[WIP] Issue #144 - Re-implement classifiers using SMILE library

build.gradle

@@ -39,7 +39,8 @@ dependencies {
     compile 'org.apache.tika:tika-parsers:1.14'
     compile 'com.syncthemall:boilerpipe:1.2.2'
     compile 'net.sourceforge.nekohtml:nekohtml:1.9.22'
-    compile 'nz.ac.waikato.cms.weka:weka-stable:3.6.13'
+    //compile 'nz.ac.waikato.cms.weka:weka-stable:3.6.13'
+    compile 'com.github.haifengl:smile-core:1.5.0'
     compile 'org.apache.lucene:lucene-core:4.10.4'
     compile 'org.elasticsearch:elasticsearch:1.4.4'
     compile 'org.elasticsearch.client:elasticsearch-rest-client:5.6.3'
@@ -55,7 +56,7 @@ dependencies {
       exclude group: 'org.apache.hadoop', module: 'hadoop-core'
       exclude group: 'junit', module: 'junit'
     }
-
+	
     // REST server dependencies
     compile "com.sparkjava:spark-core:2.5.3"
 

src/main/java/focusedCrawler/Main.java

@@ -1,6 +1,7 @@
 package focusedCrawler;
 
 import java.io.File;
+import java.io.IOException;
 import java.lang.reflect.Method;
 import java.util.Arrays;
 import java.util.List;
@@ -14,7 +15,7 @@
 import focusedCrawler.link.frontier.FrontierManagerFactory;
 import focusedCrawler.rest.RestServer;
 import focusedCrawler.seedfinder.SeedFinder;
-import focusedCrawler.target.classifier.WekaTargetClassifierBuilder;
+import focusedCrawler.target.classifier.SmileTargetClassifierBuilder;
 import focusedCrawler.tools.StartRestServer;
 import io.airlift.airline.Arguments;
 import io.airlift.airline.Cli;
@@ -143,7 +144,7 @@ public void run() {
 
     }
 
-    @Command(name = "buildModel", description = "Builds a model for a Weka target classifier")
+    @Command(name = "buildModel", description = "Builds a model for a Smile target classifier")
     public static class BuildModel implements Runnable {
 
         @Option(name = {"-t", "--trainingDataDir"}, required = true, description = "Path to folder containing training data")
@@ -155,25 +156,31 @@ public static class BuildModel implements Runnable {
         @Option(name = {"-c", "--stopWordsFile"}, required = false, description = "Path to stopwords file")
         String stopWordsFile;
 
-        @Option(name = {"-l", "--learner"}, required = false, description = "Machine-learning algorithm to be used to train the model (SMO, RandomForest)")
+        @Option(name = {"-l", "--learner"}, required = false, description = "Machine-learning algorithm to be used to train the model (SVM, RandomForest)")
         String learner;
 
         @Override
         public void run() {
 
             new File(outputPath).mkdirs();
 
-            // generate the input for weka
+            // generate the input for smile
             System.out.println("Preparing training data...");
-            WekaTargetClassifierBuilder.createInputFile(stopWordsFile, trainingPath, trainingPath + "/weka.arff" );
+            SmileTargetClassifierBuilder.createInputFile(stopWordsFile, trainingPath, trainingPath + "/smile_input.arff" );
 
             // generate the model
             System.out.println("Training model...");
-            WekaTargetClassifierBuilder.trainModel(trainingPath, outputPath, learner);
+            try {
+				SmileTargetClassifierBuilder.trainModel(trainingPath, outputPath, learner);
+			} catch (IOException | java.text.ParseException e) {
+				System.out.printf("Failed to build model.\n\n");
+                e.printStackTrace(System.out);
+                System.exit(1);
+			}
 
             // generate features file
             System.out.println("Creating feature file...");
-            WekaTargetClassifierBuilder.createFeaturesFile(outputPath,trainingPath);
+            SmileTargetClassifierBuilder.createFeaturesFile(outputPath,trainingPath);
 
             System.out.println("done.");
         }

src/main/java/focusedCrawler/link/classifier/LNClassifier.java

@@ -1,31 +1,26 @@
 package focusedCrawler.link.classifier;
 
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.ObjectInputStream;
 import java.util.Iterator;
 import java.util.Map;
 
 import focusedCrawler.link.classifier.builder.Instance;
 import focusedCrawler.link.classifier.builder.LinkNeighborhoodWrapper;
 import focusedCrawler.util.ParameterFile;
+import focusedCrawler.util.SmileUtil;
 import focusedCrawler.util.parser.LinkNeighborhood;
 import focusedCrawler.util.string.StopList;
-import weka.classifiers.Classifier;
-import weka.core.Instances;
+import smile.classification.SoftClassifier;
 
 public class LNClassifier {
 
-	private final Classifier classifier;
-	private final Instances instances;
+	private final SoftClassifier<double[]> classifier;
 	private final LinkNeighborhoodWrapper wrapper;
 	private final String[] attributes;
 
-	public LNClassifier(Classifier classifier, Instances instances,
-	                    LinkNeighborhoodWrapper wrapper, String[] attributes) {
+
+	public LNClassifier(SoftClassifier<double[]> classifier, LinkNeighborhoodWrapper wrapper,
+			String[] attributes) {
 		this.classifier = classifier;
-		this.instances = instances;
 		this.wrapper = wrapper;
 		this.attributes = attributes;
 	}
@@ -37,10 +32,9 @@ public double[] classify(LinkNeighborhood ln) throws Exception {
 		Instance instance = (Instance)urlWords.get(url);
 		double[] values = instance.getValues();
         synchronized (classifier) {
-            weka.core.Instance instanceWeka = new weka.core.Instance(1, values);
-            instanceWeka.setDataset(instances);
-            double[] probs = classifier.distributionForInstance(instanceWeka);
-            return probs;
+        	double[] prob = new double[2];
+	        int predictedValue = classifier.predict(values, prob);
+        	return prob;
         }
 	}
 
@@ -55,37 +49,9 @@ public static LNClassifier create(String featureFilePath,
 
 	public static LNClassifier create(String[] attributes, String[] classValues,
 	                                  String modelFilePath, StopList stoplist) {
-	    weka.core.FastVector vectorAtt = new weka.core.FastVector();
-	    for (int i = 0; i < attributes.length; i++) {
-	        vectorAtt.addElement(new weka.core.Attribute(attributes[i]));
-	    }
-	    weka.core.FastVector classAtt = new weka.core.FastVector();
-	    for (int i = 0; i < classValues.length; i++) {
-	        classAtt.addElement(classValues[i]);
-	    }
-	    vectorAtt.addElement(new weka.core.Attribute("class", classAtt));
-	    Instances insts = new Instances("link_classification", vectorAtt, 1);
-	    insts.setClassIndex(attributes.length);
-
 	    LinkNeighborhoodWrapper wrapper = new LinkNeighborhoodWrapper(attributes, stoplist);
-
-	    Classifier classifier = loadWekaClassifier(modelFilePath);
-
-	    return new LNClassifier(classifier, insts, wrapper, attributes);
-
+	    SoftClassifier<double[]> classifier = SmileUtil.loadSmileClassifier(modelFilePath);
+	    return new LNClassifier(classifier, wrapper, attributes);
 	}
-
-    private static Classifier loadWekaClassifier(String modelFilePath) {
-        try {
-            InputStream is = new FileInputStream(modelFilePath);
-            ObjectInputStream objectInputStream = new ObjectInputStream(is);
-            Classifier classifier = (Classifier) objectInputStream.readObject();
-            objectInputStream.close();
-            return classifier;
-        } catch (IOException | ClassNotFoundException e) {
-            throw new IllegalArgumentException(
-                    "Failed to load weka classifier instance from file: " + modelFilePath, e);
-        }
-    }
 
 }

src/main/java/focusedCrawler/link/classifier/LinkClassifierAuthority.java

@@ -10,21 +10,19 @@
 import focusedCrawler.link.frontier.LinkRelevance;
 import focusedCrawler.target.model.Page;
 import focusedCrawler.util.parser.LinkNeighborhood;
-import weka.classifiers.Classifier;
-import weka.core.Instances;
+import smile.classification.SoftClassifier;
+import smile.classification.SVM;
 
 public class LinkClassifierAuthority implements LinkClassifier{
 
 	  private LinkNeighborhoodWrapper wrapper;
 	  private String[] attributes;
-	  private Classifier classifier;
-	  private Instances instances;
+	  private SoftClassifier<double[]> classifier;
 
-	  public LinkClassifierAuthority(Classifier classifier, Instances instances, LinkNeighborhoodWrapper wrapper,String[] attributes) {
+	  public LinkClassifierAuthority(SoftClassifier<double[]> classifier,  LinkNeighborhoodWrapper wrapper,String[] attributes) {
 		  this.wrapper = wrapper;
 		  this.attributes = attributes;
 		  this.classifier = classifier;
-		  this.instances = instances;
 	  }
 
 	  public LinkClassifierAuthority() {
@@ -53,9 +51,8 @@ public LinkRelevance[] classify(Page page) throws LinkClassifierException {
 		        	  if(!page.getURL().getHost().equals(url.getHost())){
 		        		  Instance instance = entry.getValue();
 		        		  double[] values = instance.getValues();
-		        		  weka.core.Instance instanceWeka = new weka.core.Instance(1, values);
-		        		  instanceWeka.setDataset(instances);
-		        		  double[] prob = classifier.distributionForInstance(instanceWeka);
+		        		  double[] prob = new double[2];
+		        		  int predictedValue = classifier.predict(values, prob);
 		        		  relevance = LinkRelevance.DEFAULT_AUTH_RELEVANCE + (prob[0]*100);
 		        	  }
 			          linkRelevance[count] = new LinkRelevance(url, relevance);
@@ -90,9 +87,8 @@ public LinkRelevance classify(LinkNeighborhood ln) throws LinkClassifierExceptio
 		    		  if(classifier != null){
 		    			  Instance instance = (Instance) entry.getValue();
 		    			  double[] values = instance.getValues();
-		    			  weka.core.Instance instanceWeka = new weka.core.Instance(1, values);
-		    			  instanceWeka.setDataset(instances);
-		    			  double[] prob = classifier.distributionForInstance(instanceWeka);
+		    			  double[] prob = new double[2];
+		        		  int predictedValue = ((SVM<double[]>) classifier).predict(values, prob);
 		    			  if(prob[0] == 1){
 		    				  prob[0] = 0.99;
 		    			  }

src/main/java/focusedCrawler/link/classifier/LinkClassifierHub.java

@@ -9,8 +9,9 @@
 import focusedCrawler.link.frontier.LinkRelevance;
 import focusedCrawler.target.model.Page;
 import focusedCrawler.util.parser.LinkNeighborhood;
-import weka.classifiers.Classifier;
-import weka.core.Instances;
+import smile.classification.SoftClassifier;
+import smile.classification.SVM;
+
 
 /**
  * This class implements the link classifier for the hub links.
@@ -19,18 +20,16 @@
  */
 public class LinkClassifierHub implements LinkClassifier{
 
-	private Classifier classifier;
-	private Instances instances;
+	private SoftClassifier<double[]> classifier;
 	private LinkNeighborhoodWrapper wrapper;
 	private String[] attributes;
 
 	public LinkClassifierHub(){
 
 	}
 
-	public LinkClassifierHub(Classifier classifier, Instances instances, LinkNeighborhoodWrapper wrapper,String[] attributes) {
+	public LinkClassifierHub(SoftClassifier<double[]> classifier, LinkNeighborhoodWrapper wrapper,String[] attributes) {
 		this.classifier = classifier;
-		this.instances = instances;
 		this.wrapper = wrapper;
 		this.attributes = attributes;
 	}
@@ -47,9 +46,8 @@ public LinkRelevance classify(LinkNeighborhood ln) throws LinkClassifierExceptio
 					String url = (String)iter.next();
 			        Instance instance = (Instance)urlWords.get(url);
 			        double[] values = instance.getValues();
-			        weka.core.Instance instanceWeka = new weka.core.Instance(1, values);
-			        instanceWeka.setDataset(instances);
-			        double[] prob = classifier.distributionForInstance(instanceWeka);
+			        double[] prob = new double[2];
+			        int predictedValue = ((SVM<double[]>)classifier).predict(values, prob);
 			        double relevance = LinkRelevance.DEFAULT_HUB_RELEVANCE + prob[0]*100;
 			        result = new LinkRelevance(ln.getLink(),relevance);
 				}