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Example 61 with BootstrapEdgeEnsemble

use of edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble in project tetrad by cmu-phil.

the class TsImages method search.

@Override
public Graph search(DataModel dataModel, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        DataSet dataSet = (DataSet) dataModel;
        TsGFci search;
        Score score1 = score.getScore(dataSet, parameters);
        IndependenceTest test = new IndTestScore(score1);
        search = new TsGFci(test, score1);
        search.setKnowledge(dataSet.getKnowledge());
        return search.search();
    } else {
        TsImages algorithm = new TsImages(score);
        DataSet data = (DataSet) dataModel;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}
Also used : IndTestScore(edu.cmu.tetrad.search.IndTestScore) SemBicScore(edu.cmu.tetrad.algcomparison.score.SemBicScore) BdeuScore(edu.cmu.tetrad.algcomparison.score.BdeuScore) Score(edu.cmu.tetrad.search.Score) IndependenceTest(edu.cmu.tetrad.search.IndependenceTest) GeneralBootstrapTest(edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest) BootstrapEdgeEnsemble(edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble) DataSet(edu.cmu.tetrad.data.DataSet) IndTestScore(edu.cmu.tetrad.search.IndTestScore) TsGFci(edu.cmu.tetrad.search.TsGFci)

Example 62 with BootstrapEdgeEnsemble

use of edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble in project tetrad by cmu-phil.

the class Jcpc method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        DataSet continuousDataSet = DataUtils.getContinuousDataSet(dataSet);
        edu.cmu.tetrad.search.Jcpc search = new edu.cmu.tetrad.search.Jcpc(test.getTest(continuousDataSet, parameters), score.getScore(continuousDataSet, parameters));
        search.setKnowledge(knowledge);
        return search.search();
    } else {
        Jcpc jcpc = new Jcpc(test, score);
        // jcpc.setKnowledge(knowledge);
        if (initialGraph != null) {
            jcpc.setInitialGraph(initialGraph);
        }
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, jcpc, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}
Also used : GeneralBootstrapTest(edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest) BootstrapEdgeEnsemble(edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble)

Example 63 with BootstrapEdgeEnsemble

use of edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble in project tetrad by cmu-phil.

the class Pc method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        if (algorithm != null) {
        // initialGraph = algorithm.search(dataSet, parameters);
        }
        edu.cmu.tetrad.search.PcAll search = new edu.cmu.tetrad.search.PcAll(test.getTest(dataSet, parameters), initialGraph);
        search.setDepth(parameters.getInt("depth"));
        search.setKnowledge(knowledge);
        search.setFasRule(PcAll.FasRule.FAS);
        search.setColliderDiscovery(PcAll.ColliderDiscovery.FAS_SEPSETS);
        search.setConflictRule(PcAll.ConflictRule.PRIORITY);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    } else {
        Pc algorithm = new Pc(test);
        // algorithm.setKnowledge(knowledge);
        // if (initialGraph != null) {
        // algorithm.setInitialGraph(initialGraph);
        // }
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, algorithm, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}
Also used : GeneralBootstrapTest(edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest) PcAll(edu.cmu.tetrad.search.PcAll) BootstrapEdgeEnsemble(edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble) DataSet(edu.cmu.tetrad.data.DataSet) PcAll(edu.cmu.tetrad.search.PcAll)

Example 64 with BootstrapEdgeEnsemble

use of edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble in project tetrad by cmu-phil.

the class TsImagesSemBic method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (!parameters.getBoolean("bootstrapping")) {
        return search(Collections.singletonList((DataModel) DataUtils.getContinuousDataSet(dataSet)), parameters);
    } else {
        TsImagesSemBic tsImagesSemBic = new TsImagesSemBic();
        tsImagesSemBic.setKnowledge(knowledge);
        List<DataSet> dataSets = Collections.singletonList(DataUtils.getContinuousDataSet(dataSet));
        GeneralBootstrapTest search = new GeneralBootstrapTest(dataSets, tsImagesSemBic, parameters.getInt("bootstrapSampleSize"));
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}
Also used : GeneralBootstrapTest(edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest) BootstrapEdgeEnsemble(edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble)

Example 65 with BootstrapEdgeEnsemble

use of edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble in project tetrad by cmu-phil.

the class TsImagesSemBic method search.

@Override
public Graph search(List<DataModel> dataModels, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        List<DataSet> dataSets = new ArrayList<>();
        for (DataModel dataModel : dataModels) {
            dataSets.add((DataSet) dataModel);
        }
        edu.cmu.tetrad.search.TsGFci search = new edu.cmu.tetrad.search.TsGFci(new IndTestScore(new SemBicScoreImages(dataModels)), new SemBicScoreImages(dataModels));
        search.setFaithfulnessAssumed(true);
        search.setKnowledge(knowledge);
        return search.search();
    } else {
        TsImagesSemBic tsImagesSemBic = new TsImagesSemBic();
        // tsImagesSemBic.setKnowledge(knowledge);
        List<DataSet> datasets = new ArrayList<>();
        for (DataModel dataModel : dataModels) {
            datasets.add((DataSet) dataModel);
        }
        GeneralBootstrapTest search = new GeneralBootstrapTest(datasets, tsImagesSemBic, parameters.getInt("bootstrapSampleSize"));
        search.setKnowledge(knowledge);
        BootstrapEdgeEnsemble edgeEnsemble = BootstrapEdgeEnsemble.Highest;
        switch(parameters.getInt("bootstrapEnsemble", 1)) {
            case 0:
                edgeEnsemble = BootstrapEdgeEnsemble.Preserved;
                break;
            case 1:
                edgeEnsemble = BootstrapEdgeEnsemble.Highest;
                break;
            case 2:
                edgeEnsemble = BootstrapEdgeEnsemble.Majority;
        }
        search.setEdgeEnsemble(edgeEnsemble);
        search.setParameters(parameters);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    }
}
Also used : GeneralBootstrapTest(edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest) BootstrapEdgeEnsemble(edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble) IndTestScore(edu.cmu.tetrad.search.IndTestScore) ArrayList(java.util.ArrayList) SemBicScoreImages(edu.cmu.tetrad.search.SemBicScoreImages)

Aggregations

BootstrapEdgeEnsemble (edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble)66 GeneralBootstrapTest (edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest)66 DataSet (edu.cmu.tetrad.data.DataSet)26 ArrayList (java.util.ArrayList)21 EdgeListGraph (edu.cmu.tetrad.graph.EdgeListGraph)15 Graph (edu.cmu.tetrad.graph.Graph)15 TakesInitialGraph (edu.cmu.tetrad.algcomparison.utils.TakesInitialGraph)10 Lofs2 (edu.cmu.tetrad.search.Lofs2)10 Node (edu.cmu.tetrad.graph.Node)6 PrintStream (java.io.PrintStream)6 PcAll (edu.cmu.tetrad.search.PcAll)5 edu.cmu.tetrad.search (edu.cmu.tetrad.search)4 IndTestScore (edu.cmu.tetrad.search.IndTestScore)4 IndependenceTest (edu.cmu.tetrad.search.IndependenceTest)4 Fges (edu.cmu.tetrad.search.Fges)3 Score (edu.cmu.tetrad.search.Score)3 Fges (edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Fges)2 PcStableMax (edu.cmu.tetrad.search.PcStableMax)2 SemBicScoreDeterministic (edu.cmu.tetrad.search.SemBicScoreDeterministic)2 SemBicScoreImages (edu.cmu.tetrad.search.SemBicScoreImages)2