introduction to rapidminer studio v7

DublinRLightningTalksEvent

Introduction to Rapidminer Geraldine Gray, PhD

March 24th 2016

Introduc9onsGeraldineisalecturerinIns9tuteofTechnologyBlanchardstown(ITB)

CoordinatorforITB’sMScinAppliedDataScienceandAnaly9cs

[email protected] https://ie.linkedin.com/in/geraldine-gray-9b2b187

@GGrayITB geraldine.gray.itb

Overview Objec9ve:u  Introduc9ontoRapidMinerStudiofordataanaly9cs

Agenda:1.  OverviewofRapidMinerStudiointerface2.  Impor9ngadataset3.  Descrip9vesta9s9csandvisualisa9on4.  Datamodelling5.  Modelevalua9on6.  Datacleaning7.  AddingRscript

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Topic1:OverviewofRapidminerStudio

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InstallingRapidmineronyourownmachine

ThelatestversionofRapidminerStudioisV7,itcanbedownloadedfromhUps://rapidminer.com/products/comparison/

•  Forwindows:downloadtherapidminer-install.exeandinstall.DefaultsinstallittoC:\programfiles,andaddittothestart>programsmenu.

•  Formac:downloadthe.dmgandaddittoyourapplica9onsfolder.

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Background Rapidminercomeswithover:

u Over125miningalgorithms

u Over100datacleaningandprepara9onfunc9ons.

u Over30chartsfordatavisualisa9on,

u  andselec9onofmetricstoevaluatemodelperformance.

Eachfunc9onisavailableasanOPERATOR,(whichisimplementedasaJavaclass).Aprocessisbuiltbyconnec9ngoperatorstogether,withtheoutputofoneoperatorpassingasinputtothenext.Thisisalldonebydraganddrop.

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Creating a repository •  All processes created in Rapidminer are saved to a

repository. The repository will also store other objects including datasets and prediction models.

•  A repository maps to a folder on your machine created specifically for Rapidminer work.

Before starting RapidMiner studio for the first time, create a folder somewhere on your machine that will store your process and datasets from todays workshop.

•  The folder can be local to the machine, on a external drive/USB, or in the cloud.

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StartupRapidminerWhenyoustartRapidminerstudio,youarepresentedwithanini9alintroduc9onwindow.Closethiswindowtoseethemaininterface.

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RAPID MINER GUI

Processdesignwindow

Parameterseangsforselectedopera9on

Logofac9vi9es,includingerrors.Ifthisismissing,

addfromView/ShowPanel

Availableoperators

Explana9onoftheselectedoperator

Navigaterepositories

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Rapid Miner toolbars Run process

Stop process

Automatically connect operators

undo redo

save

new open

Add/remove breakpoints

Show and alter the order in which operators run

Resize the process window

Process design view

View process results

Add a note / comment

Enable/disable an operator

Rightclickop9ons:

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ProcessesandDatasets•  Yourrapidminerrepository(folder)willcontaindifferenttypesofobjects,mostcommonly:

•  Datasets–theactualdataitself•  Thesymbolisabluecylinder

•  Processes–aseriesofoperatorsthatareappliedtoadatasettoanalyseit.•  Thesymbolistwocogwheels•  Aprocesswillreadinadataset,carryoutvarioustasksonit,andoutputtheresults.AprocessdoesNOTchangetheoriginaldataset.

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Repositories•  Rapidminercomeswitharepositorycalledsamples,whichhasa

numberofdatasetsandexampleprocesses.–  Youcannoteditthesamplesrepository

Tocreateyouownrepository,selectthedropdownboxontherepositorywindow,select‘createrepository’,andbrowsetothefolderyoucreated.

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Findinganoperator•  Rapidminercomeswithmanyoperators,sofindingtheoneyouwant

canbedaun9ngatfirst.•  Onceyougetfamiliarwithoperatornames,youcanfindthemmore

easilyusingthefilteratthetopoftheoperatorwindow

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Listalloperatorsthatstartwith‘read’

Listalloperatorswhosefirstwordstartswith‘dec’,and2ndwordstartswith‘t’.

Topic2:Impor9ngadataset

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Reading in a dataset Therearetwoop9onsforaccessingadataset:1.  YoucanuseoneofthemanyReadoperatorsto

readdataintoRapidminertemporarilyforapar9cularprocess.

2. 

•  Rapidminershipswithanumberofdatasetsalready

loadedintheSAMPLESrepository

Onceadatasetisinarepository,youcanaccessitusingtheRetrieveoperator.

You can import a dataset into your repository, where it will be available to all processes via the retrieve operator. This is the most efficient method, as meta data is stored with the dataset.

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Wine Quality Dataset WearefirstgoingtoimporttheWINEQUALITYdatasetfromtheUCIrepository:hUp://archive.ics.uci.edu/ml/machine-learning-databases/wine-quality/

AUributes:1-fixedacidity2-vola9leacidity3-citricacid4-residualsugar5-chlorides6-freesulfurdioxide7-totalsulfurdioxide8-density9-pH10-sulphates11–alcoholOutputvariable(basedonsensorydata):12-quality(scorebetween0and10)

Downloadthewine-quality-red.csvfilefromtheUCIwebsite.TakealookatthedatasetinExcelorNotepad/Textpad.Thefirstrowiscolumnheadings.Columnsareseparatedby‘;’

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Google:UCIrepository,andlookforwinequality(notwine)

Importing the wine dataset into Rapidminer

1.  ReturntoRapidminer2.  Select‘adddata’;then‘mycomputer’andbrowsetothedownloaded

file.

3.  Youarepresentedwithanumberofscreenstosetthemetadataforthisdatasetasfollows...

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Thefirstscreenspecifiesimportseangs,includingthecolumndelimiter.ApreviewatboUomtellsyouiftheseangsarecorrect

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•  ThesecondscreenspecifiesdatatypeforeachaUribute,anditsroleinthedataanaly9csprocess

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Mostdatatypesareintui9ve.Binominal:binaryaUribute,itcanonlyhavetwovalues.RapidminerwillassumebinomialifanaUributehasjusttwodis9nctvaluesinthefirst100rowsscanned.Thisisnotalwayscorrect.Polynominal:anon-numericaUributewithmul9plevalues.


ROLE•  AUributeswithoutaroleareusedbyminingalgorithmstoiden9fypaUerns

inthedataset.•  Predic9onmodelswillaUempttopredicttheaUributewiththeroleof

LABEL.•  TheaUributewiththeroleofIDisaprimarykey,usedinJOINopera9ons.•  Youcanspecifyother,userdefined,rolesforaUributestobeignoredby

miningalgorithms

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ChangetheroleofthefinalaUribute,quality,tolabel.


Inthefinalscreen,specifythenameofthedataset,i.e.wine,andbrowsetotherepositoryfolderwhereitistobestored.Thedatasetwillnowappearinyourrepositorywindow

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Topic3:Descrip9veSta9s9csandVisualisa9on

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ExploringadatasetInthesamples/datarepositorythereareanumberofdatasetsalreadyimported(i.e.IntheRMformat).ClickontheTITANICdatasettoopenit.Thisautoma9callybringsyoutotheresultsview.Withintheresultsview,therearefivetabsonthelenhandside.Wewilllookatthefirstthree:1.  Data:Viewthedatainthedataset2.  Sta9s9cs:Viewsummarysta9s9csonthedataset3.  Charts:Arangeofvisualiza9onsofthedataset

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Thedataview•  Thedataviewlistsalltherowsinthedataset,andreportsonthe

numberofrows(examples),andcolumns(aUributes)inthedataset.

•  Thefiltersontherighthandsideallowyoutoinves9gaterowswithmissingvalues.

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Thesta9s9csviewThesta9s9csviewgivesmetadataoneachaUribute,specifically:

–  Datatypes–  Numberofmissingvalues–  Min,max,averagefornumberaUributes–  Least,Mostandalistofvaluesfornon-numericaUributes

ClickingonanaUributewillshowahistogramforthataUributeThisisagoodviewforanini9alqualityassessmentof:

1.  Missingvalues2.  Outliervalues3.  AUributeswhosedistribu9onofvaluesisnotasexpec9ng,

indica9ngthedatasetinnotrepresenta9veofthepopula9onofinterest.

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Thechartsview•  Thechartsviewgivesyouaccesstoarangeofvisualisa9onsforyour

dataset.

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Thechartsview

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Gotothechartviewofthe9tanicdataset.Underchartstyle,select‘histrogramcolor’.SetHistrogramto‘age’;Colorto‘Survived’;andreducetheOpaquenessofthehistrogram.a)  Doesitappearthatprioritywasgiventochildren?b)  Insteadof‘age’plot‘sex’.Doesitappearthat

prioritywasgiventowomen?c)  Lookingatahistogramof‘class’,whichclassof

passengerwasmostlikelytosurvive?

ThechartsviewWearegoingtolookatonemoredataset,theirisdataset,whichhasitsownwikipediapage:hUps://en.wikipedia.org/wiki/Iris_flower_data_set

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AUributes:a1:SepalLengtha2:SepalWidtha3:PetalLengtha4:PetalWidth

Classlabel:Iris-setosaIris-veriscolorIrish-virginica

Thechartsview

•  NavigatetotheIRISdatasetinthesamples/datarepository.Doubleclicktoopenitintheresultsview.

•  Inthechartsview,select‘ScaUerMatrix’.ThisshowsascaUerplotofallpairsofaUributes,colourcodedbyclasslabel.

a)  Arethethreeclasseswellseparated?b)  SelectaScaUer3-DColorplot.Bydefaultitcolorcodesbyclasslabel.

Useyourmousetorotatetheplotandsoviewitfromdifferentperspec9ves.

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Closealltabsintheresultsview

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Topic4

Buildingapredic9vemodel

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Classifica9onAclassifica9onalgorithmtrainsamodeltopredictaclasslabel–oneoftheaUributesinthedatasetThisclasslabeldefinesgroupsinthedatasetThealgorithmlearnswhatdifferen9atesthesegroupsfromeachother

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ClassLabel A1 A2 A3 A4Iris-setosa 5.1 3.5 1.4 0.2Iris-setosa 5 3.6 1.4 0.2Iris-setosa 5.7 3.8 1.7 0.3Iris-setosa 4.6 3.6 1 0.2Iris-setosa 5 3.3 1.4 0.2Iris-versicolor 6 2.2 4 1Iris-versicolor 6.7 3.1 4.4 1.4Iris-versicolor 6.8 2.8 4.8 1.4Iris-versicolor 5.7 3 4.2 1.2Iris-versicolor 5.7 2.9 4.2 1.3Iris-virginica 7.1 3 5.9 2.1Iris-virginica 7.2 3.6 6.1 2.5Iris-virginica 6.5 3.2 5.1 2Iris-virginica 6.7 3.3 5.7 2.1Iris-virginica 6 3 4.8 1.8

Classifica9onalgorithmsClassifica9onalgorithmsuselabeleddatatolearnhowtoiden9fyinstancesofeachclass

Willitbeeasytotrainamodeltodifferen9atebetweenthethreetypesofirisbelow?

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Iris virginica

Iris veriscolor

Iris setosa

Classifica9onalgorithmsTherearemanyclassifica9onalgorithmsimplementedinRapidminer,undermodeling/predic9ve.Wewilllookatonesuchalgorithm:aDecisionTree

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Star9ngaprocess...

•  SofarinRapidminer,wehavejustlookedatdatasets,wehaven’tactuallydoneanythingwiththedata.

•  Inthissec9onwewillcreateaRapidminerprocessthattrainsaclassifica9onmodel...

ReturntotheDesignView

Theprocesswindowshouldbeempty

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Star9ngaprocessTheprocesswillstartbyretrievingadataset.

–  Wewillusetheirisdataset

Navigatetotheirisdatasetinthedata/samplesrepository,anddragitintotheprocesswindow.

–  ThisaddsaRetrieveoperator,whichretrievesadatasetfromtherepository.

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Buildingamodel

–  Drag‘DecisionTree’fromtheoperatorswindowontotheprocesswindow,aner‘Retrieve’.

–  Connectthe‘out’portfromRetrieve(clickonthesemicircle)tothe‘tra’portofthe‘DecisionTrees’(clickonthesemicircle)

–  ConnectbothoutputportsoftheDecisionTreetotheprocessoutputport

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Aboutports...

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Process output ports Operator

input ports Operator output ports

MandatoryinputportOp9onalinputportOutputporthasavalue

Outputportdoesnothaveavalue

Ports represents input to an operator, and outputs from an operator. Data an other objects are passed from one operator to the next in a process, as indicated by ports that are connected. Colors are used to indicate the type of data/object, e.g:

purple: dataset green: model brown: model performance

Hover over a port to see the type of object required.

Connectmatchingcolours

Runtheprocesstobuildthemodel•  Runtheprocess.Rapidminerwillautoma9callybringyoutotheresults

view.•  Therearetwotabsintheresultsview(becausewehadtwooutputsfrom

theprocess:–  Thedatasetitself–  Thedecisiontreeclassifica9onmodel

•  ClickontheDecisionTreetab

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Classifica9onmodel

ThetextonLeafnodesisthepredictedclasslabel.

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AUributes:a1:SepalLengtha2:SepalWidtha3:PetalLengtha4:PetalWidth

Theheightofthebarindicatesthenumberofrowsthatmatchedthisbranch.Hoveroverthenodetogettheactualnumbers

Amixofcoloursindicatesthatnotallrowsmatchingthisbranchwereinthesameclass

Branchesonthedecisiontreerepresentif..then..rules,e.g.ifa3<=2.450thentheflowerisIrisSetosa

WhichaUributesweremostpredic9veoftheclasslabel?

Topic5

Modelaccuracy(andbuildingblocks)

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ModelaccuracyAdecisiontreeproducesanicevisualisa9onoftherulesthatpredictclassmembership.Itscanbeusedasawaytoexplorehistoricdata(Descrip9vemodeling).However,thedecisiontreeitselfdoesnottellushowaccuratethemodelwillbewhenappliedtonewdata(i.e.datathatwasnotavailabletoitduringtraining.).

i.e.canwereplyontheaccuracyofitspredic9ons?(Predic9vemodeling)Todeterminemodelaccuracywhenmakingpredic9onsonnewdata,wedothefollowing:

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Modelaccuracy

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1.Splitthedatasetintoatrainingdatasetandatestdataset

2.Trainingamodelonthetrainingdataset

3.Applythemodeltothetestdataset

4.Calculatehowmanyrowswerepredictedcorrectly.

Modelaccuracy

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Label A1 A2 A3 A4Iris-versicolor 6 2.2 4 1Iris-setosa 4.6 3.6 1 0.2Iris-versicolor 5.7 2.9 4.2 1.3Iris-versicolor 5.7 3 4.2 1.2Iris-virginica 7.1 3 5.9 2.1Iris-virginica 6 3 4.8 1.8Iris-versicolor 6.7 3.1 4.4 1.4Iris-virginica 6.5 3.2 5.1 2Iris-setosa 5 3.3 1.4 0.2Iris-virginica 6.7 3.3 5.7 2.1Iris-setosa 5.1 3.5 1.4 0.2

Training data

Label A1 A2 A3 A4Predictedvalue

Iris-setosa 5 3.6 1.4 0.2 ?Iris-versicolor 6.8 2.8 4.8 1.4 ?Iris-virginica 7.2 3.6 6.1 2.5 ?Iris-setosa 5.7 3.8 1.7 0.3 ?

Test data

Classifica9onalgorithm

Trainmodel

Classifica9onmodel

Applymodel

TrueLabel PredictedlabelIris-setosa Iris-setosaIris-versicolor Iris-virginicaIris-virginica Iris-versicolorIris-setosa Iris-setosa

Accuracy: 50%

Labeled data

ModelaccuracyinRM•  ReturntotheDesignView•  RightclickontheDecisionTreeoperatoranddeleteit•  Rightclickanywhereintheprocesswindow,selectInsertBuildingBlock,andthenNominalX-Valida9on.

•  AValida9onoperatorisaddedtotheprocesswindow.Moveittotherightoftheretrieveoperatorandconnecttheports.

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Buildingblocksaregroupsofoperatorsfrequentlyusedtogether.Youcandefineyourown,orusethe5predefinedbuildingblocks

TheiconontheboUomrightcorneroftheoperatorindicatesthereareotheroperatorsembeddedwithinthisoperator.Clickontheoperatortoviewitssub-processes

Modelaccuracy1.Thevalida9onoperatorsplitsthedatasetintopar99ons:someareusedfortrainingwhileothersareusedfortes9ng

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2. Train a Decision Tree on the training portion of the dataset

3. Apply the decision tree model to the test portion of the dataset

4. Calculate how many predictions were correct

Modelaccuracy•  Returnuptotherootlevel.•  Outputthemodel(mod)andtheperformance(ave)port.

•  Runtheprocess

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Modelaccuracy–confusionmatrixTheperformanceoperatorgivestheoverallmodelaccuracy,andaccuracywithineachclassdepictedasaconfusionmatrix:

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pred.: refers to the class label predicted by the decision tree

true: Refers to the actual class label in the original dataset

4 rows in the dataset were predicted as being Iris-virginica, but were actually iris-veriscolor

5 rows in the dataset were predicted as being Iris-veriscolor, but were actually iris-virginica

The diagonal represents correct predictions

Topic6:Datacleaning

Crea9ngaRapidminerprocessto1.  RemoveaUributes2.  RemoveRows

3.  Fillmissingvalues

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Datacleaning

•  Theirisdatasetisacleandataset,withclassesthatareeasytodis9nguish.

•  Datasetsarenotusuallysoclean,oreasytomodel.•  Thenextsec9onwillbuildaRapidminerprocesstocleanadatasetand

thentrainaclassifica9onmodel...•  ReturntotheDesignView.•  Saveyourcurrentprocesstoyourrepository,andcallitDT-IRIS

•  Startanewprocess

•  Choseablanktemplate

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Datacleaning•  Theprocesswillstartbyretrievingadataset.

–  Wewillusethe9tanicdataset,andsortoutthemissingvalues•  Navigatetothe9tanicdatasetinthedata/samplesrepository,anddrag

itintotheprocesswindow.–  ThisaddsaRetrieveoperator,whichretrievesadatasetfromtherepository.

•  The9tanicdatasethas1309rows.5aUributeshadmissingvalues

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AEeibutes Numbermissing %agemissingPassengerFare 1 0.08%PortofEmbarka9on 2 0.15%Age 263 20.09%LifeBoat 823 62.87%Cabin 1014 77.46%

Datacleaning

Step1:RemoveaUributeswith>40%missing–  Drag‘selectaUributes’ontotheprocesswindowaner‘Retrieve’.–  ConnecttheoutputfromRetrieve(clickonthesemicircle)totheInputof

‘SelectAUributes’(clickonthesemicircle)–  Clickon‘SelectAUributes’toviewitsparametersontherighthandpane.

WemustspecifywhataUributesininclude/excludeintheprocess.

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•  SetaUributefilterto‘subset’;clickon‘selectaUributes’,anddoubleclickonCabinandLifeboattomovethemtotherighthandlist.Clickapply.

•  Clickon‘invertselect’asthesearetheaUributeswedoNOTwanttoselect.

RUN THE PROCESS

Datacleaning

Step2:ReplacemissingvaluesinAGE–  Drag‘replacemissingvalues’ontotheprocesswindowaner

‘SelectAUributes’.–  Connectthe‘exa’outputfromselectaUributestothe‘exa’

inputof‘replacemissingvalues’–  Clickon‘replacemissingvalues’toviewitsparametersonthe

righthandpane.

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•  SetaUributefilterto‘single’;clickthedropdownboxbelow,andselect‘age’

•  Thedefaultisthatmissingvalueswillbereplacedbytheaveragevalueforage

RUN THE PROCESS

Datacleaning

Step3:RemoverowsforaUributeswith<5%missing–  TheonlyaUributeslenwithmissingvaluesarePassengerFareand

PortofEmbarka9on.RemovingALLrowswithmissingvalueswillhandletheremainingmissingvalues

–  DragFilterExamplesontotheprocesswindowanerReplacemissing.Selectfilterexamplestoviewitsparameters:

•  Clickthecustom_filtersdropdownboxintheoperatorsparameters,andselectno_missing_aUributes

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RUN THE PROCESS

Buildapredic9vemodelonthecleaneddata

•  Rightclickontheprocesswindow,andaddaNominalX-Valida9onblocktotheendoftheprocess.

•  Connecttheports,ensuringmodelandtheaccuracy(ave)areoupuUedfromtheprocess.

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A red port indicates there may be an error. Run the process to check . . .

Buildapredic9vemodelonthecleaneddata

•  LookfortheSetRoleoperator,anddropitontotheprocesswindow.•  ConnectitinbetweenRetrieveandSelectAUributes.•  Clickonsetroletoviewitsparameters.SetaUributenametosurvived,

andtargetroletolabel.Thedatasetnothasaclasslabel.

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HowaccurateistheDecisionTree?WhichaUributesweremostpredic9veoftheclasslabel?

RUN THE PROCESS

Topic7:AddingRcode

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RunningRscriptwithinRapidminer

•  ThereareanumberofextensionstoRapidMinerstudioavailablefreefromtheirmarketplace,includinganextensiontorunRscriptwithinRapidminer.Installedpackagesarelistedundertheextensionsfolder.

•  TheoperatortorunRscripts‘ExecuteR’.Theoperatorsparameter

providestheeditorforRscript;Inputsaretheparameterstoamandatorymainfunc9on;Areturnstatementdefinestheoutputsfromtheoperator.

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Theoperatorshelpgivesalinktotheexampleprocess.ThePolynomialdatasetissplitintotwopar99ons.LearnModelcontainsRscripttotrainalinearmodel;ApplyRModelcontainsRscripttoapplythemodelandrecorditsperformance.Thescriptforbothisonthenextslide...

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•  LearnModel

#trainalinearmodelonthetrainingdataandreturnthelearnedmodelrm_main=func9on(data){

linearModel<-lm(formula=label~.,data=data) return(linearModel)}

•  ApplyRmodel##loadthetrainedmodelandapplyitonthetestdatarm_main=func9on(model,data){#applythemodelandbuildapredic9onresult<-predict(model,data)#addthepredic9ontotheexamplesetdata$predic9on<-result#updatethemetadatametaData$data$predic9on<<-list(type="real",role="predic9on")return(data)}G. Gray 60

Learningmore...WehavejusttouchedonafewoftheoperatorsinRapidminer.•  Thesamples/processesrepositoryinRapidminerhasmanymore

examples.•  Therapidminerwebsitehastrainingmaterial.•  TheRapidminerResourceswebsitealsohastrainingmaterial,someof

whichisfree.•  Neuralmarkettrends(ThomasOU)alsohasgoodvideosonRapidminer.

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Books:1.  RapidminerDataMiningUseCasesand

BusinessAnaly9csApplica9ons.Editors:

Dr.MarkusHofmann&RalfKlinkenberg

2.  ExploringdatawithRapidminerby

AndrewChisholm(freetodownload)

introduction to rapidminer studio v7

Data & Analytics