Fast retrieval of similar subsequences in long sequence databases

Sanghyun Park; Dongwon Lee; Wesley W. Chu

doi:10.1109/KDEX.1999.836610

Fast retrieval of similar subsequences in long sequence databases

Sanghyun Park, Dongwon Lee, Wesley W. Chu

Department of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

62 Citations (Scopus)

Abstract

Although the Euclidean distance has been the most popular similarity measure in sequence databases, recent techniques prefer to use high-cost distance functions such as the time warping distance and the editing distance for wider applicability. However, if these distance functions are applied to the retrieval of similar subsequences, the number of subsequences to be inspected during the search is quadratic to the average length L~ of data sequences. We propose a novel subsequence matching scheme, called the aligned subsequence matching, where the number of subsequences to be compared with a query sequence is reduced to linear to L~. We also present an indexing technique to speed-up the aligned subsequence matching using the similarity measure of the modified time warping distance. Experiments on synthetic data sequences demonstrate the effectiveness of our proposed approach; ours consistently outperformed sequential scanning and achieved an up to 6.5 times speed-up.

Original language	English
Title of host publication	Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999
Editors	Peter Scheuermann
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	60-67
Number of pages	8
ISBN (Electronic)	0769504531, 9780769504537
DOIs	https://doi.org/10.1109/KDEX.1999.836610
Publication status	Published - 1999
Event	1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999 - Chicago, United States Duration: 1999 Nov 7 → …

Publication series

Name	Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999

Other

Other	1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999
Country/Territory	United States
City	Chicago
Period	99/11/7 → …

Bibliographical note

Publisher Copyright:
© 1999 IEEE.

All Science Journal Classification (ASJC) codes

Computer Networks and Communications
Information Systems
Information Systems and Management

Access to Document

10.1109/KDEX.1999.836610

Cite this

Park, S., Lee, D., & Chu, W. W. (1999). Fast retrieval of similar subsequences in long sequence databases. In P. Scheuermann (Ed.), Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999 (pp. 60-67). [836610] (Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/KDEX.1999.836610

Park, Sanghyun ; Lee, Dongwon ; Chu, Wesley W. / Fast retrieval of similar subsequences in long sequence databases. Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999. editor / Peter Scheuermann. Institute of Electrical and Electronics Engineers Inc., 1999. pp. 60-67 (Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999).

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abstract = "Although the Euclidean distance has been the most popular similarity measure in sequence databases, recent techniques prefer to use high-cost distance functions such as the time warping distance and the editing distance for wider applicability. However, if these distance functions are applied to the retrieval of similar subsequences, the number of subsequences to be inspected during the search is quadratic to the average length L~ of data sequences. We propose a novel subsequence matching scheme, called the aligned subsequence matching, where the number of subsequences to be compared with a query sequence is reduced to linear to L~. We also present an indexing technique to speed-up the aligned subsequence matching using the similarity measure of the modified time warping distance. Experiments on synthetic data sequences demonstrate the effectiveness of our proposed approach; ours consistently outperformed sequential scanning and achieved an up to 6.5 times speed-up.",

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Park, S, Lee, D & Chu, WW 1999, Fast retrieval of similar subsequences in long sequence databases. in P Scheuermann (ed.), Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999., 836610, Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999, Institute of Electrical and Electronics Engineers Inc., pp. 60-67, 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999, Chicago, United States, 99/11/7. https://doi.org/10.1109/KDEX.1999.836610

Fast retrieval of similar subsequences in long sequence databases. / Park, Sanghyun; Lee, Dongwon; Chu, Wesley W.

Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999. ed. / Peter Scheuermann. Institute of Electrical and Electronics Engineers Inc., 1999. p. 60-67 836610 (Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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Park S, Lee D, Chu WW. Fast retrieval of similar subsequences in long sequence databases. In Scheuermann P, editor, Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999. Institute of Electrical and Electronics Engineers Inc. 1999. p. 60-67. 836610. (Proceedings - 1999 Workshop on Knowledge and Data Engineering Exchange, KDEX 1999). https://doi.org/10.1109/KDEX.1999.836610

Fast retrieval of similar subsequences in long sequence databases

Abstract

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