Parallel Pattern Matching Algorithm with Sparse Gap Constraint
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National Key Research & Develop Plan (2016YFB1000702); National Basic Research Program of China (973)(2014CB340402); National High Technology Research and Development Program of China (863) (2014AA015204); National NaturalScience Foundation of China (61272137, 61202114, 61532021); NSSFC (12&ZD220); Fundamental Research Funds for the CentralUniversities, and the Research Funds of Renmin University of China (15XNLQ06)

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    Abstract:

    Pattern matching with wildcards is a classic problem, and matching with variable gap constraints is a popular direction in this field in recent years. In order to meet the requirement of high accuracy in some query applications, this paper proposes an algorithm (referred to as SGPM-SAI) to obtain a complete solution of pattern matching under the condition of sparse gaps constraint. SGPM-SAI firstly creates an index structure called W-SAM (wildcard suffix automation) for the preprocessed text, and then get EndPos collection for each pattern segmentation by searching string from W-SAM, and finally get the complete solution of pattern matching by means of EndPos sets intersection. Experimental results show that, regardless of pretreatment time, the performance of SGPM-SAI algorithm is at least 3~5 times higher than other competitive algorithms, such as KMP, BM, AC, suffix array. Compared with the latest version (SAIL-Gen) of SAIL algorithm, the performance of SGPM-SAI is significantly better under the condition of sparse gaps constraint. In addition, this paper introduces parallel process methods for SGPM-SAI algorithm so as to effectively utilize the massive parallel processing units of modern processors. Experimental results show that the acceleration of Parallel SGPM-SAI algorithm has significant effect, as well as good parallel scalability. This indicates that the presented method can take full advantage of the high parallel computation capability of modern many-core processors.

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周开来,陈红,熊子绎,李翠平,孙辉.一种带稀疏间隙约束的并行模式匹配算法.软件学报,2018,29(12):3799-3819

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History
  • Received:February 13,2017
  • Revised:May 25,2017
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  • Online: December 05,2018
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