Extended Kalman Filter for Estimation of Parameters in Nonlinear State-Space Models of Biochemical Networks 英文参考文献.docVIP

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Extended Kalman Filter for Estimation of Parameters in Nonlinear State-Space Models of Biochemical Networks 英文参考文献.doc

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Extended Kalman Filter for Estimation of Parameters in Nonlinear State-Space Models of Biochemical Networks 英文参考文献

ExtendedKalmanFilterforEstimationofParametersin NonlinearState-SpaceModelsofBiochemicalNetworks XiaodianSun1,LiJin1,2,MomiaoXiong1,3 * 1LaboratoryofTheoreticalSystemsBiologyandCenterforEvolutionaryBiology,SchoolofLifeScienceandInstituteforBiomedicalSciences,FudanUniversity,Shanghai, China,2CAS-MPGPartnerInstituteofComputationalBiology,SIBS,CAS,Shanghai,China,3HumanGeneticsCenter,UniversityofTexasHealthScienceCenteratHouston, Houston,Texas,UnitedStatesofAmerica Abstract It is system dynamics that determines the function of cells, tissues and organisms. To develop mathematical models and estimatetheirparametersareanessentialissueforstudyingdynamicbehaviorsofbiologicalsystemswhichincludemetabolic networks,geneticregulatorynetworksandsignaltransductionpathways,underperturbationofexternalstimuli.Ingeneral, biologicaldynamicsystemsarepartiallyobserved.Therefore,anaturalwaytomodeldynamicbiologicalsystemsistoemploy nonlinearstate-spaceequations.Althoughstatisticalmethodsforparameterestimationoflinearmodelsinbiologicaldynamic systems have been developed intensively in the recent years, the estimation of both states and parameters of nonlinear dynamicsystemsremainsachallengingtask.Inthisreport,weapplyextendedKalmanFilter(EKF)totheestimationofboth statesandparametersofnonlinearstate-spacemodels.ToevaluatetheperformanceoftheEKFforparameterestimation,we apply the EKF to a simulation dataset and two real datasets: JAK-STAT signal transduction pathway and Ras/Raf/MEK/ERK signalingtransductionpathwaysdatasets.ThepreliminaryresultsshowthatEKFcanaccuratelyestimatetheparametersand predictstatesinnonlinearstate-spaceequationsformodelingdynamicbiochemicalnetworks. Citation: Sun X, Jin L, Xiong M (2008) Extended Kalman Filter for Estimation of Parameters in Nonlinear State-Space Models of Biochemical Networks. PLoS ONE3(11):e3758.doi:10.1371/journal.pone.0003758 Editor:GustavoStolovitzky,IBMThomasJ.WatsonResearchCenter,UnitedStatesofAmerica ReceivedJune16,2008;AcceptedOctober9,2008;Pub