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arXiv 2025年

作者： Yu, Shuo Jin, Shan Li, Ming Sarwar, Tabinda Xia, Feng School of Computer Science and Technology Dalian University of Technology China Key Laboratory of Social Computing and Cognitive Intelligence Dalian University of Technology Ministry of Education China School of Software Dalian University of Technology China Zhejiang Institute of Optoelectronics China Zhejiang Key Laboratory of Intelligent Education Technology and Application Zhejiang Normal University China School of Computing Technologies RMIT University Australia

Understanding communication and information processing among brain regions of interest (ROIs) is highly dependent on long-range connectivity, which plays a crucial role in facilitating diverse functional neural integration across the entire brain. However, previous studies generally focused on the short-range dependencies within brain networks while neglecting the long-range dependencies, limiting an integrated understanding of brain-wide communication. To address this limitation, we propose Adaptive Long-range aware TransformER (ALTER), a brain graph transformer to capture long-range dependencies between brain ROIs utilizing biased random walk. Specifically, we present a novel long-range aware strategy to explicitly capture long-range dependencies between brain ROIs. By guiding the walker towards the next hop with higher correlation value, our strategy simulates the real-world brain-wide communication. Furthermore, by employing the transformer framework, ALERT adaptively integrates both short- and long-range dependencies between brain ROIs, enabling an integrated understanding of multilevel communication across the entire brain. Extensive experiments on ABIDE and ADNI datasets demonstrate that ALTER consistently outperforms generalized state-of-the-art graph learning methods (including SAN, Graphormer, GraphTrans, and LRGNN) and other graph learning based brain network analysis methods (including FBNETGEN, BrainNetGNN, BrainGNN, and BrainNETTF) in neurological disease diagnosis. Cases of long-range dependencies are also presented to further illustrate the effectiveness of ALTER. The implementation is available at https://***/yushuowiki/ALTER. Copyright © 2025, The Authors. All rights reserved.

关键词： Neurons

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ExpTopo: Explicit Topological Modeling for Bronchus Segmentation

ExpTopo: Explicit Topological Modeling for Bronchus Segmenta...

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IEEE International Symposium on Biomedical Imaging

作者： Mingyue Zhao Xiaolan Qiu S.Kevin Zhou Division of Life Sciences and Medicine School of Biomedical Engineering University of Science and Technology of China (USTC) China Center for Medical Imaging Robotics Analytic Computing & Learning (MIRACLE) Suzhou Institute for Advance Research USTC China Suzhou Key Laboratory of Microwave Imaging Processing and Application Technology Suzhou Aerospace Information Research Institute China Key Laboratory of Precision and Intelligent Chemistry University of Science and Technology of China (USTC) China Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS) Institute of Computing Technology China

ISBN: (数字)9798331520526

ISBN: (纸本)9798331520533

Airway extraction is paramount in the early diagnosis and treatment of respiratory diseases. As a tree-like structure, both topological-aware learning and voxel-wise classification are equally crucial for the airway. However, existing methods demonstrate insufficient topological learning, emphasizing only the supervision of individual key topological points. Consequently, this paper proposes a Explicit Topological Modeling (ExpTopo) approach to aid airway segmentation. It explicitly introduces topological metric space learning based on semantic segmentation, enhancing the model's structural perception by implementing global skeleton-level sparse topological learning (STL) and local voxel-level dense topological perception (DTP). Extensive experimental results demonstrate that the algorithm achieves competitive performance at both the topological and voxel levels. Code will be available in https://***/MorineZ/ExpTopo.

关键词： Codes Atmospheric modeling Semantic segmentation Pulmonary diseases Biological system modeling Extraterrestrial measurements Biomedical imaging

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LLM Knows Geometry Better than Algebra: Numerical Understanding of LLM-Based Agents in A Trading Arena

arXiv

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arXiv 2025年

作者： Ma, Tianmi Du, Jiawei Huang, Wenxin Wang, Wenjie Xie, Liang Zhong, Xian Zhou, Joey Tianyi Hubei Key Laboratory of Transportation Internet of Things Wuhan University of Technology China Hubei Key Laboratory of Big Data Intelligent Analysis and Application Hubei University China Centre for Frontier AI Research Agency for Science Technology and Research Singapore Institute of High Performance Computing Agency for Science Technology and Research Singapore School of Computing National University of Singapore Singapore School of Science Wuhan University of Technology China

Recent advancements in large language models (LLMs) have significantly improved performance in natural language processing tasks. However, their ability to generalize to dynamic, unseen tasks, particularly in numerical reasoning, remains a challenge. Existing benchmarks mainly evaluate LLMs on problems with predefined optimal solutions, which may not align with real-world scenarios where clear answers are absent. To bridge this gap, we design the Agent Trading Arena, a virtual numerical game simulating complex economic systems through zero-sum games, where agents invest in stock portfolios. Our experiments reveal that LLMs, including GPT-4o, struggle with algebraic reasoning when dealing with plain-text stock data, often focusing on local details rather than global trends. In contrast, LLMs perform significantly better with geometric reasoning when presented with visual data, such as scatter plots or K-line charts, suggesting that visual representations enhance numerical reasoning. This capability is further improved by incorporating the reflection module, which aids in the analysis and interpretation of complex data. We validate our findings on NASDAQ STOCK dataset, where LLMs demonstrate stronger reasoning with visual data compared to text. Our code and data are publicly available at https://***/wekjsdvnm/***. © 2025, CC BY.

关键词： Natural language processing systems

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Single-cell technologies: current and near future

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Science China(Life Sciences) 2025年第1期68卷 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi KeyLaboratory of Spine and Spinal CordInjury Repairand Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchoolofLifeSciencesandTechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Key Laboratory of Advanced Theory and Application in Statistics and Data Science(MOE) School of StatisticsEast China Normal UniversityShanghai 200062China

Single-cell technologies enable the indepth exploration of multiple biological hierarchies at the scale of individual cells,which have deepened our knowledge of cellular diversity,tissue organization,and overall organism function(Sun et al.,2024).In 2009,single-cell RNA sequencing(scRNA-seq)was first developed as a powerful tool to dissect gene expression and uncover transcriptional *** the rapid advancement of technology,single-cell approaches have expanded to encompass other omics,such as genomics,epigenomics,proteomics,and ***,multimodal technologies including spatially resolved transcriptomics and clustered regularly interspaced short palindromic repeats(CRISPR)screening at the single-cell level further advanced our ability to comprehensively understand cellular ***-cell methods provide deeper insights into disease mechanisms across various conditions,including cancer,developmental disorders,and aging-associated *** this issue,we focus on topics related to single-cell methods,covering the following four aspects:(i)single-cell multi-omic sequencing technology;(ii)single-cell spatial technology;(iii)singlecell CRISPR screening technology;(iv)applications of single-cell technology.

关键词： expanded enable insight

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Single-cell omics: experimental workflow, data analyses and applications

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Science China(Life Sciences) 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University(The Second People’s Hospital of Wuhu City)Wuhu 241000China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** exploration of how the genomes orchestrate the formation and maintenance of each cell,and control the cellular phenotypes of various organismsis,is both captivating and *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** technologies have expanded horizontally to include single-cell genome,epigenome,proteome,and metabolome,while vertically,they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

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Provably Secure Authenticated key-Management Mechanism for e-Healthcare Environment

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IEEE Internet of Things Journal 2025年

作者： Saleem, Muhammad Asad Li, Xiong Mahmood, Khalid Ghaffar, Zahid Xie, Yong Wang, Guijuan University of Electronic Science and Technology of China School of Computer Science and Engineering Sichuan Chengdu611731 China National Yunlin University of Science and Technology Graduate School of Intelligent Data Science Yunlin Douliu64002 Taiwan National Yunlin University of Science and Technology Graduate School of Engineering Science and Technology Douliu64002 Taiwan Qinghai Institute of Technology School of Computer and Information Science China Qinghai Provincial Laboratory for Intelligent Computing and Application China Key Laboratory of Computing Power Network and Information Security Jinan250353 China Shandong Provincial Key Laboratory of Industrial Network and Information System Security China Shandong Fundamental Research Center for Computer Science Jinan250353 China

The Internet of Things (IoT) is rapidly permeating all aspects of human life, involving a network of devices that share sensitive data. A notable application is the e-healthcare systems, which employ connected sensors, medical servers, and wearable devices. However, the public nature of communication in e-healthcare systems poses challenges such as security, privacy, and authentication of participating entities. Recently, many authentication protocols have been introduced to address these challenges. However, most of these protocols remain vulnerable to various security attacks, including device or medical server impersonation, denial of service, physical or cloning, and de-synchronization attacks. Therefore, we introduce an authenticated key-management protocol utilizing hash functions and Cipher-Block Chaining-Advanced Encryption Standard encryption (CBC-AES) encryption. The proposed protocol also employs the Physical Unclonable Function (PUF), which makes it more robust and efficient in resisting physical or cloning attacks. Additionally, the proposed scheme resists various security threats, including impersonation, session key leakage, ephemeral secret leakage, and de-synchronization attacks. We analyze the scheme’s security and reliability through formal and informal analysis. The informal analysis demonstrates that the scheme encompasses crucial security features, while the formal analysis substantiates. Moreover, performance analysis of the proposed protocol with various competing results indicates that our protocol achieves an average reduction in communication and computation overheads by 36.03.% and 41.79%, respectively. © 2014 IEEE.

关键词： Electronic health record

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A Unified Framework for Exploratory Learning-Aided Community Detection Under Topological Uncertainty

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IEEE Transactions on Network Science and Engineering 2025年

作者： Hou, Yu Tran, Cong Li, Ming Shin, Won-Yong Yonsei University School of Mathematics and Computing Computational Science and Engineering Seoul03722 Korea Republic of Posts and Telecommunications Institute of Technology Faculty of Information Technology Hanoi100000 Viet Nam Zhejiang Institute of Optoelectronics Jinhua321004 China Zhejiang Normal University Zhejiang Key Laboratory of Intelligent Education Technology and Application Jinhua321004 China Graduate School of Artificial Intelligence Pohang37673 Korea Republic of

In social networks, the discovery of community structures has received considerable attention as a fundamental problem in various network analysis tasks. However, due to privacy concerns or access restrictions, the network structure is often uncertain, thereby rendering established community detection approaches ineffective without costly network topology acquisition. To tackle this challenge, we present META-CODE, a unified framework for detecting overlapping communities via exploratory learning aided by easy-to-collect node metadata when networks are topologically unknown (or only partially known). Specifically, META-CODE consists of three iterative steps in addition to the initial network inference step: 1) node-level community-affiliation embeddings based on graph neural networks (GNNs) trained by our new reconstruction loss, 2) network exploration via community-affiliation-based node queries, and 3) network inference using an edge connectivity-based Siamese neural network model from the explored network. Through extensive experiments on three real-world datasets including two large networks, we demonstrate: (a) the superiority of META-CODE over benchmark community detection methods, achieving remarkable gains up to 65.55% on the Facebook dataset over the best competitor among our selected competitive methods in terms of normalized mutual information (NMI), (b) the impact of each module in META-CODE, (c) the effectiveness of node queries in META-CODE based on empirical evaluations and theoretical findings, and (d) the convergence of the inferred network. © 2013 IEEE.

关键词： Structured Query Language

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Modeling Fine-Grained Relations in Dynamic Space-Time Graphs for Video-Based Facial Expression Recognition

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IEEE Transactions on Affective computing 2025年

作者： Huang, Changqin Jiang, Fan Han, Zhongmei Huang, Xiaodi Wang, Shijin Zhu, Yanlai Jiang, Yunliang Hu, Bin Zhejiang Normal University Key Laboratory of Intelligent Education Technology and Application of Zhejiang Province Zhejiang Jinhua321004 China Charles Sturt University School of Computing Mathematics and Engineering AlburyNSW2640 Australia State Key Laboratory of Cognitive Intelligence Anhui Hefei230088 China Hangzhou Hikvision Digital Technology Co. Ltd Education Business Department Hangzhou310051 China Zhejiang Normal University School of Computer Science and Technology Jinhua321004 China Beijing Institute of Technology School of Medical Technology Beijing10081 China

Facial expressions in videos inherently mirror the dynamic nature of real-world facial events. Consequently, facial expression recognition (FER) should employ a dynamic graph-based representation to effectively capture the relational structure of facial expressions rather than relying on conventional grid or sequence methods. However, existing graph-based approaches have their limitations. Frame-level graph methods provide a coarse representation of the facial graph across time and space, while landmark-based graph methods need to introduce additional facial landmarks, resulting in a static graph structure. To address these challenges, we propose spatial-temporal relation-aware dynamic graph convolutional networks (ST-RDGCN). This fine-grained relation modeling approach enables the dynamic modeling of evolving facial expressions in videos through dynamic space-time graphs, eliminating the need for facial landmarks. ST-RDGCN encompasses three graph construction paradigms: dynamic independent space graph, dynamic joint space-time graph, and dynamic cross space-time graph. Furthermore, we propose a relation-aware space-time graph convolution (RSTG-Conv) operator to learn informative spatiotemporal correlations in dynamic space-time graphs. In extensive experimental evaluations, our ST-RDGCN demonstrates state-of-the-art performance on the five popular video-based FER datasets, achieving overall accuracy scores of 99.69%, 91.67%, 56.51%, 69.37%, and 49.03% on the CK+, Oulu-CASIA, AFEW, DFEW, and FERV39 k datasets, respectively. In particular, our ST-RDGCN outperforms the current best method by 3.6% in UAR on the most challenging FERV39 k dataset. Furthermore, our analysis reveals that the dynamic cross space-time graph scheme is the most effective among the three dynamic graph construction schemes. © 2010-2012 IEEE.

关键词： Graphic methods

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Adaptive Backdoor Attacks with Reasonable Constraints on Graph Neural Networks

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IEEE Transactions on Dependable and Secure computing 2025年

作者： Dong, Xuewen Li, Jiachen Li, Shujun You, Zhichao Qu, Qiang Kholodov, Yaroslav Shen, Yulong The School of Computer Science and Technology Xidian University The Engineering Research Center of Blockchain Technology Application and Evaluation Ministry of Education China The Shaanxi Key Laboratory of Blockchain and Secure Computing Xi’an710071 China The School of Computing Kent Interdisciplinary Research Centre in Cyber Security University of Kent CanterburyCT2 7NF United Kingdom Shenzhen Institute of Advanced Technology Chinese Academy of Sciences China The Intelligent Transportation Systems Lab Innopolis University Innopolis Russia The School of Computer Science and Technology Xidian University China

Recent studies show that graph neural networks (GNNs) are vulnerable to backdoor attacks. Existing backdoor attacks against GNNs use fixed-pattern triggers and lack reasonable trigger constraints, overlooking individual graph characteristics and rendering insufficient evasiveness. To tackle the above issues, we propose ABARC, the first Adaptive Backdoor Attack with Reasonable Constraints, applying to both graph-level and node-level tasks in GNNs. For graph-level tasks, we propose a subgraph backdoor attack independent of the graph’s topology. It dynamically selects trigger nodes for each target graph and modifies node features with constraints based on graph similarity, feature range, and feature type. For node-level tasks, our attack begins with an analysis of node features, followed by selecting and modifying trigger features, which are then constrained by node similarity, feature range, and feature type. Furthermore, an adaptive edge-pruning mechanism is designed to reduce the impact of neighbors on target nodes, ensuring a high attack success rate (ASR). Experimental results show that even with reasonable constraints for attack evasiveness, our attack achieves a high ASR while incurring a marginal clean accuracy drop (CAD). When combined with the state-of-the-art defense randomized smoothing (RS) method, our attack maintains an ASR over 94%, surpassing existing attacks by more than 7%. © 2004-2012 IEEE. All rights reserved.

关键词： Graph neural networks

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Adaptive Backdoor Attacks with Reasonable Constraints on Graph Neural Networks

arXiv

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arXiv 2025年

作者： Dong, Xuewen Li, Jiachen Li, Shujun You, Zhichao Qu, Qiang Kholodov, Yaroslav Shen, Yulong School of Computer Science and Technology Xidian University The Engineering Research Center of Blockchain Technology Application and Evaluation Ministry of Education China The Shaanxi Key Laboratory of Blockchain and Secure Computing Xi’an710071 China University of Kent CanterburyCT2 7NP United Kingdom Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences China Intelligent Transportation Systems Lab Innopolis University Innopolis Russia School of Computer Science and Technology Xidian University China The Shaanxi Key Laboratory of Network and System Security Xi’an710071 China

关键词： Graph neural networks

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