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///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard //
// Scheines, Joseph Ramsey, and Clark Glymour. //
// //
// This program is free software; you can redistribute it and/or modify //
// it under the terms of the GNU General Public License as published by //
// the Free Software Foundation; either version 2 of the License, or //
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// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
// GNU General Public License for more details. //
// //
// You should have received a copy of the GNU General Public License //
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///////////////////////////////////////////////////////////////////////////////
package edu.cmu.tetradapp.model;
import edu.cmu.tetrad.data.Knowledge;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.IndependenceTest;
import edu.cmu.tetrad.search.test.MsepTest;
import edu.cmu.tetrad.search.utils.GraphSearchUtils;
import edu.cmu.tetrad.search.utils.MeekRules;
import edu.cmu.tetrad.search.work_in_progress.VcPcFast;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.Params;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import edu.cmu.tetradapp.util.IndTestType;
import java.io.Serial;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
/**
* Extends AbstractAlgorithmRunner to produce a wrapper for the PC algorithm.
*
* @author josephramsey
* @version $Id: $Id
*/
public class VcpcFastRunner extends AbstractAlgorithmRunner
implements IndTestProducer {
@Serial
private static final long serialVersionUID = 23L;
/**
* The graph to be searched.
*/
private Graph dag;
/**
* The independence facts model.
*/
private IndependenceFactsModel independenceFactsModel;
/**
* The true graph, if any.
*/
private Graph trueGraph;
/**
* The adjacent triples.
*/
private Set fvcpcAdjacent;
/**
* The apparent nonadjacent triples.
*/
private Set fvcpcApparent;
/**
* The definite nonadjacent triples.
*/
private Set fvcpcDefinite;
//============================CONSTRUCTORS============================//
/**
* Constructs a wrapper for the given DataWrapper. The DataWrapper must contain a DataSet that is either a DataSet
* or a DataSet or a DataList containing either a DataSet or a DataSet as its selected model.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(DataWrapper dataWrapper, Parameters params) {
super(dataWrapper, params, null);
}
/**
* Constructor for VcpcFastRunner.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public VcpcFastRunner(DataWrapper dataWrapper, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(dataWrapper, params, knowledgeBoxModel);
}
/**
* Constructor for VcpcFastRunner.
*
* @param indModel a {@link edu.cmu.tetradapp.model.IndependenceFactsModel} object
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(IndependenceFactsModel indModel, GraphWrapper graphWrapper, Parameters params) {
super(graphWrapper.getGraph(), params);
this.dag = graphWrapper.getGraph();
this.independenceFactsModel = indModel;
}
/**
* /** Constucts a wrapper for the given EdgeListGraph.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(Graph graph, Parameters params) {
super(graph, params);
}
/**
* Constucts a wrapper for the given EdgeListGraph.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public VcpcFastRunner(Graph graph, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(graph, params, knowledgeBoxModel);
}
/**
* Constucts a wrapper for the given EdgeListGraph.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(GraphWrapper graphWrapper, Parameters params) {
super(graphWrapper.getGraph(), params);
}
/**
* Constucts a wrapper for the given EdgeListGraph.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public VcpcFastRunner(GraphWrapper graphWrapper, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(graphWrapper.getGraph(), params, knowledgeBoxModel);
}
/**
* Constucts a wrapper for the given EdgeListGraph.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public VcpcFastRunner(GraphSource graphWrapper, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(graphWrapper.getGraph(), params, knowledgeBoxModel);
}
/**
* Constructor for VcpcFastRunner.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param model a {@link edu.cmu.tetradapp.model.IndependenceFactsModel} object
*/
public VcpcFastRunner(GraphSource graphWrapper, Parameters params, IndependenceFactsModel model) {
super(graphWrapper.getGraph(), params);
this.independenceFactsModel = model;
}
/**
* Constucts a wrapper for the given EdgeListGraph.
*
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphSource} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(GraphSource graphWrapper, Parameters params) {
super(graphWrapper.getGraph(), params);
}
/**
* Constructor for VcpcFastRunner.
*
* @param dagWrapper a {@link edu.cmu.tetradapp.model.DagWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(DagWrapper dagWrapper, Parameters params) {
super(dagWrapper.getDag(), params);
}
/**
* Constructor for VcpcFastRunner.
*
* @param dagWrapper a {@link edu.cmu.tetradapp.model.DagWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public VcpcFastRunner(DagWrapper dagWrapper, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(dagWrapper.getDag(), params, knowledgeBoxModel);
}
/**
* Constructor for VcpcFastRunner.
*
* @param dagWrapper a {@link edu.cmu.tetradapp.model.SemGraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(SemGraphWrapper dagWrapper, Parameters params) {
super(dagWrapper.getGraph(), params);
}
/**
* Constructor for VcpcFastRunner.
*
* @param dagWrapper a {@link edu.cmu.tetradapp.model.SemGraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public VcpcFastRunner(SemGraphWrapper dagWrapper, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(dagWrapper.getGraph(), params, knowledgeBoxModel);
}
/**
* Constructor for VcpcFastRunner.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(DataWrapper dataWrapper, GraphWrapper graphWrapper, Parameters params) {
super(dataWrapper, params, null);
this.trueGraph = graphWrapper.getGraph();
}
/**
* Constructor for VcpcFastRunner.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param graphWrapper a {@link edu.cmu.tetradapp.model.GraphWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public VcpcFastRunner(DataWrapper dataWrapper, GraphWrapper graphWrapper, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(dataWrapper, params, knowledgeBoxModel);
this.trueGraph = graphWrapper.getGraph();
}
/**
* Constructor for VcpcFastRunner.
*
* @param model a {@link edu.cmu.tetradapp.model.IndependenceFactsModel} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public VcpcFastRunner(IndependenceFactsModel model, Parameters params) {
super(model, params, null);
}
/**
* Constructor for VcpcFastRunner.
*
* @param model a {@link edu.cmu.tetradapp.model.IndependenceFactsModel} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
* @param knowledgeBoxModel a {@link edu.cmu.tetradapp.model.KnowledgeBoxModel} object
*/
public VcpcFastRunner(IndependenceFactsModel model, Parameters params, KnowledgeBoxModel knowledgeBoxModel) {
super(model, params, knowledgeBoxModel);
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.VcpcFastRunner} object
* @see TetradSerializableUtils
*/
public static VcpcFastRunner serializableInstance() {
return new VcpcFastRunner(Dag.serializableInstance(), new Parameters());
}
//===================PUBLIC METHODS OVERRIDING ABSTRACT================//
/**
* execute.
*/
public void execute() {
Knowledge knowledge = (Knowledge) getParams().get("knowledge", new Knowledge());
VcPcFast fvcpc = new VcPcFast(getIndependenceTest());
fvcpc.setKnowledge(knowledge);
fvcpc.setMeekPreventCycles(this.isMeekPreventCycles());
fvcpc.setDepth(getParams().getInt("depth", -1));
if (this.independenceFactsModel != null) {
fvcpc.setFacts(this.independenceFactsModel.getFacts());
}
Graph graph = null;
try {
graph = fvcpc.search();
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
if (getSourceGraph() != null) {
LayoutUtil.arrangeBySourceGraph(graph, getSourceGraph());
} else if (knowledge.isDefaultToKnowledgeLayout()) {
GraphSearchUtils.arrangeByKnowledgeTiers(graph, knowledge);
} else {
LayoutUtil.defaultLayout(graph);
}
setResultGraph(graph);
setVcpcFastFields(fvcpc);
}
/**
* getIndependenceTest.
*
* @return a {@link edu.cmu.tetrad.search.IndependenceTest} object
*/
public IndependenceTest getIndependenceTest() {
if (this.dag != null) {
return new MsepTest(getGraph());
}
Object dataModel = getDataModel();
if (dataModel == null) {
dataModel = getSourceGraph();
}
IndTestType testType = (IndTestType) (getParams()).get("indTestType", IndTestType.FISHER_Z);
return new IndTestChooser().getTest(dataModel, getParams(), testType);
}
/**
* getGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getGraph() {
return getResultGraph();
}
/**
* Getter for the field independenceFactsModel.
*
* @return a {@link edu.cmu.tetradapp.model.IndependenceFactsModel} object
*/
public IndependenceFactsModel getIndependenceFactsModel() {
return this.independenceFactsModel;
}
/**
* getTriplesClassificationTypes.
*
* @return the names of the triple classifications. Coordinates with
*/
public List getTriplesClassificationTypes() {
List names = new ArrayList<>();
names.add("Ambiguous Triples");
return names;
}
/**
* {@inheritDoc}
*/
public List> getTriplesLists(Node node) {
List> triplesList = new ArrayList<>();
Graph graph = getGraph();
triplesList.add(GraphUtils.getAmbiguousTriplesFromGraph(node, graph));
return triplesList;
}
/**
* getAdj.
*
* @return a {@link java.util.Set} object
*/
public Set getAdj() {
return new HashSet<>(this.fvcpcAdjacent);
}
/**
* getAppNon.
*
* @return a {@link java.util.Set} object
*/
public Set getAppNon() {
return new HashSet<>(this.fvcpcApparent);
}
/**
* getDefNon.
*
* @return a {@link java.util.Set} object
*/
public Set getDefNon() {
return new HashSet<>(this.fvcpcDefinite);
}
/**
* supportsKnowledge.
*
* @return a boolean
*/
public boolean supportsKnowledge() {
return true;
}
/**
* getMeekRules.
*
* @return a {@link edu.cmu.tetrad.search.utils.MeekRules} object
*/
public MeekRules getMeekRules() {
MeekRules meekRules = new MeekRules();
meekRules.setMeekPreventCycles(this.isMeekPreventCycles());
meekRules.setKnowledge((Knowledge) getParams().get("knowledge", new Knowledge()));
meekRules.setVerbose(false);
return meekRules;
}
/**
* {@inheritDoc}
*/
@Override
public String getAlgorithmName() {
return "VCPC-Fast";
}
//========================== Private Methods ===============================//
private boolean isMeekPreventCycles() {
Parameters params = getParams();
return params instanceof Parameters && params.getBoolean(Params.GUARANTEE_CPDAG, false);
}
private void setVcpcFastFields(VcPcFast fvcpc) {
this.fvcpcAdjacent = fvcpc.getAdjacencies();
this.fvcpcApparent = fvcpc.getApparentNonadjacencies();
this.fvcpcDefinite = fvcpc.getDefiniteNonadjacencies();
List fvcpcNodes = getGraph().getNodes();
}
}
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