Bayesianstatistics

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Dr.DavidSpiegelhalter,CambridgeUniversity,UK
KennethRice,UniversityofWashington,Seattle,WA,USA
Bayesianstatisticsisasystemfordescribingepistemologicaluncertaintyusingthemathematicallanguageof
probability.Inthe'Bayesianparadigm,'degreesofbeliefinstatesofnaturearespecifiedthesearenonnegative,and
thetotalbeliefinallstatesofnatureisfixedtobeone.Bayesianstatisticalmethodsstartwithexisting'prior'beliefs,
andupdatetheseusingdatatogive'posterior'beliefs,whichmaybeusedasthebasisforinferentialdecisions.

Background
In1763,ThomasBayespublishedapaperontheproblemofinduction,thatis,arguingfromthespecifictothe
general.Inmodernlanguageandnotation,BayeswantedtouseBinomialdatacomprising successesoutof
attemptstolearnabouttheunderlyingchance ofeachattemptsucceeding.Bayes'keycontributionwastousea
probabilitydistributiontorepresentuncertaintyabout Thisdistributionrepresents'epistemological'uncertainty,
duetolackofknowledgeabouttheworld,ratherthan'aleatory'probabilityarisingfromtheessentialunpredictability
offutureevents,asmaybefamiliarfromgamesofchance.
n

Modern'Bayesianstatistics'isstillbasedonformulatingprobabilitydistributionstoexpressuncertaintyabout
unknownquantities.Thesecanbeunderlyingparametersofasystem(induction)orfutureobservations(prediction).

Bayes'Theorem
Initsrawform,Bayes'Theoremisaresultinconditionalprobability,statingthatfortworandomquantities and

,)y(p/) (p) |y(p = )y| (p

where
denotesaprobabilitydistribution(http://en.wikipedia.org/wiki/Probability_distribution),and
a
conditionaldistribution.When representsdataand representsparametersinastatisticalmodel,BayesTheorem
providesthebasisforBayesianinference.The'prior'distribution
(epistemologicaluncertainty)iscombinedwith
'likelihood'
toprovidea'posterior'distribution
(updatedepistemologicaluncertainty):thelikelihoodis
derivedfromanaleatorysamplingmodel
butconsideredasfunctionof forfixed
)|(p

)(p

) (p

)y| (p

. y

) |y(p

) |y(p

Whileaninnocuoustheory,practicaluseoftheBayesianapproachrequiresconsiderationofcomplexpracticalissues,
includingthesourceofthepriordistribution,thechoiceofalikelihoodfunction,computationandsummaryofthe
posteriordistributioninhighdimensionalproblems,andmakingaconvincingpresentationoftheanalysis.
Bayestheoremcanbethoughtofaswayofcoherentlyupdatingouruncertaintyinthelightofnewevidence.Theuse
ofaprobabilitydistributionasa'language'toexpressouruncertaintyisnotanarbitrarychoice:itcaninfactbe
determinedfromdeeperprinciplesoflogicalreasoningorrationalbehaviorseeJaynes(2003)orLindley(1953).In
particular,DeFinetti(1937)showedthatmakingaqualitativeassumptionsofexchangeabilityofbinaryobservations
(i.e.thattheirjointdistributionisunaffectedbylabelpermutation)isequivalenttoassumingtheyareeach
independentconditionalonsomeunknownparameter where hasapriordistributionandisthelimiting
frequencywithwhichtheeventsoccur.

UseofBayes'Theorem:asimpleexample

Supposeahospitalhasaround200bedsoccupiedeachday,andwewanttoknowtheunderlyingriskthatapatient
willbeinfectedbyMRSA(methicillinresistantStaphylococcusaureus).Lookingbackatthefirstsixmonthsofthe
year,wecount
20infectionsin40,000bed
days.Asimpleestimateoftheunderlyingrisk
wouldbe20/40,000 5infectionsper10,000
beddays.Thisisalsothemaximumlikelihood
estimate,ifweassumethattheobservation is
drawnfromaPoissondistributionwithmean
where
isthenumberofbeddays/
sothat
= y

4 = N

,000 ,01

. !y/

e ) N ( = ) |y(p

However,otherevidenceabouttheunderlying
riskmayexist,suchasthepreviousyear'sratesor
ratesinsimilarhospitalswhichmaybeincluded
aspartofahierarchicalmodel(seebelow).
Supposethisotherinformation,onitsown,
suggestsplausiblevaluesof ofaround10per
10,000,with95%ofthesupportfor lying
between5and17.Thisjudgementabout maybe
expressedasapriorprobabilitydistribution.Say,
forconvenience,theGamma
familyof
distributionsischosentoformallydescribeour
knowledgeabout Thisfamilyhasdensity

Figure1:Prior,likelihoodandposteriordistributionsfor therate
ofinfectionsper10,000beddays.Theposteriordistributionisa
formalcompromisebetweenthelikelihood,summarizingtheevidence
inthedataalone,andthepriordistribution,whichsummarizes
externalevidencewhichsuggestedhigherrates.
,

)b ,a(

1 a

b = ) (p

givesapriordistributionwithappropriateproperties,asshowninFigure1.

1 = b

and

; )a( /

choosing

01 = a

Figure1alsoshowsadensityproportionaltothelikelihoodfunction,underanassumedPoissonmodel.UsingBayes
Theorem,theposteriordistribution
is
)y| (p

)b + N(

1 a +y

1 a

i.e.aGamma
distributionthisclosedformposterior,withinthesameparametricfamilyastheprior,
isanexampleofaconjugateBayesiananalysis.Figure1showsthatthisposteriorisprimarilyinfluencedbythe
likelihoodfunctionbutis'shrunk'towardsthepriordistributiontoreflectthattheexpectationbasedonexternal
evidencewasofahigherratethanthatactuallyobserved.Thiscanbethoughtofasanautomaticadjustmentfor
'Regressiontothemean(http://en.wikipedia.org/wiki/Regression_to_the_mean%7C)',inthatthepriordistribution
willtendtocounteractchancehighsorlowsinthedata.
)b + N ,a + y(

Priordistributions
ThepriordistributioniscentraltoBayesianstatisticsandyetremainscontroversialunlessthereisaphysical
samplingmechanismtojustifyachoiceof
Oneoptionistoseek'objective'priordistributionsthatcanbeusedin
situationswherejudgementalinputissupposedtobeminimized,suchasinscientificpublications.Whileprogressin
ObjectiveBayesmethodshasbeenmadeforsimplesituations,auniversaltheoryofpriorsthatrepresentzeroor
minimalinformationhasbeenelusive.
. ) (p

Acompletealternativeisthefullysubjectivistposition,whichcompelsonetoelicitpriorsonallparametersbasedon
thepersonaljudgementofappropriateindividuals.ApragmaticcompromiserecognizesthatBayesianstatistical
analysesmustusuallybejustifiedtoexternalbodiesandthereforethepriordistributionshould,asfaraspossible,be

basedonconvincingexternalevidenceoratleastbeguaranteedtobeweaklyinformative:ofcourse,exactlythesame
holdsforthechoiceoffunctionalformforthesamplingdistributionwhichwillalsobeasubjectofjudgementandwill
needtobejustified.Bayesiananalysisisperhapsbestseenasaprocessforobtainingposteriordistributionsor
predictionsbasedonarangeofassumptionsaboutbothpriordistributionsandlikelihoods:arguinginthisway,
sensitivityanalysisandreasonedjustificationforbothpriorandlikelihoodbecomevital.
Setsofpriordistributionscanthemselvesshareunknownparameters,forminghierarchicalmodels
(http://en.wikipedia.org/wiki/Hierarchical_models%7C).ThesefeaturestronglywithinappliedBayesiananalysis
andprovideapowerfulbasisforpoolingevidencefrommultiplesourcesinordertoreachmorepreciseconclusions.
Essentiallyacompromiseisreachedbetweenthetwoextremesofassumingthesourcesareestimating(a)precisely
thesame,or(b)totallyunrelated,parameters.Thedegreeofpoolingisitselfestimatedfromthedataaccordingtothe
similarityofthesources,butthisdoesnotavoidtheneedforcarefuljudgementaboutwhetherthesourcesareindeed
exchangeable,inthesensethatwehavenoexternalreasonstobelievethatcertainsourcesaresystematicallydifferent
fromothers.

Prediction
OneofthestrengthsoftheBayesianparadigmisitseaseinmakingpredictions.Ifcurrentuncertaintyabout is
summarizedbyaposteriordistribution
apredictivedistributionforanyquantity thatdependson through
asamplingdistribution
canbeobtainedasfollows

, )y| (p

) | z(p

d )y| (p) | z(p

= )y| z(p

providedthat and areconditionallyindependentgiven

models.

whichwillgenerallyholdexceptintimeseriesorspatial

IntheMRSAexampleabove,supposewewantedtopredictthenumberofinfections overthenextsixmonths,or
40,000beddays.Thispredictionisgivenby
z

)p 1(

a +y

)b + N(

)a + y + z(

1 a +y

a +y

)b + N(

e ) N (
= )y| z(p

= d
! z)a + y(

)a + y(

!z

ThisNegativeBinomialpredictivedistributionfor isshowninFigure2.
z

where

. )b + N2(/)b + N( = p

MakingBayesianDecisions
Forinference,afullreportoftheposteriordistributionisthecorrectandfinalconclusionofastatisticalanalysis.
However,thismaybeimpractical,particularlywhentheposteriorishighdimensional.Instead,posteriorsummaries
arecommonlyreported,forexampletheposteriormeanandvariance,orparticulartailareas.Iftheanalysisis
performedwiththegoalofmakingaspecificdecision,measuresofutility,orlossfunctionscanbeusedtoderivethe
posteriorsummarythatisthe'best'decision,giventhedata.
InDecisionTheory,thelossfunctiondescribeshowbadaparticulardecisionwouldbe,givenatruestateofnature.
Givenaparticularposterior,theBayesruleisthedecisionwhichminimizestheexpectedlosswithrespecttothat
posterior.Ifaruleisadmissible(meaningthatthereisnorulewithstrictlygreaterutility,foratleastsomestateof
nature)itcanbeshowntobeaBayesruleforsomeproperpriorandutilityfunction.
ManyintuitivelyreasonablesummariesofposteriorscanalsobemotivatedasBayesrules.Theposteriormeanfor
someparameter istheBayesrulewhenthelossfunctionisthesquareofthedistancefrom tothedecision.As
noted,forexample,bySchervish(1995),quantilebasedcredibleintervalscanbejustifiedasaBayesrulefora
bivariatedecisionproblem,andHighestPosteriorDensityintervalscanbejustifiedasaBayesruleforasetvalued
decisionproblem.

Asaspecificexample,supposewehadtoprovide
apointpredictionforthenumberofMRSAcases
inthenext6months.Foreverycasethatweover
estimate,wewilllose10unitsofwasted
resources,butforeverycasethatweunder
estimatewewilllose50unitsthroughhavingto
makeemergencyprovision.Ourselectedestimate
isthat whichwillminimisetheexpectedtotal
cost,givenby
t

)y| z(p)t z(05

1 t

+ )y| z(p) z t(01

1+ t= z

0= z

Theoptimalchoiceof canbecalculatedtobe
30,considerablymorethantheexpectedvalue
24,reflectingourfearofunderestimation.
t

Figure2:Predictivedistributionfornumberofinfectionsinthenext
N+ b
N 2+ b

,1 + y + a (

distributionwith
10,
1,
20,
4.Themeanis25and
standarddeviationis6.7,andtheprobabilitythattherearemore
than20infectionsis73%.Essentially,moreinfectionsarepredicted
forthesecondsixmonths,becauseexternalevidencesuggeststhe
observationswereluckyinthefirsthalfoftheyear.
= N

= y

= b

= a

ComputationforBayesian
statistics

sixmonths,expressedasNegativeBinomial

Bayesiananalysisrequiresevaluating
expectationsoffunctionsofrandomquantitiesas
abasisforinference,wherethesequantitiesmayhaveposteriordistributionswhicharemultivariateorofcomplex
formoroftenboth.ThismeantthatformanyyearsBayesianstatisticswasessentiallyrestrictedtoconjugateanalysis,
wherethemathematicalformofthepriorandlikelihoodarejointlychosentoensurethattheposteriormaybe
evaluatedwithease.Numericalintegrationmethodsbasedonanalyticapproximationsorquadratureweredeveloped
in70sand80swithsomesuccess,butarevolutionarychangeoccurredintheearly1990swiththeadoptionof
indirectmethods,notablyMonteCarloMarkovChain).

TheMonteCarlomethod
Anyposteriordistribution
maybeapproximatedbytakingaverylargerandomsampleofrealizationsof from
theapproximatepropertiesof
bytherespectivesummariesoftherealizations.Forexample,the
posteriormeanandvarianceof maybeapproximatedbythemeanandvarianceofalargenumberofrealizations
from
Similarly,quantilesoftherealizationsestimatequantilesoftheposterior,andthemodeofasmoothed
histogramoftherealizationsmaybeusedtoestimatetheposteriormode.

)y| (p

)y| (p

; )y| (p

. )y| (p

Samplesfromtheposteriorcanbegeneratedinseveralways,withoutexactknowledgeof
Directmethods
includerejectionsampling,whichgeneratesindependentproposalsfor andacceptsthemataratewherebythose
retainedareproportionaltothedesiredposterior.Importancesamplingcanalsobeusedtonumericallyevaluate
relevantintegralsbyappropriatelyweightingindependentsamplesfromauserchosendistributionon properties
oftheposterior
canbeestimated.
. )y| (p

)y| (p

MarkovChainMonteCarlo(MCMC)
RealizationsfromtheposteriorusedinMonteCarlomethodsneednotbeindependent,orgenerateddirectly.Ifthe
conditionaldistributionofeachparameterisknown(conditionalonallotherparameters),onesimplewaytogenerate
apossiblydependentsampleofdatapointsisviaGibbsSampling.Thisalgorithmgeneratesoneparameteratatime

asitsequentiallyupdateseachparameter,theentireparameterspaceisexplored.Itisappropriatetostartfrom
multiplestartingpointsinordertocheckconvergence,andinthelongrun,the'chains'ofrealizationsproducedwill
reflecttheposteriorofinterest.
MoregeneralversionsofthesameargumentincludetheMetropolisHastingsalgorithmdevelopingpractical
algorithmstoapproximateposteriordistributionsforcomplexproblemsremainsanactiveareaofresearch.

ApplicationsofBayesianstatisticalmethods
ExplicitlyBayesianstatisticalmethodstendtobeusedinthreemainsituations.Thefirstiswhereonehasno
alternativebuttoincludequantitativepriorjudgments,duetolackofdataonsomeaspectofamodel,orbecausethe
inadequaciesofsomeevidencehastobeacknowledgedthroughmakingassumptionsaboutthebiasesinvolved.These
situationscanoccurwhenapolicydecisionmustbemadeonthebasisofacombinationofimperfectevidencefrom
multiplesources,anexamplebeingtheencouragementofBayesianmethodsbytheFoodandDrugAdministration
(FDA)divisionresponsibleformedicaldevices.
Thesecondsituationiswithmoderatesizeproblemswithmultiplesourcesofevidence,wherehierarchicalmodels
canbeconstructedontheassumptionofsharedpriordistributionswhoseparameterscanbeestimatedfromthedata.
Commonapplicationareasincludemetaanalysis,diseasemapping,multicentrestudies,andsoon.Withweakly
informativepriordistributionstheconclusionsmayoftenbenumericallysimilartoclassictechniques,evenifthe
interpretationsmaybedifferent.
Thethirdareaconcernswhereahugejointprobabilitymodelisconstructed,relatingpossiblythousandsof
observationsandparameters,andtheonlyfeasiblewayofmakinginferencesontheunknownquantitiesisthrough
takingaBayesianapproach:examplesincludeimageprocessing,spamfiltering,signalanalysis,andgeneexpression
data.Classicalmodelfittingfails,andMCMCorotherapproximatemethodsbecomeessential.
ThereisalsoextensiveuseofBayesianideasofparameteruncertaintybutwithoutexplicituseofBayestheorem.Ifa
deterministicpredictionmodelhasbeenconstructed,butsomeoftheparameterinputsareuncertain,thenajointprior
distributioncanbeplacedonthoseparametersandtheresultinguncertaintypropagatedthroughthemodel,often
usingMonteCarlomethods,toproduceapredictiveprobabilitydistribution.Thistechniqueisusedwidelyinrisk
analysis,healtheconomicmodellingandclimateprojections,andissometimesknownasprobabilisticsensitivity
analysis.
Anothersettingwherethe'updating'inherentintheBayesianapproachissuitableisinmachinelearningsimple
examplescanbefoundinmodernsoftwareforspamfiltering,suggestingwhichbooksormoviesausermightenjoy
givenhisorherpastpreferences,orrankingschemesformillionsofonlinegamers.Formalinferencemayonlybe
approximatelycarriedout,buttheBayesianperspectiveallowsaflexibleandadaptiveresponsetoeachadditionalitem
ofinformation.

OpenAreasinBayesianStatistics
ThephilosophicalrationaleforusingBayesianmethodswaslargelyestablishedandsettledbythepioneeringworkof
DeFinetti,Savage,JaynesandLindley.However,widespreadconcernremainoverhowtoapplythesemethodsin
practice,wherevariousconcernsoversensitivitytoassumptionscandetractfromtherhetoricalimpactofBayesians'
epistemologicalvalidity.

Hypothesistestingandmodelchoice
Jeffreys(1939)developedaprocedureforusingdata totestbetweenalternativescientifichypotheses
and
bycomputingtheBayesfactor
Hesuggestedthresholdsforstrengthofevidencefororagainstthe
hypotheses.TheBayesfactorcanbecombinedwiththepriorodds
togiveposteriorprobabilitiesofeach
,

1H

0H

. ) 1 H|y(p/) 0 H|y(p

) 1 H(p/) 0 H(p

hypothesis,thatcanbeusedtoweightpredictionsinBayesianModelAveraging(BMA).AlthoughBMAcanbean
effectivepragmaticdeviceforprediction,theuseofposteriormodelprobabilitiesforscientifichypothesistestingis
controversialevenamongtheBayesiancommunity,forbothphilosophicalandpracticalreasons:first,itmaynot
makesensetotalkofprobabilitiesofhypothesesthatweknowarenotstrictly'true',andsecond,thecalculationofthe
Bayesfactorcanbeextremelysensitivetoapparentlyinnocuouspriorassumptionsaboutparameterswithineach
hypothesis.Forexample,theordinateofawidelydisperseduniformpriordistributionwouldbeirrelevantfor
estimationwithinasinglemodel,butbecomescrucialwhencomparingmodels.
Ithasalsobeenarguedthatmodelchoiceisnotnecessarilythesameasidentifyingthe'true'model,particularlyasin
mostcircumstancesnotruemodelexistsandsoposteriormodelprobabilitiesarenotinterpretableoruseful.Instead,
othercriteria,suchastheAkaikeInformationCriterionortheDevianceInformationCriterion,areconcernedwith
selectingmodelsthatareexpectedtomakegoodshorttermpredictions.

Robustnessandreporting
Intheuncommonsituationthatthedataareextensiveandofsimplestructure,thepriorassumptionswillbe
unimportantandtheassumedsamplingmodelwillbeuncontroversial.Moregenerallywewouldliketoreportthat
anyconclusionsarerobusttoreasonablechangesinbothpriorandassumedmodel:thishasbeentermedinference
robustnesstodistinguishitfromthefrequentistideaofrobustnessofprocedureswhenappliedtodifferentdata.
(Frequentiststatisticsusesthepropertiesofstatisticalproceduresoverrepeatedapplicationstomakeinferencebased
onthedataathand)
Bayesianstatisticalanalysiscanbecomplextocarryout,andexplicitlyincludesbothqualitativeandquantitative
judgement.Thissuggeststheneedforagreedstandardsforanalysisandreporting,butthesehavenotyetbeen
developed.Inparticular,audiencesshouldideallyfullyunderstandthecontributionofthepriordistributiontothe
conclusions,thereasonablenessofthepriorassumptions,therobustnesstoalternativemodelsandpriors,andthe
adequacyofthecomputationalmethods.

Modelcriticism
InthearchetypalBayesianparadigmthereisnoneedfortestingwhetherasinglemodeladequatelyfitsthedata,since
weshouldbealwayscomparingtwocompetingmodelsusinghypothesistestingmethods.Howevertherehasbeen
recentgrowthintechniquesfortestingabsoluteadequacy,generallyinvolvingthesimulationofreplicatedataand
checkingwhetherspecificcharacteristicsoftheobserveddatamatchthoseofthereplicates.Proceduresformodel
criticismincomplexhierarchicalmodelsarestillbeingdeveloped.Itisalsoreasonabletocheckthereisnotstrong
conflictbetweendifferentdatasourcesorbetweenprioranddata,andgeneralmeasuresofconflictincomplexmodels
isalsoasubjectofcurrentresearch.

Connectionsandcomparisonswithotherschoolsofstatisticalinference
Atasimplelevel,'classical'likelihoodbasedinferencecloselyresemblesBayesianinferenceusingaflatprior,making
theposteriorandlikelihoodproportional.However,thisunderestimatesthedeepphilosophicaldifferencesbetween
BayesianandfrequentistinferenceBayesianmakestatementsabouttherelativeevidenceforparametervaluesgivena
dataset,whilefrequentistscomparetherelativechanceofdatasetsgivenaparametervalue.
Theincompatibilityofthesetwoviewshaslongbeenasourceofcontentionbetweendifferentschoolsofstatisticians
thereislittleagreementoverwhichis'right','mostappropriate'oreven'mostuseful'.Nevertheless,inmanycases,
estimates,intervals,andotherdecisionswillbeextremelysimilarforBayesianandfrequentistanalyses.Bernstein
vonMisesTheoremsgivegeneralresultsprovingapproximatelargesampleagreementbetweenBayesianand
frequentistmethods,forlargeclassesofstandardparametricandsemiparametricmodels.Anotableexceptionisin

hypothesistesting,wheredefaultBayesianandfrequentistmethodscangivestronglydiscordantconclusions.Also,
establishingBayesianinterpretationsofnonmodelbasedfrequentistanalyses(suchasGeneralizedEstimating
Equations)remainsanopenarea.
SomequalitiessoughtinnonBayesianinference(suchasadherencetothelikelihoodprinciple
(http://en.wikipedia.org/wiki/Likelihood_principle%7C)andexploitationofsufficiency)arenaturalconsequencesof
followingaBayesianapproach.Also,manyBayesianprocedurescanalso,quitestraightforwardly,becalibratedto
havedesiredfrequentistproperties,suchasintervalswith95%coverage.ThiscanbeusefulwhenjustifyingBayesian
methodstoexternalbodiessuchasregulatoryagencies,andwemightexpectanincreaseduseof'hybrid'techniques
inwhichaBayesianinterpretationisgiventotheinferences,butthelongrunbehaviouroftheprocedureisalsotaken
intoaccount.

References
ThomasBayes(1763),"AnEssaytowardssolvingaProblemintheDoctrineofChances"Phil.Trans.Royal
SocietyLondon
B.deFinetti,LaPrevision:SesLoisLogiques,SesSourcesSubjectives(1937)Annalesdel'InstitutHenriPoincare,
7:168.TranslatedasForesight:ItsLogicalLaws,ItsSubjectiveSources,inKyburg,H.E.andSmokler,H.E.
eds.,(1964).StudiesinSubjectiveProbability.Wiley,NewYork,91158
E.T.JaynesProbabilityTheory:TheLogicofScience(2003)CambridgeUniversityPress,Cambridge,UK
H.Jeffreys(1939)TheoryofProbabilityOxford,ClarendonPress
D.V.Lindley:StatisticalInference(1953)JournaloftheRoyalStatisticalSociety,SeriesB,16:3076
Schervish,M.J.(1995)TheoryofStatistics.SpringerVerlag,NewYork.

Furtherreading
BernardoandSmith(1994)BayesianTheory,Wiley
Berger(1993)StatisticalDecisionTheoryandBayesianAnalysis,SpringerVerlag
CarlinandLouis(2008)BayesianMethodsforDataAnalysis(ThirdEdition)ChapmanandHall/CRC
Gelman,Carlin,SternandRubin(2003)BayesianDataAnalysis(SecondEdition)ChapmanandHall/CRC
GelmanandHill(2007)DataAnalysisUsingRegressionandMultilevel/HierarchicalModels,Cambridge
UniversityPress
Lindley(1991)MakingDecisions(2ndEdition)Wiley
Robert(2007)TheBayesianChoice:FromDecisionTheoreticFoundationstoComputationalImplementation
(SecondEdition),SpringerVerlag

Seealso
Sponsoredby:EugeneM.Izhikevich,EditorinChiefofScholarpedia,thepeerreviewedopenaccessencyclopedia
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Gelman,UniversityofColumbia,NewYork,NY
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