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Revisiting multiple pattern matching Algorithms for Multi-Core Architecture

Journal of Computer Science & Technology 2011年第5期26卷 866-874页

作者：谭光明刘萍卜东波刘燕兵 Key Laboratory of Computer System and Architecture Institute of Computing TechnologyChinese Academy of Sciences Key Laboratory of Network Technology Institute of Computing TechnologyChinese Academy of Sciences

Due to the huge size of patterns to be searched,multiple pattern searching remains a challenge to several newly-arising applications like network intrusion *** this paper,we present an attempt to design efficient multiple pattern searching algorithms on multi-core *** observe an important feature which indicates that the multiple pattern matching time mainly depends on the number and minimal length of *** multi-core algorithm proposed in this paper leverages this feature to decompose pattern set so that the parallel execution time is *** formulate the problem as an optimal decomposition and scheduling of a pattern set,then propose a heuristic algorithm,which takes advantage of dynamic programming and greedy algorithmic techniques,to solve the optimization *** results suggest that our decomposition approach can increase the searching speed by more than 200% on a 4-core AMD Barcelona system.

关键词： parallel algorithm multi-core multiple pattern matching

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New multi-pattern matching algorithm

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Journal of Systems Engineering and Electronics 2006年第2期17卷 437-442页

作者： Liu Gongshen Li Jianhua Li Shenghong School of Information Security Engineering Shanghai Jiaotong University Shanghai 200030 P. R. China

The traditional multiple pattern matching algorithm, deterministic finite state automata, is implemented by tree structure. A new algorithm is proposed by substituting sequential binary tree for traditional tree. It is proved by experiment that the algorithm has three features, its construction process is quick, its cost of memory is small. At the same time, its searching process is as quick as the traditional algorithm. The algorithm is suitable for the application which requires preprocessing the patterns dynamically.

关键词： multiple pattern matching finite state automata sequential binary tree.

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TahcoRoll: fast genomic signature profiling viathinned automaton and rolling hash

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Medical Review 2021年第2期1卷 114-125页

作者： Chelsea J.-T.Ju Jyun-Yu Jiang Ruirui Li Zeyu Li Wei Wang Department of omputer Science University of CaliforniaLos AngelesUSA

Objectives:Genomic signatures like k-mers have become one of the most prominent approaches to describe genomic *** a result,myriad real-world applications,such as the construction of de Bruijn graphs in genome assembly,have been benefited by recognizing genomic *** other words,an efficient approachof genomic signatureprofiling is an essential need for tackling high-throughput sequencing ***,most of the existing approaches only recognize fixed-size k-merswhile many research studies have shown the importance of considering variable-length ***:In this paper,we present a novel genomic signature profiling approach,TahcoRoll,by extending the Aho–Corasick algorithm(AC)for the task of profiling variable-length *** first group nucleotides into two clusters and represent each cluster with a *** rolling hash technique is further utilized to encode signatures and read patterns for efficient ***:In extensive experiments,TahcoRoll significantly outperforms the most state-of-the-art k-mer counters and has the capability of processing reads across different sequencing platforms on a budget desktop ***:The single-thread version of TahcoRoll is as efficient as the eight-thread version of the state-of-the-art,JellyFish,while the eight-thread TahcoRoll outperforms the eight-thread JellyFish by at least four times.

关键词： Aho-Corasick algorithm genome sequencing k-mers multiple pattern matching rolling hash.

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