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Bioimage-based protein subcellular location prediction： a comprehensive review

Frontiers of Computer Science 2018年第1期12卷 26-39页

作者： Ying-Ying XU Li-Xiu YAO Hong-Bin SHEN Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai 200240 China Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai 200240 China

Subcellular localization of proteins can provide key hints to infer their functions and structures in cells. With the breakthrough of recent molecule imaging techniques, the usage of 2D bioimages has become increasingly popular in automatically analyzing the protein subcellular location pat- terns. Compared with the widely used protein 1D amino acid sequence data, the images of protein distribution are more intuitive and interpretable, making the images a better choice at many applications for revealing the dynamic char- acteristics of proteins, such as detecting protein translocation and quantification of proteins. In this paper, we systemati- cally reviewed the recent progresses in the field of automated image-based protein subcellular location prediction, and clas- sified them into four categories including growing of bioim- age databases, description of subcellular location distribution patterns, classification methods, and applications of the pre- diction systems. Besides, we also discussed some potential directions in this field.

关键词： bioimage informatics protein subcellular loca-tion prediction global and local features multi-location pro-tein recognition

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Shadow detection using regression tree fields with paired regions

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Journal of Computational information Systems 2013年第11期9卷 4309-4317页

作者： Tao, Wei Zhou, Yue Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Shanghai 200240 China

In this paper, we try to deal with the problem of shadow detection from static images and video sequences. In instead to considering individual regions separately, we use relative illumination conditions between segmented regions and perform pair-wise classification based on such information. We use Regression Tree Fields to solve the labeling of shadow and non-shadow regions. And we use continuous value to describe the possibility of the shadow of the region. We evaluate our method on static images and a series of video sequences. © 2013 by Binary information Press.

关键词： Classification (of information)

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Cyber-physical System Security for Networked Industrial Processes

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International Journal of Automation and computing 2015年第6期12卷 567-578页

作者： Shuang Huang Chun-Jie Zhou Shuang-Hua Yang Yuan-Qing Qin School of Automation Huazhong University of Science and Technology Key Laboratory of Ministry of Education for Image Processing and Intelligent Control Department of Computer Science Loughborough University

Cyber-physical systems(CPSs) are integrations of networks, computation and physical processes, where embedded computing devices continually sense, monitor, and control the physical processes through networks. Networked industrial processes combining internet, real-time computer control systems and industrial processes together are typical CPSs. With the increasingly frequent cyber-attack, security issues have gradually become key problems for CPSs. In this paper, a cyber-physical system security protection approach for networked industrial processes, i.e., industrial CPSs, is proposed. In this approach, attacks are handled layer by layer from general information technology(IT) security protection, to active protection, then to intrusion tolerance and physical security protection. The intrusion tolerance implemented in real-time control systems is the most critical layer because the real time control system directly affects the physical layer. This novel intrusion tolerance scheme with a closed loop defense framework takes into account the special requirements of industrial CPSs. To illustrate the effectiveness of the CPS security protection approach, a networked water level control system is described as a case study in the architecture analysis and design language(AADL) environment. Simulation results show that 3 types of injected attacks can be quickly defended by using the proposed protection approach.

关键词： Critical infrastructures cyber-physical systems(CP

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Mem Brain: An Easy-to-Use Online Webserver for Transmembrane Protein Structure Prediction

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Nano-Micro Letters 2018年第1期10卷 12-19页

作者： Xi Yin Jing Yang Feng Xiao Yang Yang Hong-Bin Shen Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Department of Computer Science Shanghai Jiao Tong University Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering

Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels,transporters, receptors. Because it is difficult to determinate the membrane protein's structure by wet-lab experiments,accurate and fast amino acid sequence-based computational methods are highly desired. In this paper, we report an online prediction tool called Mem Brain, whose input is the amino acid sequence. Mem Brain consists of specialized modules for predicting transmembrane helices, residue–residue contacts and relative accessible surface area of a-helical membrane proteins. Mem Brain achieves aprediction accuracy of 97.9% of ATMH, 87.1% of AP,3.2 ± 3.0 of N-score, 3.1 ± 2.8 of C-score. Mem BrainContact obtains 62%/64.1% prediction accuracy on training and independent dataset on top L/5 contact prediction,respectively. And Mem Brain-Rasa achieves Pearson correlation coefficient of 0.733 and its mean absolute error of13.593. These prediction results provide valuable hints for revealing the structure and function of membrane *** Brain web server is free for academic use and available at ***/bioinf/Mem Brain/.

关键词： Transmembrane a-helices Structure prediction Machine learning Contact map prediction Relative accessible surface area

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Self-organization of Reconfigurable Protocol Stack for Networked control Systems

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International Journal of Automation and computing 2011年第2期8卷 221-235页

作者： Chun-Jie Zhou Hui Chen Yuan-Qing Qin Yu-Feng Shi Guang-Can Yu Key Laboratory of Ministry of Education for Image Processing and Intelligent Control Department of Control Science and Engineering Huazhong University Science and Technology Wuhan 430074 PRC

In networked control systems （NCS）,the control performance depends on not only the control algorithm but also the communication protocol *** performance degradation introduced by the heterogeneous and dynamic communication environment has intensified the need for the reconfigurable protocol *** this paper,a novel architecture for the reconfigurable protocol stack is proposed,which is a unified specification of the protocol components and service interfaces supporting both static and dynamic reconfiguration for existing industrial communication *** the architecture,a triple-level self-organization structure is designed to manage the dynamic reconfiguration procedure based on information exchanges inside and outside the protocol ***,the protocol stack can be self-adaptive to various environment and system requirements through the reconfiguration of working mode,routing and scheduling ***,the study on the protocol of dynamic address management is conducted for the system of controller area network （CAN）.The results show the efficiency of our self-organizing architecture for the implementation of a reconfigurable protocol stack.

关键词： Networked control system (NCS) communication network self-organization protocol stack reconfiguration

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An improved column generation algorithm for crew scheduling problems

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Journal of information and Computational Science 2013年第1期10卷 175-183页

作者： Chen, Shijun Shen, Yindong Image Processing and Intelligent Control Key Laboratory of Education Ministry Department of Control Science and Engineering Huazhong University of Science and Technology Wuhan 430074 China

Column Generation (CG) technique is popularly applied in solving the crew scheduling problem of large size, which is generally modeled as an Integer Linear Programming (ILP) problem. The traditional CG algorithms for bus and rail crew scheduling encounter difficulties on either the generation of all potential shifts or solving subproblems. A subproblem embedded in the CG is generally represented as a Resource-constrained Shortest Path Problem (RCSPP), which is NP-hard and constitutes a major reason for the CG's slow convergence. This paper presents a novel CG strategy to improve the efficiency of the proposed crew scheduling approach. The main idea is that a reasonably large set of "good" potential shifts (called a shift-pool) is pre-compiled using problem-specific knowledge. During the CG process, the RCSPP is not constructed to generate potential shifts as new columns until no columns with Negative Reduced Cost (NRC) exist in the shift-pool. Experiments are carried out on a series of Chinese real-world problem instances, and the computational results show that the solving process is significantly accelerated. © 2013 by Binary information Press.

关键词： Integer programming

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A novel model and behavior analysis for a swarm of multi-agent systems with finite velocity

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Chinese Physics B 2014年第9期23卷 590-593页

作者：王良顺吴治海 Key Laboratory of Image Processing and Intelligent Control of the Ministry of Education School of AutomationHuazhong University of Science and Technology Key Laboratory for Advanced Process Control of Light Industry of the Ministry of Education School of Internet of Things EngineeringJiangnan University

Inspired by the fact that in most existing swarm models of multi-agent systems the velocity of an agent can be infinite, which is not in accordance with the real applications, we propose a novel swarm model of multi-agent systems where the velocity of an agent is finite. The Lyapunov function method and LaSalle＇s invariance principle are employed to show that by using the proposed model all of the agents eventually enter into a bounded region around the swarm center and finally tend to a stationary state. Numerical simulations are provided to demonstrate the effectiveness of the theoretical results.

关键词： multi-agent systems swarm finite velocity attraction and repulsion

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Motion cue based pedestrian detection with two-frame-filtering

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High Technology Letters 2015年第3期21卷 328-332页

作者：吕敬钦 Zhang Miaohui Yang Jie Institute of Image Processing and Pattern Recognition Shanghai Jiaotong Universityand Key Laboratory of System Control and Information ProcessingMinistry of Education of China

This study proposes a motion cue based pedestrian detection method with two-trame-filtering （Tff） for video surveillance. The novel motion cue is exploited by the gray value variation between two frames. Then Tff processing filters the gradient magnitude image by the variation map. Summa- tions of the Tff gradient magnitudes in cells are applied to train a pre-deteetor to exclude most of the background regions. Histogram of Tff oriented gradient （HTffOG） feature is proposed for pedestrian detection. Experimental results show that this method is effective and suitable for real-time surveil- lance applications.

关键词： pedestrian detection two-frame-filtering (TFF) Tff magnitude vector (TffMV) Histogram of Tff oriented gradient ( HTffOG) SVM video surveillance

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A uniform solution to the independent set problem through tissue P systems with cell separation

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Frontiers of Computer Science 2012年第4期6卷 477-488页

作者： Xingyi ZHANG Xiangxiang ZENG Bin LUO Zheng ZHANG Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and TechnologyAnhui UniversityHefei 230039China Department of Computer Science Xiamen UniversityXiamen 361005China Key Laboratory of Image Processing and Intelligent Control Department of Control Science and EngineeringHuazhong University of Science and TechnologyWuhan 430074China

Membrane computing is an emergent branch of natural computing, which is inspired by the structure and the functioning of living cells, as well as the organization of cells in tissues, organs, and other higher order structures. Tissue P systems are a class of the most investigated computing mod- els in the framework of membrane computing, especially in the aspect of efficiency. To generate an exponential resource in a polynomial time, cell separation is incorporated into such systems, thus obtaining so called tissue P systems with cell separation. In this work, we exploit the computational efficiency of this model and construct a uniform family of such tissue P systems for solving the independent set problem, a well-known NP-complete problem, by which an efficient so- lution can be obtained in polynomial time.

关键词： membrane computing tissue P system cell sep- aration independent set problem

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Optical Music Recognition Based On Localityconstrained Linear Coding and Double Distribution Support Vector Machine 5

Optical Music Recognition Based On Localityconstrained Linea...

引用

The 5th International Symposium on Electromagnetic Compatibility

作者： XiaXia Zeng Fanyong Cheng Wenzhong Lin Haibo Luo Zhiqiang Ruan Fujian Provincial Key Laboratory of Information Processing and Intelligent Control（Minjiang University）

ISBN: (纸本)9781509051861;9781509051854

Optical Music Recognition（OMR） has received increasing attention in recent *** this paper,we adopt the descriptor of Locality-constrained Linear Coding（LLC） and Double Distribution Support Vector Machine（DDSVM） to address music symbol classification in *** can obtain stronger feature representation ability compared with original music ***,DDSVM is presented to obtain stronger robustness and generalization ***,DDSVM is adopted to improve the classification performance in ***,One Versus Rest Double Distribution Support Vector Machine（OVR-DDSVM） is proposed for multi-class music symbol ***-DDSVM can obtain high accuracy only using linear kernel due to LLC descriptor,and this speeds the classification ***-DDSVM is tested on more than10000 music symbol images of 20 classes,and experimental results verify the superiority of LLC+DDSVM to other algorithms.

关键词： OMR SVM classification

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