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arXiv 2025年

作者： Guo, Cong Huang, Changqin Zhou, Wenhua Huang, Xiaodi Key Laboratory of Intelligent Education Technology and Application of Zhejiang Province Zhejiang Normal University Jinhua China School of Computing Mathematics and Engineering Charles Sturt University Albury Australia

Multi-label learning poses significant challenges in extracting reliable supervisory signals from the label space. Existing approaches often employ continuous pseudo-labels to replace binary labels, improving supervisory information representation. However, these methods can introduce noise from irrelevant labels and lead to unreliable graph structures. To overcome these limitations, this study introduces a novel multi-label feature selection method called Binary Hashing and Dynamic Graph Constraint (BHDG), the first method to integrate binary hashing into multi-label learning. BHDG utilizes low-dimensional binary hashing codes as pseudo-labels to reduce noise and improve representation robustness. A dynamically constrained sample projection space is constructed based on the graph structure of these binary pseudo-labels, enhancing the reliability of the dynamic graph. To further enhance pseudo-label quality, BHDG incorporates label graph constraints and inner product minimization within the sample space. Additionally, an l2,1-norm regularization term is added to the objective function to facilitate the feature selection process. The augmented Lagrangian multiplier (ALM) method is employed to optimize binary variables effectively. Comprehensive experiments on 10 benchmark datasets demonstrate that BHDG outperforms ten state-of-the-art methods across six evaluation metrics. BHDG achieves the highest overall performance ranking, surpassing the next-best method by an average of at least 2.7 ranks per metric, underscoring its effectiveness and robustness in multi-label feature selection. Copyright © 2025, The Authors. All rights reserved.

关键词： Graph theory

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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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Long-range Brain Graph Transformer

arXiv

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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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Ingredient-Guided RGB-D Fusion Network for Nutritional Assessment

IEEE Transactions on AgriFood Electronics

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IEEE Transactions on AgriFood Electronics 2025年第1期3卷 156-166页

作者： Feng, Zhihui Xiong, Hao Min, Weiqing Hou, Sujuan Duan, Huichuan Liu, Zhonghua Jiang, Shuqiang Shandong Normal University School of Information Science and Enginering Jinan250358 China Macquarie University Centre for Health Informatics Macquarie ParkNSW2109 Australia Chinese Academy of Sciences Key Laboratory of Intelligent Information Processing Institute of Computing Technology Beijing100190 China University of Chinese Academy of Sciences Beijing100049 China Zhejiang Ocean University School of Information Engineering Zhoushan316022 China

The nutritional value of agricultural products is an important indicator for evaluating their quality, which directly affects people's dietary choices and overall well-being. Nutritional assessment studies provide a scientific basis for the production, processing, and marketing of food by analyzing the nutrients they contain. Traditional methods often struggle with suboptimal accuracy and can be time consuming, as well as a shortage of professionals. The progress in artificial intelligence has revolutionized dietary health by offering more accessible methods for food nutritional assessment using vision-based approaches. However, existing vision-based methods using RGB images often face challenges due to varying lighting conditions, impacting the accuracy of nutritional assessment. An alternative is the RGB-D fusion method, which combines RGB images and depth maps. Yet, these methods typically rely on simple fusion techniques that do not ensure precise assessment. Additionally, current vision-based methods struggle to detect small components like oils and sugars on food surfaces, crucial for determining ingredient information and ensuring accurate nutritional assessment. In this pursuit, we propose a novel ingredient-guided RGB-D fusion network that integrates RGB images with depth maps and enables more reliable nutritional assessment guided by ingredient information. Specifically, the multifrequency bimodality fusion module is designed to leverage the correlation between the RGB image and the depth map within the frequency domain. Furthermore, the progressive-fusion module and ingredient-guided module leverage ingredient information to explore the potential correlation between ingredients and nutrients, thereby enhancing the guidance for nutritional assessment learning. We evaluate our approach on a variety of ablation settings on Nutrition5k, where it consistently outperforms state-of-the-art methods. © 2023 IEEE.

关键词： Medicinal chemistry

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Non-Hermitian Physics in Mesoscopic Electron Transport Through Coupled Quantum Dots

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Chinese Physics Letters 2025年第4期42卷 114-124页

作者： Yiyang Li Jincheng Lu Chen Wang Jian-Hua Jiang School of Physical Science and Technology&Collaborative Innovation Center of Suzhou Nano Science and Technology Soochow UniversitySuzhou215006China Key Laboratory of Intelligent Optoelectronic Devices and Chips of Jiangsu Higher Education Institutions School of Physical Science and TechnologySuzhou University of Science and TechnologySuzhou215009China Advanced Technology Research Institute of Taihu Photon Center School of Physical Science and TechnologySuzhou University of Science and TechnologySuzhou 215009China Department of Physics Zhejiang Normal UniversityJinhua321004China School of Biomedical Engineering Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei230026China Suzhou Institute for Advanced Research University of Science and Technology of ChinaSuzhou215123China School of Physical Sciences University of Science and Technology of ChinaHefei 230026China

We investigate electron mesoscopic transport in a three-terminal setup with coupled quantum dots and a magnetic *** mapping the original transport problem into a non-Hermitian Hamiltonian form,we study the interplay between the coherent couplings between quantum dots,the magnetic flux,and the dissipation due to the tunnel coupling with the reservoirs.

关键词： quantum dots magnetic fluxby electron mesoscopic transport non hermitian physics magnetic fluxand coherent couplings transport problem tunnel coupling

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GoPIM: GCN-Oriented Pipeline Optimization for PIM Accelerators

GoPIM: GCN-Oriented Pipeline Optimization for PIM Accelerato...

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IEEE Symposium on High-Performance Computer Architecture

作者： Siling Yang Shuibing He Wenjiong Wang Yanlong Yin Tong Wu Weijian Chen Xuechen Zhang Xian-He Sun Dan Feng The State Key Laboratory of Blockchain and Data Security Zhejiang University Zhejiang Lab Hangzhou High-Tech Zone (Binjiang) Institute of Blockchain and Data Security Zhejiang Key Laboratory of Big Data Intelligent Computing Washington State University Vancouver Illinois Institute of Technology Huazhong University of Science and Technology Wuhan National Laboratory for Optoelectronics

ISBN: (数字)9798331506476

ISBN: (纸本)9798331506483

Graph convolutional networks (GCNs) are popular for a variety of graph learning tasks. ReRAM-based processing-in-memory (PIM) accelerators are promising to expedite GCN training owing to their in-situ computing capability. However, existing accelerators can be severely underutilized even with pipelines, due to the oversight of the skewed execution times of various GCN stages and the ignorance of skewed degrees of graph vertices. In this work, we propose GOPIM, a GCN-oriented pipeline optimization for PIM accelerators to expedite GCN training. First, GOPIM proposes an ML-based scheme that allocates crossbar resources to the most needed stages to streamline the overall pipeline. Second, GOPIM utilizes a selective vertex updating technique that evenly distributes vertices on crossbars by interleaved mapping. These techniques collectively reduce the overall execution time without losing much accuracy. We also provide a practical architecture design for GOPIM. Our experimental results show that, GoPIM achieves up to 191 × speedup and 16.1 × energy saving, compared to the state-of-the-art work.

关键词： Training Accuracy Graph convolutional networks Pipelines Energy conservation Computer architecture Machine learning Parallel processing Optimization

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K-ON: Stacking Knowledge On the Head Layer of Large Language Model

arXiv

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arXiv 2025年

作者： Guo, Lingbing Zhang, Yichi Bo, Zhongpu Chen, Zhuo Sun, Mengshu Zhang, Zhiqiang Zhang, Wen Chen, Huajun College of Computer Science and Technology Zhejiang University China ZJU-Ant Group Joint Lab of Knowledge Graph China Ant Group China School of Software Technology Zhejiang University China Zhejiang Key Laboratory of Big Data Intelligent Computing China

Recent advancements in large language models (LLMs) have significantly improved various natural language processing (NLP) tasks. Typically, LLMs are trained to predict the next token, aligning well with many NLP tasks. However, in knowledge graph (KG) scenarios, entities are the fundamental units and identifying an entity requires at least several tokens. This leads to a granularity mismatch between KGs and natural languages. To address this issue, we propose K-ON, which integrates KG knowledge into the LLM by employing multiple head layers for next k-step prediction. K-ON can not only generate entity-level results in one step, but also enables contrastive loss against entities, which is the most powerful tool in KG representation learning. Experimental results show that K-ON outperforms state-of-the-art methods that incorporate text and even the other modalities. Copyright © 2025, The Authors. All rights reserved.

关键词： Knowledge graph

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Engineered bioorthogonal cell delivery system for in situ antimicrobial peptide recruitment during systemic bacterial infection

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Acta Biomaterialia 2025年 198卷 115-130页

作者： Peng, Wenchang Fu, Yun Du, Yajing Pan, Jingye Li, Bowen Gu, Yun Bai, Yang Zheng, Bin Wang, Tao School of Life Sciences Tianjin University Tianjin300072 China Fujian Provincial Human Sperm Bank Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics Fujian Medical University Fujian Fuzhou350001 China Academy of Medical Engineering and Translational Medicine Tianjin University Tianjin300072 China Department of Stomatology Tianjin Medical University General Hospital Tianjin300052 China School of Biomedical Engineering and Technology Tianjin Medical University Tianjin300070 China Tianjin Key Laboratory of Pathogenic Microbiology of Infectious Disease 300011 China Key Laboratory of Intelligent Treatment and Life Support for Critical Diseases of Zhejiang Province The First Affiliated Hospital of Wenzhou Medical University Zhejiang Wenzhou325000 China

Allogeneic cells represent promising intelligent delivery platforms owing to their intrinsic target homing ability, ready-to-use, scalability and broad applicability. However, implanted allogeneic cells are susceptible to rapid clearance by mononuclear phagocytic system (MPS), resulting in short half-life and compromised therapeutic efficacy. To overcome this limitation, we constructed genetically engineered allogeneic cells with surface-expressed CD24, a "don't eat me" signal protein, to evade phagocytosis by macrophages. Additionally, we modified the allogeneic cells with azide groups, creating a binding site for dibenzocyclooctyne (DBCO)-modified drugs through copper-free click chemistry. The results showed that mesenchymal stem cells (MSCs) have natural inflammation-targeting properties, and modification of allogeneic MSCs (M24N3 cells) significantly prolonged their retention at the site of inflammation. Moreover, DBCO-modified antimicrobial peptides (DBCO-LL37) were more effectively recruited to inflammation sites via bioorthogonal reactions, resulting in sustained bacterial clearance. The M24N3@DBCO-LL37 treatment cleared multiple sepsis mediators, extended circulation time, and increased tissue retention, ultimately protecting against organ damage and delaying sepsis-induced lethality, subsequently resulting in remarkable survival rate elevation. These findings underscore the potential of bioorthogonal system based on engineered allogeneic cells for the treatment of complex inflammatory diseases, highlighting their promising applications in evading rapid clearance systems in vivo. Statement of Significance: In recent years, allogeneic cells have garnered significant research interest as emerging drug delivery carriers due to their off-the-shelf availability, scalable production, and broad therapeutic applicability. However, recognition and elimination mediated by the mononuclear phagocyte system (MPS) brings a substantial challenge to their clinical applicati

关键词： Macrophages

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Virtualizing Next-Generation Programmable Networks: Techniques, Use Cases, and Promising Future Directions

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IEEE Network 2025年第3期39卷 148-155页

作者： Chen, Xiang Du, Hongyang Liu, Wenjing Liu, Hongyan Zhang, Jianshan Yang, Xu Zhang, Dong Wu, Chunming Liu, Xuan Niyato, Dusit Zhejiang University College of Computer Science and Technology Hangzhou310027 China The University of Hong Kong Department of Electrical and Electronic Engineering Pokfulam Hong Kong Zhejiang Media Group Hangzhou310005 China Minjiang University Fujian Provincial Key Laboratory of Information Processing and Intelligent Control College of Computer and Data Science Fuzhou350108 China Fuzhou University College of Computer and Data Science Fuzhou350108 China Yangzhou University College of Information Engineering College of Artificial Intelligence Yangzhou225009 China Nanyang Technological University College of Computing and Data Science Jurong West 639798 Singapore

For decades, network virtualization plays a crucial role in modern networks, e.g., 6G mobile networks: tenants construct arbitrary virtual networks on the same physical network. However, production networks are becoming programmable and need more ways of network configurations. So prior techniques like SDN hypervisors are deprecated since they cannot configure programmable networks. In response, a new category of network virtualization techniques has emerged recently to virtualize programmable networks, i.e., programmable network hypervisors (PNHs). This article first reviews this trend to comprehensively survey PNHs. To understand their benefits, we build a testbed with hardware switches and sophisticated topologies. Our testbed experiments stress-test hypervisors and demonstrate that they outperform prior works with higher acceptance ratios of virtual networks under large-scale scenarios and heavy loads. Finally, we highlight the open issues of these techniques to shed light on the future directions in this promising topic. © 1986-2012 IEEE.

关键词： Virtualization

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