Boss parallel

docs/manual/index.html

@@ -4548,6 +4548,25 @@ <h3>Zhang-Shen Bound Score</h3>
 
     <div id="parameters"><h2>Search Parameters</h2>
 
+        <h3 class="parameter_description"
+            id="numThreads">numThreads</h3>
+        <ul
+                class="parameter_description_list">
+            <li>Short Description: <span
+                    id="numThreads_short_desc">The number of threads (>= 1) to use for the search</span></li>
+            <li>Long Description: <span
+                    id="numThreads_long_desc">The number of threads to use for the search.</span>
+            </li>
+            <li>Default Value: <span
+                    id="numThreads_default_value">1</span></li>
+            <li>Lower
+                Bound: <span id="numThreads_lower_bound">1</span></li>
+            <li>Upper Bound: <span
+                    id="numThreads_upper_bound">1000000</span></li>
+            <li>Value Type:
+                <span id="numThreads_value_type">Integer</span></li>
+        </ul>
+
         <p>Note: You must specify the "Value Type" of each parameter, and
             the value type must be one of the following: Integer, Long, Double, String,
             Boolean.</p> <!-- Insert the parameter descriptions here, must follow
@@ -7435,24 +7454,24 @@ <h3 class="parameter_description" id="useBes">useBes</h3>
         </ul>
 
         <h3 class="parameter_description"
-            id="graspUseDataOrder">graspUseDataOrder</h3>
+            id="useDataOrder">useDataOrder</h3>
         <ul
                 class="parameter_description_list">
             <li>Short Description: <span
-                    id="graspUseDataOrder_short_desc"> Yes just in case data variable
+                    id="useDataOrder_short_desc"> Yes just in case data variable
         order should be used for the first initial permutation. </span></li>
-            <li>Long Description: <span id="graspUseDataOrder_long_desc"> In
+            <li>Long Description: <span id="useDataOrder_long_desc"> In
         either case, if multiple starting points are used, taking the best
         scoring model from among these, subsequent starting points will all
         be random shuffles. </span></li>
             <li>Default Value: <span
-                    id="graspUseDataOrder_default_value">true</span></li>
+                    id="useDataOrder_default_value">true</span></li>
             <li>Lower
-                Bound: <span id="graspUseDataOrder_lower_bound"></span></li>
+                Bound: <span id="useDataOrder_lower_bound"></span></li>
             <li>Upper Bound: <span
-                    id="graspUseDataOrder_upper_bound"></span></li>
+                    id="useDataOrder_upper_bound"></span></li>
             <li>Value Type: <span
-                    id="graspUseDataOrder_value_type">Boolean</span></li>
+                    id="useDataOrder_value_type">Boolean</span></li>
         </ul>
 
         <h3 class="parameter_description"

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Boss.java

@@ -70,7 +70,8 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             edu.cmu.tetrad.search.Boss boss = new edu.cmu.tetrad.search.Boss(score);
             boss.setUseBes(parameters.getBoolean(Params.USE_BES));
             boss.setNumStarts(parameters.getInt(Params.NUM_STARTS));
-            boss.setAllowInternalRandomness(parameters.getBoolean(Params.ALLOW_INTERNAL_RANDOMNESS));
+            boss.setNumThreads(parameters.getInt(Params.NUM_THREADS));
+            boss.setUseDataOrder(parameters.getBoolean(Params.USE_DATA_ORDER));
             PermutationSearch permutationSearch = new PermutationSearch(boss);
             permutationSearch.setKnowledge(this.knowledge);
 
@@ -111,8 +112,9 @@ public List<String> getParameters() {
         // Parameters
         params.add(Params.USE_BES);
         params.add(Params.NUM_STARTS);
-        params.add(Params.ALLOW_INTERNAL_RANDOMNESS);
         params.add(Params.TIME_LAG);
+        params.add(Params.NUM_THREADS);
+        params.add(Params.USE_DATA_ORDER);
 
         return params;
     }

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Grasp.java

@@ -80,7 +80,7 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             grasp.setOrdered(parameters.getBoolean(Params.GRASP_ORDERED_ALG));
             grasp.setUseScore(parameters.getBoolean(Params.GRASP_USE_SCORE));
             grasp.setUseRaskuttiUhler(parameters.getBoolean(Params.GRASP_USE_RASKUTTI_UHLER));
-            grasp.setUseDataOrder(parameters.getBoolean(Params.GRASP_USE_DATA_ORDER));
+            grasp.setUseDataOrder(parameters.getBoolean(Params.USE_DATA_ORDER));
             grasp.setAllowInternalRandomness(parameters.getBoolean(Params.ALLOW_INTERNAL_RANDOMNESS));
             grasp.setVerbose(parameters.getBoolean(Params.VERBOSE));
 
@@ -130,7 +130,7 @@ public List<String> getParameters() {
         params.add(Params.GRASP_NONSINGULAR_DEPTH);
         params.add(Params.GRASP_ORDERED_ALG);
         params.add(Params.GRASP_USE_RASKUTTI_UHLER);
-        params.add(Params.GRASP_USE_DATA_ORDER);
+        params.add(Params.USE_DATA_ORDER);
         params.add(Params.ALLOW_INTERNAL_RANDOMNESS);
         params.add(Params.TIME_LAG);
         params.add(Params.VERBOSE);

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/RestrictedBoss.java

@@ -84,7 +84,7 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             // variables as Tier 2 and the rest as Tier 1, and run BOSS again and return
             // the result.
 
-            Knowledge knowledge = new Knowledge();;
+            Knowledge knowledge = new Knowledge();
             for (Node node : targets) knowledge.addToTier(2, node.getName());
             for (Node node : dataSet.getVariables()) {
                 if (!targets.contains(node)) knowledge.addToTier(1, node.getName());
@@ -96,7 +96,6 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             edu.cmu.tetrad.search.Boss boss = new edu.cmu.tetrad.search.Boss(score);
             boss.setUseBes(parameters.getBoolean(Params.USE_BES));
             boss.setNumStarts(parameters.getInt(Params.NUM_STARTS));
-            boss.setAllowInternalRandomness(parameters.getBoolean(Params.ALLOW_INTERNAL_RANDOMNESS));
             PermutationSearch permutationSearch = new PermutationSearch(boss);
             permutationSearch.setKnowledge(knowledge);
             permutationSearch.search();
@@ -126,7 +125,6 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             boss = new edu.cmu.tetrad.search.Boss(score);
             boss.setUseBes(parameters.getBoolean(Params.USE_BES));
             boss.setNumStarts(parameters.getInt(Params.NUM_STARTS));
-            boss.setAllowInternalRandomness(parameters.getBoolean(Params.ALLOW_INTERNAL_RANDOMNESS));
             permutationSearch = new PermutationSearch(boss);
             permutationSearch.setKnowledge(knowledge);
 
@@ -169,7 +167,6 @@ public List<String> getParameters() {
         // Parameters
         params.add(Params.USE_BES);
         params.add(Params.NUM_STARTS);
-        params.add(Params.ALLOW_INTERNAL_RANDOMNESS);
         params.add(Params.TARGETS);
         params.add(Params.TRIMMING_STYLE);
 

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/Bfci.java

@@ -83,7 +83,6 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             search.setCompleteRuleSetUsed(parameters.getBoolean(Params.COMPLETE_RULE_SET_USED));
             search.setDoDiscriminatingPathRule(parameters.getBoolean(Params.DO_DISCRIMINATING_PATH_RULE));
             search.setDepth(parameters.getInt(Params.DEPTH));
-            search.setAllowInternalRandomness(parameters.getBoolean(Params.ALLOW_INTERNAL_RANDOMNESS));
             search.setVerbose(parameters.getBoolean(Params.VERBOSE));
 
             search.setKnowledge(knowledge);
@@ -129,7 +128,6 @@ public List<String> getParameters() {
         params.add(Params.COMPLETE_RULE_SET_USED);
         params.add(Params.DO_DISCRIMINATING_PATH_RULE);
         params.add(Params.DEPTH);
-        params.add(Params.ALLOW_INTERNAL_RANDOMNESS);
         params.add(Params.TIME_LAG);
         params.add(Params.VERBOSE);
 
@@ -147,7 +145,7 @@ public Knowledge getKnowledge() {
 
     @Override
     public void setKnowledge(Knowledge knowledge) {
-        this.knowledge = new Knowledge((Knowledge) knowledge);
+        this.knowledge = new Knowledge(knowledge);
     }
 
     @Override

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/pag/GraspFci.java

@@ -88,7 +88,7 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             search.setOrdered(parameters.getBoolean(Params.GRASP_ORDERED_ALG));
             search.setUseScore(parameters.getBoolean(Params.GRASP_USE_SCORE));
             search.setUseRaskuttiUhler(parameters.getBoolean(Params.GRASP_USE_RASKUTTI_UHLER));
-            search.setUseDataOrder(parameters.getBoolean(Params.GRASP_USE_DATA_ORDER));
+            search.setUseDataOrder(parameters.getBoolean(Params.USE_DATA_ORDER));
             search.setNumStarts(parameters.getInt(Params.NUM_STARTS));
 
             // FCI
@@ -143,7 +143,7 @@ public List<String> getParameters() {
         params.add(Params.GRASP_NONSINGULAR_DEPTH);
         params.add(Params.GRASP_ORDERED_ALG);
         params.add(Params.GRASP_USE_RASKUTTI_UHLER);
-        params.add(Params.GRASP_USE_DATA_ORDER);
+        params.add(Params.USE_DATA_ORDER);
         params.add(Params.NUM_STARTS);
 
         // FCI

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/examples/TestBoss.java

@@ -23,7 +23,6 @@
 
 import edu.cmu.tetrad.algcomparison.Comparison;
 import edu.cmu.tetrad.algcomparison.algorithm.Algorithms;
-import edu.cmu.tetrad.algcomparison.algorithm.continuous.dag.Dagma;
 import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Boss;
 import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges;
 import edu.cmu.tetrad.algcomparison.graph.RandomForward;
@@ -44,18 +43,22 @@ public static void main(String... args) {
         Parameters parameters = new Parameters();
         parameters.set(Params.NUM_RUNS, 1);
         parameters.set(Params.DIFFERENT_GRAPHS, true);
-        parameters.set(Params.NUM_MEASURES, 100);
+        parameters.set(Params.NUM_MEASURES, 1000);
         parameters.set(Params.AVG_DEGREE, 10);
         parameters.set(Params.SAMPLE_SIZE, 1000);
         parameters.set(Params.COEF_LOW, 0);
         parameters.set(Params.COEF_HIGH, 1);
         parameters.set(Params.VAR_LOW, 1);
         parameters.set(Params.VAR_HIGH, 3);
 
-        parameters.set(Params.PENALTY_DISCOUNT, 2);
+        parameters.set(Params.PENALTY_DISCOUNT, 8);
         parameters.set(Params.SEM_BIC_STRUCTURE_PRIOR, 0);
         parameters.set(Params.ALPHA, 1e-2);
 
+        parameters.set(Params.USE_BES, false);
+        parameters.set(Params.NUM_STARTS, 1);
+        parameters.set(Params.NUM_THREADS, 400);
+
         parameters.set(Params.VERBOSE, false);
 
         Statistics statistics = new Statistics();
@@ -67,9 +70,9 @@ public static void main(String... args) {
 
         Algorithms algorithms = new Algorithms();
 //        algorithms.add(new DirectLingam(new SemBicScore()));
-        algorithms.add(new Fges(new SemBicScore()));
+//        algorithms.add(new Fges(new SemBicScore()));
         algorithms.add(new Boss(new SemBicScore()));
-        algorithms.add(new Dagma());
+//        algorithms.add(new Dagma());
 
         Simulations simulations = new Simulations();
         simulations.add(new SemSimulation(new RandomForward()));

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

@@ -83,7 +83,6 @@ public final class BFci implements IGraphSearch {
     private int depth = -1;
     private boolean doDiscriminatingPathRule = true;
     private boolean bossUseBes = false;
-    private boolean allowInternalRandomness = false;
 
 
     /**
@@ -119,7 +118,6 @@ public Graph search() {
         Boss subAlg = new Boss(this.score);
         subAlg.setUseBes(bossUseBes);
         subAlg.setNumStarts(this.numStarts);
-        subAlg.setAllowInternalRandomness(this.allowInternalRandomness);
         PermutationSearch alg = new PermutationSearch(subAlg);
         alg.setKnowledge(this.knowledge);
 
@@ -214,7 +212,4 @@ public void setBossUseBes(boolean useBes) {
         this.bossUseBes = useBes;
     }
 
-    public void setAllowInternalRandomness(boolean allowInternalRandomness) {
-        this.allowInternalRandomness = allowInternalRandomness;
-    }
 }