Merge branch 'master' of github.com:EpistasisLab/srbench

cavalab · Sep 22, 2021 · c63a3d2 · c63a3d2
2 parents 607b790 + bafbad2
commit c63a3d2
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Showing 3 changed files with 40 additions and 15 deletions.
diff --git a/experiment/methods/src/mrgp/mrgp.jar b/experiment/methods/src/mrgp/mrgp.jar
diff --git a/experiment/methods/src/mrgp/mrgp.py b/experiment/methods/src/mrgp/mrgp.py
@@ -12,7 +12,7 @@
 class MRGPRegressor(BaseEstimator):
   def __init__(self, g=10, popsize=100, rt_mut=0.5, 
                rt_cross=0.5, max_len=10, time_out=10*60,
-               tmp_dir=None
+               tmp_dir=None, n_jobs=1, random_state=None
                ):
     self.g = g
     self.popsize = popsize
@@ -21,6 +21,8 @@ def __init__(self, g=10, popsize=100, rt_mut=0.5,
     self.max_len = max_len
     self.time_out = time_out  #in seconds
     self.tmp_dir = tmp_dir
+    self.n_jobs = n_jobs
+    self.random_state = random_state
 
   def fit(self, features, target, sample_weight=None, groups=None):
     data=pd.DataFrame(features)
@@ -40,17 +42,19 @@ def fit(self, features, target, sample_weight=None, groups=None):
     data.to_csv(self.dataset+'-train',
                 header=None, 
                 index=None)
-    subprocess.check_output(['java', '-jar', 
-                             THIS_DIR+'/mrgp.jar',
-                             '-train', 
-                             self.dataset, 
-                             str(self.g), 
-                             str(self.popsize), 
-                             str(self.rt_mut), 
-                             str(self.rt_cross), 
-                             str(self.max_len),
-                             str(self.time_out)
-                            ])
+    output = ['java', '-jar', THIS_DIR+'/mrgp.jar',
+             '-train',
+             self.dataset,
+             str(self.g),
+             str(self.popsize),
+             str(self.rt_mut),
+             str(self.rt_cross),
+             str(self.max_len),
+             str(self.time_out),
+             str(self.n_jobs)
+             ]
+    output = output+[str(self.random_state)] if self.random_state != None else output
+    subprocess.check_output(output)
     # get model and complexity
     self.model_, self.complexity_ = self._get_model()
 

diff --git a/experiment/methods/src/mrgp/mrgp/src/main/SRLearnerMenuManager.java b/experiment/methods/src/mrgp/mrgp/src/main/SRLearnerMenuManager.java
@@ -54,7 +54,7 @@ public void printUsage(){
 
     public void parseSymbolicRegressionTrain(String args[]) throws IOException{
         String dataPath;
-        int numMinutes=0;
+        int numMinutes = 10*60;
         String propsFile = "";
         SymbRegMOO srEvoGPj;
         dataPath = args[1];
@@ -63,6 +63,21 @@ public void parseSymbolicRegressionTrain(String args[]) throws IOException{
         String  mut_rate = args[4];
         String  crossover_rate = args[5];
         String  max_length = args[6];
+        String  external_threads = "4";
+        String  rng_seed = "";
+        // Add a time limit if specified by user
+        if (args.length >= 8){
+        	    numMinutes = Integer.parseInt(args[7]);
+	    }
+	// Add a maximum number of threads if specified by user
+        if (args.length >= 9){
+                   external_threads = args[8];
+           }
+      	// Add a seed if specified by user
+        if (args.length >= 10){
+                   rng_seed = args[9];
+           }
+
         // run evogpj with standard properties
         Properties props = new Properties();
         //System.out.print(dataPath);
@@ -74,6 +89,12 @@ public void parseSymbolicRegressionTrain(String args[]) throws IOException{
         props.put(Parameters.Names.TREE_INIT_MAX_DEPTH, max_length);
         props.put(Parameters.Names.TREE_MUTATE_MAX_DEPTH, max_length);
         props.put(Parameters.Names.TREE_XOVER_MAX_DEPTH, max_length);
+        if (args.length >= 9){
+                   props.put(Parameters.Names.EXTERNAL_THREADS, external_threads);
+           }
+        if (args.length >= 10){
+                   props.put(Parameters.Names.SEED, rng_seed);
+           }
 
 /*            if (args[2].equals("-minutes")) {
                 ;
@@ -105,8 +126,8 @@ public void parseSymbolicRegressionTrain(String args[]) throws IOException{
             System.exit(-1);
         }
      */
-        //allow each job to run <10mins
-        srEvoGPj = new SymbRegMOO(props,10*60);
+        //allow each job to run around numMinutes
+        srEvoGPj = new SymbRegMOO(props,numMinutes);
         Individual bestIndi = srEvoGPj.run_population();
 
     }