algebraic statistics for computational biology - lior pachter and bernd sturmfels

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1、AlgebraicStatisticsforComputationalBiology“Ifyoucan’tstandalgebra,keepoutofevolutionarybiology”–JohnMaynardSmith[Smith,1998,pageix]AlgebraicStatisticsforComputationalBiologyEditedbyLiorPachterandBerndSturmfelsUniversityofCaliforniaatBerkeleycambridgeuniversitypressCambridge,NewYork,Melbo

2、urne,Madrid,CapeTown,Singapore,S˜aoPauloCambridgeUniversityPress,ThePittBuilding,TrumpingtonStreet,Cambridge,UnitedKingdomwww.cambridge.orgInformationonthistitle:www.cambridge.org/9780521857000cCambridgeUniversityPress2005Thisbookisincopyright.Subjecttostatutoryexceptionandtotheprovision

3、sofrelevantcollectivelicensingagreements,noreproductionofanypartmaytakeplacewithoutthewrittenpermissionofCambridgeUniversityPress.Firstpublished2005PrintedintheUSATypefaceComputerModern10/13ptSystemLATEX2ε[author]AcataloguerecordforthisbookisavailablefromtheBritishLibraryISBN-13978–0–521

4、–85700–0hardbackISBN-100-521-85700-7hardbackCambridgeUniversityPresshasnoresponsibilityforthepersistenceoraccuracyofURLSforexternalorthird-partyinternetwebsitesreferredtointhisbook,anddoesnotguaranteethatanycontentonsuchwebsitesis,orwillremain,accurateorappropriate.ContentsPrefacepageixG

5、uidetothechaptersxiAcknowledgmentofsupportxiiPartIIntroductiontothefourthemes11StatisticsL.PachterandB.Sturmfels31.1Statisticalmodelsfordiscretedata41.2Linearmodelsandtoricmodels91.3ExpectationMaximization171.4Markovmodels241.5Graphicalmodels332ComputationL.PachterandB.Sturmfels432.1Trop

6、icalarithmeticanddynamicprogramming442.2Sequencealignment492.3Polytopes592.4Treesandmetrics672.5Software743AlgebraL.PachterandB.Sturmfels853.1VarietiesandGr¨obnerbases863.2Implicitization943.3Maximumlikelihoodestimation1023.4Tropicalgeometry1093.5Thetreeoflifeandothertropicalvarieties117

7、4BiologyL.PachterandB.Sturmfels1254.1Genomes1264.2Thedata1324.3Theproblems1374.4Statisticalmodelsforabiologicalsequence1414.5Statisticalmodelsofmutation147vviContentsPartIIStudiesonthefourthemes1595ParametricInferenceR.Mihaescu1635.1Tropicalsum-productdecompositions1645.2