[Draft]: Calculate local markov blanket against true graph for parted nodes that passed AD Test

tetrad-lib/src/main/java/edu/cmu/tetrad/graph/GraphUtils.java

@@ -103,7 +103,7 @@ public static boolean isClique(Collection<Node> set, Graph graph) {
      * @param graph  a DAG, CPDAG, MAG, or PAG.
      * @return a {@link edu.cmu.tetrad.graph.Graph} object
      */
-    public static Graph markovBlanketSubgraph(Node target, Graph graph) {
+    public static Graph markovBlanketSubgraph(Node target, Graph graph) { // TODO VBC: @Joe is this the more general method you recommended?
         Set<Node> mb = markovBlanket(target, graph);
 
         Graph mbGraph = new EdgeListGraph();
@@ -2253,7 +2253,7 @@ public static Graph trimGraph(List<Node> targets, Graph graph, int trimmingStyle
                 graph = trimAdjacentToTarget(targets, graph);
                 break;
             case 3:
-                graph = trimMarkovBlanketGraph(targets, graph);
+                graph = trimMarkovBlanketGraph(targets, graph); // TODO VBC currently using this
                 break;
             case 4:
                 graph = trimSemidirected(targets, graph);
@@ -2298,7 +2298,7 @@ private static Graph trimAdjacentToTarget(List<Node> targets, Graph graph) {
      * @param graph   the original graph from which the Markov blanket graph is derived
      * @return the trimmed Markov blanket graph
      */
-    private static Graph trimMarkovBlanketGraph(List<Node> targets, Graph graph) {
+    private static Graph trimMarkovBlanketGraph(List<Node> targets, Graph graph) { // TODO vbc this is
         Graph mbDag = new EdgeListGraph(graph);
 
         M:

tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java

@@ -6,6 +6,7 @@
 import edu.cmu.tetrad.graph.GraphUtils;
 import edu.cmu.tetrad.graph.IndependenceFact;
 import edu.cmu.tetrad.graph.Node;
+import edu.cmu.tetrad.graph.Edge;
 import edu.cmu.tetrad.search.test.*;
 import edu.cmu.tetrad.util.SublistGenerator;
 import edu.cmu.tetrad.util.TetradLogger;
@@ -251,6 +252,62 @@ public Double checkAgainstAndersonDarlingTest(List<Double> pValues) {
         return generalAndersonDarlingTest.getP();
     }
 
+    public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodes(IndependenceTest independenceTest, Graph graph, Double threshold) {
+        // when calling, default reject null as <=0.05
+        List<List<Node>> accepts_rejects = new ArrayList<>();
+        List<Node> accepts = new ArrayList<>();
+        List<Node> rejects = new ArrayList<>();
+        List<Node> allNodes = graph.getNodes();
+        for (Node x : allNodes) {
+            List<IndependenceFact> localIndependenceFacts = getLocalIndependenceFacts(x);
+            List<Double> localPValues = getLocalPValues(independenceTest, localIndependenceFacts);
+            Double ADTest = checkAgainstAndersonDarlingTest(localPValues);
+            if (ADTest  <= threshold) {
+                rejects.add(x);
+            } else {
+                accepts.add(x);
+            }
+        }
+        accepts_rejects.add(accepts);
+        accepts_rejects.add(rejects);
+        return accepts_rejects;
+    }
+
+    public Double getPrecisionOrRecallOnMarkovBlanketGraph(Node x, Graph estimatedGraph, Graph trueGraph, boolean getPrecision) {
+        List<Node> singleNode = Arrays.asList(x);
+        // Lookup graph is the same structure as trueGraph's structure but node objects replaced by estimated graph nodes.
+        Graph lookupGraph = GraphUtils.replaceNodes(trueGraph, estimatedGraph.getNodes());
+
+        // TODO VBC use the recurssion method
+        Graph xMBLookupGraph = GraphUtils.trimGraph(singleNode, lookupGraph, 3);
+        Set<Edge> xMBLookupGraphEdges = xMBLookupGraph.getEdges();
+        System.out.println("@@@@@@@@@@@@@@@@");
+        System.out.println("True Graph:" + trueGraph);
+        System.out.println("LookupGraph:" + lookupGraph); // this print should be the same as the true graph
+
+        System.out.println("xMBLookupGraphEdges size: " + xMBLookupGraphEdges.size());
+        System.out.println("xMBLookupGraph Nodes size: " + xMBLookupGraph.getNodes().size());
+        System.out.println("xMBLookupGraph:" + xMBLookupGraph); // The MB trim of the lookup graph, so it should be a subset of the lookup graph print
+
+        // Get Markov Blanket Subgraph for this node x.
+        Graph xMBEstimatedGraph = GraphUtils.trimGraph(singleNode, estimatedGraph, 3);
+        Set<Edge> xMBEstimatedGraphEdges = xMBEstimatedGraph.getEdges();
+        System.out.println("xMBEstimatedGraphEdges size: " + xMBEstimatedGraphEdges.size());
+        System.out.println("xMBEstimatedGraph Nodes size: " + xMBEstimatedGraph.getNodes().size());
+        System.out.println("xMBEstimatedGraph:" + xMBEstimatedGraph); // This should be compared with the xMBLookupGraph
+        System.out.println("@@@@@@@@@@@@@@@@");
+
+        HashSet<Edge> truePositive = new HashSet<>(xMBEstimatedGraphEdges);
+        // TODO VBC: QUESTION FOr DISCUSSION
+        //  Here it would only be retained if the points and direction of an edge is exactly the same.
+        // Do we want to only check for points? If not, a lot wrong/no direction edges would be filtered out at this step.
+        truePositive.retainAll(xMBLookupGraphEdges);
+
+        double precision = (double) truePositive.size() / xMBLookupGraphEdges.size();
+        double recall = (double) truePositive.size() / xMBEstimatedGraphEdges.size();
+        return getPrecision ? precision : recall;
+    }
+
 
     /**
      * Returns the variables of the independence test.

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

@@ -14,8 +14,10 @@
 import edu.cmu.tetrad.sem.SemIm;
 import edu.cmu.tetrad.sem.SemPm;
 import edu.cmu.tetrad.util.NumberFormatUtil;
+import edu.cmu.tetrad.util.Parameters;
 import org.junit.Test;
 
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -110,4 +112,43 @@ public void test2() {
 
         System.out.println(markovCheck.getMarkovCheckRecordString());
     }
+
+    @Test
+    public void testPrecissionRecallForLocal() {
+        Graph trueGraph = RandomGraph.randomDag(10, 0, 10, 100, 100, 100, false);
+        System.out.println("Test True Graph: " + trueGraph);
+        System.out.println("Test True Graph size: " + trueGraph.getNodes().size());
+
+        SemPm pm = new SemPm(trueGraph);
+        SemIm im = new SemIm(pm, new Parameters());
+        DataSet data = im.simulateData(1000, false);
+        edu.cmu.tetrad.search.score.SemBicScore score = new SemBicScore(data, false);
+        score.setPenaltyDiscount(2);
+        Graph estimatedCpdag = new PermutationSearch(new Boss(score)).search(); // Estimated graph
+        System.out.println("Test Estimated CPDAG Graph: " + estimatedCpdag);
+        System.out.println("Test Estimated Graph size: " + estimatedCpdag.getNodes().size());
+        System.out.println("=====================================");
+
+        IndependenceTest fisherZTest = new IndTestFisherZ(data, 0.05);
+        MarkovCheck markovCheck = new MarkovCheck(estimatedCpdag, fisherZTest, ConditioningSetType.LOCAL_MARKOV); // TODO Also try MB for settype
+        List<List<Node>> accepts_rejects = markovCheck.getAndersonDarlingTestAcceptsRejectsNodesForAllNodes(fisherZTest, estimatedCpdag, 0.05);
+        List<Node> accepts = accepts_rejects.get(0);
+        List<Node> rejects = accepts_rejects.get(1);
+        System.out.println("Accepts size: " + accepts.size());
+        System.out.println("Rejects size: " + rejects.size());
+
+        List<Double> acceptsPrecision = new ArrayList<>();
+        List<Double> acceptsRecall = new ArrayList<>();
+        for(Node a: accepts) {
+            double precision = markovCheck.getPrecisionOrRecallOnMarkovBlanketGraph(a, estimatedCpdag, trueGraph, true);
+            double recall = markovCheck.getPrecisionOrRecallOnMarkovBlanketGraph(a, estimatedCpdag, trueGraph, false);
+            acceptsPrecision.add(precision);
+            acceptsRecall.add(recall);
+        }
+        System.out.println("Accepts Precisions: " + acceptsPrecision);
+        System.out.println("Accepts Recall: " + acceptsRecall);
+        System.out.println("****************************************************");
+
+
+    }
 }