Merge pull request #1799 from cmu-phil/vbc-2024-07-16

Include specify file for test check nodewise markov

testTrueGraphForCheckNodewiseMarkov.txt

@@ -0,0 +1,49 @@
+Graph Nodes:
+X1;X2;X3;X4;X5;X6;X7;X8;X9;X10
+
+Graph Edges:
+1. X1 --> X2
+2. X1 --> X3
+3. X1 --> X5
+4. X1 --> X6
+5. X1 --> X7
+6. X1 --> X8
+7. X1 --> X9
+8. X1 --> X10
+9. X2 --> X3
+10. X2 --> X4
+11. X2 --> X5
+12. X2 --> X8
+13. X2 --> X9
+14. X2 --> X10
+15. X3 --> X4
+16. X3 --> X5
+17. X3 --> X6
+18. X3 --> X7
+19. X3 --> X8
+20. X3 --> X9
+21. X3 --> X10
+22. X4 --> X5
+23. X4 --> X6
+24. X4 --> X9
+25. X4 --> X10
+26. X5 --> X6
+27. X5 --> X7
+28. X5 --> X8
+29. X5 --> X9
+30. X5 --> X10
+31. X6 --> X7
+32. X6 --> X8
+33. X6 --> X9
+34. X6 --> X10
+35. X7 --> X8
+36. X7 --> X9
+37. X7 --> X10
+38. X8 --> X9
+39. X8 --> X10
+40. X9 --> X10
+
+
+Test True Graph size: 10
+Test Estimated CPDAG Graph: Graph Nodes:
+X1;X2;X3;X4;X5;X6;X7;X8;X9;X10

tetrad-lib/src/test/java/edu/cmu/tetrad/test/TestCheckNodewiseMarkov.java

@@ -12,14 +12,56 @@
 import edu.cmu.tetrad.util.Params;
 import org.junit.Test;
 
+import java.io.File;
 import java.util.List;
 
 
 
 public class TestCheckNodewiseMarkov {
 
     public static void main(String... args) {
-        testGaussianDAGPrecisionRecallForLocalOnMarkovBlanket(10, 40, 40, 0.5, 1.0, 0.8);
+//        testGaussianDAGPrecisionRecallForLocalOnMarkovBlanket(10, 40, 40, 0.5, 1.0, 0.8);
+        String filePath = "testTrueGraphForCheckNodewiseMarkov.txt";
+        File file = new File(filePath);
+        if (file.exists()) {
+            System.out.println("Loading true graph file: " + filePath);
+            testGaussianDAGPrecisionRecallForLocalOnMarkovBlanket(file, 0.5, 1.0, 0.8);
+        } else {
+            System.out.println("File does not exist at the specified path.");
+        }
+    }
+
+    public static void testGaussianDAGPrecisionRecallForLocalOnMarkovBlanket(File txtFile, double threshold, double shuffleThreshold, double lowRecallBound) {
+        Graph trueGraph = GraphSaveLoadUtils.loadGraphTxt(txtFile);
+        System.out.println("Test True Graph: " + trueGraph);
+        System.out.println("Test True Graph size: " + trueGraph.getNodes().size());
+
+        SemPm pm = new SemPm(trueGraph);
+        // Parameters without additional setting default tobe Gaussian
+        SemIm im = new SemIm(pm, new Parameters());
+        DataSet data = im.simulateData(10000, false);
+        SemBicScore score = new SemBicScore(data, false);
+        score.setPenaltyDiscount(2);
+        Graph estimatedCpdag = new PermutationSearch(new Boss(score)).search();
+//        TODO VBC: Next check different search algo to generate estimated graph. e.g. PC
+        System.out.println("Test Estimated CPDAG Graph: " + estimatedCpdag);
+        System.out.println("~~~~~~~~~~~~~~~~~~~~~~~~~~~~");
+        testGaussianDAGPrecisionRecallForLocalOnMarkovBlanketUsingAdjAHConfusionMatrix(data, trueGraph, estimatedCpdag, threshold, shuffleThreshold, lowRecallBound);
+        testGaussianDAGPrecisionRecallForLocalOnMarkovBlanketUsingLGConfusionMatrix(data, trueGraph, estimatedCpdag, threshold, shuffleThreshold, lowRecallBound);
+        System.out.println("~~~~~~~~~~~~~Full Graph~~~~~~~~~~~~~~~");
+        estimatedCpdag = GraphUtils.replaceNodes(estimatedCpdag, trueGraph.getNodes());
+        double whole_ap = new AdjacencyPrecision().getValue(trueGraph, estimatedCpdag, null);
+        double whole_ar = new AdjacencyRecall().getValue(trueGraph, estimatedCpdag, null);
+        double whole_ahp = new ArrowheadPrecision().getValue(trueGraph, estimatedCpdag, null);
+        double whole_ahr = new ArrowheadRecall().getValue(trueGraph, estimatedCpdag, null);
+        double whole_lgp = new LocalGraphPrecision().getValue(trueGraph, estimatedCpdag, null);
+        double whole_lgr = new LocalGraphRecall().getValue(trueGraph, estimatedCpdag, null);
+        System.out.println("whole_ap: " + whole_ap);
+        System.out.println("whole_ar: " + whole_ar );
+        System.out.println("whole_ahp: " + whole_ahp);
+        System.out.println("whole_ahr: " + whole_ahr);
+        System.out.println("whole_lgp: " + whole_lgp);
+        System.out.println("whole_lgr: " + whole_lgr);
     }
 
     public static void testGaussianDAGPrecisionRecallForLocalOnMarkovBlanket(int numNodes, int maxNumEdges, int maxDegree, double threshold, double shuffleThreshold, double lowRecallBound) {