ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010最新文献

Implementation of a DNA-based anomaly identification system utilizing associative string processor (ASP) 基于dna的关联字符串处理器异常识别系统的实现

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5586949

Z. Trabelsi, R. Hamdy

{"title":"Implementation of a DNA-based anomaly identification system utilizing associative string processor (ASP)","authors":"Z. Trabelsi, R. Hamdy","doi":"10.1109/AICCSA.2010.5586949","DOIUrl":"https://doi.org/10.1109/AICCSA.2010.5586949","url":null,"abstract":"The genetic material that encodes the unique characteristics of each individual, such as gender, eye color, and other human features is the well-known DNA. In this work, we introduce an anomaly intrusion detection system, built on the notion of a DNA sequence or gene, which is responsible for the normal network traffic patterns. Subsequently, the system detects suspicious activities by searching the “normal behavior DNA sequence” through string matching. Conversely, string matching is a computationally intensive task and can be converted into a potential bottleneck without high-speed processing. Furthermore, conventional software implemented string matching algorithms have not kept pace with the ever increasing network speeds. As a result, we adopt a monitoring phase that is hardware implemented with the intention that DNA pattern matching is performed at wire-speed. Finally, we provide the details of our FPGA implementation of the bioinformatics-based string matching technique. The associative string processor (ASP) is an associative memory-based micro-architecture with long fixed-length words that can be partially searched. We show that the proposed micro-architecture can handle fixed-length patterns at a rate of more than one character per cycle.","PeriodicalId":352946,"journal":{"name":"ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010","volume":"82 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115677672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Evolutionary placement of short sequence reads on multi-core architectures 多核结构上短序列读取的进化定位

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5586973

A. Stamatakis, Zsolt Komornik, S. Berger

{"title":"Evolutionary placement of short sequence reads on multi-core architectures","authors":"A. Stamatakis, Zsolt Komornik, S. Berger","doi":"10.1109/AICCSA.2010.5586973","DOIUrl":"https://doi.org/10.1109/AICCSA.2010.5586973","url":null,"abstract":"The application of high performance computing methods in bioinformatics becomes increasingly important because of the masses of data generated by novel short-read DNA sequencers. One important application of such short reads, is the analysis of microbial communities where the anonymous short reads need to be identified by sequence comparison to a set of reference sequences. This identification is required to analyze the microbial composition and biological diversity of the sample. We briefly introduce a new algorithm for evolutionary (phylogenetic) placement of short reads under the Maximum Likelihood criterion and implement it in RAxML. While this algorithm is significantly more accurate than plain pair-wise sequence comparison it can become highly compute-intensive when a typical number of 100,000 reads and more need to be placed into an existing phylogenetic tree. Therefore, we deploy multi-grain parallelism to improve parallel efficiency of this algorithm on 16-core and 32-core architectures. Via this multi-grain approach, we achieve parallel execution time improvements of 25% and super-linear speedups on 16 cores, as well as near-linear speedups and improvements exceeding 50% on 32-cores on two large real-world microbial datasets. Evolutionary placement of 100,000 reads into a tree with more than 4,000 taxa now only requires less than 2 hours of execution time on 32 cores.","PeriodicalId":352946,"journal":{"name":"ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124873719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 14

Towards a formal framework for developing concurrent programs: Modeling dynamic behavior 面向开发并发程序的正式框架:动态行为建模

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5586965

H. Haghighi

引用次数: 2

A hybrid performance modeling approach for adaptive algorithm selection on hierarchical clusters 层次聚类自适应算法选择的混合性能建模方法

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5587043

W. Nasri, Sami Achour

{"title":"A hybrid performance modeling approach for adaptive algorithm selection on hierarchical clusters","authors":"W. Nasri, Sami Achour","doi":"10.1109/AICCSA.2010.5587043","DOIUrl":"https://doi.org/10.1109/AICCSA.2010.5587043","url":null,"abstract":"Recent advances in parallel and distributed computing have made it very challenging for programmers to reach the performance potential of current systems. In addition, recent advances in numerical algorithms and software optimizations have tremendously increased the number of alternatives for solving a problem, which further complicates the software tuning process. Indeed, no single algorithm can represent the universal best choice for efficient solution of a given problem on all compute substrates. In this paper, we develop a framework that addresses the design of efficient parallel algorithms in hierarchical computing environments. More specifically, given multiple choices for solving a particular problem, the framework uses a judicious combination of analytical performance models and empirical approaches to automate the algorithm selection by determining the most suitable execution scheme expected to perform the best at the specific setting. Preliminary experimental results obtained by implementing two different numerical kernels demonstrated the interest of the hybrid performance modeling approach integrated in the framework.","PeriodicalId":352946,"journal":{"name":"ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010","volume":"176 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116010837","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Managing conversational streams by explorative mind-maps 通过探索性思维导图管理会话流

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5587033

Jayanta Poray, Christoph Schommer

引用次数: 5

Event-based adaptation policies for Fractal components 分形组件的基于事件的适应策略

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5586944

Julien Dormoy, O. Kouchnarenko

引用次数: 8

Design of codebook using Centroid Neural Network with state dependence measure 带状态依赖度量的质心神经网络设计码本

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5586957

Dong-Chul Park

引用次数: 0

A hybrid genetic algorithm for Golomb ruler problem Golomb标尺问题的混合遗传算法

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5586955

N. Ayari, Thé Van Luong, A. Jemai

引用次数: 31

A layered cluster based routing for an ad hoc environment 用于临时环境的基于分层集群的路由

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5587016

I. Jemili, A. Belghith, M. Mosbah

引用次数: 4

Towards a parameterizable cycle-accurate ISS in ArchC 在ArchC中实现可参数化周期精确的ISS

ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010 Pub Date : 2010-05-16 DOI: 10.1109/AICCSA.2010.5586945

C. Bechara, N. Ventroux, D. Etiemble

引用次数: 7