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Identification of Transcription Factor Binding Sites Using GA and PSO

Identification of Transcription Factor Binding Sites Using G...

引用

International Conference on Intelligent Systems Design and Applications (ISDA)

作者： Xiao-yu Chang Chun-guang Zhou Yan-wen Li Ping Hu College of Computer Science Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Jilin University China College of Computer Science Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education department of computer science Northeast Normal University Changchun China

Identification of transcription factor binding sites from the upstream regions of genes is a highly important and unsolved problem. In this paper, we propose a novel framework for using evolutionary algorithm to solve this challenging issue. Under this framework, we use two prevalent evolutionary algorithms: genetic algorithm (GA) and particle swarm optimization (PSO) to find unknown sites in a collection of relatively long intergenic sequences that are suspected of being bound by the same factor. This paper represents binding sites motif to position weight matrix (PWM) and introduces how to code PWM to genome for GA and how to code it to particle for PSO. We apply these two algorithms to 5 different yeast saccharomyces cerevisiae transcription factor binding sites and CRP binding sites. The results on saccharomyces cerevisiae show that it can find the correct binding sites motifs, and the result on CRP shows that these two algorithms can achieve more accuracy than MEME and Gibbs sampler

关键词： Evolutionary computation Pulse width modulation Genomics Bioinformatics Genetic algorithms Particle swarm optimization Biology computing Evolution (biology) educational institutions Computer science

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Virtual storage image implementation in a SAN system to improve storage capacity, fault tolerance and bandwidth

Virtual storage image implementation in a SAN system to impr...

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INTERMAG 2006 - IEEE International Magnetics Conference

作者： Deng, Y. Wang, F. Zhou, K. Wu, S. Center for Grid Computing Cambridge-Cranfteld High Performance Computing Facilities Cranfield University Campus Bedfordshire MK430AL United Kingdom Key Laboratory of Data Storage System Ministry of Education Huazhong University of Science and Technology Wuhan 430074 China

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ISBN: (纸本)1424414792

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Combining Greedy Method and Genetic Algorithm to Identify Transcription Factor Binding Sites

Combining Greedy Method and Genetic Algorithm to Identify Tr...

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International Conference on Hybrid Intelligent Systems (HIS)

作者： Wanyu Wang Xiaoyu Chang Chunguang Zhou College of Computer Science Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Jilin University Changchun China

Identification of Transcription Factor Binding Sites (TFBS) from the upstream region of genes remains a highly important and unsolved problem particularly in higher eukaryotic genomes. In this paper, we propose a novel approach to identify transcription factor binding sites. This approach combines greedy method and genetic algorithm (CGGA) to search conserved segment in the given sequence set. A new greedy method which can efficiently search a local optimal result is proposed. In order to solve the high complexity of this algorithm, we also give an effective improvement for this method. Then, we describe how to combine genetic algorithm with this greedy method to find the more optimal results. Greedy method is combined to the fitness function of the genetic algorithm. We apply this approach on two different TFBS sets and the results show that it can find correct result both effective and efficient, and for CRP binding sites, it get a more accurate result than Gibbs Sampler, AlignACE and MDGA.

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SLNN: A Neural Network for Fuzzy Neural Network's Structure Learning

SLNN: A Neural Network for Fuzzy Neural Network's Structure ...

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International Conference on Intelligent Systems Design and Applications (ISDA)

作者： Daxin Tian Yanheng Liu Jian Wang College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China

A novel structure learning algorithm for fuzzy neural networks (SLNN) is presented in this paper. The neurons of SLNN are created and adapted as online learning proceeds. The learning rule of SLNN is based on Hebbian learning and a kernel winner-take-all algorithm - KWTA. KWTA not only can let SLNN be able to learn from new data but also can prevent losing the knowledge which has been learned earlier. To obtain a concise fuzzy rule, a pruning algorithm is adopted in SLNN which doesn't disobey the basic design philosophy of fuzzy system. Simulations are performed on the primary benchmark: circle-in-the-square. Comparison with ARTMAP and BP neural network indicates that better performance is achieved

关键词： Neural networks Fuzzy neural networks Fuzzy systems Clustering algorithms Signal processing algorithms Computer networks Neurons Partitioning algorithms Learning Fuzzy control

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Research of Mobile IPv6 Application Based On Diameter Protocol

Research of Mobile IPv6 Application Based On Diameter Protoc...

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International Multi-Symposiums on Computer and Computational Sciences (IMSCCS)

作者： Da Wei Yanheng Liu Xuegang Yu Xiaodong Li College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University China

The diameter protocol is recommended by IETF as AAA (authentication, authorization and accounting) protocol criterion for the next generation network. Because the IPv6 protocol will be widely applied in the intending all-IP network, mobile IPv6 application based on diameter protocol will play more important role in authentication, authorization and accounting. In this paper, the implementation of mobile node's authentication and authorization is presented with PANA (protocol for carrying authentication for network access) protocol. It is based on diameter protocol for the application expansion of mobile IPv6, which provides the supports to the basic AAA process of mobile IPv6 nodes and dynamic home agent distribution in the visited network and the secret key distribution. Finally, the correctness of this application expansion is testified with developing the design of protocol based on opendiameter

关键词： Access protocols Authentication Cryptographic protocols Authorization Network servers Application software IP networks Peer to peer computing Transport protocols Computer science

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A hybrid discrete particle swarm algorithm for open-shop problems

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6th International Conference Simulated Evolution and Learning, SEAL 2006

作者： Qingyun, Yang Jigui, Sun Juyang, Zhang Chunjie, Wang College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory for Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 China Open Laboratory for Intelligence Information Processing Fudan University Shanghai 200433 China Basic Sciences of ChangChun University of Technology ChangChun University of Technology Changchun 130012 China

ISBN: (纸本)3540473319

A hybrid discrete particle swarm algorithm is presented in this paper to solve open-shop problems. The operations are redefined in the discrete particle swarm algorithm. To improve the performance the simulated annealing algorithm is combined with discrete particle swarm. We use SA to enhance the results of local best positions instead of current positions. The experimental results show that our hybrid discrete particle swarm algorithm is effective and efficient to solve open-shop problems. © Springer-Verlag Berlin Heidelberg 2006.

关键词： Open systems

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Design and Implementation of Geo-Objects Simulation and Interactive Visual Editing Tools

Design and Implementation of Geo-Objects Simulation and Inte...

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International Conference on Artificial Reality and Telexistence (ICAT)

作者： Song Shi Chongchen Chen Qingmin Wang Jieyun Yan Key Laboratory of Data Mining & Information Sharing of Ministry of Education Spatial Information Research Center of Fujian Fuzhou University Fuzhou China

Terrain is the carrier of virtual environment, and terrain modeling is the base of constructing model in synthetic natural environment (SNE). The goal of SNE modeling is not only to reconstruct real environment elements such as terrain in virtual environment, but also to construct multi-level interactive channels between human and virtual environment. In this paper, a prototype called geo-objects simulation and visual editing system (GSVES) is developed, in which a technological approach for integrating modeling, editing and analyzing environment elements is explored. Further more, this paper goes into a description of the different levels of interactive behavior between human and virtual environment as follows: data level, analysis level and collaboration level, from low to high. We proposed the real environment elements should be organized sequentially in the context of SNE, which lays the foundation for interaction between human and virtual environment harmoniously finally

关键词： Virtual environment Humans Analytical models Object oriented modeling data processing Tin data mining Virtual prototyping Virtual reality Computer architecture

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A framework for accessing general object storage

A framework for accessing general object storage

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International Workshop on Networking, Architecture, and Storages (IWNAS)

作者： Qun Liu Dan Feng Qin Ling-jun Zeng Ling-fang Key Laboratory of Data Storage System Ministry of EducationCollege of Computer Huazhong University of Science슠and슠Technology Wuhan China

With computer application popularizing and storage capacity increasing, research for NAS and SAN storage system are gradually turning to OBS. The OBS will become the next wave of network storage technology. In this paper a framework for accessing general object storage (GOS) is presented. The GOS system adopts a basic unit called storage device object (SDO) and proposes an access model that contains upper layer, middle layer and lower layer. It not only enriches the concept of object, but also gives a compatible object interface in the network storage systems. So it allows applications to access to different SDO according their attributes. Therefore it is more universal

关键词： Storage area networks File servers Application software Protocols Network servers data structures Image storage File systems Laboratories data storage systems

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I/O Scheduling in Huge Object-based Storage System

I/O Scheduling in Huge Object-based Storage System

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Japan-china Joint Workshop on Frontier of Computer Science and Technology (FCST)

作者： Dan Feng Hanbo Liu Key Laboratory of Data Storage System Ministry of Education School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China

Huge object-based storage system (HOSS), using objects which possess their own attributes and methods as storage interface, absorbs the advantages of both blocks and files interface. HOSS adopts the interaction among clients, metadata servers and object-based storage device, which has decreased the overload of servers in large measure. After the interactions' flows concerned with I/O operations among the three components described in detail the design and implementation of parallel I/O scheduling is described and discussed. With the buffer, the results show that it enhances the whole system performance efficiently. The performance is better when it's compared with the Lustre system

关键词： Buffer storage Computer architecture Processor scheduling Computer science educational technology System performance Protocols Quality of service Laboratories data storage systems

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Prediction of Transcription Factor Binding Sites Using Genetic Algorithm

Prediction of Transcription Factor Binding Sites Using Genet...

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IEEE Conference on Industrial Electronics and Applications (ICIEA)

作者： Xiaoyu Chang Wengang Zhou Chunguang Zhou Yanchun Liang College of Computer Science and Technology Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Jilin University Changchun China

Identification of transcription factor binding sites (TFBS) from the upstream region of genes remains a highly important and unsolved problem particularly in higher eukaryotic genomes. In this paper, we propose a new approach to predict TFBS. This approach uses position weight matrix (PWM) to represent binding sites and uses genetic algorithm (GA) to search the best matrix. A new coding method so called multiple-variable coding is proposed in GA. We apply it on two transcription factors rebl and mgl. The result shows that this approach can find most of the known sites, which indicates that this method is very effective

关键词： Genetic algorithms Pulse width modulation Sequences Genomics Bioinformatics Hidden Markov models Proteins Computer science educational technology knowledge engineering

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