Examples with DataSet edu.cmu.tetrad.data.DataSet used on opensource projects

Example 36 with DataSet

use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.

the class TsFci method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        edu.cmu.tetrad.search.TsFci search = new edu.cmu.tetrad.search.TsFci(test.getTest(dataSet, parameters));
        search.setDepth(parameters.getInt("depth"));
        search.setKnowledge(dataSet.getKnowledge());
        return search.search();
    } else {
        TsFci tsFci = new TsFci(test, algorithm);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, tsFci, 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 37 with DataSet

use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.

the class CpcStable method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        Graph init = null;
        if (algorithm != null) {
        // init = algorithm.search(dataSet, parameters);
        }
        edu.cmu.tetrad.search.PcAll search = new edu.cmu.tetrad.search.PcAll(test.getTest(dataSet, parameters), init);
        search.setDepth(parameters.getInt("depth"));
        search.setKnowledge(knowledge);
        search.setFasRule(PcAll.FasRule.FAS_STABLE);
        search.setColliderDiscovery(edu.cmu.tetrad.search.PcAll.ColliderDiscovery.CONSERVATIVE);
        search.setConflictRule(edu.cmu.tetrad.search.PcAll.ConflictRule.PRIORITY);
        search.setVerbose(parameters.getBoolean("verbose"));
        return search.search();
    } else {
        CpcStable cpcStable = new CpcStable(test, algorithm);
        // cpcStable.setKnowledge(knowledge);
        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();
    }
}

Example 38 with DataSet

use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.

the class Fges 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.Fges search = new edu.cmu.tetrad.search.Fges(score.getScore(dataSet, parameters));
        search.setFaithfulnessAssumed(parameters.getBoolean("faithfulnessAssumed"));
        search.setKnowledge(knowledge);
        search.setVerbose(parameters.getBoolean("verbose"));
        search.setMaxDegree(parameters.getInt("maxDegree"));
        search.setSymmetricFirstStep(parameters.getBoolean("symmetricFirstStep"));
        Object obj = parameters.get("printStream");
        if (obj instanceof PrintStream) {
            search.setOut((PrintStream) obj);
        }
        if (initialGraph != null) {
            search.setInitialGraph(initialGraph);
        }
        return search.search();
    } else {
        Fges fges = new Fges(score, algorithm);
        // fges.setKnowledge(knowledge);
        DataSet data = (DataSet) dataSet;
        GeneralBootstrapTest search = new GeneralBootstrapTest(data, fges, 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 39 with DataSet

use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.

the class Lingam method search.

public Graph search(DataModel dataSet, Parameters parameters) {
    if (parameters.getInt("bootstrapSampleSize") < 1) {
        edu.cmu.tetrad.search.Lingam lingam = new edu.cmu.tetrad.search.Lingam();
        lingam.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
        return lingam.search(DataUtils.getContinuousDataSet(dataSet));
    } else {
        Lingam algorithm = new Lingam();
        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();
    }
}

Example 40 with DataSet

use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.

the class StabilitySelection method search.

@Override
public Graph search(DataModel dataSet, Parameters parameters) {
    DataSet _dataSet = (DataSet) dataSet;
    double percentageB = parameters.getDouble("percentSubsampleSize");
    int numSubsamples = parameters.getInt("numSubsamples");
    Map<Edge, Integer> counts = new HashMap<>();
    List<Graph> graphs = new ArrayList<>();
    final ForkJoinPool pool = ForkJoinPoolInstance.getInstance().getPool();
    class StabilityAction extends RecursiveAction {

        private int chunk;

        private int from;

        private int to;

        private StabilityAction(int chunk, int from, int to) {
            this.chunk = chunk;
            this.from = from;
            this.to = to;
        }

        @Override
        protected void compute() {
            if (to - from <= chunk) {
                for (int s = from; s < to; s++) {
                    BootstrapSampler sampler = new BootstrapSampler();
                    sampler.setWithoutReplacements(true);
                    DataSet sample = sampler.sample(_dataSet, (int) (percentageB * _dataSet.getNumRows()));
                    Graph graph = algorithm.search(sample, parameters);
                    graphs.add(graph);
                }
            } else {
                final int mid = (to + from) / 2;
                StabilityAction left = new StabilityAction(chunk, from, mid);
                StabilityAction right = new StabilityAction(chunk, mid, to);
                left.fork();
                right.compute();
                left.join();
            }
        }
    }
    final int chunk = 2;
    pool.invoke(new StabilityAction(chunk, 0, numSubsamples));
    // }
    for (Graph graph : graphs) {
        for (Edge edge : graph.getEdges()) {
            increment(edge, counts);
        }
    }
    initialGraph = new EdgeListGraph(dataSet.getVariables());
    double percentStability = parameters.getDouble("percentStability");
    for (Edge edge : counts.keySet()) {
        if (counts.get(edge) > percentStability * numSubsamples) {
            initialGraph.addEdge(edge);
        }
    }
    return initialGraph;
}