add seed support (seedForRandom) in java

egeulgen · May 5, 2023 · a6a548a · a6a548a
1 parent 8cbac07
commit a6a548a
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Showing 17 changed files with 20 additions and 12 deletions.
diff --git a/inst/java/ActiveSubnetworkSearch.jar b/inst/java/ActiveSubnetworkSearch.jar
diff --git a/java/ActiveSubnetworkSearchAlgorithms/ActiveSubnetworkSearch.java b/java/ActiveSubnetworkSearchAlgorithms/ActiveSubnetworkSearch.java
diff --git a/java/ActiveSubnetworkSearchAlgorithms/GAIndividual.java b/java/ActiveSubnetworkSearchAlgorithms/GAIndividual.java
diff --git a/java/ActiveSubnetworkSearchAlgorithms/GeneticAlgorithm.java b/java/ActiveSubnetworkSearchAlgorithms/GeneticAlgorithm.java
@@ -34,7 +34,7 @@ public ArrayList<Subnetwork> geneticAlgorithm(){
         networkNodeList = ActiveSubnetworkSearch.networkNodeList;
         populationSize=Parameters.ga_populationSize;
         ArrayList<GAIndividual> population=new ArrayList<>();
-        random=new Random();
+        random=new Random(Parameters.seedForRandom);
 
         initializePopulation(population, populationSize);
 

diff --git a/java/ActiveSubnetworkSearchAlgorithms/GreedySearch.java b/java/ActiveSubnetworkSearchAlgorithms/GreedySearch.java
diff --git a/java/ActiveSubnetworkSearchAlgorithms/SimulatedAnnealing.java b/java/ActiveSubnetworkSearchAlgorithms/SimulatedAnnealing.java
@@ -34,7 +34,10 @@ public class SimulatedAnnealing {
      * @param scoreCalculations 
      */
     public ArrayList<Subnetwork> simulatedAnnealing() {
-
+
+        Random rand = new Random(Parameters.seedForRandom);
+
+
         Network network=ActiveSubnetworkSearch.network;
         ScoreCalculations scoreCalculations=ActiveSubnetworkSearch.scoreCalculations;
 
@@ -51,7 +54,7 @@ public ArrayList<Subnetwork> simulatedAnnealing() {
             }
         }else{
             for (Node node : nodesOffSet) {
-                if(Math.random()<Parameters.geneInitialAdditionProbability){
+                if(rand.nextDouble()<Parameters.geneInitialAdditionProbability){
                     nodesOnSet.add(node);
                 }
             }
@@ -78,7 +81,7 @@ public ArrayList<Subnetwork> simulatedAnnealing() {
 
         double T = initialTemperature;
         double temp_step = 1 - Math.pow((finalTemperature / initialTemperature), (1.0 / totalIterations));
-        Random rand = new Random();
+
 
         System.out.println("Percentage of finished job, node number and score of modules that have more than one node are as follows:");
         int percent=0;

diff --git a/java/ActiveSubnetworkSearchMisc/Gaussian.java b/java/ActiveSubnetworkSearchMisc/Gaussian.java
diff --git a/java/ActiveSubnetworkSearchMisc/ScoreCalculations.java b/java/ActiveSubnetworkSearchMisc/ScoreCalculations.java
@@ -7,6 +7,7 @@
 import java.util.HashMap;
 import java.util.AbstractMap.SimpleEntry;
 import java.util.Collections;
+import java.util.Random;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
@@ -128,15 +129,18 @@ private void calculateMeanAndStdForMonteCarlo() {
         }
 //        System.out.println(""+significantNodesList.size()+" "+nonsignificantNodesList.size());
 
+        Random random=new Random(Parameters.seedForRandom);
+
+
         for (int trial = 0; trial < numberOfTrials; trial++) {
 //            long start=System.nanoTime();
 
-            Collections.shuffle(nodeListForSampling);
+            Collections.shuffle(nodeListForSampling, random);
 
             //These code can be used to first add significant nodes and start 
             //sampling with positive scored nodes
-//            Collections.shuffle(significantNodesList);
-//            Collections.shuffle(nonsignificantNodesList);
+//            Collections.shuffle(significantNodesList, random);
+//            Collections.shuffle(nonsignificantNodesList, random);
 //            nodeListForSampling.clear();
 //            nodeListForSampling.addAll(significantNodesList);
 //            nodeListForSampling.addAll(nonsignificantNodesList);

diff --git a/java/ActiveSubnetworkSearchMisc/Subnetwork.java b/java/ActiveSubnetworkSearchMisc/Subnetwork.java
diff --git a/java/ActiveSubnetworkSearchMisc/ZStatistics.java b/java/ActiveSubnetworkSearchMisc/ZStatistics.java
diff --git a/java/Application/AppActiveSubnetworkSearch.java b/java/Application/AppActiveSubnetworkSearch.java
@@ -27,9 +27,7 @@ public static void main(String[] args) {
 
     public static void processArguments(String[] args) throws Exception {
         String helpText;
-        helpText = "It is recommended to increase Stack size while running. You can use\n"
-                + "java -Xss4m -jar ActiveSubnetworkSearch.jar\n"
-                + "Options of the application are\n"
+        helpText = "Options of the application are\n"
                 + "-sif=<path>            \tuses the given interaction file\n"
                 + "-sig=<path>            \tuses the given experiment file (gene p-value pairs)\n"
                 + "-method=[GR|SA|GA]     \truns greedy search, simulated annealing or genetic algorithm for the search (default GR)\n"
@@ -46,7 +44,8 @@ public static void processArguments(String[] args) throws Exception {
                 + "-grMaxDepth=<value>    \tsets max depth in greedy search, 0 for no limit (default 1)\n"
                 + "-grSearchDepth=<value> \tsets search depth in greedy search (default 1)\n"
                 + "-grOverlap=<value>     \tsets overlap threshold for results of greedy search (default 0.5)\n"
-                + "-grSubNum=<value>      \tsets number of subnetworks to be presented in the results (default 1000)\n";
+                + "-grSubNum=<value>      \tsets number of subnetworks to be presented in the results (default 1000)\n"
+                + "-seedForRandom=<value>      \tsets the seed for random number generators, useful for reproducibility (default 1234)\n";
         if(args.length==0 || args[0].equals("-h") || args[0].equals("help") || args[0].equals("-help")){
             System.out.println(helpText);
         }else{
@@ -78,6 +77,7 @@ public static void processArguments(String[] args) throws Exception {
                     case "-grSearchDepth":Parameters.gr_searchDepth=Integer.parseInt(value);break;
                     case "-grOverlap":Parameters.gr_overlapThreshold=Double.parseDouble(value);break;
                     case "-grSubNum":Parameters.gr_subnetworkNum=Integer.parseInt(value);break;
+                    case "-seedForRandom":Parameters.seedForRandom=Integer.parseInt(value);break;
                     default:System.out.println("Unknown argument: "+argType);
                 }
             }

diff --git a/java/Application/Parameters.java b/java/Application/Parameters.java
@@ -5,7 +5,6 @@
  * @author Ozan Ozisik
  */
 
-
 public class Parameters {
     public static String sifPath="BIOGRID-ORGANISM-Homo_sapiens-3.4.155.OzCleaned.sif";
     public static String experimentFilePath="Behcet_jp_GWASPvalue.txt";
@@ -36,4 +35,6 @@ public enum SearchMethod{GR, SA, GA};
     public static double gr_overlapThreshold=0.5;//(default 0.5)
     public static double gr_subnetworkNum=1000;//(default 1000)
 
+    public static int seedForRandom=1234;
+
 }
diff --git a/java/File/ExperimentFileReader.java b/java/File/ExperimentFileReader.java
diff --git a/java/File/SIFReader.java b/java/File/SIFReader.java
diff --git a/java/Network/Network.java b/java/Network/Network.java
diff --git a/java/Network/Node.java b/java/Network/Node.java
diff --git a/java/Network/SubnetworkFinder.java b/java/Network/SubnetworkFinder.java