Graph Constrained Discriminant Analysis A New Method for the Integration of a Graph into a Classification Process 英文参考文献.docVIP

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Graph Constrained Discriminant Analysis A New Method for the Integration of a Graph into a Classification Process 英文参考文献.doc

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Graph Constrained Discriminant Analysis A New Method for the Integration of a Graph into a Classification Process 英文参考文献

GraphConstrainedDiscriminantAnalysis:ANewMethod fortheIntegrationofaGraphintoaClassification Process VincentGuillemot1,2*,ArthurTenenhaus1,2,LaurentLeBrusquet2,VincentFrouin1* 1LaboratoryofFunctionalGenomics–CEA,DSV,IRCM,Evry,France,2DepartmentofSignalsandElectronicsSystems–Supe′lec,Gif-sur-Yvette,France Abstract Integrating gene regulatory networks (GRNs) into the classification process of DNA microarrays is an important issue in bioinformatics,bothbecausethisinformationhasatruebiologicalinterestandbecauseithelpsintheinterpretationofthe final classifier. We present a method called graph-constrained discriminant analysis (gCDA), which aims to integrate the information contained in one or several GRNs into a classification procedure. We show that when the integrated graph includeserroneousinformation,gCDA’sperformanceisonlyslightlyworse,thusshowingrobustnesstomisspecificationsin thegivenGRNs.ThegCDAframeworkalsoallowstheclassificationprocesstotakeintoaccountasmanyapriorigraphsas there are classes in the dataset. The gCDA procedure was applied to simulated data and to three publicly available microarraydatasets.gCDAshowsveryinterestingperformancewhencomparedtostate-of-the-artclassificationmethods. Thesoftwarepackagegcda,alongwiththerealdatasetsthatwereusedinthisstudy,areavailableonline:http://biodev.cea. fr/gcda/. Citation:GuillemotV,TenenhausA,LeBrusquetL,FrouinV(2011)GraphConstrainedDiscriminantAnalysis:ANewMethodfortheIntegrationofaGraphintoa ClassificationProcess.PLoSONE6(10):e26146.doi:10.1371/journal.pone.0026146 Editor:ArkadyB.Khodursky,UniversityofMinnesota,UnitedStatesofAmerica ReceivedFebruary11,2011;AcceptedSeptember20,2011;PublishedOctober14,2011 Copyright: ? 2011 Guillemot et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:ThisworkwasfundedbyaCEA-Re′gionIledeFrancegrant.T