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Subject: svn commit: r1140264 - in /mahout/trunk:
 core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/
 src/conf/
Date: Mon, 27 Jun 2011 18:46:46 -0000
To: commits@mahout.apache.org
From: srowen@apache.org
Message-Id: <20110627184646.ABFE223888CB@eris.apache.org>

Author: srowen
Date: Mon Jun 27 18:46:46 2011
New Revision: 1140264

URL: http://svn.apache.org/viewvc?rev=1140264&view=rev
Log:
MAHOUT-734 add HMM command lines

Added:
    mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/BaumWelchTrainer.java
    mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/LossyHmmSerializer.java
    mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/RandomSequenceGenerator.java
    mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/ViterbiEvaluator.java
Modified:
    mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmModel.java
    mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmTrainer.java
    mahout/trunk/src/conf/driver.classes.props

Added: mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/BaumWelchTrainer.java
URL: http://svn.apache.org/viewvc/mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/BaumWelchTrainer.java?rev=1140264&view=auto
==============================================================================
--- mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/BaumWelchTrainer.java (added)
+++ mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/BaumWelchTrainer.java Mon Jun 27 18:46:46 2011
@@ -0,0 +1,169 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.mahout.classifier.sequencelearning.hmm;
+
+import com.google.common.io.Closeables;
+import org.apache.commons.cli2.CommandLine;
+import org.apache.commons.cli2.Group;
+import org.apache.commons.cli2.Option;
+import org.apache.commons.cli2.OptionException;
+import org.apache.commons.cli2.builder.ArgumentBuilder;
+import org.apache.commons.cli2.builder.DefaultOptionBuilder;
+import org.apache.commons.cli2.builder.GroupBuilder;
+import org.apache.commons.cli2.commandline.Parser;
+import org.apache.mahout.common.CommandLineUtil;
+
+import java.io.DataOutputStream;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.Scanner;
+
+/**
+ * A class for EM training of HMM from console
+ */
+public final class BaumWelchTrainer {
+
+  private BaumWelchTrainer() {
+  }
+
+  public static void main(String[] args) throws IOException {
+    DefaultOptionBuilder optionBuilder = new DefaultOptionBuilder();
+    ArgumentBuilder argumentBuilder = new ArgumentBuilder();
+
+    Option inputOption = optionBuilder.withLongName("input").
+      withDescription("Text file with space-separated integers to train on").
+      withShortName("i").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("path").create()).withRequired(true).create();
+
+    Option outputOption = optionBuilder.withLongName("output").
+      withDescription("Path trained HMM model should be serialized to").
+      withShortName("o").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("path").create()).withRequired(true).create();
+
+    Option stateNumberOption = optionBuilder.withLongName("nrOfHiddenStates").
+      withDescription("Number of hidden states").
+      withShortName("nh").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("number").create()).withRequired(true).create();
+
+    Option observedStateNumberOption = optionBuilder.withLongName("nrOfObservedStates").
+      withDescription("Number of observed states").
+      withShortName("no").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("number").create()).withRequired(true).create();
+
+    Option epsilonOption = optionBuilder.withLongName("epsilon").
+      withDescription("Convergence threshold").
+      withShortName("e").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("number").create()).withRequired(true).create();
+
+    Option iterationsOption = optionBuilder.withLongName("max-iterations").
+      withDescription("Maximum iterations number").
+      withShortName("m").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("number").create()).withRequired(true).create();
+
+    Group optionGroup = new GroupBuilder().withOption(inputOption).
+      withOption(outputOption).withOption(stateNumberOption).withOption(observedStateNumberOption).
+      withOption(epsilonOption).withOption(iterationsOption).
+      withName("Options").create();
+
+    try {
+      Parser parser = new Parser();
+      parser.setGroup(optionGroup);
+      CommandLine commandLine = parser.parse(args);
+
+      String input = (String) commandLine.getValue(inputOption);
+      String output = (String) commandLine.getValue(outputOption);
+
+      int nrOfHiddenStates = Integer.parseInt((String) commandLine.getValue(stateNumberOption));
+      int nrOfObservedStates = Integer.parseInt((String) commandLine.getValue(observedStateNumberOption));
+
+      double epsilon = Double.parseDouble((String) commandLine.getValue(epsilonOption));
+      int maxIterations = Integer.parseInt((String) commandLine.getValue(iterationsOption));
+
+      //constructing random-generated HMM
+      HmmModel model = new HmmModel(nrOfHiddenStates, nrOfObservedStates, new Date().getTime());
+      List<Integer> observations = new ArrayList<Integer>();
+
+      //reading observations
+      Scanner scanner = new Scanner(new FileInputStream(input));
+      try {
+        while (scanner.hasNextInt()) {
+          observations.add(scanner.nextInt());
+        }
+      } finally {
+        scanner.close();
+      }
+
+      int[] observationsArray = new int[observations.size()];
+      for (int i = 0; i < observations.size(); ++i) {
+        observationsArray[i] = observations.get(i);
+      }
+
+      //training
+      HmmModel trainedModel = HmmTrainer.trainBaumWelch(model,
+        observationsArray, epsilon, maxIterations, true);
+
+      //serializing trained model
+      DataOutputStream stream  = new DataOutputStream(new FileOutputStream(output));
+      try {
+        LossyHmmSerializer.serialize(trainedModel, stream);
+      } finally {
+        Closeables.closeQuietly(stream);
+      }
+
+      //printing tranied model
+      System.out.println("Initial probabilities: ");
+      for (int i = 0; i < trainedModel.getNrOfHiddenStates(); ++i)
+        System.out.print(i + " ");
+      System.out.println();
+      for (int i = 0; i < trainedModel.getNrOfHiddenStates(); ++i)
+        System.out.print(trainedModel.getInitialProbabilities().get(i) + " ");
+      System.out.println();
+
+      System.out.println("Transition matrix:");
+      System.out.print("  ");
+      for (int i = 0; i < trainedModel.getNrOfHiddenStates(); ++i)
+        System.out.print(i + " ");
+      System.out.println();
+      for (int i = 0; i < trainedModel.getNrOfHiddenStates(); ++i) {
+        System.out.print(i + " ");
+        for (int j = 0; j < trainedModel.getNrOfHiddenStates(); ++j) {
+          System.out.print(trainedModel.getTransitionMatrix().get(i, j) + " ");
+        }
+        System.out.println();
+      }
+      System.out.println("Emission matrix: ");
+      System.out.print("  ");
+      for (int i = 0; i < trainedModel.getNrOfOutputStates(); ++i)
+        System.out.print(i + " ");
+      System.out.println();
+      for (int i = 0; i < trainedModel.getNrOfHiddenStates(); ++i) {
+        System.out.print(i + " ");
+        for (int j = 0; j < trainedModel.getNrOfOutputStates(); ++j) {
+          System.out.print(trainedModel.getEmissionMatrix().get(i, j) + " ");
+        }
+        System.out.println();
+      }
+    } catch (OptionException e) {
+      CommandLineUtil.printHelp(optionGroup);
+    }
+  }
+}

Modified: mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmModel.java
URL: http://svn.apache.org/viewvc/mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmModel.java?rev=1140264&r1=1140263&r2=1140264&view=diff
==============================================================================
--- mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmModel.java (original)
+++ mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmModel.java Mon Jun 27 18:46:46 2011
@@ -78,8 +78,7 @@ public class HmmModel implements Cloneab
    * Get a copy of this model
    */
   @Override
-  public HmmModel clone() throws CloneNotSupportedException {
-    super.clone();
+  public HmmModel clone() {
     HmmModel model = new HmmModel(transitionMatrix.clone(), emissionMatrix.clone(), initialProbabilities.clone());
     if (hiddenStateNames != null) {
       model.hiddenStateNames = HashBiMap.create(hiddenStateNames);

Modified: mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmTrainer.java
URL: http://svn.apache.org/viewvc/mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmTrainer.java?rev=1140264&r1=1140263&r2=1140264&view=diff
==============================================================================
--- mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmTrainer.java (original)
+++ mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/HmmTrainer.java Mon Jun 27 18:46:46 2011
@@ -220,14 +220,8 @@ public final class HmmTrainer {
     pseudoCount = pseudoCount == 0 ? Double.MIN_VALUE : pseudoCount;
 
     // allocate space for iteration models
-    HmmModel lastIteration;
-    HmmModel iteration;
-    try {
-      lastIteration = initialModel.clone();
-      iteration = initialModel.clone();
-    } catch (CloneNotSupportedException e) {
-      throw new UnknownError("Cloning HmmModels broke. Check for programming errors, changed APIs.");
-    }
+    HmmModel lastIteration = initialModel.clone();
+    HmmModel iteration = initialModel.clone();
 
     // allocate space for Viterbi path calculation
     int[] viterbiPath = new int[observedSequence.length];
@@ -301,14 +295,9 @@ public final class HmmTrainer {
   public static HmmModel trainBaumWelch(HmmModel initialModel,
                                         int[] observedSequence, double epsilon, int maxIterations, boolean scaled) {
     // allocate space for the iterations
-    HmmModel lastIteration;
-    HmmModel iteration;
-    try {
-      lastIteration = initialModel.clone();
-      iteration = initialModel.clone();
-    } catch (CloneNotSupportedException e) {
-      throw new UnknownError("Cloning HmmModels broke. Check for programming errors, changed APIs etc.");
-    }
+    HmmModel lastIteration = initialModel.clone();
+    HmmModel iteration = initialModel.clone();
+
     // allocate space for baum-welch factors
     int hiddenCount = initialModel.getNrOfHiddenStates();
     int visibleCount = observedSequence.length;

Added: mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/LossyHmmSerializer.java
URL: http://svn.apache.org/viewvc/mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/LossyHmmSerializer.java?rev=1140264&view=auto
==============================================================================
--- mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/LossyHmmSerializer.java (added)
+++ mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/LossyHmmSerializer.java Mon Jun 27 18:46:46 2011
@@ -0,0 +1,62 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.mahout.classifier.sequencelearning.hmm;
+
+import org.apache.mahout.math.Matrix;
+import org.apache.mahout.math.MatrixWritable;
+import org.apache.mahout.math.Vector;
+import org.apache.mahout.math.VectorWritable;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+
+/**
+ * Utils for serializing Writable parts of HmmModel (that means without hidden state names and so on)
+ */
+final class LossyHmmSerializer {
+
+  private LossyHmmSerializer() {
+  }
+
+  static void serialize(HmmModel model, DataOutput output) throws IOException {
+    MatrixWritable matrix = new MatrixWritable(model.getEmissionMatrix());
+    matrix.write(output);
+    matrix.set(model.getTransitionMatrix());
+    matrix.write(output);
+
+    VectorWritable vector = new VectorWritable(model.getInitialProbabilities());
+    vector.write(output);
+  }
+
+  static HmmModel deserialize(DataInput input) throws IOException {
+    MatrixWritable matrix = new MatrixWritable();
+    matrix.readFields(input);
+    Matrix emissionMatrix = matrix.get();
+
+    matrix.readFields(input);
+    Matrix transitionMatrix = matrix.get();
+
+    VectorWritable vector = new VectorWritable();
+    vector.readFields(input);
+    Vector initialProbabilities = vector.get();
+
+    return new HmmModel(transitionMatrix, emissionMatrix, initialProbabilities);
+  }
+
+}

Added: mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/RandomSequenceGenerator.java
URL: http://svn.apache.org/viewvc/mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/RandomSequenceGenerator.java?rev=1140264&view=auto
==============================================================================
--- mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/RandomSequenceGenerator.java (added)
+++ mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/RandomSequenceGenerator.java Mon Jun 27 18:46:46 2011
@@ -0,0 +1,106 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+package org.apache.mahout.classifier.sequencelearning.hmm;
+
+import com.google.common.io.Closeables;
+import org.apache.commons.cli2.CommandLine;
+import org.apache.commons.cli2.Group;
+import org.apache.commons.cli2.Option;
+import org.apache.commons.cli2.OptionException;
+import org.apache.commons.cli2.builder.ArgumentBuilder;
+import org.apache.commons.cli2.builder.DefaultOptionBuilder;
+import org.apache.commons.cli2.builder.GroupBuilder;
+import org.apache.commons.cli2.commandline.Parser;
+import org.apache.mahout.common.CommandLineUtil;
+
+import java.io.DataInputStream;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintWriter;
+
+/**
+ * Command-line tool for generating random sequences by given HMM
+ */
+public final class RandomSequenceGenerator {
+
+  private RandomSequenceGenerator() {
+  }
+
+  public static void main(String[] args) throws IOException {
+    DefaultOptionBuilder optionBuilder = new DefaultOptionBuilder();
+    ArgumentBuilder argumentBuilder = new ArgumentBuilder();
+
+    Option outputOption = optionBuilder.withLongName("output").
+      withDescription("Output file with sequence of observed states").
+      withShortName("o").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("path").create()).withRequired(false).create();
+
+    Option modelOption = optionBuilder.withLongName("model").
+      withDescription("Path to serialized HMM model").
+      withShortName("m").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("path").create()).withRequired(true).create();
+
+    Option lengthOption = optionBuilder.withLongName("length").
+      withDescription("Length of generated sequence").
+      withShortName("l").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("number").create()).withRequired(true).create();
+
+    Group optionGroup = new GroupBuilder().
+      withOption(outputOption).withOption(modelOption).withOption(lengthOption).
+      withName("Options").create();
+
+    try {
+      Parser parser = new Parser();
+      parser.setGroup(optionGroup);
+      CommandLine commandLine = parser.parse(args);
+
+      String output = (String) commandLine.getValue(outputOption);
+
+      String modelPath = (String) commandLine.getValue(modelOption);
+
+      int length = Integer.parseInt((String) commandLine.getValue(lengthOption));
+
+      //reading serialized HMM
+      DataInputStream modelStream = new DataInputStream(new FileInputStream(modelPath));
+      HmmModel model;
+      try {
+        model = LossyHmmSerializer.deserialize(modelStream);
+      } finally {
+        Closeables.closeQuietly(modelStream);
+      }
+
+      //generating observations
+      int[] observations = HmmEvaluator.predict(model, length, System.currentTimeMillis());
+
+      //writing output
+      PrintWriter writer = new PrintWriter(new FileOutputStream(output));
+      try {
+        for (int observation : observations) {
+          writer.print(observation);
+          writer.print(' ');
+        }
+      } finally {
+        Closeables.closeQuietly(writer);
+      }
+    } catch (OptionException e) {
+      CommandLineUtil.printHelp(optionGroup);
+    }
+  }
+}

Added: mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/ViterbiEvaluator.java
URL: http://svn.apache.org/viewvc/mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/ViterbiEvaluator.java?rev=1140264&view=auto
==============================================================================
--- mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/ViterbiEvaluator.java (added)
+++ mahout/trunk/core/src/main/java/org/apache/mahout/classifier/sequencelearning/hmm/ViterbiEvaluator.java Mon Jun 27 18:46:46 2011
@@ -0,0 +1,133 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.mahout.classifier.sequencelearning.hmm;
+
+import com.google.common.io.Closeables;
+import org.apache.commons.cli2.CommandLine;
+import org.apache.commons.cli2.Group;
+import org.apache.commons.cli2.Option;
+import org.apache.commons.cli2.OptionException;
+import org.apache.commons.cli2.builder.ArgumentBuilder;
+import org.apache.commons.cli2.builder.DefaultOptionBuilder;
+import org.apache.commons.cli2.builder.GroupBuilder;
+import org.apache.commons.cli2.commandline.Parser;
+import org.apache.mahout.common.CommandLineUtil;
+
+import java.io.DataInputStream;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Scanner;
+
+/**
+ * Command-line tool for Viterbi evaluating
+ */
+public final class ViterbiEvaluator {
+
+  private ViterbiEvaluator() {
+  }
+
+  public static void main(String[] args) throws IOException {
+    DefaultOptionBuilder optionBuilder = new DefaultOptionBuilder();
+    ArgumentBuilder argumentBuilder = new ArgumentBuilder();
+
+    Option inputOption = optionBuilder.withLongName("input").
+      withDescription("Text file with space-separated integers to segment").
+      withShortName("i").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("path").create()).withRequired(true).create();
+
+    Option outputOption = optionBuilder.withLongName("output").
+      withDescription("Output file with decoded sequence of hidden states").
+      withShortName("o").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("path").create()).withRequired(true).create();
+
+    Option modelOption = optionBuilder.withLongName("model").
+      withDescription("Path to serialized HMM model").
+      withShortName("m").withArgument(argumentBuilder.withMaximum(1).withMinimum(1).
+      withName("path").create()).withRequired(true).create();
+
+    Option likelihoodOption = optionBuilder.withLongName("likelihood").
+      withDescription("Compute likelihood of observed sequence").
+      withShortName("l").withRequired(false).create();
+
+    Group optionGroup = new GroupBuilder().withOption(inputOption).
+      withOption(outputOption).withOption(modelOption).withOption(likelihoodOption).
+      withName("Options").create();
+
+    try {
+      Parser parser = new Parser();
+      parser.setGroup(optionGroup);
+      CommandLine commandLine = parser.parse(args);
+
+      String input = (String) commandLine.getValue(inputOption);
+      String output = (String) commandLine.getValue(outputOption);
+
+      String modelPath = (String) commandLine.getValue(modelOption);
+
+      boolean computeLikelihood = commandLine.hasOption(likelihoodOption);
+
+      //reading serialized HMM
+      DataInputStream modelStream = new DataInputStream(new FileInputStream(modelPath));
+      HmmModel model;
+      try {
+        model = LossyHmmSerializer.deserialize(modelStream);
+      } finally {
+        Closeables.closeQuietly(modelStream);
+      }
+
+      //reading observations
+      List<Integer> observations = new ArrayList<Integer>();
+      Scanner scanner = new Scanner(new FileInputStream(input));
+      try {
+        while (scanner.hasNextInt()) {
+          observations.add(scanner.nextInt());
+        }
+      } finally {
+        scanner.close();
+      }
+
+      int[] observationsArray = new int[observations.size()];
+      for (int i = 0; i < observations.size(); ++i) {
+        observationsArray[i] = observations.get(i);
+      }
+
+      //decoding
+      int[] hiddenStates = HmmEvaluator.decode(model, observationsArray, true);
+
+      //writing output
+      PrintWriter writer = new PrintWriter(new FileOutputStream(output));
+      try {
+        for (int hiddenState : hiddenStates) {
+          writer.print(hiddenState);
+          writer.print(' ');
+        }
+      } finally {
+        Closeables.closeQuietly(writer);
+      }
+
+      if (computeLikelihood) {
+        System.out.println("Likelihood: " + HmmEvaluator.modelLikelihood(model, observationsArray, true));
+      }
+    } catch (OptionException e) {
+      CommandLineUtil.printHelp(optionGroup);
+    }
+  }
+}

Modified: mahout/trunk/src/conf/driver.classes.props
URL: http://svn.apache.org/viewvc/mahout/trunk/src/conf/driver.classes.props?rev=1140264&r1=1140263&r2=1140264&view=diff
==============================================================================
--- mahout/trunk/src/conf/driver.classes.props (original)
+++ mahout/trunk/src/conf/driver.classes.props Mon Jun 27 18:46:46 2011
@@ -37,4 +37,7 @@ org.apache.mahout.math.hadoop.stochastic
 org.apache.mahout.clustering.spectral.eigencuts.EigencutsDriver = eigencuts : Eigencuts spectral clustering
 org.apache.mahout.clustering.spectral.kmeans.SpectralKMeansDriver = spectralkmeans : Spectral k-means clustering 
 org.apache.mahout.cf.taste.hadoop.als.ParallelALSFactorizationJob = parallelALS : ALS-WR factorization of a rating matrix
-org.apache.mahout.cf.taste.hadoop.als.PredictionJob = predictFromFactorization : predict preferences from a factorization of a rating matrix
\ No newline at end of file
+org.apache.mahout.cf.taste.hadoop.als.PredictionJob = predictFromFactorization : predict preferences from a factorization of a rating matrix
+org.apache.mahout.classifier.sequencelearning.hmm.BaumWelchTrainer = baumwelch : Baum-Welch algorithm for unsupervised HMM training
+org.apache.mahout.classifier.sequencelearning.hmm.ViterbiEvaluator = viterbi : Viterbi decoding of hidden states from given output states sequence
+org.apache.mahout.classifier.sequencelearning.hmm.RandomSequenceGenerator = hmmpredict : Generate random sequence of observations by given HMM