/
IcaLingam.java
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/
IcaLingam.java
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package edu.cmu.tetrad.algcomparison.algorithm.continuous.dag;
import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
import edu.cmu.tetrad.algcomparison.algorithm.ReturnsBootstrapGraphs;
import edu.cmu.tetrad.annotation.AlgType;
import edu.cmu.tetrad.annotation.Bootstrapping;
import edu.cmu.tetrad.data.DataModel;
import edu.cmu.tetrad.data.DataSet;
import edu.cmu.tetrad.data.DataType;
import edu.cmu.tetrad.data.SimpleDataLoader;
import edu.cmu.tetrad.graph.EdgeListGraph;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.search.IcaLingD;
import edu.cmu.tetrad.search.utils.LogUtilsSearch;
import edu.cmu.tetrad.util.Matrix;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.Params;
import edu.cmu.tetrad.util.TetradLogger;
import edu.pitt.dbmi.algo.resampling.GeneralResamplingTest;
import java.util.ArrayList;
import java.util.List;
/**
* LiNGAM.
*
* @author josephramsey
*/
@edu.cmu.tetrad.annotation.Algorithm(
name = "ICA-LiNGAM",
command = "ica-lingam",
algoType = AlgType.forbid_latent_common_causes,
dataType = DataType.Continuous
)
@Bootstrapping
public class IcaLingam implements Algorithm, ReturnsBootstrapGraphs {
private static final long serialVersionUID = 23L;
private List<Graph> bootstrapGraphs = new ArrayList<>();
public Graph search(DataModel dataSet, Parameters parameters) {
if (parameters.getInt(Params.NUMBER_RESAMPLING) < 1) {
DataSet data = SimpleDataLoader.getContinuousDataSet(dataSet);
int maxIter = parameters.getInt(Params.FAST_ICA_MAX_ITER);
double alpha = parameters.getDouble(Params.FAST_ICA_A);
double tol = parameters.getDouble(Params.FAST_ICA_TOLERANCE);
Matrix W = IcaLingD.estimateW(data, maxIter, tol, alpha);
edu.cmu.tetrad.search.IcaLingam icaLingam = new edu.cmu.tetrad.search.IcaLingam();
icaLingam.setBThreshold(parameters.getDouble(Params.THRESHOLD_B));
icaLingam.setAcyclicityGuaranteed(parameters.getBoolean(Params.GUARANTEE_ACYCLIC));
Matrix bHat = icaLingam.fitW(W);
Graph graph = IcaLingD.makeGraph(bHat, data.getVariables());
TetradLogger.getInstance().forceLogMessage(bHat.toString());
TetradLogger.getInstance().forceLogMessage(graph.toString());
LogUtilsSearch.stampWithBic(graph, dataSet);
return graph;
} else {
IcaLingam algorithm = new IcaLingam();
DataSet data = (DataSet) dataSet;
GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm,
parameters.getInt(Params.NUMBER_RESAMPLING), parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE),
parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT), parameters.getInt(Params.RESAMPLING_ENSEMBLE),
parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));
search.setParameters(parameters);
search.setVerbose(parameters.getBoolean(Params.VERBOSE));
if (parameters.getBoolean(Params.SAVE_BOOTSTRAP_GRAPHS)) this.bootstrapGraphs = search.getGraphs();
return search.search();
}
}
@Override
public Graph getComparisonGraph(Graph graph) {
return new EdgeListGraph(graph);
}
public String getDescription() {
return "ICA-LiNGAM (ICA Linear Non-Gaussian Acyclic Model";
}
@Override
public DataType getDataType() {
return DataType.Continuous;
}
@Override
public List<String> getParameters() {
List<String> parameters = new ArrayList<>();
parameters.add(Params.VERBOSE);
parameters.add(Params.FAST_ICA_MAX_ITER);
parameters.add(Params.FAST_ICA_A);
parameters.add(Params.FAST_ICA_TOLERANCE);
parameters.add(Params.THRESHOLD_B);
parameters.add(Params.GUARANTEE_ACYCLIC);
return parameters;
}
@Override
public List<Graph> getBootstrapGraphs() {
return this.bootstrapGraphs;
}
}