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

Example 16 with GeneralBootstrapTest

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

the class R4 method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        Graph graph = algorithm.search(dataSet, parameters);
        if (graph != null) {
            initialGraph = graph;
        } else {
            throw new IllegalArgumentException("This R4 algorithm needs both data and a graph source as inputs; it \n" + "will orient the edges in the input graph using the data");
        }
        List<DataSet> dataSets = new ArrayList<>();
        dataSets.add(DataUtils.getContinuousDataSet(dataSet));
        Lofs2 lofs = new Lofs2(initialGraph, dataSets);
        lofs.setRule(Lofs2.Rule.R4);
        return lofs.orient();
    } else {
        R4 r4 = new R4(algorithm);
        if (initialGraph != null) {
            r4.setInitialGraph(initialGraph);
        }
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, r4, 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 17 with GeneralBootstrapTest

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

the class RSkewE method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        Graph graph = algorithm.search(dataSet, parameters);
        if (graph != null) {
            initialGraph = graph;
        } else {
            throw new IllegalArgumentException("This RSkewE algorithm needs both data and a graph source as inputs; it \n" + "will orient the edges in the input graph using the data");
        }
        List<DataSet> dataSets = new ArrayList<>();
        dataSets.add(DataUtils.getContinuousDataSet(dataSet));
        Lofs2 lofs = new Lofs2(initialGraph, dataSets);
        lofs.setRule(Lofs2.Rule.RSkewE);
        return lofs.orient();
    } else {
        RSkewE rSkewE = new RSkewE(algorithm);
        if (initialGraph != null) {
            rSkewE.setInitialGraph(initialGraph);
        }
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, rSkewE, 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 18 with GeneralBootstrapTest

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

the class FgesMeasurement method search.

@Override
public Graph search(DataModel dataModel, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        DataSet dataSet = DataUtils.getContinuousDataSet(dataModel);
        dataSet = dataSet.copy();
        dataSet = DataUtils.standardizeData(dataSet);
        double variance = parameters.getDouble("measurementVariance");
        if (variance > 0) {
            for (int i = 0; i < dataSet.getNumRows(); i++) {
                for (int j = 0; j < dataSet.getNumColumns(); j++) {
                    double d = dataSet.getDouble(i, j);
                    double norm = RandomUtil.getInstance().nextNormal(0, Math.sqrt(variance));
                    dataSet.setDouble(i, j, d + norm);
                }
            }
        }
        Fges search = new Fges(score.getScore(dataSet, parameters));
        search.setFaithfulnessAssumed(parameters.getBoolean("faithfulnessAssumed"));
        search.setKnowledge(knowledge);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    } else {
        FgesMeasurement fgesMeasurement = new FgesMeasurement(score, algorithm);
        // fgesMeasurement.setKnowledge(knowledge);
        if (initialGraph != null) {
            fgesMeasurement.setInitialGraph(initialGraph);
        }
        DataSet data = (DataSet) dataModel;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, fgesMeasurement, 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 19 with GeneralBootstrapTest

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

the class FasLofsConcatenated 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);
        }
        DataSet dataSet = DataUtils.concatenate(dataSets);
        edu.cmu.tetrad.search.FasLofs search = new FasLofs(dataSet, rule);
        search.setDepth(parameters.getInt("depth"));
        search.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
        search.setKnowledge(knowledge);
        return getGraph(search);
    } else {
        FasLofsConcatenated algorithm = new FasLofsConcatenated(rule);
        // algorithm.setKnowledge(knowledge);
        List<DataSet> datasets = new ArrayList<>();
        for (DataModel dataModel : dataModels) {
            datasets.add((DataSet) dataModel);
        }
        GeneralBootstrapTest search = new GeneralBootstrapTest(datasets, 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();
    }
}

Example 20 with GeneralBootstrapTest

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

the class Ccd method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        edu.cmu.tetrad.search.Ccd search = new edu.cmu.tetrad.search.Ccd(test.getTest(dataSet, parameters));
        search.setDepth(parameters.getInt("depth"));
        search.setApplyR1(parameters.getBoolean("applyR1"));
        return search.search();
    } else {
        Ccd algorithm = new Ccd(test);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, 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();
    }
}