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BSPM:A NEW MECHANISM FOR “OVERLAP-MATCHING EXPRESSIONS”IN DPI

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Journal of Electronics(China) 2010年第3期27卷 289-297页

作者： Li Zheng Yu Nenghai Li Yang moe-microsoft key lab of multimedia computing and communication University of Science and Technology of China Hefei 230027 China

Nowadays, using Deterministic Finite Automata (DFA) or Non-deterministic Finite Automata (NFA) to parse regular expressions is the most popular way for Deep Packet Inspection (DPI), and the research about DPI focuses on the improvement of DFA to reduce memory. However, most of the existing literature ignores a special kind of "overlap-matching expression", which causes states explosion and takes quite a large part in the DPI rules. To solve this problem, in this paper a new mechanism is proposed based on bitmap. We start with a simple regular expression to describe "overlap-matching expressions" and state the problem. Then, after calculating the terrible number of exploded states for this kind of expressions, the procedure of Bitmap-based Soft Parallel Mechanism (BSPM) is described. Based on BSPM, we discuss all the different types of "overlap-matching ex- pressions" and give optimization suggestions of them separately. Finally, experiment results prove that BSPM can give an excellent performance on solving the problem stated above, and the optimization suggestions are also effective for the memory reduction on all types of "overlap-matching expressions".

关键词： Intrusion detection Deep Packet Inspection (DPI) Regular expressions Bitmap-based Deterministic Finite Automata (DFA)

A ROBUST EYE LOCALIZATION ALGORITHM FOR FACE RECOGNITION

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Journal of Electronics(China) 2008年第3期25卷 337-342页

作者： Zhang Wencong Li Xin Yao Peng Li Bin Zhuang Zhenquan moe-microsoft key laboratory of multimedia computing and communication University of Science and Technology of China Hefei 230026 China

The accuracy of face alignment affects greatly the performance of a face recognition system. Since the face alignment is usually conducted using eye positions, the algorithm for accurate eye lo- calization is essential for the accurate face recognition. In this paper, an algorithm is proposed for eye localization. First, the proper AdaBoost detection is adaptively trained to segment the region based on the special gray distribution in the region. After that, a fast radial symmetry operator is used to pre- cisely locate the center of eyes. Experimental results show that the method can accurately locate the eyes, and it is robust to the variations of face poses, illuminations, expressions, and accessories.

关键词： Eye localization AdaBoost Fast radial symmetry

ASYMBOOST-BASED FISHER LINEAR CLASSIFIER FOR FACE RECOGNITION

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Journal of Electronics(China) 2008年第3期25卷 352-357页

作者： Wang Xianji Ye Xueyi Li Bin Li Xin Zhuang Zhenquan moe-Microsofl key laboratory of multimedia computing and communication University of Science and Technology of China Hefei 230025 China

When using AdaBoost to select discriminant features from some feature space (e.g. Gabor feature space) for face recognition, cascade structure is usually adopted to leverage the asymmetry in the distribution of positive and negative samples. Each node in the cascade structure is a classifier trained by AdaBoost with an asymmetric learning goal of high recognition rate but only moderate low false positive rate. One limitation of AdaBoost arises in the context of skewed example distribution and cascade classifiers: AdaBoost minimizes the classification error, which is not guaranteed to achieve the asymmetric node learning goal. In this paper, we propose to use the asymmetric AdaBoost (Asym- Boost) as a mechanism to address the asymmetric node learning goal. Moreover, the two parts of the selecting features and forming ensemble classifiers are decoupled, both of which occur simultaneously in AsymBoost and AdaBoost. Fisher Linear Discriminant Analysis (FLDA) is used on the selected fea- tures to learn a linear discriminant function that maximizes the separability of data among the different classes, which we think can improve the recognition performance. The proposed algorithm is dem- onstrated with face recognition using a Gabor based representation on the FERET database. Ex- perimental results show that the proposed algorithm yields better recognition performance than AdaBoost itself.

关键词： AsymBoost AdaBoost Gabor feature Face recognition

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) Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University key laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent computing Zhejiang Lab Shanghai Research Institute for Intelligent Autonomous Systems Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of Medicine National key laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University Beijing Institutes of Life Science Chinese Academy of Sciences Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology (CQB)Peking University Zhejiang key laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women's HospitalZhejiang University School of Medicine key laboratory of Advanced Theory and Application in Statistics and Data Science-moe School of StatisticsEast China Normal University

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our 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 intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These 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 sc RNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This 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

AN ENHANCEMENT SCHEME OF TCP PROTOCOL IN MOBILE AD HOC NETWORKS:MME-TCP

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Journal of Electronics(China) 2007年第1期24卷 1-9页

作者： Kai Caihong Yu Nenghai Chen Yuzhong moe-microsoft key lab. of multimedia computing and communication Information Processing Center University of Science ＆ Technology of China Hefer 230027 China

Transmission Control Protocol (TCP) optimization in Mobile Ad hoc NETworks (MANETs) is a challenging issue because of some unique characteristics of MANETs. In this paper,a new end-to-end mechanism based on multiple metrics measurement is proposed to improve TCP performance in MANETs. Multi-metric Measurement based Enhancement of TCP (MME-TCP) designs the metrics and the identification algorithm according to the characteristics of MANETs and the experiment results. Furthermore,these metrics are measured at the sender node to reduce the overhead of control information over networks. Simulation results show that MME-TCP mechanism achieves a significant performance improvement over standard TCP in MANETs.

关键词： Ad hoc networks Transmission Control Protocol (TCP) Network states End-to-end metrics Identification algorithms

Single-cell technologies: current and near future

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Science China Life Sciences 2025年第01期 1-4页

作者： Chenfei Wang Qi Liu Xiaohui Fan Tieliu Shi key laboratory of Spine and Spinal Cord Injury Repair and Regeneration Ministry of EducationOrthopedics DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji University Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji University Research Institute of Intelligent computing Zhejiang Lab Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang University National key laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang University Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal University key laboratory of Advanced Theory and Application in Statistics and Data Science (moe) School of StatisticsEast China Normal University

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(sc RNA-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 metabolomics.

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Surface-confined persistent luminescence with amplified FRET efficiency for cell-cell communication monitoring

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Science China Chemistry 2025年

作者： Ziyun Miao Wenjing Dai Yubin Jin Bing Qi Jiayi Chen Lingling Qiu Yurong Wei Jie Wang The key lab of Health Chemistry&Molecular Diagnosis of Suzhou College of ChemistryChemical Engineering&Materials ScienceSoochow University

Microbial communication monitoring is vital for understanding the mechanisms beneath gut microbiota equilibrium, infections,and biomanufacturing. Herein, we reported monitoring bacterial communication by surface-confined persistent ***, we constructed core-shell structured Zn1.4Ga1.2Ge0.4O4@Zn1.4Ga1.2Ge0.4O4:Cr（ZGGO@ZGGO:Cr） persistent luminescence nanoparticles（PLNPs） with amplified FRET efficiency for the detection of azoreductase（AzoR） that participates in bacterial communication. ZGGO@ZGGO:Cr nanoparticles were functionalized with an azo black hole quencher（ZGGO@ZGGO:Cr-BHQ-3）. Due to the proximity of surface-confined persistent luminescence with the surface-bound BHQ-3,ZGGO@ZGGO:Cr-BHQ-3 exhibited a FRET efficiency up to 1.6 times that of traditional ZGGO:Cr-BHQ-3. Further, the specific catalytic reduction of azo bonds in BHQ-3 by bacterial extracellular AzoR recovers the persistent luminescence of ZGGO@ZGGO:Cr. ZGGO@ZGGO:Cr-BHQ-3 displayed superior sensitivity and speed in detecting extracellular AzoR over ZGGO:Cr-BHQ-3, attributed to its surface-confined persistent luminescence. We found that the peak secretion of AzoR occurs during the exponential growth period of bacteria including S. aureus and E. coli based on the persistent luminescence recovery rate of ZGGO@ZGGO:Cr-BHQ-3. Furthermore, ZGGO@ZGGO:Cr-BHQ-3 was used to probe the communication between different bacterial species. R. palustris is a kind of lycopene-production bacteria. We found that the cohabitation of R. palustris and S. putrefaciens boosted both AzoR secretion and lycopene production. Moreover, the secretion and activity of AzoR positively correlated with lycopene production, suggesting that AzoR may participate in the communication between R. palustris and S. putrefaciens to promote lycopene production. This study offers a robust method to enhance PLNP-based biosensing sensitivity and provides a promising strategy for microbial communication monitoring.

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Efficient implementation of the Barnes-Hut octree algorithm for Monte Carlo simulations of charged systems

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Science China Mathematics 2014年第7期57卷 1331-1340页

作者： GAN ZeCheng XU ZhenLi Department of Mathematics Institute of Natural Sciencesand MoE Key Lab of Scientific and Engineering ComputingShanghai Jiao Tong University

Computer simulation with Monte Carlo is an important tool to investigate the function and equilibrium properties of many biological and soft matter materials solvable in *** appropriate treatment of long-range electrostatic interaction is essential for these charged systems,but remains a challenging problem for large-scale *** develop an efficient Barnes-Hut treecode algorithm for electrostatic evaluation in Monte Carlo simulations of Coulomb many-body *** algorithm is based on a divide-and-conquer strategy and fast update of the octree data structure in each trial move through a local adjustment *** test the accuracy of the tree algorithm,and use it to perform computer simulations of electric double layer near a spherical *** is shown that the computational cost of the Monte Carlo method with treecode acceleration scales as log N in each *** a typical system with ten thousand particles,by using the new algorithm,the speed has been improved by two orders of magnitude from the direct summation.

关键词： electrostatics Monte Carlo fast algorithms octree colloidal interfaces

A RESEARCH OF UWB RAKE RECEIVER BASED ON NOVEL RLS ADAPTIVE ALGORITHM

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Journal of Electronics(China) 2006年第3期23卷 341-345页

作者： Yin Yong Yu Nenghai Dong Weijie moe-microsoft key laboratory of multimedia computing and communication Information Processing Center University of Science and Technology of China Hefei 230027 China

A modified RAKE receiver based on novel Recursive Least Squares （RLS） adaptive algorithm is proposed. The receiver uses L-fingered correlators, which are composed of RLS adaptive filters, to enhance the performance of multipath receiving. It can also track the amplitude of the received signal to form a real-time amplitude estimation which is correlated with the power of excess delay bin. The simulation results based on the IEEE UltraWide Band （UWB） channel models （CMI to CM4） show that the novel RLS algorithm can alter the attenuation estimation with the finger＇s power delay profile, and RAKE receiver with few fingers can be employed to get high performance.

关键词： UltraWide Band (UWB) RAKE receiver Recursive Least Squares (RLS)