NDLI: Parallel Algorithm for Approximate String Matching with K Differences

Content Provider	IEEE Xplore Digital Library
Author	Longjiang Guo Shufang Du Meirui Ren Yu Liu Jinbao Li Jing He Ning Tian Keqin Li
Copyright Year	2013
Description	Author affiliation: Sch. of Comput. Sci. & Technol., Heilongjiang Univ., Harbin, China (Longjiang Guo; Shufang Du; Meirui Ren; Yu Liu; Jinbao Li; Ning Tian) \|\| Dept. of Comput. Sci., Kennesaw State Univ., Kennesaw, GA, USA (Jing He) \|\| Dept. of Comput. Sci., State Univ. of New York, New Paltz, NY, USA (Keqin Li)
Abstract	Approximate string matching using the k-difference technique has been widely applied to many fields such as pattern recognition and computational biology. Data dependency exists in the traditional sequential algorithm. Therefore, it is hard to design a parallel algorithm for approximate string matching with k differences. This paper presents a technique to eliminate data dependency. Based on this technique, this paper also presents a parallel algorithm which can calculate the elements in the same row of the edit distance matrix in parallel by eliminating data dependency. The algorithm has high parallelism, but requires synchronization. To validate the proposed algorithm, it is implemented on GPU and multiple-core CPUs. Moreover, the CUDA optimization techniques are also presented in the paper. Finally, experimental results show that, compared with the traditional sequential algorithm on CPU with twenty-four cores, the proposed parallel algorithm achieves speedup of 7-42 on GPU.
Starting Page	257
Ending Page	261
File Size	276012
Page Count	5
File Format	PDF
ISBN	9780769550343
DOI	10.1109/NAS.2013.40
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-07-17
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Algorithm design and analysis edit distance Heuristic algorithms Approximate string matching Graphics processing units parallel algorithm Approximation algorithms k differences Parallel algorithms GPU Pattern matching
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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