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Proceedings of the ACM Symposium on Applied Computing 2007年 133-137页

作者： Fang, Xiaoyong Wang, Zhenghua Luo, Zhigang Yuan, Bo Ding, Fan National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China Department of Biomedical Informatics College of Medicine and Public Health Ohio State University Columbus OH 43210-1239 United States

ISBN: (纸本)1595934804;9781595934802

We here devise a new method for detecting and assessing RNA secondary structure by using multiple sequence alignment. The central idea of the method is to first detect conserved stems in the alignment using a special matrix and then assess them by evaluating the ratio of the signal to the noise. We tested the method on data sets composed of pairwise and three-way alignments of known ncRNAs. For the pairwise tests, our method has sensitivity 61.42% and specificity 97.05% for structural alignments, and sensitivity 42.05% and specificity 98.15% for BLAST alignments. For the three-way tests, our method has sensitivity 65.17% and specificity 97.96% for structural alignments, and sensitivity 40.70% and specificity 97.87% for CLUSTALW alignments. Our method can detect conserved secondary structures in gapped or ungapped RNA alignments. Copyright 2007 ACM.

关键词： RNA

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Compositional Verification of UML Dynamic Models

Compositional Verification of UML Dynamic Models

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Asia-Pacific Conference on Software Engineering

作者： Wei Dong Ji Wang Zhichang Qi Ni Rong School of Computer National University of Defense Technology China National Laboratory for Parallel and Distributed Processing China

UML dynamic models are important for software analysis and design. Verifying UML dynamic models to find design errors earlier is a key issue for ensuring software quality. Because of the characteristics such as concurrency and hierarchy, model checking of UML Statecharts and collaboration diagrams faces the problem of state explosion. In this paper, UML Statecharts is firstly structurally expressed by hierarchical automata and its semantics for open systems is introduced. Then, the synchronization composition of objects in UML collaboration diagrams is expatiated, based on which the global system behaviors can be constructed. Based on hierarchical automata and simulation relation between semantics structures, the compositional rules for verifying concurrent object systems are proposed. It makes possible that the construction of global state space will be unnecessary in model checking of UML collaboration diagrams. The hierarchical structures of UML Statecharts are also brought into the compositional verification, which makes the model checking of implementation models can be carried out through replacing detailed components by abstract specifications.

关键词： Unified modeling language Concurrent computing Automata State-space methods Explosions International collaboration Software systems Software engineering distributed computing Laboratories

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Are filter methods very effective in gene selection of microarray data?

Are filter methods very effective in gene selection of micro...

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IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

作者： Zhou-Jun Li Li-Juan Zhang Huo-Wang Chen School of Computer Science & Engineering Beihang University Beijing China National Laboratory for Parallel and Distributed Processing Changsha China

Feature (gene) selection is a frequently used preprocessing technology for successful cancer classification task in microarray gene expression data analysis. Widely used gene selection approaches are mainly focused on the filter methods. Filter methods are usually considered to be very effective and efficient for high-dimensional data. This paper reviews the existing filter methods, and shows the performance of the representative algorithms on microarray data by extensive experimental study. Surprisingly, the experimental results show that filter methods are not very effective on microarray data. We analyze the cause of the result and provide the basic ideas for potential solutions.

关键词： Filters Data analysis Classification algorithms Cancer Algorithm design and analysis computer science Data engineering Laboratories distributed processing Gene expression

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Collaborative Search in Large-scale Unstructured Peer-to-Peer Networks

Collaborative Search in Large-scale Unstructured Peer-to-Pee...

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International Conference on parallel processing (ICPP)

作者： Yiming Zhang Dongsheng Li Lei Chen Xicheng Lu National Laboratory for Parallel and Distributed Processing National University of Defense Technology China Department of Computer Science Hong Kong University of Science and Technology Hong Kong China

Searching in large-scale unstructured peer-to-peer networks is challenging due to the lack of effective hint information to guide queries. In this paper, we propose POP, a parallel, collaborative and Probabilistic search mechanism, in which query messages are viewed as search units to collaborate with each other and aggregate the distributed hints during the search process. A scheme called distributed Bloom filter (DBF) is presented to propagate the hints with a bandwidth-aware manner, in which a node divides the received Bloom filter vector into subvectors and disseminates the fragments to its neighbors according to their bandwidth capacity. The effectiveness of POP is demonstrated through theoretical analysis and extensive simulations.

关键词： Large-scale systems Peer to peer computing Bandwidth Information filtering Information filters Analytical models Aggregates Space technology International collaboration Laboratories

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Game-based axiomatization of μ-calculus

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Jisuanji Yanjiu yu Fazhan/computer Research and Development 2007年第11期44卷 1896-1902页

作者： Liu, Wanwei Wang, Ji Chen, Huowang National Laboratory of Parallel and Distributed Processing School of Computer Science National University of Defense Technology Changsha 410073 China

With the never-ending growth of the complexity of modern hardware and software systems, more and more sophisticated methods of verification are required. Model checking has been proved to be an effective approach to guaranteeing the correctness of design and implementation of software and hardware system. Model and temporal logics are used as specification languages in software and hardware verification. Modal μ-calculus is an extremely popular and important one among these logics. It is succinct in syntax and powerful in expressiveness. Since Kozen's paper on modal μ-calculus, it has received ever growing interest in both theoretical and application aspects. Based on the focus game theory, Lange and Stirling proposed the axiom systems for LTL and CTL. This paper extends that idea to that for modal μ-calculus. A game-theoretic approach is presented to test the satisfiability of modal μ-calculus formulas. In addition, this approach converts the satisfiability problem for μ-calculus into a solving problem for focus games. Consequently, based on these game rules, an axiom system for μ-calculus is developed, and the completeness of this deductive system can be proved via the game based satisfiability testing procedure. By comparison, this axiom system is much more intuitive and succinct than the existing μ-calculus axiom systems.

关键词： Temporal logic

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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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Two layered P2P model for semantic service discovery

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Ruan Jian Xue Bao/Journal of Software 2007年第8期18卷 1922-1932页

作者： Liu, Zhi-Zhong Wang, Huai-Min Zhou, Bin Institute of Network and Information Security School of Computer National University of Defense Technology Changsha 410073 China National Laboratory for Parallel and Distributed Processing School of Computer National University of Defense Technology Changsha 410073 China

In open Internet environment, it is inevitable that multiple ontologies coexist. Centralized service discovery mechanism becomes the bottleneck of SOC (service oriented computing), which results in poor scalability of system. Aiming at solving these problems, a two layered P2P based model for semantic service discovery is proposed in this paper. The model is based on ontology community and integrates iVCE (Internet-based virtual computing environment) core concepts into a P2P model. Based on this model, a service discovery algorithm composed of two stages and three steps is proposed. It matches services across communities as well as within community. Within a community, algorithm locates registers holding service information with a high probability of satisfying a request firstly. Then it captures semantic matching between service advertisements and service requests by logical reasoning. Service discovery across communities occurs according to some policies. The model is suitable for opening environment with coexistent multiple ontologies. Experimental results show that given an appropriate setting, the model can make a tradeoff between recall and responding time. In addition, the model will release the mean load of registers efficiently while holding recall.

关键词： Semantics

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Internet-based virtual computing environment(iVCE):Concepts and architecture

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Science in China(Series F) 2006年第6期49卷 681-701页

作者： LU Xicheng WANG Huaimin WANG Ji National Laboratory for Parallel and Distributed Processing Changsha 410073 China College of Computer National University of Defense Technology Changsha 410073 China

Resources over Internet have such intrinsic characteristics as growth, autonomy and diversity, which have brought many challenges to the efficient sharing and comprehensive utilization of these resources. This paper presents a novel approach for the construction of the Internet-based Virtual Computing Environment （iVCE）, whose sig- nificant mechanisms are on-demand aggregation and autonomic collaboration. The iVCE is built on the open infrastructure of the Internet and provides harmonious, transparent and integrated services for end-users and applications. The concept of iVCE is presented and its architectural framework is described by introducing three core concepts, i.e., autonomic element, virtual commonwealth and virtual executor. Then the connotations, functions and related key technologies of each components of the architecture are deeply analyzed with a case study, iVCE for Memory.

关键词： resource aggregation collaboration virtual computing environment Internet

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Automated WCET analysis based on program modes

Automated WCET analysis based on program modes

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1st International Workshop on Automation of Software Test, AST'06, Co-located with the 28th International Conference on Software Engineering, ICSE 2009

作者： Ji, Meng-Luo Wang, Ji Li, Shuhao Qi, Zhi-Chang School of Computer National University of Defense Technology China National Laboratory for Parallel and Distributed Processing China

ISBN: (纸本)1595934081

Program mode is a regular trajectory of the execution of a program that is determined by the values of its input variables. By exploiting program modes we may make Worst Case Execution Time (WCET) analysis more precise. This paper presents a novel method to automatically find program modes and calculate the WCET of programs. It consists of two phases. In phase one, we firstly automatically find the modes of a program by mode-relevant program slicing;then we compute the precondition for each mode using a path-wise test data generation method;after that, we can either conclude that it is an infeasible path, or get its precondition. In phase two, we calculate the WCET estimate of each given mode for modern RISC processors with caches and pipelines. The experiments are demonstrated to show the effectiveness of the method. Copyright 2006 ACM.

关键词： Real time systems

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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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