Examples with Fges edu.cmu.tetrad.search.Fges used on opensource projects

Example 11 with Fges

use of edu.cmu.tetrad.search.Fges 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 12 with Fges

use of edu.cmu.tetrad.search.Fges in project tetrad by cmu-phil.

the class TestFges method checkSearch.

/**
 * Presents the input graph to FCI and checks to make sure the output of FCI is equivalent to the given output
 * graph.
 */
private void checkSearch(String inputGraph, String outputGraph) {
    // Set up graph and node objects.
    Graph graph = GraphConverter.convert(inputGraph);
    // Set up search.
    Fges fges = new Fges(new GraphScore(graph));
    // Run search
    Graph resultGraph = fges.search();
    // Build comparison graph.
    Graph trueGraph = GraphConverter.convert(outputGraph);
    // PrintUtil out problem and graphs.
    // System.out.println("\nInput graph:");
    // System.out.println(graph);
    // System.out.println("\nResult graph:");
    // System.out.println(resultGraph);
    // System.out.println("\nTrue graph:");
    // System.out.println(trueGraph);
    resultGraph = GraphUtils.replaceNodes(resultGraph, trueGraph.getNodes());
    // Do test.
    assertTrue(resultGraph.equals(trueGraph));
}

Example 13 with Fges

use of edu.cmu.tetrad.search.Fges in project tetrad by cmu-phil.

the class TestFges method clarkTest.

@Test
public void clarkTest() {
    RandomGraph randomGraph = new RandomForward();
    Simulation simulation = new LinearFisherModel(randomGraph);
    Parameters parameters = new Parameters();
    parameters.set("numMeasures", 100);
    parameters.set("numLatents", 0);
    parameters.set("coefLow", 0.2);
    parameters.set("coefHigh", 0.8);
    parameters.set("avgDegree", 2);
    parameters.set("maxDegree", 100);
    parameters.set("maxIndegree", 100);
    parameters.set("maxOutdegree", 100);
    parameters.set("connected", false);
    parameters.set("numRuns", 1);
    parameters.set("differentGraphs", false);
    parameters.set("sampleSize", 1000);
    parameters.set("faithfulnessAssumed", false);
    parameters.set("maxDegree", -1);
    parameters.set("verbose", false);
    parameters.set("alpha", 0.01);
    simulation.createData(parameters);
    DataSet dataSet = (DataSet) simulation.getDataModel(0);
    Graph trueGraph = simulation.getTrueGraph(0);
    // trueGraph = SearchGraphUtils.patternForDag(trueGraph);
    ScoreWrapper score = new edu.cmu.tetrad.algcomparison.score.SemBicScore();
    IndependenceWrapper test = new FisherZ();
    Algorithm fges = new edu.cmu.tetrad.algcomparison.algorithm.oracle.pattern.Fges(score, false);
    Graph fgesGraph = fges.search(dataSet, parameters);
    clarkTestForAlpha(0.05, parameters, dataSet, trueGraph, fgesGraph, test);
    clarkTestForAlpha(0.01, parameters, dataSet, trueGraph, fgesGraph, test);
}

Example 14 with Fges

use of edu.cmu.tetrad.search.Fges in project tetrad by cmu-phil.

the class TestFges method searchMGMFges.

public Graph searchMGMFges(DataSet ds, double penalty) {
    MGM m = new MGM(ds, new double[] { 0.1, 0.1, 0.1 });
    // m.setVerbose(this.verbose);
    Graph gm = m.search();
    DataSet dataSet = MixedUtils.makeContinuousData(ds);
    SemBicScore score = new SemBicScore(new CovarianceMatrixOnTheFly(dataSet));
    score.setPenaltyDiscount(penalty);
    Fges fg = new Fges(score);
    fg.setBoundGraph(gm);
    fg.setVerbose(false);
    return fg.search();
}

Example 15 with Fges

use of edu.cmu.tetrad.search.Fges in project tetrad by cmu-phil.

the class TestFges method testFromGraph.

@Test
public void testFromGraph() {
    int numNodes = 20;
    int numIterations = 20;
    for (int i = 0; i < numIterations; i++) {
        // System.out.println("Iteration " + (i + 1));
        Graph dag = GraphUtils.randomDag(numNodes, 0, numNodes, 10, 10, 10, false);
        Fges fges = new Fges(new GraphScore(dag));
        fges.setFaithfulnessAssumed(true);
        Graph pattern1 = fges.search();
        Graph pattern2 = new Pc(new IndTestDSep(dag)).search();
        // System.out.println(pattern2);
        assertEquals(pattern2, pattern1);
    }
}