and safety-oriented standards may increase long-term learning capacity by improving legitimacy, interoperability, and social trust. The central claim is not that a country follows neural-network equations, but that AI sovereignty depends on how effectively it converts distributed information into absorbed, coordinated, and socially legitimate capability. The paper connects HCLM with neural scaling laws, endogenous growth theory, creative destruction, absorptive capacity, and coordination mechanisms. It offers a formal heuristic, policy indicators, illustrative scenarios, and implications for France. The numerical results are diagnostic scenarios, not econometric estimates or official rankings. The proposed viewpoint reframes AI policy as the governance of an open, strategic, non-equilibrium learning system that should be tested with historical and cross-country data.

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20.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2606.18554

Forged Calamity: Benchmark for Cross-Domain Synthetic Disaster Detection in the Age of Diffusion

Authors:

Duc-Manh Phan ↗Quoc-Duy Tran ↗Duy-Khang Do ↗Anh-Tuan Vo ↗Hai-Dang Nguyen ↗Trong Le Do ↗Mai-Khiem Tran ↗Vinh-Tiep Nguyen ↗Tam V. Nguyen ↗Isao Echizen ↗Minh-Triet Tran ↗Trung-Nghia Le ↗…

The rapid advancement of text-to-image diffusion models has enabled the creation of highly photorealistic synthetic images that closely resemble real photographs, making it increasingly difficult to distinguish authentic content from AI-generated fabrications. This poses challenges for cybersecurity, digital forensics, and disaster response, where fake imagery of floods, fires, or earthquakes can spread misinformation or disrupt emergency operations. To address this, we introduce Forged Calamity, a benchmark dataset for synthetic disaster detection containing 30,000 images, including 6,000 real and 24,000 synthetic samples generated by four diffusion models. Comprehensive experiments across fine-tuned and zero-shot settings reveal consistent weaknesses in current forensic approaches. Fine-tuned detectors perform well in-distribution but lose up to 50\% accuracy on unseen generators or disaster types, showing overfitting to model-specific artifacts. Zero-shot generalized detectors also struggle to maintain stable accuracy, with only limited resilience in a few representation-robust models. These findings highlight persistent generalization gaps and the urgent need for domain- and model-agnostic detection methods to ensure visual authenticity in the diffusion era.

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21.

arXiv (CS.LG) 2026-06-18 DOI: arXiv:2606.19036

Geometric and Stochastic Analysis of Discontinuities in Sparse Mixture-of-Experts

Authors:

Tho Tran Huu ↗Huu-Tuan Nguyen ↗Thien-Hai Nguyen ↗Nhat-Tri Ho ↗Viet-Hoang Tran ↗Tho Quan ↗Tan Minh Nguyen ↗

arXiv:2606.19036v1 Announce Type: new Abstract: Sparse Mixture-of-Experts (SMoE) architectures are now widely deployed in state-of-the-art language and vision models, where conditional routing allows scaling to very large networks. However, this very Top-$k$ expert selection that enables conditional routing also renders the SMoE map inherently discontinuous. In the vicinity of these discontinuity surfaces, even inputs that are arbitrarily close may activate substantially different sets of experts resulting in significantly different outputs. In this work we give a rigorous geometric and stochastic analysis of these discontinuities. We first classify them by order, determined by the number of tied experts at a switching event. Using measure-theoretic slicing arguments, we establish asymptotic volume estimates for the thickened discontinuity surfaces, showing that lower-order discontinuity sets dominate, whereas higher-order ones occupy a vanishingly small relative volume. Next, modeling random perturbations in the input space via a diffusion process, we prove that the path eventually encounter a discontinuity, and moreover that the first hit almost surely occurs on an order-1 discontinuity with explicit finite-time probability bounds. We further derive occupation-time bounds that quantify the duration the random path spend in the neighborhoods of each discontinuity order. These theoretical results imply that inputs are more likely to lie near lower order discontinuities. Motivated by this insight, we propose a simple smoothing mechanism that can be directly applied to existing SMoEs, softly incorporating experts near discontinuities; our analysis guarantees that the added computational overhead remains small while providing localized smoothing near discontinuities, and experiments across language and vision tasks show that smoothing not only enforces continuity of the SMoE map but also enhances empirical performance.

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22.

medRxiv (Medicine) 2026-06-23 DOI: HASH:9043ea844aa60af2f0075ccab453b4a1

The Target ALS Global Natural History Study: Cross-platform proteomics to accelerate biofluid biomarker and drug target discovery in amyotrophic lateral sclerosis

Authors:

Yasui ↗Weatherill ↗Dugom ↗Weiner ↗Gopalakrishnan ↗Tran ↗Oskarsson ↗Nagle ↗Miller ↗Gutierrez ↗Ravits ↗Hoover ↗…

Amyotrophic lateral sclerosis (ALS) is a fatal, rapidly progressive neurodegenerative disease of motor neurons for which therapeutics are limited. Improved biomarkers are imperative to improve patient care and therapeutic development. Here, we employed 35-plex isobaric tandem mass tag labeling based on isobutyl-proline reporter group (TMTpro) to perform unbiased proteomic analysis of cerebrospinal fluid (CSF) and plasma from control (n= 28, n= 31) and sporadic ALS (sALS) (n= 39, n= 41), from the Target ALS Global Natural History Study (TALS GNHS). We identified 2,875 proteins in CSF and 1,118 proteins in plasma and identified known and novel differentially expressed proteins (DEPs) between controls and sALS, some of which were orthogonally validated using immunoassay. Comparison of TMTpro-MS and Olink proximity extension assay proteomics revealed common and non-overlapping differentially expressed proteins illustrating strengths unique to each platform. This initial cross-sectional proteomic study of biofluids from the TALS GNHS, with unrestricted availability of study results to the research community, highlights the potential of this resource as a potent platform for ALS biomarker discovery.

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23.

arXiv (CS.CV) 2026-06-25 DOI: arXiv:2510.11047

Benchmarking Deep Learning Models for Laryngeal Cancer Staging Using the LaryngealCT Dataset

Authors:

Nivea Roy ↗Son Tran ↗Atul Sajjanhar ↗K. Devaraja ↗Prakashini Koteshwara ↗Yong Xiang ↗Divya Rao ↗

Laryngeal cancer imaging research lacks standardised public datasets to enable reproducible deep learning (DL) model development. We present LaryngealCT, a curated benchmark of 1,029 computed tomography (CT) scans aggregated from six collections from The Cancer Imaging Archive (TCIA). Uniform 1 mm isotropic volumes of interest encompassing the larynx were extracted using a weakly supervised parameter search framework validated by clinical experts. Six 3D DL architectures (custom 3D CNN, ResNet18,50,101, DenseNet121 and MedicalNet-pretrained ResNet50) were benchmarked on (i) early (Tis,T1,T2) vs. advanced (T3,T4) and (ii) T4 vs. non-T4 classification tasks. On the independent test set, the 3D CNN achieved the strongest overall performance across global and per-class metrics (Accuracy 0.854, F1-macro 0.841) in early vs. advanced classification. In the T4 task, AU-ROC values exceeded 0.82 for most models, but sensitivity for T4 disease remained limited (less than or equal to 0.412), with ResNet101 showing the most promising calibrated T4 recall (0.706. Model explainability assessed using GradCAMpp with thyroid cartilage overlays for T4 classification task revealed anatomically plausible peri-cartilage activations, although spatial overlap was modest. Through open-source data, pretrained models, and integrated explainability tools, LaryngealCT offers a reproducible foundation for AI-driven research to support future clinical decision-making in laryngeal oncology.

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24.

medRxiv (Medicine) 2026-06-15 DOI: HASH:f8d0c6985f19f9da44f919de87373ece

International Consensus Guideline on Management of Genitourinary Adverse Events Associated with Prostate Cancer Radiotherapy

Authors:

Dornisch ↗A. M ↗Alongi ↗Ballas ↗Birtle ↗Blanchard ↗Bryant ↗R. J ↗Choudhury ↗Cooperberg ↗M. R ↗Dal Pra ↗…

Purpose/Objective: Genitourinary (GU) adverse events (AEs) are common during and after pelvic radiation therapy (RT) for prostate cancer and can substantially impact quality of life. We convened an international committee to establish consensus in the prevention, mitigation, and management of radiation-related acute and late GU AEs, as there are no relevant evidence-based consensus guidelines to inform treating providers. Materials/Methods: A systematic evidence review focused on mitigation and management of radiation-related acute and late GU AEs was performed in PubMed, Embase and Cochrane. The following topics were addressed: management of acute GU AEs in the intact and post-operative settings; RT techniques; bladder outlet obstruction procedures; and indications for urology referral or hyperbaric oxygen therapy (HBO). Evidence-based consensus recommendations were developed using a Delphi process. We highlight the current state of evidence and evidence gaps worthy of future study. Results: Consensus was reached for 31 key questions. For management of lower urinary tract symptoms (LUTS), most evidence comes from trials in patients without cancer and not undergoing RT. A consensus algorithm for medical management of acute GU AEs was developed with the following highlights: (a) alpha blockers as 1st-line for obstructive symptoms in the intact setting, (b) anti-spasmodics as 1st -line for irritative symptoms in the intact setting, and (c) anti-spasmodics as 1st -line in the post-operative setting. The consensus algorithm provides an ordered list of medications to offer if 1st -line options afford inadequate relief. For RT fractionation, randomized clinical trial (RCT) data are available. 40% of panelists rarely or never use standard fractionation over moderate hypofractionation for patients with baseline LUTS, but most consider moderate hypofractionation over SBRT for AUA IPSS > 15. For patients with severe obstructive LUTS (most commonly AUA IPSS >20), the panel recommends a prophylactic bladder outlet obstruction procedure and, if obstructive symptoms improve, consideration of moderate hypofractionation or SBRT, based on retrospective data. There is one RCT supporting use of HBO for late radiation cystitis. Conclusions: The consensus guideline synthesizes available evidence and expert opinion across key clinical decision points to provide practical guidance in the prevention, mitigation, and management of radiation-related acute and late GU AEs in prostate cancer RT. Envisioned as a living document with periodic updates, this guideline serves as a resource for practicing radiation oncologists by outlining expert-derived consensus recommendations of evidence-based care in areas where high-quality data is limited.

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25.

arXiv (CS.CV) 2026-06-24 DOI: arXiv:2604.00725

A Benchmark of State-Space Models vs. Transformers and BiLSTM-based Models for Historical Newspaper OCR

Authors:

Merveilles Agbeti-Messan ↗Pierrick Tranouez ↗St\'ephane Nicolas ↗Cl\'ement Chatelain ↗Thierry Paquet ↗

End-to-end OCR for historical newspapers remains challenging, as models must handle long text sequences, degraded print quality, and complex layouts. While Transformer-based recognizers dominate current research, their quadratic complexity limits efficient paragraph-level transcription and large-scale deployment. We investigate linear-time State-Space Models (SSMs), specifically Mamba, as a scalable alternative to Transformer-based sequence modeling for OCR. We present to our knowledge, the first OCR architecture based on SSMs, combining a CNN visual encoder with bi-directional and autoregressive Mamba sequence modeling, and conduct a large-scale benchmark comparing SSMs with Transformer- and BiLSTM-based recognizers. Multiple decoding strategies (CTC, autoregressive, and non-autoregressive) are evaluated under identical training conditions alongside strong neural baselines (VAN, DAN, DANIEL) and widely used off-the-shelf OCR engines (PERO-OCR, Tesseract OCR, TrOCR, Gemini). Experiments on historical newspapers from the Bibliotheque nationale du Luxembourg, with newly released >99% verified gold-standard annotations, and cross-dataset tests on Fraktur and Antiqua lines, show that all neural models achieve low error rates (~2% CER), making computational efficiency the main differentiator. Mamba-based models maintain competitive accuracy while halving inference time and exhibiting superior memory scaling (1.26x vs 2.30x growth at 1000 chars), reaching 6.07% CER at the severely degraded paragraph level compared to 5.24% for DAN, while remaining 2.05x faster. We release code, trained models, and standardized evaluation protocols to enable reproducible research and guide practitioners in large-scale cultural heritage OCR available at https://github.com/MarcoPerson/ssm-ocr-benchmark.

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