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International Conference on BioMedical Engineering and Informatics (BMEI)

作者： Qijun Liu Zhenghua Wang Hanchang Sun Hao Guo Wanlin Liu Yunping Zhu National Laboratory of Parallel & Distributed Processing National University of Defence Technology Changsha China State Key Laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing China

To conduct a systemic analysis of biological networks function distribution and function modules, we present a semiautomatic method to achieve independent and intact GO slim (InitGO) based on graph operations and GO hierarchy structure. Our method is packed into a user-friendly Cytoscape plugin named InitGO. The application of InitGO to yeast transcriptional factors regulatory network shows that the network has function modularity, offering evidence that our method is effective for defining function modules. InitGO plugin and source codes are available on request from the authors.

关键词： Ontologies Biological information theory Independent component analysis Fungi Data visualization Systems biology Bioinformatics Laboratories distributed processing Transfer functions

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Revealing the functional modularity of yeast transcriptional regulatory network by using a novel topological measurement

Revealing the functional modularity of yeast transcriptional...

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International Conference on Computer Science and Information technology (CSIT)

作者： Qijun Liu Zhenghua Wang Mansheng Li Dong Li Yunping Zhu National Laboratory of Parallel & Distributed Processing National University of Defence Technology Changsha China State Key Laboratory of Proteomics Beijing Proteomics Research Center Beijing Institute of Radiation Medicine Beijing China

It has been reported that function implementations in biological systems, including transcriptional regulatory networks (TRN), show modular architecture. Analyzing functional modularity of biological networks can describe characteristics of function implementation and their "position" in biology systems from the systems perspective. Defining functional modules naturally, we bring up a novel measurement, cohesive degree (CD), to characterize the modularity. From this character, we know that not all of the corresponding modules of function annotations take on good modularity. Considering the ratio of the non-cohesive (zero-CD value) modules, TRN's functional modularity is also weaker than that of other biological network and integral ones. And, this is not caused by data integrity, but by the topology of itself. In fact, the modularity implementation of biological systems is mainly accomplished through the cooperation of several types of networks, not by TRN alonely.

关键词： Fungi Biochemistry Biological systems Proteins Gene expression Laboratories Electronic mail Proteomics Network topology Systems biology

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Scalable unbiased sampling method based on multi-peer adaptive random walk

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Ruan Jian Xue Bao/Journal of Software 2009年第3期20卷 630-643页

作者： Fu, Yong-Quan Wang, Yi-Jie Zhou, Jing National Key Laboratory for Parallel and Distributed Processing School of Computer National University of Defense Technology Changsha 410073 China Staff Room of Computer Command Academy of the Corps of Engineers Xuzhou 221000 China

To deal with the scalable and fast unbiased sampling problems in unstructured P2P systems, a sampling method based on multi-peer adaptive random walk (SMARW) is proposed. In the method, based on the multi-peer random walk process, a set of provisional peers are selected as agents which start the sampling processes, by which the sampling process is speeded up with receiving a set of tunable number samples each time;Meanwhile, after receiving new samples earlier agents are replaced with these new samples which repeat the sampling process. With this simple replacement, it can be guaranteed with high probability that the system can reach the optimal load balance;furthermore, SMARW adopts an adaptive distributed random walk adjustment process to increase the convergence rate of the sampling process. A detailed theorical analysis and performance evaluation confirm that SMARW has a high level of unbiased sampling and near-optimal load balancing capability. © by Institute of Software, the Chinese Academy of Sciences. All rights reserved.

关键词： Peer to peer networks

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Optimistic data consistency maintenance method based on data dependence

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Jisuanji Xuebao/Chinese Journal of Computers 2008年第5期31卷 741-753页

作者： Zhou, Jing Wang, Yi-Jie Li, Si-Kun National Key Laboratory for Parallel and Distributed Processing School of Computer National University of Defense Technology Changsha 410073 China

This paper proposes an optimistic data consistency method according to the question about data dependence in data consistency. In the method, data object is partitioned into data blocks by fixed size as the basic unit of data management. Updates are compressed by Bloom filter technique and propagated in double-path. Negotiation algorithms detect and reconcile update conflicts, and dynamic data management algorithms accommodate dynamic data processing. The results of the performance evaluation show that it is an efficient method to achieve consistency, good dynamic property, and strong robustness when choosing the size of data block appropriately. At the same time, a feasible way is put forward on how to choose appropriate data block size.

关键词： Data processing

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Optimistic data consistency maintenance method based on key-attributes

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Ruan Jian Xue Bao/Journal of Software 2008年第8期19卷 2114-2126页

作者： Zhou, Jing Wang, Yi-Jie Li, Si-Kun National Key Laboratory for Parallel and Distributed Processing School of Computer National University of Defense Technology Changsha 410073 China

The features of simple description, small updates item and weak dependence are the main characteristics of updates of key-attributes in P2P systems. Accordingly, an optimistic data consistency maintenance method based on key-attributes is proposed. In the method, the update of key-attributes is separated from user update requests. key-Updates are propagated by latency-overlay update propagation model, that is, updates are always propagated to the nodes having maximum or minimum latency, and assured and uncertain propagation paths of updates are all taken into account. Based on classifying key-update conflicts, a double-level reconciling mechanism including buffer preprocessing and update-log processing is applied to detect and reconcile conflicts, and then conflicts are solved by policies as last-writer-win and divide-and-rule. Lastly, update-log management method and maintenance method brought by node failure and network partitioning are discussed for the above is deployed based on the information storied in update-log. Delaying key-attributes updates cannot occur by the optimistic disposal method, and then it cannot depress efficiency of resource location based on key-attributes, which adapts well to P2P systems for Internet. The simulation results show that it is an effective optimistic data consistency maintenance method, achieving good consistency overhead, resource location and resource access overhead, and having strong robustness.

关键词： Maintenance

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Optimization approaches of organizing streams on imagine processor

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Jisuanji Xuebao/Chinese Journal of Computers 2008年第7期31卷 1092-1100页

作者： Yang, Xue-Jun Zeng, Li-Fang Deng, Yu Tang, Yu-Hua National Key Laboratory of Parallel and Distributed Processing School of Computer Science National University of Defense Technology Changsha 410073 China Jiangnan Remote Sensing Institute Shanghai 200072 China

Due to the characteristics of stream applications and the insufficiency of conventional processors when running stream programs, stream processors which support data-level parallelism become the research hotspot. This paper presents two means, stream partition (SP) and stream compression (SC), to optimize streams on Imagine. The results of simulation show that SP and SC can make stream applications take full advantage of the parallel clusters, pipelines and three-level memory hierarchy of the Imagine processor, and then reduce the execution time of stream programs.

关键词： parallel processing systems

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An Efficient Approximation for Weapon-Target Assignment

An Efficient Approximation for Weapon-Target Assignment

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ISECS International Colloquium on Computing, Communication, Control, and Management, CCCM

作者： Lina Chen ChuanJun Ren Su Deng C4ISR Technology National Defense Science and Technology Key Laboratory National University of Defense Technology Changsha Hunan China National Laboratory of Parallel and Distributed Processing National University of Defense Technology Changsha Hunan China

The weapon-target assignment (WTA) problem is a fundamental problem arising in defense-related applications of operations research. The WTA problem can be formulated as a nonlinear integer programming problem and is known to be NP-complete. We present firstly a technique founded on the use weapon cell, which enables one-to-many mapping about weapon-target to become one-to-one mapping. Next, we introduce a framework of solving the WTA problem. Based on this framework, an approximation algorithm that is grounded on the rules about weapon cells and targets is proposed. Finally, the simulative results show that the proposed algorithm indeed is very efficient.

关键词： Weapons Heuristic algorithms Algorithm design and analysis Resource management Artificial neural networks Genetic algorithms Operations research

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Multi-replica clustering management method based on limited-coding

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Ruan Jian Xue Bao/Journal of Software 2007年第6期18卷 1456-1467页

作者： Zhou, Jing Wang, Yi-Jie Li, Si-Kun School of Computer National University of Defense Technology Changsha 410073 China National Key Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China

In this paper, according to the resource management problems brought by a large number of replicas, a multi-replica clustering management method based on limited-coding is proposed. In this method, according to the process of creating new replicas from existent single replica, replicas are partitioned into different hierarchies and clusters. Then replicas are coded and managed based on the user-defined limited-coding rule consisting of replica hierarchy and replica sequence, which can also dispose the alteration of clusters caused by dynamic adjustments on replicas (replica addition or replica removal) effectively. After that, a management model of centralization in local and peer to peer in wide area is adopted to organize replicas, and the cost of reconciling consistency can be greatly depressed combining with defined minimal-time of update propagation. The relevance between the coding rule and the number of replicas, and the solutions to replica failure and replica recover are discussed. The results of the performance evaluation show that the clustering method is an efficient way to manage a large number of replicas, achieving good scalability, not sensitive to moderate node failure, and adapting well to applications with frequent updates.

关键词： Data processing

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Relativity between gene expression level and combinatorial regulatory relationship

Relativity between gene expression level and combinatorial r...

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第五届中国蛋白质组学大会暨首届粤港蛋白质组学学术交流会

作者： Liu Wan-Lin Li Dong Liu Qi-Jun Zhu Yun-Ping He Fu-Chu State Key Laboratory of Proteomics Beijing Proteome Research CenterBeijing Institute of Radiation MedicineBeijingChina100850 State Key Laboratory of ProteomicsBeijing Proteome Research CenterBeijing Institute of Radiation MedicineBeijingChina100850 National Key Laboratory for Parallel & Distributed Processing National University of Deference and TechnologyChangshaChina410073

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Data dependence-based optimistic data consistency maintenance method

Data dependence-based optimistic data consistency maintenanc...

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6th IEEE International Conference on Computer and Information technology, CIT 2006

作者： Zhou, Jing Wang, Yijie Li, Sikun National Key Laboratory for Parallel and Distributed Processing School of Computer Science National University of Defense Technology China

ISBN: (纸本)076952687X

Data replication introduces well-known consistency issues. This paper puts forward the question about data dependence in data consistency, which embodies pseudo-conflict updates and update dependency. According to that, an optimistic data consistency method is proposed. In our method, data object is partitioned into data blocks by fixed size, as the basic unit of data management. Updates are compressed by Bloom filter technique and propagated in double-path. Negotiation algorithms detect and reconcile update conflicts, and dynamic data management algorithms accommodate dynamic data processing. The results of the performance evaluation show that our method is an efficient method to achieve consistency, good dynamic property, and strong robustness. © 2006 IEEE.

关键词： Information technology

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