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A reconfigurable index FLASH memory tailored to seed-based genomic sequence comparison algorithms

Journal of VLSI Signal Processing systems for Signal, Image, and Video technology 2007年第3期48卷 255-269页

作者： Lavenier, D. Georges, G. Liu, X. IRISA/CNRS Campus de Beaulieu Rennes 35042 France Key Laboratory of Computer System and Architecture Institute of Computing Technology CAS Beijing China

Genomic sequence comparison algorithms represent the basic toolbox for processing large volume of DNA or protein sequences. They are involved both in the systematic scan of databases, mostly for detecting similarities with an unknown sequence, and in preliminary processing before advanced bioinformatics analysis. Due to the exponential growth of genomic data, new solutions are required to keep the computation time reasonable. This paper presents a specific hardware architecture to speed-up seed-based algorithms which are currently the most popular heuristics for detecting alignments. The architecture regroups FLASH and FPGA technologies on a common support, allowing a large amount of data to be rapidly accessed and quickly processed. Experiments on database search and intensive sequence comparison demonstrate a good cost/performance ratio compared to standard approaches. © 2007 Springer Science + Business Media, LLC.

关键词： Flash memory

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Macro liveness graph and liveness of ω-independent unbounded nets

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Science China(Information Sciences) 2015年第3期58卷 132-141页

作者： WANG ShouGuang GAN MengDi ZHOU MengChu School of Information and Electronic Engineering Zhejiang Gongshang University Key Laboratory of Embedded System and Service Computing Ministry of EducationTongji University Department of Electrical and Computer Engineering New Jersey Institute of Technology

Liveness is a basic property of a system and the liveness issue of unbounded Petri nets remains one of the most difficult problems in this *** work proposes a novel method to decide the liveness of a class of unbounded generalized Petri nets calledω-independent unbounded nets,breaking the existing limits to one-place-unbounded *** algorithm to construct a macro liveness graph(MLG)is developed and a critical condition based on MLG deciding the liveness ofω-independent unbounded nets is *** are provided to demonstrate its effectiveness.

关键词： discrete event system(DES) Petri nets complex systems liveness property analysis

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Improved structural modeling based on conserved domain clusters and structure-anchored alignments

Proceedings of the ACM Symposium on Applied Computing

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Proceedings of the ACM Symposium on Applied computing 2007年 128-132页

作者： Zhang, Fa Xu, Lin Liu, Zhiyong Yuan, Bo Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy of Science Graduate School Chinese Academy of Science Institute of Computing Technology Chinese Academy of Science Department of Computer Science and Engineering Shanghai Jiaotong University

ISBN: (纸本)1595934804;9781595934802

In this paper, we presented a method to improve structural modeling based on conserved domain clusters and structure-anchored alignments. We first constructed a template library of structural clusters for all conserved sequence domains. Then, for each cluster, we built the profile using the structure and sequence information. Finally we use the profile and structural alignments as anchors to increase the alignment accuracy between a query and its templates. Our preliminary results show that this method can be used for the partial prediction for a majority of known protein sequences with better qualities. Copyright 2007 ACM.

关键词： Proteins

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Identity-Based key-Insulated Proxy Signature Without Random Oracles

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Journal of Shanghai Jiaotong university(Science) 2011年第5期16卷 557-566页

作者：陈剑洪龙宇陈克非王永涛 Department of Computer Science and Engineering Shanghai Jiaotong University School of Computer Engineering Huaiyin Institute of Technology Shanghai Key Laboratory of Scalable Computing and System Shanghai Jiaotong University

In an identity based proxy signature (IBPS) scheme, a designated proxy signer can generate the signature on behalf of an original signer. Traditional IBPS schemes normally rely on the assumption that private keys are kept perfectly secure. However, due to viruses, worms or other break-ins allowed by operating-system holes, key exposure seems inevitable. To minimize the damage caused by key exposure in IBPS, we propose an identity-based key-insulated proxy signature (IBKIPS) scheme in the standard model, i.e. without random oracles.

关键词： key-insulated proxy signature identity-based standard model

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An efficient error control scheme for chip-to-chip optical interconnects

An efficient error control scheme for chip-to-chip optical i...

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2007 IEEE International Symposium on Circuits and systems, ISCAS 2007

作者： Jun, Wang Ge, Zhang Weiwu, Hu Key Laboratory of Computer System and Architecture Institute of Computing Technology CAS Beijing 100080 China

As the gap between processing capability and bandwidth requirement of microprocessor increases, optical interconnects are used more and more widely in chip-to-chip data links. Trade-offs are made among latency, area, power consumption and reliability in the high frequency interconnect system in which error control schemes are always implemented to make it tolerate PER (packet error rate). In this paper, a scalable system for chip-to-chip optical interconnects is proposed and different types of error control schemes are compared using 90nm CMOS process. The goals are set to low latency, small area and low power consumption as well as acceptable MTTF (mean time to failure) for USR (ultra-short-reach) with very low BER (bit error rate). After that the ECS-HC based system is picked out and validated based on FPGA and 4.25Gbps 850nm optical transceivers. © 2007 IEEE.

关键词： Error correction

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Computation pattern driven reuse of manual optimizations for GPGPUs

Computation pattern driven reuse of manual optimizations for...

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2011 12th International Conference on Parallel and Distributed computing, Applications and Technologies, PDCAT 2011

作者： Xu, Shixiong Han, Dongni Chen, Li Key Laboratory of Computer System and Architecture Institute of Computing Technology University of Chinese Beijing China

ISBN: (纸本)9780769545646

The wide application of General Purpose Graphic Processing Units (GPGPUs) results in large manual efforts on porting and optimizing algorithms on them. However, most existing automatic ways of generating GPGPU code fail to conduct optimization strategies regarding a specific computation and to reuse constantly evolving manual optimizations. In this paper, we present a computation pattern driven approach for computation-specific GPGPU code generation and optimization, which in turn reuses manual optimizations to a certain extent. We suggest language extensions to OpenMP, high-level data structure attributes, in order to assist the process of computation pattern matching and to help give users intuitive performance tuning parameters in the view of data structure attributes. We illustrate the feasibility of this approach through three important computation dwarfs, which are dense matrix, sparse matrix, and structured mesh computation in scientific computing. We also build a prototype OpenMP-to-CUDA translator that consists of computation pattern recognition and code template instantiation. The experimental results demonstrate the performance benefits of computation pattern driven method. To our best knowledge, it is the first work on reusing manual optimizations for GPGPUs with computation pattern driven approach. © 2011 IEEE.

关键词： Data structures

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A New ETL Approach Based on Data Virtualization

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Journal of computer Science & technology 2015年第2期30卷 311-323页

作者：郭树盛袁子牧孙傲冰岳强 State Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China University of Chinese Academy of Sciences Beijing 100190 China Cloud Computing Center Chinese Academy of Sciences Dongguan 523808 China

ETL （Extract-Transform-Load） usually includes three phases： extraction, transformation, and loading. In building data warehouse, it plays the role of data injection and is the most time-consuming activity. Thus it is necessary to improve the performance of ETL. In this paper, a new ETL approach, TEL （Transform-Extract-Load） is proposed. The TEL approach applies virtual tables to realize the transformation stage before extraction stage and loading stage, without data staging area or staging database which stores raw data extracted from each of the disparate source data systems. The TEL approach reduces the data transmission load, and improves the performance of query from access layers. Experimental results based on our proposed benchmarks show that the TEL approach is feasible and practical.

关键词： cloud computing big data ETL heterogeneous database data virtualization

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A Dependability Model for TMR system

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International Journal of Automation and computing 2012年第3期9卷 315-324页

作者： Peng, Jun-Jie Liu, Yan-Ping Chen, Yuan-Yuan School of Computer Engineering and Science Shanghai University Shanghai 200072 China Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China

Much research has been done on the dependability evaluation of computer systems. However, much of this is gone no further than study of the fault coverage of such systems, with little focus on the relationship between fault coverage and overall system dependability. In this paper, a Markovian dependability model for triple-modular-redundancy (TMR) system is presented. Having fully considered the effects of fault coverage, working time, and constant failure rate of single module on the dependability of the target TMR system, the model is built based on the stepwise degradation strategy. Through the model, the relationship between the fault coverage and the dependability of the system is determined. What is more, the dependability of the system can be dynamically and precisely predicted at any given time with the fault coverage set. This will be of much benefit for the dependability evaluation and improvement, and be helpful for the system design and maintenance.

关键词： Dependability Markovian model coverage triple-modular-redundancy (TMR) failure rate.

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A parallel algorithm for computing betweenness centrality

A parallel algorithm for computing betweenness centrality

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38th International Conference on Parallel Processing, ICPP-2009

作者： Tan, Guangming Tu, Dengbiao Sun, Ninghui Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy of Science Beijing China

ISBN: (纸本)9780769538020

In this paper we present a multi-grained parallel algorithm for computing betweenness centrality, which is extensively used in large-scale network analysis. Our method is based on a novel algorithmic handling of access conflicts for a CREW PRAM algorithm. We propose a proper data-processor mapping, a novel edge-numbering strategy and a new triple array data structure recording the shortest path for eliminating conflicts to access the shared memory. The algorithm requires O(n + m) space and O(nm/p ) ( or O(nm+n2logn /p )) time for unweighted (or weighted) graphs, and it is a work-optimal CREW PRAM algorithm. On current multi-core platforms, our algorithm outperforms the previous algorithm by 2-3 times. © 2009 IEEE.

关键词： Parallel algorithms

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Software and hardware cooperate for 1-D FFT algorithm optimization on multicore processors

Software and hardware cooperate for 1-D FFT algorithm optimi...

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IEEE 9th International Conference on computer and Information technology, CIT 2009

作者： Zhou, Yongbin Zhang, Junchao Fan, Dongrui Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing China

ISBN: (纸本)9780769538365

Multicore architecture is becoming a promise to keep Moore's Law and brings a revolution in both research and industry which results new design space for software and architecture. Fast Fourier Transform (FFT), computing intensive and bandwidth intensive, is one of the most popular and important applications in the world. Compared with the computing resource on multicore architecture, the on-chip memory resource is much more expensive because of the limitation of physical chip size. Efficient implementation of FFT algorithm on multicore with good scalability is a challenge for both software and hardware developers. In this paper, supported by the Godson-T architecture, an optimized implementation of 1-D FFT has been developed with matrix transpose conceal and computation/communication overlapping, which achieve more than 30% performance improvement as well as almost 1/3 L2 cache consumption reduce comparing with the base six-step FFT. The limitation of scalability is also analyzed and the conclusion is that on Godson-T when frequency and simultaneous data access happen, the limited access bandwidth of L2 cache is the bottleneck and result in the longer on-chip network latency. © 2009 IEEE.

关键词： Fast Fourier transforms

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