Program: 51050
Project: 51050
Buggy source:
/** 
 * @param args
 */
public static void main(String[] args){
  RDFDataSet testSetA=new RDFFileDataSet(DATA_DIR + "String_Node_Str",RDFFormat.RDFXML);
  RDFDataSet testSetB=new RDFFileDataSet(DATA_DIR + "String_Node_Str",RDFFormat.N3);
  List<LinkPredictionDataSetParameters> dataSetsParams=new ArrayList<LinkPredictionDataSetParameters>();
  List<String> bl=new ArrayList<String>();
  bl.add("String_Node_Str");
  bl.add("String_Node_Str");
  long[] seeds={11,21,31,41,51,61,71,81,91,101};
  double[] cs={0.01,0.1,1,10,100};
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,1,false,false));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,2,false,false));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,1,false,true));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,2,false,true));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,1,true,false));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,2,true,false));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,1,true,true));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,2,true,true));
  LinkPredictionDataSet dataset;
  LinkPredictionExperiment exp;
  ResultsTable resultsWL=new ResultsTable();
  ResultsTable resultsSTF=new ResultsTable();
  ResultsTable resultsSTP=new ResultsTable();
  ResultsTable resultsIGW=new ResultsTable();
  ResultsTable resultsIGP=new ResultsTable();
  Experimenter experimenter=new Experimenter(NUMBER_OF_PROC);
  Thread expT=new Thread(experimenter);
  expT.setDaemon(true);
  expT.start();
  try {
    for (    LinkPredictionDataSetParameters params : dataSetsParams) {
      dataset=DataSetFactory.createLinkPredictonDataSet(params);
      for (int i=0; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new WLSubTreeKernel(i),new WLSubTreeKernel(i),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsWL.addResult(exp.getResults().getAccuracy());
          resultsWL.addResult(exp.getResults().getF1());
          resultsWL.addResult(exp.getResults().getrPrecision());
          resultsWL.addResult(exp.getResults().getAveragePrecision());
        }
      }
      for (int i=0; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new IntersectionSubTreeKernel(i,1),new IntersectionSubTreeKernel(i,1),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsSTF.addResult(exp.getResults().getAccuracy());
          resultsSTF.addResult(exp.getResults().getF1());
          resultsSTF.addResult(exp.getResults().getrPrecision());
          resultsSTF.addResult(exp.getResults().getAveragePrecision());
        }
      }
      for (int i=0; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new IntersectionPartialSubTreeKernel(i,0.01),new IntersectionPartialSubTreeKernel(i,0.01),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsSTP.addResult(exp.getResults().getAccuracy());
          resultsSTP.addResult(exp.getResults().getF1());
          resultsSTP.addResult(exp.getResults().getrPrecision());
          resultsSTP.addResult(exp.getResults().getAveragePrecision());
        }
      }
      for (int i=1; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new IntersectionGraphWalkKernel(i,1),new IntersectionGraphWalkKernel(i,1),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsIGW.addResult(exp.getResults().getAccuracy());
          resultsIGW.addResult(exp.getResults().getF1());
          resultsIGW.addResult(exp.getResults().getrPrecision());
          resultsIGW.addResult(exp.getResults().getAveragePrecision());
        }
      }
      for (int i=1; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new IntersectionGraphPathKernel(i,1),new IntersectionGraphPathKernel(i,1),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsIGP.addResult(exp.getResults().getAccuracy());
          resultsIGP.addResult(exp.getResults().getF1());
          resultsIGP.addResult(exp.getResults().getrPrecision());
          resultsIGP.addResult(exp.getResults().getAveragePrecision());
        }
      }
    }
  }
 catch (  Exception e) {
    e.printStackTrace();
  }
  experimenter.stop();
  while (expT.isAlive()) {
    try {
      Thread.sleep(1000);
    }
 catch (    Exception e) {
      e.printStackTrace();
    }
  }
  System.out.println(resultsWL);
  System.out.println(resultsSTF);
  System.out.println(resultsSTP);
  System.out.println(resultsIGW);
  System.out.println(resultsIGP);
}

Fixed version (ground truth):
/** 
 * @param args
 */
public static void main(String[] args){
  RDFDataSet testSetA=new RDFFileDataSet(DATA_DIR + "String_Node_Str",RDFFormat.RDFXML);
  RDFDataSet testSetB=new RDFFileDataSet(DATA_DIR + "String_Node_Str",RDFFormat.N3);
  List<LinkPredictionDataSetParameters> dataSetsParams=new ArrayList<LinkPredictionDataSetParameters>();
  List<String> bl=new ArrayList<String>();
  bl.add("String_Node_Str");
  bl.add("String_Node_Str");
  long[] seeds={11,21,31,41,51,61,71,81,91,101};
  double[] cs={0.01,0.1,1,10,100};
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,1,false,false));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,2,false,false));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,1,false,true));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,2,false,true));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,1,true,false));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,2,true,false));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,1,true,true));
  dataSetsParams.add(new LinkPredictionDataSetParameters(testSetA,"String_Node_Str","String_Node_Str","String_Node_Str",bl,2,true,true));
  LinkPredictionDataSet dataset;
  LinkPredictionExperiment exp;
  ResultsTable resultsWL=new ResultsTable();
  ResultsTable resultsSTF=new ResultsTable();
  ResultsTable resultsSTP=new ResultsTable();
  ResultsTable resultsIGW=new ResultsTable();
  ResultsTable resultsIGP=new ResultsTable();
  Experimenter experimenter=new Experimenter(NUMBER_OF_PROC);
  Thread expT=new Thread(experimenter);
  expT.setDaemon(true);
  expT.start();
  try {
    for (    LinkPredictionDataSetParameters params : dataSetsParams) {
      dataset=DataSetFactory.createLinkPredictonDataSet(params);
      resultsWL.newRow(dataset.getLabel() + "String_Node_Str");
      for (int i=0; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new WLSubTreeKernel(i),new WLSubTreeKernel(i),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsWL.addResult(exp.getResults().getAccuracy());
          resultsWL.addResult(exp.getResults().getF1());
          resultsWL.addResult(exp.getResults().getrPrecision());
          resultsWL.addResult(exp.getResults().getAveragePrecision());
        }
      }
      resultsSTF.newRow(dataset.getLabel() + "String_Node_Str");
      for (int i=0; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new IntersectionSubTreeKernel(i,1),new IntersectionSubTreeKernel(i,1),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsSTF.addResult(exp.getResults().getAccuracy());
          resultsSTF.addResult(exp.getResults().getF1());
          resultsSTF.addResult(exp.getResults().getrPrecision());
          resultsSTF.addResult(exp.getResults().getAveragePrecision());
        }
      }
      resultsSTP.newRow(dataset.getLabel() + "String_Node_Str");
      for (int i=0; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new IntersectionPartialSubTreeKernel(i,0.01),new IntersectionPartialSubTreeKernel(i,0.01),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsSTP.addResult(exp.getResults().getAccuracy());
          resultsSTP.addResult(exp.getResults().getF1());
          resultsSTP.addResult(exp.getResults().getrPrecision());
          resultsSTP.addResult(exp.getResults().getAveragePrecision());
        }
      }
      resultsIGW.newRow(dataset.getLabel() + "String_Node_Str");
      for (int i=1; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new IntersectionGraphWalkKernel(i,1),new IntersectionGraphWalkKernel(i,1),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsIGW.addResult(exp.getResults().getAccuracy());
          resultsIGW.addResult(exp.getResults().getF1());
          resultsIGW.addResult(exp.getResults().getrPrecision());
          resultsIGW.addResult(exp.getResults().getAveragePrecision());
        }
      }
      resultsIGP.newRow(dataset.getLabel() + "String_Node_Str");
      for (int i=1; i < 3; i++) {
        if (experimenter.hasSpace()) {
          int fileId=(int)(Math.random() * 100000000);
          File file=new File(DATA_DIR + "String_Node_Str" + "String_Node_Str"+ fileId+ "String_Node_Str"+ i+ "String_Node_Str");
          exp=new LinkPredictionExperiment(new LinkPredictionDataSet(dataset),new IntersectionGraphPathKernel(i,1),new IntersectionGraphPathKernel(i,1),0.5,0.5,seeds,cs,new FileOutputStream(file));
          experimenter.addExperiment(exp);
          resultsIGP.addResult(exp.getResults().getAccuracy());
          resultsIGP.addResult(exp.getResults().getF1());
          resultsIGP.addResult(exp.getResults().getrPrecision());
          resultsIGP.addResult(exp.getResults().getAveragePrecision());
        }
      }
    }
  }
 catch (  Exception e) {
    e.printStackTrace();
  }
  experimenter.stop();
  while (expT.isAlive()) {
    try {
      Thread.sleep(1000);
    }
 catch (    Exception e) {
      e.printStackTrace();
    }
  }
  System.out.println(resultsWL);
  System.out.println(resultsSTF);
  System.out.println(resultsSTP);
  System.out.println(resultsIGW);
  System.out.println(resultsIGP);
}