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

Example 51 with GeneralBootstrapTest

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

the class Glasso method search.

public Graph search(DataModel ds, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        DoubleMatrix2D cov = new DenseDoubleMatrix2D(DataUtils.getContinuousDataSet(ds).getCovarianceMatrix().toArray());
        edu.cmu.tetrad.search.Glasso glasso = new edu.cmu.tetrad.search.Glasso(cov);
        glasso.setMaxit((int) parameters.getInt("maxit"));
        glasso.setIa(parameters.getBoolean("ia"));
        glasso.setIs(parameters.getBoolean("is"));
        glasso.setItr(parameters.getBoolean("itr"));
        glasso.setIpen(parameters.getBoolean("ipen"));
        glasso.setThr(parameters.getDouble("thr"));
        glasso.setRhoAllEqual(1.0);
        edu.cmu.tetrad.search.Glasso.Result result = glasso.search();
        TetradMatrix wwi = new TetradMatrix(result.getWwi().toArray());
        List<Node> variables = ds.getVariables();
        Graph resultGraph = new EdgeListGraph(variables);
        for (int i = 0; i < variables.size(); i++) {
            for (int j = i + 1; j < variables.size(); j++) {
                if (wwi.get(i, j) != 0.0 && wwi.get(i, j) != 0.0) {
                    resultGraph.addUndirectedEdge(variables.get(i), variables.get(j));
                }
            }
        }
        return resultGraph;
    } else {
        Glasso algorithm = new Glasso();
        DataSet data = (DataSet) ds;
        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();
    }
}

Example 52 with GeneralBootstrapTest

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

the class R3 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 R3 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.R3);
        return lofs.orient();
    } else {
        R3 r3 = new R3(algorithm);
        if (initialGraph != null) {
            r3.setInitialGraph(initialGraph);
        }
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, r3, 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 53 with GeneralBootstrapTest

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

the class CcdMaxConcatenated 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);
        IndependenceTest test = this.test.getTest(dataSet, parameters);
        edu.cmu.tetrad.search.CcdMax search = new edu.cmu.tetrad.search.CcdMax(test);
        search.setDoColliderOrientations(parameters.getBoolean("doColliderOrientation"));
        search.setUseHeuristic(parameters.getBoolean("useMaxPOrientationHeuristic"));
        search.setMaxPathLength(parameters.getInt("maxPOrientationMaxPathLength"));
        search.setKnowledge(knowledge);
        search.setDepth(parameters.getInt("depth"));
        search.setApplyOrientAwayFromCollider(parameters.getBoolean("applyR1"));
        search.setUseOrientTowardDConnections(parameters.getBoolean("orientTowardDConnections"));
        return search.search();
    } else {
        CcdMaxConcatenated algorithm = new CcdMaxConcatenated(test);
        // 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 54 with GeneralBootstrapTest

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

the class MixedFgesTreatingDiscreteAsContinuous method search.

public Graph search(DataModel Dk, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        DataSet mixedDataSet = DataUtils.getMixedDataSet(Dk);
        mixedDataSet = DataUtils.convertNumericalDiscreteToContinuous(mixedDataSet);
        SemBicScore score = new SemBicScore(new CovarianceMatrixOnTheFly(mixedDataSet));
        score.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
        Fges fges = new Fges(score);
        Graph p = fges.search();
        return convertBack(mixedDataSet, p);
    } else {
        MixedFgesTreatingDiscreteAsContinuous algorithm = new MixedFgesTreatingDiscreteAsContinuous();
        DataSet data = (DataSet) Dk;
        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();
    }
}

Example 55 with GeneralBootstrapTest

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

the class FasLofs method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        edu.cmu.tetrad.search.FasLofs search = new edu.cmu.tetrad.search.FasLofs((DataSet) dataSet, rule);
        search.setDepth(parameters.getInt("depth"));
        search.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
        search.setKnowledge(knowledge);
        return getGraph(search);
    } else {
        FasLofs fasLofs = new FasLofs(rule);
        // fasLofs.setKnowledge(knowledge);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, fasLofs, 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();
    }
}