Merge pull request #1521 from cmu-phil/parameter_disappearing_issue

Fixed problem of SEM and Bayes simultion parameters going missing after simulation and re-opening the Simulation box.
cmu-phil · Feb 14, 2023 · e1f308c · e1f308c
2 parents 5da6ae6 + 6889e8e
commit e1f308c
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diff --git a/docs/manual/index.html b/docs/manual/index.html
@@ -7246,7 +7246,7 @@ <h3 id="zSRiskBound" class="parameter_description">zSRiskBound</h3>
             <li>Long Description: <span id="zSRiskBound_long_desc">
                 This is the probability of getting the true model if a correct model is discovered. Could underfit.</span>
             </li>
-            <li>Default Value: <span id="zSRiskBound_default_value">0.001</span></li>
+            <li>Default Value: <span id="zSRiskBound_default_value">0.1</span></li>
             <li>Lower Bound: <span id="zSRiskBound_lower_bound">0</span></li>
             <li>Upper Bound: <span id="zSRiskBound_upper_bound">1</span></li>
             <li>Value Type: <span id="zSRiskBound_value_type">Double</span></li>

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/StatsListEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/StatsListEditor.java
@@ -172,15 +172,15 @@ private List<Statistic> statistics() {
 
 
         // 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());
+//        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());
 
 //        statistics.add(new LegalPag());
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/simulation/ParameterTab.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/simulation/ParameterTab.java
@@ -217,6 +217,7 @@ private void showParameters() {
         this.parameterBox.removeAll();
         if (this.simulation.getSimulation() != null) {
             Set<String> params = new LinkedHashSet<>(this.simulation.getSimulation().getParameters());
+
             if (params.isEmpty()) {
                 this.parameterBox.add(ParameterTab.NO_PARAM_LBL, BorderLayout.NORTH);
             } else {

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/FgesRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/FgesRunner.java
@@ -200,7 +200,7 @@ public void execute() {
             }
         }
 
-        this.fges.setInitialGraph(this.externalGraph);
+        this.fges.setExternalGraph(this.externalGraph);
         this.fges.setKnowledge((Knowledge) getParams().get("knowledge", new Knowledge()));
         this.fges.setVerbose(true);
         Graph graph = this.fges.search();

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/multi/FgesConcatenated.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/multi/FgesConcatenated.java
@@ -75,7 +75,7 @@ public Graph search(List<DataModel> dataModels, Parameters parameters) {
             }
 
             if (initial != null) {
-                search.setInitialGraph(initial);
+                search.setExternalGraph(initial);
             }
 
             return search.search();

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/BOSSDC.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/BOSSDC.java
@@ -54,6 +54,8 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             boss.setAlgType(Boss.AlgType.BOSS1);
         } else if (parameters.getInt(Params.BOSS_ALG) == 2) {
             boss.setAlgType(Boss.AlgType.BOSS2);
+        } else if (parameters.getInt(Params.BOSS_ALG) == 3) {
+            boss.setAlgType(Boss.AlgType.BOSS3);
         } else {
             throw new IllegalArgumentException("Unrecognized boss algorithm type.");
         }

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Fges.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Fges.java
@@ -40,7 +40,7 @@ public class Fges implements Algorithm, HasKnowledge, UsesScoreWrapper {
     private ScoreWrapper score;
     private Knowledge knowledge = new Knowledge();
 
-    private Graph initialGraph = null;
+    private Graph wxternalGraph = null;
 
     public Fges() {
 
@@ -68,7 +68,7 @@ public Graph search(DataModel dataModel, Parameters parameters) {
 
             edu.cmu.tetrad.search.Fges search
                     = new edu.cmu.tetrad.search.Fges(score);
-//            search.setInitialGraph(initialGraph);
+            search.setExternalGraph(wxternalGraph);
             search.setKnowledge(this.knowledge);
             search.setVerbose(parameters.getBoolean(Params.VERBOSE));
             search.setMeekVerbose(parameters.getBoolean(Params.MEEK_VERBOSE));
@@ -150,7 +150,7 @@ public void setScoreWrapper(ScoreWrapper score) {
         this.score = score;
     }
 
-    public void setInitialGraph(Graph initialGraph) {
-        this.initialGraph = initialGraph;
+    public void setExternalGraph(Graph externalGraph) {
+        this.wxternalGraph = externalGraph;
     }
 }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/PC.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/PC.java
@@ -39,7 +39,7 @@ public class PC implements Algorithm, HasKnowledge, TakesIndependenceWrapper {
     private IndependenceWrapper test;
     private Knowledge knowledge = new Knowledge();
 
-    private Graph initialGraph = null;
+    private Graph externalGraph = null;
 
     public PC() {
     }
@@ -102,7 +102,7 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             search.setUseHeuristic(parameters.getBoolean(Params.USE_MAX_P_ORIENTATION_HEURISTIC));
             search.setMaxPathLength(parameters.getInt(Params.MAX_P_ORIENTATION_MAX_PATH_LENGTH));
             search.setMaxPathLength(parameters.getInt(Params.MAX_P_ORIENTATION_MAX_PATH_LENGTH));
-            search.setInitialGraph(initialGraph);
+            search.setExternalGraph(externalGraph);
             search.setVerbose(parameters.getBoolean(Params.VERBOSE));
 
             return search.search();
@@ -171,7 +171,7 @@ public void setIndependenceWrapper(IndependenceWrapper test) {
         this.test = test;
     }
 
-    public void setInitialGraph(Graph initialGraph) {
-        this.initialGraph = initialGraph;
+    public void setExternalGraph(Graph externalGraph) {
+        this.externalGraph = externalGraph;
     }
 }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/examples/TestBoss.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/examples/TestBoss.java
@@ -30,6 +30,7 @@
 import edu.cmu.tetrad.algcomparison.graph.RandomForward;
 import edu.cmu.tetrad.algcomparison.independence.FisherZ;
 import edu.cmu.tetrad.algcomparison.score.SemBicScore;
+import edu.cmu.tetrad.algcomparison.score.ZhangShenBoundScore;
 import edu.cmu.tetrad.algcomparison.simulation.SemSimulation;
 import edu.cmu.tetrad.algcomparison.simulation.Simulations;
 import edu.cmu.tetrad.algcomparison.statistic.*;

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/simulation/BayesNetSimulation.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/simulation/BayesNetSimulation.java
@@ -107,13 +107,13 @@ public List<String> getParameters() {
             parameters.addAll(this.randomGraph.getParameters());
         }
 
-        if (this.pm == null) {
-            parameters.addAll(BayesPm.getParameterNames());
-        }
+//        if (this.pm == null) {
+        parameters.addAll(BayesPm.getParameterNames());
+//        }
 
-        if (this.im == null) {
-            parameters.addAll(MlBayesIm.getParameterNames());
-        }
+//        if (this.im == null) {
+        parameters.addAll(MlBayesIm.getParameterNames());
+//        }
 
         parameters.add(Params.NUM_RUNS);
         parameters.add(Params.DIFFERENT_GRAPHS);

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/simulation/SemSimulation.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/simulation/SemSimulation.java
@@ -125,9 +125,9 @@ public List<String> getParameters() {
             parameters.addAll(this.randomGraph.getParameters());
         }
 
-        if (this.im == null) {
-            parameters.addAll(SemIm.getParameterNames());
-        }
+//        if (this.im == null) {
+        parameters.addAll(SemIm.getParameterNames());
+//        }
 
         parameters.add(Params.MEASUREMENT_VARIANCE);
         parameters.add(Params.NUM_RUNS);
@@ -175,7 +175,7 @@ private DataSet simulate(Graph graph, Parameters parameters) {
         // Not setting this im messes up algcomparison. -JR 20230206
 
 //        if (this.im == null) {
-            this.im = im;
+        this.im = im;
 //        }
 
         // Need this in case the SEM IM is given externally.

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/annotation/AlgorithmAnnotations.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/annotation/AlgorithmAnnotations.java
@@ -54,7 +54,7 @@ public boolean takesKnowledge(Class clazz) {
         return clazz != null && HasKnowledge.class.isAssignableFrom(clazz);
     }
 
-    public boolean takesInitialGraph(Class clazz) {
+    public boolean takesExternalGraph(Class clazz) {
         return clazz != null && TakesExternalGraph.class.isAssignableFrom(clazz);
     }
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Paths.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Paths.java
@@ -20,7 +20,7 @@ public Paths(Graph graph) {
     }
 
     /**
-     * Returns a valid causal order for either a DAG or a CPDAG.
+     * Returns a valid causal order for either a DAG or a CPDAG. (bryanandrews)
      * @param initialOrder Variables in the order will be kept as close to this
      *                     initial order as possible, either the forward order
      *                     or the reverse order, depending on the next parameter.

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Boss.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Boss.java
@@ -36,6 +36,7 @@ public class Boss {
     private int numStarts = 1;
     private AlgType algType = AlgType.BOSS1;
     private boolean caching = true;
+    private double epsilon = 1e-10;
 
     public Boss(@NotNull IndependenceTest test, Score score) {
         this.test = test;
@@ -89,7 +90,7 @@ public List<Node> bestOrder(@NotNull List<Node> order) {
                 shuffle(order);
             }
 
-            this.start =  MillisecondTimes.timeMillis();
+            this.start = MillisecondTimes.timeMillis();
 
             makeValidKnowledgeOrder(order);
 
@@ -131,7 +132,7 @@ public List<Node> bestOrder(@NotNull List<Node> order) {
 
         this.scorer.score(bestPerm);
 
-        this.stop =  MillisecondTimes.timeMillis();
+        this.stop = MillisecondTimes.timeMillis();
 
         if (this.verbose) {
             TetradLogger.getInstance().forceLogMessage("\nFinal " + algType + " order = " + this.scorer.getPi());
@@ -225,7 +226,7 @@ public void betterMutation1(@NotNull TeyssierScorer scorer) {
 
                     tuck(x, j, scorer, range);
 
-                    if (scorer.score() > bestScore || violatesKnowledge(scorer.getPi())) {
+                    if (scorer.score() > bestScore + epsilon || violatesKnowledge(scorer.getPi())) {
                         for (int l = range[0]; l <= range[1]; l++) {
                             introns2.add(scorer.get(l));
                         }
@@ -244,63 +245,47 @@ public void betterMutation1(@NotNull TeyssierScorer scorer) {
             if (verbose) {
                 System.out.println();
             }
-        } while (bestScore > originalScore);
+        } while (bestScore > originalScore + epsilon);
     }
 
 
-
     public void betterMutation2(@NotNull TeyssierScorer scorer) {
         scorer.bookmark();
         double s1, s2;
 
-        Set<Node> introns1;
-        Set<Node> introns2;
-
-        introns2 = new HashSet<>(scorer.getPi());
-
         do {
             s1 = scorer.score();
             scorer.bookmark(1);
 
-            introns1 = introns2;
-            introns2 = new HashSet<>();
-
             for (Node k : scorer.getPi()) {
                 double _sp = NEGATIVE_INFINITY;
                 scorer.bookmark();
 
-                if (!introns1.contains(k)) continue;
-
                 for (int j = 0; j < scorer.size(); j++) {
                     scorer.moveTo(k, j);
 
-                    if (scorer.score() >= _sp) {
+                    if (scorer.score() >= _sp + epsilon) {
                         if (!violatesKnowledge(scorer.getPi())) {
                             _sp = scorer.score();
                             scorer.bookmark();
 
-                            if (scorer.index(k) <= j) {
-                                for (int m = scorer.index(k); m <= j; m++) {
-                                    introns2.add(scorer.get(m));
-                                }
-                            } else if (scorer.index(k) > j) {
-                                for (int m = j; m <= scorer.index(k); m++) {
-                                    introns2.add(scorer.get(m));
-                                }
+                            if (verbose) {
+                                System.out.print("\rIndex = " + (scorer.index(k) + 1) + " Score = " + scorer.score() + " (betterMutation2)" + " Elapsed " + ((MillisecondTimes.timeMillis() - start) / 1000.0 + " s"));
                             }
                         }
-                    }
+                   }
 
-                    if (verbose) {
-                        System.out.print("\rIndex = " + (j + 1) + " Score = " + scorer.score() + " (betterMutation2)" + " Elapsed " + ((MillisecondTimes.timeMillis() - start) / 1000.0 + " s"));
-                    }
                 }
 
                 scorer.goToBookmark();
             }
 
+            if (verbose) {
+                System.out.println();
+            }
+
             s2 = scorer.score();
-        } while (s2 > s1);
+        } while (s2 > s1 + epsilon);
 
         scorer.goToBookmark(1);
     }