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Conference Paper: Short adjacent repeat identification based on chemical reaction optimization

TitleShort adjacent repeat identification based on chemical reaction optimization
Authors
KeywordsShort adjacent repeats
Chemical reaction optimization
Maximum a posteriori
Computational time
Globaloptimum
Issue Date2012
PublisherIEEE. The Journal's web site is located at http://ieeexplore.ieee.org/xpl/conhome.jsp?punumber=1000284
Citation
The 2012 IEEE Congress on Evolutionary Computation (CEC 2012), Brisbane, Australia, 10-15 June 2012. In IEEE CEC Proceedings, 2012, p. 1-8 How to Cite?
AbstractThe analysis of short tandem repeats (STRs) in DNA sequences has become an attractive method for determining the genetic profile of an individual. Here we focus on a more general and practical issue named short adjacent repeats identification problem (SARIP), which is extended from STR by allowing short gaps between neighboring units. Presently, the best available solution to SARIP is BASARD, which uses Markov chain Monte Carlo algorithms to determine the posterior estimate. However, the computational complexity and the tendency to get stuck in a local mode lower the efficiency of BASARD and impede its wide application. In this paper, we prove that SARIP is NP-hard, and we also solve it with Chemical Reaction Optimization (CRO), a recently developed metaheuristic approach. CRO mimics the interactions of molecules in a chemical reaction and it can explore the solution space efficiently to find the optimal or near optimal solution(s). We test the CRO algorithm with both synthetic and real data, and compare its performance in mode searching with BASARD. Simulation results show that CRO enjoys dozens of times, or even a hundred times shorter computational time compared with BASARD. It is also demonstrated that CRO can obtain the global optima most of the time. Moreover, CRO is more stable in different runs, which is of great importance in practical use. Thus, CRO is by far the best method on SARIP. © 2012 IEEE.
DescriptionIEEE World Congress on Computational Intelligence (WCCI 2012), Brisbane, Australia, 10-15 June 2012 hosted three conferences: the 2012 International Joint Conference on Neural Networks (IJCNN 2012), the 2012 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE 2012), and the 2012 IEEE Congress on Evolutionary Computation (IEEE CEC 2012)
Persistent Identifierhttp://hdl.handle.net/10722/165308
ISBN

 

DC FieldValueLanguage
dc.contributor.authorXu, Jen_US
dc.contributor.authorLam, AYSen_US
dc.contributor.authorLi, VOKen_US
dc.contributor.authorLi, Qen_US
dc.contributor.authorFan, X-
dc.date.accessioned2012-09-20T08:16:53Z-
dc.date.available2012-09-20T08:16:53Z-
dc.date.issued2012en_US
dc.identifier.citationThe 2012 IEEE Congress on Evolutionary Computation (CEC 2012), Brisbane, Australia, 10-15 June 2012. In IEEE CEC Proceedings, 2012, p. 1-8en_US
dc.identifier.isbn978-1-4673-1509-8-
dc.identifier.urihttp://hdl.handle.net/10722/165308-
dc.descriptionIEEE World Congress on Computational Intelligence (WCCI 2012), Brisbane, Australia, 10-15 June 2012 hosted three conferences: the 2012 International Joint Conference on Neural Networks (IJCNN 2012), the 2012 IEEE International Conference on Fuzzy Systems (FUZZ-IEEE 2012), and the 2012 IEEE Congress on Evolutionary Computation (IEEE CEC 2012)-
dc.description.abstractThe analysis of short tandem repeats (STRs) in DNA sequences has become an attractive method for determining the genetic profile of an individual. Here we focus on a more general and practical issue named short adjacent repeats identification problem (SARIP), which is extended from STR by allowing short gaps between neighboring units. Presently, the best available solution to SARIP is BASARD, which uses Markov chain Monte Carlo algorithms to determine the posterior estimate. However, the computational complexity and the tendency to get stuck in a local mode lower the efficiency of BASARD and impede its wide application. In this paper, we prove that SARIP is NP-hard, and we also solve it with Chemical Reaction Optimization (CRO), a recently developed metaheuristic approach. CRO mimics the interactions of molecules in a chemical reaction and it can explore the solution space efficiently to find the optimal or near optimal solution(s). We test the CRO algorithm with both synthetic and real data, and compare its performance in mode searching with BASARD. Simulation results show that CRO enjoys dozens of times, or even a hundred times shorter computational time compared with BASARD. It is also demonstrated that CRO can obtain the global optima most of the time. Moreover, CRO is more stable in different runs, which is of great importance in practical use. Thus, CRO is by far the best method on SARIP. © 2012 IEEE.-
dc.languageengen_US
dc.publisherIEEE. The Journal's web site is located at http://ieeexplore.ieee.org/xpl/conhome.jsp?punumber=1000284-
dc.relation.ispartofIEEE Congress on Evolutionary Computationen_US
dc.rightsIEEE Congress on Evolutionary Computation. Copyright © IEEE.-
dc.rights©2012 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.-
dc.rightsCreative Commons: Attribution 3.0 Hong Kong License-
dc.subjectShort adjacent repeats-
dc.subjectChemical reaction optimization-
dc.subjectMaximum a posteriori-
dc.subjectComputational time-
dc.subjectGlobaloptimum-
dc.titleShort adjacent repeat identification based on chemical reaction optimizationen_US
dc.typeConference_Paperen_US
dc.identifier.emailXu, J: xujin@eee.hku.hken_US
dc.identifier.emailLam, AYS: ayslam@eee.hku.hk-
dc.identifier.emailLi, VOK: vli@eee.hku.hk-
dc.identifier.authorityLam, AYS=rp02083en_US
dc.identifier.authorityLi, VOK=rp00150-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1109/CEC.2012.6256614-
dc.identifier.scopuseid_2-s2.0-84866858687-
dc.identifier.hkuros210470en_US
dc.identifier.hkuros261766-
dc.identifier.spage1-
dc.identifier.epage8-
dc.publisher.placeUnited States-
dc.customcontrol.immutablesml 130508 ; sml 160909 - merged-

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