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edu.cmu.tetrad.algcomparison.CompareTwoGraphs Maven / Gradle / Ivy
package edu.cmu.tetrad.algcomparison;
import edu.cmu.tetrad.algcomparison.statistic.*;
import edu.cmu.tetrad.data.DataModel;
import edu.cmu.tetrad.graph.*;
import edu.cmu.tetrad.search.utils.GraphSearchUtils;
import edu.cmu.tetrad.util.TextTable;
import org.jetbrains.annotations.NotNull;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.List;
import static java.util.Collections.sort;
/**
* Gives the comparison of a target graph to a reference graph that is implemented in the interface. Three methods are
* given, one to return the edgewise comparison, one to return the stats list comparison, and one to return the
* misclassification comparison. Each returns a String, which can be printed.
*
* @author josephramsey
*/
public class CompareTwoGraphs {
/**
* Returns an edgewise comparison of two graphs. This says, edge by edge, what the differences and similarities are
* between the two graphs.
*
* @param trueGraph The true graph.
* @param targetGraph The target graph.
* @return The comparison string.
*/
@NotNull
public static String getEdgewiseComparisonString(Graph trueGraph, Graph targetGraph) {
boolean printStars = false;
StringBuilder builder = new StringBuilder();
GraphUtils.GraphComparison comparison = GraphSearchUtils.getGraphComparison(trueGraph, targetGraph);
List edgesAdded = comparison.getEdgesAdded();
List edgesAdded2 = new ArrayList<>();
for (Edge e1 : edgesAdded) {
Node n1 = e1.getNode1();
Node n2 = e1.getNode2();
boolean twoCycle1 = trueGraph.getDirectedEdge(n1, n2) != null && trueGraph.getDirectedEdge(n2, n1) != null;
boolean twoCycle2 = targetGraph.getDirectedEdge(n1, n2) != null && targetGraph.getDirectedEdge(n2, n1) != null;
if (!(twoCycle1 || twoCycle2)) {
edgesAdded2.add(e1);
}
}
sort(edgesAdded2);
builder.append("\nAdjacencies added (not involving 2-cycles and not reoriented):");
if (edgesAdded2.isEmpty()) {
builder.append("\n --NONE--");
} else {
for (int i = 0; i < edgesAdded2.size(); i++) {
Edge _edge = edgesAdded2.get(i);
builder.append("\n").append(i + 1).append(". ").append(_edge.toString());
}
}
builder.append("\n\nAdjacencies removed:");
List edgesRemoved = comparison.getEdgesRemoved();
sort(edgesRemoved);
if (edgesRemoved.isEmpty()) {
builder.append("\n --NONE--");
} else {
for (int i = 0; i < edgesRemoved.size(); i++) {
Edge edge = edgesRemoved.get(i);
Node node1 = trueGraph.getNode(edge.getNode1().getName());
Node node2 = trueGraph.getNode(edge.getNode2().getName());
builder.append("\n").append(i + 1).append(". ").append(edge);
if (printStars) {
boolean directedInGraph1 = false;
if (Edges.isDirectedEdge(edge) && trueGraph.paths().existsSemiDirectedPath(node1, node2)) {
directedInGraph1 = true;
} else if ((Edges.isUndirectedEdge(edge) || Edges.isBidirectedEdge(edge))
&& (trueGraph.paths().existsSemiDirectedPath(node1, node2)
|| trueGraph.paths().existsSemiDirectedPath(node2, node1))) {
directedInGraph1 = true;
}
if (directedInGraph1) {
builder.append(" *");
}
}
}
}
List edges1 = new ArrayList<>(trueGraph.getEdges());
List twoCycles = new ArrayList<>();
List allSingleEdges = new ArrayList<>();
for (Edge edge : edges1) {
if (edge.isDirected() && targetGraph.containsEdge(edge) && targetGraph.containsEdge(edge.reverse())) {
twoCycles.add(edge);
} else if (trueGraph.containsEdge(edge)) {
allSingleEdges.add(edge);
}
}
builder.append("\n\n"
+ "Two-cycles in true correctly adjacent in estimated");
sort(allSingleEdges);
if (twoCycles.isEmpty()) {
builder.append("\n --NONE--");
} else {
for (int i = 0; i < twoCycles.size(); i++) {
Edge adj = edges1.get(i);
builder.append("\n").append(i + 1).append(". ").append(adj).append(" ").append(adj.reverse())
.append(" ====> ").append(trueGraph.getEdge(twoCycles.get(i).getNode1(), twoCycles.get(i).getNode2()));
}
}
List incorrect = new ArrayList<>();
for (Edge adj : allSingleEdges) {
Edge edge1 = trueGraph.getEdge(adj.getNode1(), adj.getNode2());
Edge edge2 = targetGraph.getEdge(adj.getNode1(), adj.getNode2());
if (!edge1.equals(edge2)) {
incorrect.add(adj);
}
}
{
builder.append("\n\n" + "Edges incorrectly oriented");
if (incorrect.isEmpty()) {
builder.append("\n --NONE--");
} else {
int j1 = 0;
sort(incorrect);
for (Edge adj : incorrect) {
Edge edge1 = trueGraph.getEdge(adj.getNode1(), adj.getNode2());
Edge edge2 = targetGraph.getEdge(adj.getNode1(), adj.getNode2());
if (edge1 == null || edge2 == null) continue;
builder.append("\n").append(++j1).append(". ").append(edge1).append(" ====> ").append(edge2);
}
}
}
{
builder.append("\n\n" + "Edges correctly oriented");
List correct = new ArrayList<>();
for (Edge adj : allSingleEdges) {
Edge edge1 = trueGraph.getEdge(adj.getNode1(), adj.getNode2());
Edge edge2 = targetGraph.getEdge(adj.getNode1(), adj.getNode2());
if (edge1.equals(edge2)) {
correct.add(edge1);
}
}
if (correct.isEmpty()) {
builder.append("\n --NONE--");
} else {
sort(correct);
int j2 = 0;
for (Edge edge : correct) {
builder.append("\n").append(++j2).append(". ").append(edge);
}
}
}
return builder.toString();
}
/**
* Returns a string representing a table of statistics that can be printed.
*
* @param trueGraph The true graph.
* @param targetGraph The target graph.
* @return The comparison string.
*/
public static String getStatsListTable(Graph trueGraph, Graph targetGraph) {
return getStatsListTable(trueGraph, targetGraph, null);
}
/**
* Returns a string representing a table of statistics that can be printed.
*
* @param trueGraph The true graph.
* @param targetGraph The target graph.
* @param dataModel The data model; some statistics (like BIC) may use this.
* @return The comparison string.
*/
public static String getStatsListTable(Graph trueGraph, Graph targetGraph, DataModel dataModel) {
Graph _targetGraph = GraphUtils.replaceNodes(targetGraph, trueGraph.getNodes());
List statistics = statistics();
TextTable table = new TextTable(statistics.size(), 3);
NumberFormat nf = new DecimalFormat("0.###");
List abbr = new ArrayList<>();
List desc = new ArrayList<>();
List values = new ArrayList<>();
for (Statistic statistic : statistics) {
try {
values.add(statistic.getValue(trueGraph, _targetGraph, dataModel));
abbr.add(statistic.getAbbreviation());
desc.add(statistic.getDescription());
} catch (Exception ignored) {
}
}
for (int i = 0; i < abbr.size(); i++) {
double value = values.get(i);
table.setToken(i, 1, Double.isNaN(value) ? "-" : "" + nf.format(value));
table.setToken(i, 0, abbr.get(i));
table.setToken(i, 2, desc.get(i));
}
table.setJustification(TextTable.LEFT_JUSTIFIED);
return table.toString();
}
private static List statistics() {
List statistics = new ArrayList<>();
// Others
statistics.add(new AdjacencyPrecision());
statistics.add(new AdjacencyRecall());
statistics.add(new ArrowheadPrecision());
statistics.add(new ArrowheadRecall());
statistics.add(new ArrowheadPrecisionCommonEdges());
statistics.add(new ArrowheadRecallCommonEdges());
statistics.add(new AdjacencyTn());
statistics.add(new AdjacencyTp());
statistics.add(new AdjacencyTpr());
statistics.add(new AdjacencyFpr());
statistics.add(new AdjacencyFn());
statistics.add(new AdjacencyFp());
statistics.add(new AdjacencyFn());
statistics.add(new ArrowheadTn());
statistics.add(new ArrowheadTp());
statistics.add(new F1Adj());
statistics.add(new F1All());
statistics.add(new F1Arrow());
statistics.add(new MathewsCorrAdj());
statistics.add(new MathewsCorrArrow());
statistics.add(new NumberOfEdgesEst());
statistics.add(new NumberOfEdgesTrue());
statistics.add(new NumCorrectVisibleAncestors());
statistics.add(new PercentBidirectedEdges());
statistics.add(new TailPrecision());
statistics.add(new TailRecall());
statistics.add(new TwoCyclePrecision());
statistics.add(new TwoCycleRecall());
statistics.add(new TwoCycleFalsePositive());
statistics.add(new TwoCycleFalseNegative());
statistics.add(new TwoCycleTruePositive());
statistics.add(new AverageDegreeEst());
statistics.add(new AverageDegreeTrue());
statistics.add(new DensityEst());
statistics.add(new DensityTrue());
statistics.add(new StructuralHammingDistance());
// Joe table.
statistics.add(new NumDirectedEdges());
statistics.add(new NumUndirectedEdges());
statistics.add(new NumPartiallyOrientedEdges());
statistics.add(new NumNondirectedEdges());
statistics.add(new NumBidirectedEdgesEst());
statistics.add(new TrueDagPrecisionTails());
statistics.add(new TrueDagPrecisionArrow());
statistics.add(new BidirectedLatentPrecision());
// Greg table
// statistics.add(new AncestorPrecision());
// statistics.add(new AncestorRecall());
// statistics.add(new AncestorF1());
// statistics.add(new SemidirectedPrecision());
// statistics.add(new SemidirectedRecall());
// statistics.add(new SemidirectedPathF1());
// statistics.add(new NoSemidirectedPrecision());
// statistics.add(new NoSemidirectedRecall());
// statistics.add(new NoSemidirectedF1());
return statistics;
}
/**
* Returns a misclassification comparison of two graphs. This includes both an edge misclassiifcation matrix as well
* as an endpoint misclassification matrix.
*
* @param trueGraph The true graph.
* @param targetGraph The target graph.
* @return The comparison string.
*/
@NotNull
public static String getMisclassificationTable(Graph trueGraph, Graph targetGraph) {
return "Edge Misclassification Table:" +
"\n" +
MisclassificationUtils.edgeMisclassifications(targetGraph, trueGraph) +
"\n\n" +
"Endpoint Misclassification Table:" +
"\n\n" +
MisclassificationUtils.endpointMisclassification(targetGraph, trueGraph);
}
}
