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A parallel approximation hitting set algorithm for gene expression analysis 14

A parallel approximation hitting set algorithm for gene expr...

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14th symposium on computer architecture and high performance computing

作者： Ruchkys, DP Song, SW Univ Sao Paulo Inst Matemat & Estatist Dept Ciencia Computacao BR-05508090 Sao Paulo Brazil

ISBN: (纸本)0769517722

With the recent DNA-microarray technology, it is possible to measure the expression levels of thousands of genes simultaneously in the same experiment. A genetic network is a model that describes how the expression level of each gene is affected by the expression levels of other genes in the network. Given, the results of an experiment with n genes and m measures over time (m << n), we consider the problem of finding a subset of genes (k genes, where k << n) that explain the expression level of a given target gene under study. We consider the coarse-grained multicomputer (CGM) model, with p processors. In this paper we first present a sequential approximation algorithm of O(m(4) n) time and O(m(2)n) space. the main result is a new parallel approximation algorithm that determines the k genes in O(m(4) n/p) local computing time plus O(k) communication rounds, and with space requirement of O(m(2) n/p). the p factor in the parallel time and space complexities indicates a,good parallelization. We also show preliminary, promising,experimental results on a Beowulf machine. To our knowledge there are no CGM algorithms for the problem considered in this paper.

关键词： Algorithm design and analysis Approximation algorithms computer networks DNA computing Gene expression Genetics Monitoring Space technology Time measurement User-generated content

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Scalability of a distributed neural information retrieval system 11

Scalability of a distributed neural information retrieval sy...

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11th IEEE International symposium on high performance Distributed computing (HPDC-11)

作者： Weeks, M Hodge, VJ Austin, J Univ York Dept Comp Sci York YO1 5DD N Yorkshire England

ISBN: (纸本)0769516866

Summary form only given. AURA (Advanced Uncertain Reasoning architecture) is a generic family of techniques and implementations intended for high-speed approximate search and match operations on large unstructured datasets. AURA technology is fast, economical, and offers unique advantages for finding near-matches not available with other methods. AURA is based upon a high-performance binary neural network called a correlation matrix memory (CMM). Typically, several CMM elements are used in combination to solve soft or fuzzy pattern-matching problems. AURA takes large volumes of data and constructs a special type of compressed index. AURA finds exact and near-matches between indexed records and a given query, where the query itself may have omissions and errors. the degree of nearness required during matching can be varied through thresholding techniques. the PCI-based PRESENCE (Parallel Structured Neural computing Engine) card is a hardware-accelerator architecture for the core CMM computations needed in AURA-based applications. the card is designed for use in low-cost workstations and incorporates 128 MByte of low-cost DRAM for CMM storage. To investigate the scalability of the distributed AURA system, we implement a word-to-document index of an AURA-based information retrieval system, called MinerTaur, over a distributed PRESENCE CMM. © 2002 IEEE.

关键词： Aircraft Artificial neural networks computer architecture computer science Concurrent computing Coordinate measuring machines Environmental economics Information retrieval Neural networks Scalability

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Coven - a framework for high performance problem solving environments 11

Coven - a framework for high performance problem solving env...

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11th IEEE International symposium on high performance Distributed computing (HPDC-11)

作者： DeBardeleben, NA Ligon, WB Pandit, S Stanzione, DC Clemson Univ Holcombe Dept Elect & Comp Engn Parallel Architecture Res Lab Clemson SC 29634 USA

ISBN: (纸本)0769516866

this work presents the design of the Coven framework for construction of Problem Solving Environments (PSEs) for parallel computers. PSEs are an integral part of modern high performance computing (HPC) and Coven attempts to simplify PSE construction. Coven targets Beowulf cluster parallel computers but independent of any particular domain for the PSE. Multi-threaded parallel applications are created with Coven that are capable of supporting most of the constructs in a typical parallel programming language. Coven uses an agent-based front-end which allows multiple custom interfaces to be constructed Examples of the use of Coven in the construction of prototype PSEs are shown, and the effectiveness of these PSEs is evaluated in terms of the performance of the applications they generate.

关键词： Application software Computational modeling computer simulation Concurrent computing high performance computing Parallel architectures Parallel programming Problem-solving Prototypes Writing

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Software architecture-based adaptation for grid computing 11

Software architecture-based adaptation for grid computing

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11th IEEE International symposium on high performance Distributed computing (HPDC-11)

作者： Cheng, SW Garlan, D Schmerl, B Steenkiste, P Hu, NN Carnegie Mellon Univ Sch Comp Sci Pittsburgh PA 15213 USA

ISBN: (纸本)0769516866

Grid applications must increasingly self-adapt dynamically to changing environments. In most cases, adaptation has been implemented in an ad hoc fashion, on a per-application basis. this paper describes work which generalizes adaptation so that it can be used across applications by providing an adaptation framework. this framework uses a software architectural model of the system to analyze whether the application requires adaptation, and allows repairs to be written in the context of the architectural model and propagated to the running system. In this paper, we exemplify our framework by applying it to the domain of load-balancing a client-server system. We report on an experiment conducted using our framework, which illustrates that this approach maintains architectural requirements.

关键词： Application software Availability computer networks computer science Grid computing Humans Mechanical factors Monitoring Network servers Runtime

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Portals 3.0: Protocol building blocks for low overhead communication 16

Portals 3.0: Protocol building blocks for low overhead commu...

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16th International Parallel and Distributed Processing symposium, IPDPS 2002

作者： Brightwell, R. Riesen, R. Lawry, B. Maccabe, A.B. Sandia National Laboratories Scalable Computing Systems Department PO Box 5800 AlbuquerqueNM87185-1110 United States University of New Mexico Computer Science Department FEC 313 AlbuquerqueNM87131 United States

ISBN: (纸本)0769515738

this paper describes the evolution of the Portals message passing architecture and programming interface from its initial development on tightly-coupled massively parallel platforms to the current implementation running on a 1792-node commodity PC Linux cluster. Portals provides the basic building blocks needed for higher-level protocols to implement scalable, low-overhead communication. Portals has several unique characteristics that differentiate it from other high-performance system-area data movement layers. this paper discusses several of these features and illustrates how they can impact the scalability and performance of higher-level message passing protocols. © 2002 IEEE.

关键词： massively parallel message passing network protocol os bypass workstation cluster

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Self-adaptive arallel rocessing architecture for high-speed networking 16

Self-adaptive arallel rocessing architecture for high-speed ...

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16th Annual International symposium on high performance computing Systems and Applications, HPCS 2002

作者： Foag, Jürgen Pazos, Nuria Wild, thomas Brunnbauer, Winthir Inst. for Integrated Circuits Techn. University of Munich Bavaria Munich80290 Germany Infineon Technologies San JoseCA United States

ISBN: (纸本)0769516262

this article describes a packet processing methodology, which executes the required protocol layer functions of a networking device in parallel. Based on the dynamic prediction of the inherent protocol-stack of receiving packets, the data dependency of the layers is speculatively resolved and the functions are processed. Consequently, packet processing latency can be minimized and end-to-end transmission delays can be optimized without sacrificing flexibility in the supported networking protocols and applications. Utilizing the self-adaptive processing methodology, presented in this paper, transmission systems may realize a mean system processing time reduction and consequently a transmission rate increase of up to 40 percent dependent on the quality of the prediction. © 2002 IEEE.

关键词： Internet protocols

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Grid-based knowledge discovery services for high throughput informatics 11

Grid-based knowledge discovery services for high throughput ...

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11th IEEE International symposium on high performance Distributed computing (HPDC-11)

作者： Ghanem, M Guo, Y Rowe, A Wendel, P Univ London Imperial Coll Sci Technol & Med London England

ISBN: (纸本)0769516866

Discovery Net is an application layer for providing grid-based knowledge discovery services. these services allow scientists to create and manage complex knowledge discovery workflows that integrate data and analysis routines provided as remote services. they also allow scientists to store, share and execute these workflows as well as publish them as new services. Discovery Net provides a higher level of abstraction of the Grid for knowledge discovery activities, thus separating the end-users from resource management issues already handled by existing and emerging standards.

关键词： Biomedical informatics computer architecture Data analysis Data mining Educational institutions Knowledge management Prototypes Remote sensing Resource management throughput

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Beyond the "device as portal": Meeting the requirements of wireless and mobile devices in the legion grid computing system 16

Beyond the "device as portal": Meeting the requirements of w...

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16th International Parallel and Distributed Processing symposium, IPDPS 2002

作者： Clarke, B. Humphrey, M. Department of Computer Science University of Virginia CharlottesvilleVA22903 United States

ISBN: (纸本)0769515738

Grid computing is an emerging paradigm in which resources in multiple organizations are combined into a single, seamless computing environment. As the storage, processing, and networking capabilities of wireless and mobile devices continue to expand, there will soon be the ability to use such devices as first-class compute- and data-servers (albeit for restricted problem sizes). However, without the proper software architecture for Grid computing, such devices will continue to be only usable as Web portals to high-power backend servers. this paper describes the unique capabilities of the Legion Grid computing infrastructure that will directly support these next-generation, poweful devices as first-class entities. © 2002 IEEE.

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Handoff in mobile ATM networks: Framework for performance optimization 16

Handoff in mobile ATM networks: Framework for performance op...

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16th Annual International symposium on high performance computing Systems and Applications, HPCS 2002

作者： Medidi, Sirisha R. Golshani, Forouzan School of Electrical Engineering and Computer Science Washington State University PullmanWA99164-2752 United States Department of Computer Science and Engineering Arizona State University TempeAZ85287-5406 United States

ISBN: (纸本)0769516262

Current handoff rerouting techniques in Mobile ATM networks fail to optimize some or all of the following parameters: handoff latency, route length, computational complexity, communication disruption period, network buffer requirements, and bandwidth *** s paper focuses on the optimization of the above parameters in the context of efficient handoff in Mobile ATM networks.W e propose a framework for efficient handoff, in which the route information of a call in progress can be released to the communicating mobile hosts and their corresponding *** switch covering the mobile host requesting handoff selects an appropriate rerouting process based on the route information and the location of the mobile hosts.A comparitive evaluation of our scheme with the existing schemes is presented. © 2002 IEEE.

关键词： Asynchronous transfer mode

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Let's study whole-program cache behaviour analytically 8

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8th International symposium on high-performance computer architecture

作者： Vera, X Xue, JL Malardalens Kogskola Inst Datatek Vasteras Sweden

ISBN: (纸本)0769515258

Based on a new characterisation of data reuse across multiple loop nests, we present a method, a prototyping implementation and some experimental results for analysing the cache behaviour of whole programs with regular computations. Validation against cache simulation using real codes shows the efficiency and accuracy of our method. the largest program we have analysed, Applu from SPECfp95, has 3868 lines, 16 subroutines and 2565 references. In the case of a 32KB cache with a 32B line size, our method obtains the miss ratio with an absolute error of about 0.80% in about 128 seconds while the simulator used runs for nearly 5 hours on a 933MHz Pentium III PC. Our method can be used to guide compiler locality optimisations and improve cache simulation performance.

关键词： Boolean functions computer architecture Data structures

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