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Article: Mining periodic patterns with gap requirement from sequences

TitleMining periodic patterns with gap requirement from sequences
Authors
KeywordsGap Requirement
Periodic Pattern
Sequence Mining
Issue Date2007
PublisherAssociation for Computing Machinery, Inc. The Journal's web site is located at http://tkdd.cs.uiuc.edu
Citation
Acm Transactions On Knowledge Discovery From Data, 2007, v. 1 n. 2 How to Cite?
AbstractWe study a problem of mining frequently occurring periodic patterns with a gap requirement from sequences. Given a character sequence S of length L and a pattern P of length l, we consider P a frequently occurring pattern in S if the probability of observing P given a randomly picked length-l subsequence of S exceeds a certain threshold. In many applications, particularly those related to bioinformatics, interesting patterns are periodic with a gap requirement. That is to say, the characters in P should match subsequences of S in such a way that the matching characters in S are separated by gaps of more or less the same size. We show the complexity of the mining problem and discuss why traditional mining algorithms are computationally infeasible. We propose practical algorithms for solving the problem and study their characteristics. We also present a case study in which we apply our algorithms on some DNA sequences. We discuss some interesting patterns obtained from the case study. © 2007 ACM.
Persistent Identifierhttp://hdl.handle.net/10722/152360
ISSN
2015 Impact Factor: 1.0
2015 SCImago Journal Rankings: 1.292
References

 

DC FieldValueLanguage
dc.contributor.authorZhang, Men_US
dc.contributor.authorKao, Ben_US
dc.contributor.authorCheung, DWen_US
dc.contributor.authorYip, KYen_US
dc.date.accessioned2012-06-26T06:37:37Z-
dc.date.available2012-06-26T06:37:37Z-
dc.date.issued2007en_US
dc.identifier.citationAcm Transactions On Knowledge Discovery From Data, 2007, v. 1 n. 2en_US
dc.identifier.issn1556-4681en_US
dc.identifier.urihttp://hdl.handle.net/10722/152360-
dc.description.abstractWe study a problem of mining frequently occurring periodic patterns with a gap requirement from sequences. Given a character sequence S of length L and a pattern P of length l, we consider P a frequently occurring pattern in S if the probability of observing P given a randomly picked length-l subsequence of S exceeds a certain threshold. In many applications, particularly those related to bioinformatics, interesting patterns are periodic with a gap requirement. That is to say, the characters in P should match subsequences of S in such a way that the matching characters in S are separated by gaps of more or less the same size. We show the complexity of the mining problem and discuss why traditional mining algorithms are computationally infeasible. We propose practical algorithms for solving the problem and study their characteristics. We also present a case study in which we apply our algorithms on some DNA sequences. We discuss some interesting patterns obtained from the case study. © 2007 ACM.en_US
dc.languageengen_US
dc.publisherAssociation for Computing Machinery, Inc. The Journal's web site is located at http://tkdd.cs.uiuc.eduen_US
dc.relation.ispartofACM Transactions on Knowledge Discovery from Dataen_US
dc.subjectGap Requirementen_US
dc.subjectPeriodic Patternen_US
dc.subjectSequence Miningen_US
dc.titleMining periodic patterns with gap requirement from sequencesen_US
dc.typeArticleen_US
dc.identifier.emailKao, B:kao@cs.hku.hken_US
dc.identifier.emailCheung, DW:dcheung@cs.hku.hken_US
dc.identifier.authorityKao, B=rp00123en_US
dc.identifier.authorityCheung, DW=rp00101en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1145/1267066.1267068en_US
dc.identifier.scopuseid_2-s2.0-34548236885en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-34548236885&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume1en_US
dc.identifier.issue2en_US
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridZhang, M=20434954000en_US
dc.identifier.scopusauthoridKao, B=35221592600en_US
dc.identifier.scopusauthoridCheung, DW=34567902600en_US
dc.identifier.scopusauthoridYip, KY=7101909946en_US

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