Examples with GeneralBootstrapTest edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest used on opensource projects

Example 41 with GeneralBootstrapTest

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

the class FaskConcatenated method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (!parameters.getBoolean("bootstrapping")) {
        return search(Collections.singletonList((DataModel) DataUtils.getContinuousDataSet(dataSet)), parameters);
    } else {
        FaskConcatenated algorithm = new FaskConcatenated(score);
        algorithm.setKnowledge(knowledge);
        List<DataSet> dataSets = Collections.singletonList(DataUtils.getContinuousDataSet(dataSet));
        GeneralBootstrapTest search = new GeneralBootstrapTest(dataSets, algorithm, 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();
    }
}

Example 42 with GeneralBootstrapTest

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

the class FaskConcatenated method search.

@Override
public Graph search(List<DataModel> dataSets, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        List<DataSet> centered = new ArrayList<>();
        for (DataModel dataSet : dataSets) {
            centered.add(DataUtils.standardizeData((DataSet) dataSet));
        }
        DataSet dataSet = DataUtils.concatenate(centered);
        dataSet.setNumberFormat(new DecimalFormat("0.000000000000000000"));
        Fask search = new Fask(dataSet, score.getScore(dataSet, parameters));
        search.setDepth(parameters.getInt("depth"));
        search.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
        search.setExtraEdgeThreshold(parameters.getDouble("extraEdgeThreshold"));
        search.setDelta(parameters.getDouble("faskDelta"));
        search.setAlpha(parameters.getDouble("twoCycleAlpha"));
        search.setKnowledge(knowledge);
        return search.search();
    } else {
        FaskConcatenated algorithm = new FaskConcatenated(score);
        algorithm.setKnowledge(knowledge);
        List<DataSet> datasets = new ArrayList<>();
        for (DataModel dataModel : dataSets) {
            datasets.add((DataSet) dataModel);
        }
        GeneralBootstrapTest search = new GeneralBootstrapTest(datasets, algorithm, 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();
    }
}

Example 43 with GeneralBootstrapTest

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

the class ImagesBDeu method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (!parameters.getBoolean("bootstrapping")) {
        return search(Collections.singletonList((DataModel) DataUtils.getDiscreteDataSet(dataSet)), parameters);
    } else {
        ImagesBDeu imagesBDeu = new ImagesBDeu();
        imagesBDeu.setKnowledge(knowledge);
        List<DataSet> dataSets = Collections.singletonList(DataUtils.getContinuousDataSet(dataSet));
        GeneralBootstrapTest search = new GeneralBootstrapTest(dataSets, imagesBDeu, 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();
    }
}

Example 44 with GeneralBootstrapTest

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

the class ImagesBDeu method search.

@Override
public Graph search(List<DataModel> dataSets, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        BdeuScoreImages score = new BdeuScoreImages(dataSets);
        score.setSamplePrior(parameters.getDouble("samplePrior"));
        score.setStructurePrior(parameters.getDouble("structurePrior"));
        edu.cmu.tetrad.search.Fges search = new edu.cmu.tetrad.search.Fges(score);
        search.setFaithfulnessAssumed(true);
        search.setKnowledge(knowledge);
        return search.search();
    } else {
        ImagesBDeu imagesBDeu = new ImagesBDeu();
        // imagesBDeu.setKnowledge(knowledge);
        List<DataSet> datasets = new ArrayList<>();
        for (DataModel dataModel : dataSets) {
            datasets.add((DataSet) dataModel);
        }
        GeneralBootstrapTest search = new GeneralBootstrapTest(datasets, imagesBDeu, 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();
    }
}

Example 45 with GeneralBootstrapTest

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

the class ImagesPcStableMax method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (!parameters.getBoolean("bootstrapping")) {
        return search(Collections.singletonList((DataModel) DataUtils.getContinuousDataSet(dataSet)), parameters);
    } else {
        ImagesPcStableMax imagesPcStableMax = new ImagesPcStableMax();
        imagesPcStableMax.setKnowledge(knowledge);
        List<DataSet> dataSets = Collections.singletonList(DataUtils.getContinuousDataSet(dataSet));
        GeneralBootstrapTest search = new GeneralBootstrapTest(dataSets, imagesPcStableMax, 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();
    }
}