/*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* IBk.java
* Copyright (C) 1999-2012 University of Waikato, Hamilton, New Zealand
*
*/
package weka.classifiers.lazy;
import java.util.Enumeration;
import java.util.Vector;
import weka.classifiers.AbstractClassifier;
import weka.classifiers.UpdateableClassifier;
import weka.classifiers.rules.ZeroR;
import weka.core.AdditionalMeasureProducer;
import weka.core.Attribute;
import weka.core.Capabilities;
import weka.core.Capabilities.Capability;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionUtils;
import weka.core.SelectedTag;
import weka.core.Tag;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.core.WeightedInstancesHandler;
import weka.core.neighboursearch.LinearNNSearch;
import weka.core.neighboursearch.NearestNeighbourSearch;
/**
<!-- globalinfo-start -->
* K-nearest neighbours classifier. Can select appropriate value of K based on cross-validation. Can also do distance weighting.<br/>
* <br/>
* For more information, see<br/>
* <br/>
* D. Aha, D. Kibler (1991). Instance-based learning algorithms. Machine Learning. 6:37-66.
* <p/>
<!-- globalinfo-end -->
*
<!-- technical-bibtex-start -->
* BibTeX:
* <pre>
* @article{Aha1991,
* author = {D. Aha and D. Kibler},
* journal = {Machine Learning},
* pages = {37-66},
* title = {Instance-based learning algorithms},
* volume = {6},
* year = {1991}
* }
* </pre>
* <p/>
<!-- technical-bibtex-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -I
* Weight neighbours by the inverse of their distance
* (use when k > 1)</pre>
*
* <pre> -F
* Weight neighbours by 1 - their distance
* (use when k > 1)</pre>
*
* <pre> -K <number of neighbors>
* Number of nearest neighbours (k) used in classification.
* (Default = 1)</pre>
*
* <pre> -E
* Minimise mean squared error rather than mean absolute
* error when using -X option with numeric prediction.</pre>
*
* <pre> -W <window size>
* Maximum number of training instances maintained.
* Training instances are dropped FIFO. (Default = no window)</pre>
*
* <pre> -X
* Select the number of nearest neighbours between 1
* and the k value specified using hold-one-out evaluation
* on the training data (use when k > 1)</pre>
*
* <pre> -A
* The nearest neighbour search algorithm to use (default: weka.core.neighboursearch.LinearNNSearch).
* </pre>
*
<!-- options-end -->
*
* @author Stuart Inglis (singlis@cs.waikato.ac.nz)
* @author Len Trigg (trigg@cs.waikato.ac.nz)
* @author Eibe Frank (eibe@cs.waikato.ac.nz)
* @version $Revision: 8034 $
*/
public class IBk
extends AbstractClassifier
implements OptionHandler, UpdateableClassifier, WeightedInstancesHandler,
TechnicalInformationHandler, AdditionalMeasureProducer {
/** for serialization. */
static final long serialVersionUID = -3080186098777067172L;
/** The training instances used for classification. */
protected Instances m_Train;
/** The number of class values (or 1 if predicting numeric). */
protected int m_NumClasses;
/** The class attribute type. */
protected int m_ClassType;
/** The number of neighbours to use for classification (currently). */
protected int m_kNN;
/**
* The value of kNN provided by the user. This may differ from
* m_kNN if cross-validation is being used.
*/
protected int m_kNNUpper;
/**
* Whether the value of k selected by cross validation has
* been invalidated by a change in the training instances.
*/
protected boolean m_kNNValid;
/**
* The maximum number of training instances allowed. When
* this limit is reached, old training instances are removed,
* so the training data is "windowed". Set to 0 for unlimited
* numbers of instances.
*/
protected int m_WindowSize;
/** Whether the neighbours should be distance-weighted. */
protected int m_DistanceWeighting;
/** Whether to select k by cross validation. */
protected boolean m_CrossValidate;
/**
* Whether to minimise mean squared error rather than mean absolute
* error when cross-validating on numeric prediction tasks.
*/
protected boolean m_MeanSquared;
/** Default ZeroR model to use when there are no training instances */
protected ZeroR m_defaultModel;
/** no weighting. */
public static final int WEIGHT_NONE = 1;
/** weight by 1/distance. */
public static final int WEIGHT_INVERSE = 2;
/** weight by 1-distance. */
public static final int WEIGHT_SIMILARITY = 4;
/** possible instance weighting methods. */
public static final Tag [] TAGS_WEIGHTING = {
new Tag(WEIGHT_NONE, "No distance weighting"),
new Tag(WEIGHT_INVERSE, "Weight by 1/distance"),
new Tag(WEIGHT_SIMILARITY, "Weight by 1-distance")
};
/** for nearest-neighbor search. */
protected NearestNeighbourSearch m_NNSearch = new LinearNNSearch();
/** The number of attributes the contribute to a prediction. */
protected double m_NumAttributesUsed;
/**
* IBk classifier. Simple instance-based learner that uses the class
* of the nearest k training instances for the class of the test
* instances.
*
* @param k the number of nearest neighbors to use for prediction
*/
public IBk(int k) {
init();
setKNN(k);
}
/**
* IB1 classifer. Instance-based learner. Predicts the class of the
* single nearest training instance for each test instance.
*/
public IBk() {
init();
}
/**
* Returns a string describing classifier.
* @return a description suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return "K-nearest neighbours classifier. Can "
+ "select appropriate value of K based on cross-validation. Can also do "
+ "distance weighting.\n\n"
+ "For more information, see\n\n"
+ getTechnicalInformation().toString();
}
/**
* Returns an instance of a TechnicalInformation object, containing
* detailed information about the technical background of this class,
* e.g., paper reference or book this class is based on.
*
* @return the technical information about this class
*/
public TechnicalInformation getTechnicalInformation() {
TechnicalInformation result;
result = new TechnicalInformation(Type.ARTICLE);
result.setValue(Field.AUTHOR, "D. Aha and D. Kibler");
result.setValue(Field.YEAR, "1991");
result.setValue(Field.TITLE, "Instance-based learning algorithms");
result.setValue(Field.JOURNAL, "Machine Learning");
result.setValue(Field.VOLUME, "6");
result.setValue(Field.PAGES, "37-66");
return result;
}
/**
* Returns the tip text for this property.
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String KNNTipText() {
return "The number of neighbours to use.";
}
/**
* Set the number of neighbours the learner is to use.
*
* @param k the number of neighbours.
*/
public void setKNN(int k) {
m_kNN = k;
m_kNNUpper = k;
m_kNNValid = false;
}
/**
* Gets the number of neighbours the learner will use.
*
* @return the number of neighbours.
*/
public int getKNN() {
return m_kNN;
}
/**
* Returns the tip text for this property.
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String windowSizeTipText() {
return "Gets the maximum number of instances allowed in the training " +
"pool. The addition of new instances above this value will result " +
"in old instances being removed. A value of 0 signifies no limit " +
"to the number of training instances.";
}
/**
* Gets the maximum number of instances allowed in the training
* pool. The addition of new instances above this value will result
* in old instances being removed. A value of 0 signifies no limit
* to the number of training instances.
*
* @return Value of WindowSize.
*/
public int getWindowSize() {
return m_WindowSize;
}
/**
* Sets the maximum number of instances allowed in the training
* pool. The addition of new instances above this value will result
* in old instances being removed. A value of 0 signifies no limit
* to the number of training instances.
*
* @param newWindowSize Value to assign to WindowSize.
*/
public void setWindowSize(int newWindowSize) {
m_WindowSize = newWindowSize;
}
/**
* Returns the tip text for this property.
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String distanceWeightingTipText() {
return "Gets the distance weighting method used.";
}
/**
* Gets the distance weighting method used. Will be one of
* WEIGHT_NONE, WEIGHT_INVERSE, or WEIGHT_SIMILARITY
*
* @return the distance weighting method used.
*/
public SelectedTag getDistanceWeighting() {
return new SelectedTag(m_DistanceWeighting, TAGS_WEIGHTING);
}
/**
* Sets the distance weighting method used. Values other than
* WEIGHT_NONE, WEIGHT_INVERSE, or WEIGHT_SIMILARITY will be ignored.
*
* @param newMethod the distance weighting method to use
*/
public void setDistanceWeighting(SelectedTag newMethod) {
if (newMethod.getTags() == TAGS_WEIGHTING) {
m_DistanceWeighting = newMethod.getSelectedTag().getID();
}
}
/**
* Returns the tip text for this property.
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String meanSquaredTipText() {
return "Whether the mean squared error is used rather than mean "
+ "absolute error when doing cross-validation for regression problems.";
}
/**
* Gets whether the mean squared error is used rather than mean
* absolute error when doing cross-validation.
*
* @return true if so.
*/
public boolean getMeanSquared() {
return m_MeanSquared;
}
/**
* Sets whether the mean squared error is used rather than mean
* absolute error when doing cross-validation.
*
* @param newMeanSquared true if so.
*/
public void setMeanSquared(boolean newMeanSquared) {
m_MeanSquared = newMeanSquared;
}
/**
* Returns the tip text for this property.
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String crossValidateTipText() {
return "Whether hold-one-out cross-validation will be used " +
"to select the best k value.";
}
/**
* Gets whether hold-one-out cross-validation will be used
* to select the best k value.
*
* @return true if cross-validation will be used.
*/
public boolean getCrossValidate() {
return m_CrossValidate;
}
/**
* Sets whether hold-one-out cross-validation will be used
* to select the best k value.
*
* @param newCrossValidate true if cross-validation should be used.
*/
public void setCrossValidate(boolean newCrossValidate) {
m_CrossValidate = newCrossValidate;
}
/**
* Returns the tip text for this property.
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String nearestNeighbourSearchAlgorithmTipText() {
return "The nearest neighbour search algorithm to use " +
"(Default: weka.core.neighboursearch.LinearNNSearch).";
}
/**
* Returns the current nearestNeighbourSearch algorithm in use.
* @return the NearestNeighbourSearch algorithm currently in use.
*/
public NearestNeighbourSearch getNearestNeighbourSearchAlgorithm() {
return m_NNSearch;
}
/**
* Sets the nearestNeighbourSearch algorithm to be used for finding nearest
* neighbour(s).
* @param nearestNeighbourSearchAlgorithm - The NearestNeighbourSearch class.
*/
public void setNearestNeighbourSearchAlgorithm(NearestNeighbourSearch nearestNeighbourSearchAlgorithm) {
m_NNSearch = nearestNeighbourSearchAlgorithm;
}
/**
* Get the number of training instances the classifier is currently using.
*
* @return the number of training instances the classifier is currently using
*/
public int getNumTraining() {
return m_Train.numInstances();
}
/**
* Returns default capabilities of the classifier.
*
* @return the capabilities of this classifier
*/
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
result.disableAll();
// attributes
result.enable(Capability.NOMINAL_ATTRIBUTES);
result.enable(Capability.NUMERIC_ATTRIBUTES);
result.enable(Capability.DATE_ATTRIBUTES);
result.enable(Capability.MISSING_VALUES);
// class
result.enable(Capability.NOMINAL_CLASS);
result.enable(Capability.NUMERIC_CLASS);
result.enable(Capability.DATE_CLASS);
result.enable(Capability.MISSING_CLASS_VALUES);
// instances
result.setMinimumNumberInstances(0);
return result;
}
/**
* Generates the classifier.
*
* @param instances set of instances serving as training data
* @throws Exception if the classifier has not been generated successfully
*/
public void buildClassifier(Instances instances) throws Exception {
// can classifier handle the data?
getCapabilities().testWithFail(instances);
// remove instances with missing class
instances = new Instances(instances);
instances.deleteWithMissingClass();
m_NumClasses = instances.numClasses();
m_ClassType = instances.classAttribute().type();
m_Train = new Instances(instances, 0, instances.numInstances());
// Throw away initial instances until within the specified window size
if ((m_WindowSize > 0) && (instances.numInstances() > m_WindowSize)) {
m_Train = new Instances(m_Train,
m_Train.numInstances()-m_WindowSize,
m_WindowSize);
}
m_NumAttributesUsed = 0.0;
for (int i = 0; i < m_Train.numAttributes(); i++) {
if ((i != m_Train.classIndex()) &&
(m_Train.attribute(i).isNominal() ||
m_Train.attribute(i).isNumeric())) {
m_NumAttributesUsed += 1.0;
}
}
m_NNSearch.setInstances(m_Train);
// Invalidate any currently cross-validation selected k
m_kNNValid = false;
m_defaultModel = new ZeroR();
m_defaultModel.buildClassifier(instances);
}
/**
* Adds the supplied instance to the training set.
*
* @param instance the instance to add
* @throws Exception if instance could not be incorporated
* successfully
*/
public void updateClassifier(Instance instance) throws Exception {
if (m_Train.equalHeaders(instance.dataset()) == false) {
throw new Exception("Incompatible instance types\n" + m_Train.equalHeadersMsg(instance.dataset()));
}
if (instance.classIsMissing()) {
return;
}
m_Train.add(instance);
m_NNSearch.update(instance);
m_kNNValid = false;
if ((m_WindowSize > 0) && (m_Train.numInstances() > m_WindowSize)) {
boolean deletedInstance=false;
while (m_Train.numInstances() > m_WindowSize) {
m_Train.delete(0);
deletedInstance=true;
}
//rebuild datastructure KDTree currently can't delete
if(deletedInstance==true)
m_NNSearch.setInstances(m_Train);
}
}
/**
* Calculates the class membership probabilities for the given test instance.
*
* @param instance the instance to be classified
* @return predicted class probability distribution
* @throws Exception if an error occurred during the prediction
*/
public double [] distributionForInstance(Instance instance) throws Exception {
if (m_Train.numInstances() == 0) {
//throw new Exception("No training instances!");
return m_defaultModel.distributionForInstance(instance);
}
if ((m_WindowSize > 0) && (m_Train.numInstances() > m_WindowSize)) {
m_kNNValid = false;
boolean deletedInstance=false;
while (m_Train.numInstances() > m_WindowSize) {
m_Train.delete(0);
}
//rebuild datastructure KDTree currently can't delete
if(deletedInstance==true)
m_NNSearch.setInstances(m_Train);
}
// Select k by cross validation
if (!m_kNNValid && (m_CrossValidate) && (m_kNNUpper >= 1)) {
crossValidate();
}
m_NNSearch.addInstanceInfo(instance);
Instances neighbours = m_NNSearch.kNearestNeighbours(instance, m_kNN);
double [] distances = m_NNSearch.getDistances();
double [] distribution = makeDistribution( neighbours, distances );
return distribution;
}
/**
* Returns an enumeration describing the available options.
*
* @return an enumeration of all the available options.
*/
public Enumeration listOptions() {
Vector newVector = new Vector(8);
newVector.addElement(new Option(
"\tWeight neighbours by the inverse of their distance\n"+
"\t(use when k > 1)",
"I", 0, "-I"));
newVector.addElement(new Option(
"\tWeight neighbours by 1 - their distance\n"+
"\t(use when k > 1)",
"F", 0, "-F"));
newVector.addElement(new Option(
"\tNumber of nearest neighbours (k) used in classification.\n"+
"\t(Default = 1)",
"K", 1,"-K <number of neighbors>"));
newVector.addElement(new Option(
"\tMinimise mean squared error rather than mean absolute\n"+
"\terror when using -X option with numeric prediction.",
"E", 0,"-E"));
newVector.addElement(new Option(
"\tMaximum number of training instances maintained.\n"+
"\tTraining instances are dropped FIFO. (Default = no window)",
"W", 1,"-W <window size>"));
newVector.addElement(new Option(
"\tSelect the number of nearest neighbours between 1\n"+
"\tand the k value specified using hold-one-out evaluation\n"+
"\ton the training data (use when k > 1)",
"X", 0,"-X"));
newVector.addElement(new Option(
"\tThe nearest neighbour search algorithm to use "+
"(default: weka.core.neighboursearch.LinearNNSearch).\n",
"A", 0, "-A"));
return newVector.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -I
* Weight neighbours by the inverse of their distance
* (use when k > 1)</pre>
*
* <pre> -F
* Weight neighbours by 1 - their distance
* (use when k > 1)</pre>
*
* <pre> -K <number of neighbors>
* Number of nearest neighbours (k) used in classification.
* (Default = 1)</pre>
*
* <pre> -E
* Minimise mean squared error rather than mean absolute
* error when using -X option with numeric prediction.</pre>
*
* <pre> -W <window size>
* Maximum number of training instances maintained.
* Training instances are dropped FIFO. (Default = no window)</pre>
*
* <pre> -X
* Select the number of nearest neighbours between 1
* and the k value specified using hold-one-out evaluation
* on the training data (use when k > 1)</pre>
*
* <pre> -A
* The nearest neighbour search algorithm to use (default: weka.core.neighboursearch.LinearNNSearch).
* </pre>
*
<!-- options-end -->
*
* @param options the list of options as an array of strings
* @throws Exception if an option is not supported
*/
public void setOptions(String[] options) throws Exception {
String knnString = Utils.getOption('K', options);
if (knnString.length() != 0) {
setKNN(Integer.parseInt(knnString));
} else {
setKNN(1);
}
String windowString = Utils.getOption('W', options);
if (windowString.length() != 0) {
setWindowSize(Integer.parseInt(windowString));
} else {
setWindowSize(0);
}
if (Utils.getFlag('I', options)) {
setDistanceWeighting(new SelectedTag(WEIGHT_INVERSE, TAGS_WEIGHTING));
} else if (Utils.getFlag('F', options)) {
setDistanceWeighting(new SelectedTag(WEIGHT_SIMILARITY, TAGS_WEIGHTING));
} else {
setDistanceWeighting(new SelectedTag(WEIGHT_NONE, TAGS_WEIGHTING));
}
setCrossValidate(Utils.getFlag('X', options));
setMeanSquared(Utils.getFlag('E', options));
String nnSearchClass = Utils.getOption('A', options);
if(nnSearchClass.length() != 0) {
String nnSearchClassSpec[] = Utils.splitOptions(nnSearchClass);
if(nnSearchClassSpec.length == 0) {
throw new Exception("Invalid NearestNeighbourSearch algorithm " +
"specification string.");
}
String className = nnSearchClassSpec[0];
nnSearchClassSpec[0] = "";
setNearestNeighbourSearchAlgorithm( (NearestNeighbourSearch)
Utils.forName( NearestNeighbourSearch.class,
className,
nnSearchClassSpec)
);
}
else
this.setNearestNeighbourSearchAlgorithm(new LinearNNSearch());
Utils.checkForRemainingOptions(options);
}
/**
* Gets the current settings of IBk.
*
* @return an array of strings suitable for passing to setOptions()
*/
public String [] getOptions() {
String [] options = new String [11];
int current = 0;
options[current++] = "-K"; options[current++] = "" + getKNN();
options[current++] = "-W"; options[current++] = "" + m_WindowSize;
if (getCrossValidate()) {
options[current++] = "-X";
}
if (getMeanSquared()) {
options[current++] = "-E";
}
if (m_DistanceWeighting == WEIGHT_INVERSE) {
options[current++] = "-I";
} else if (m_DistanceWeighting == WEIGHT_SIMILARITY) {
options[current++] = "-F";
}
options[current++] = "-A";
options[current++] = m_NNSearch.getClass().getName()+" "+Utils.joinOptions(m_NNSearch.getOptions());
while (current < options.length) {
options[current++] = "";
}
return options;
}
/**
* Returns an enumeration of the additional measure names
* produced by the neighbour search algorithm, plus the chosen K in case
* cross-validation is enabled.
*
* @return an enumeration of the measure names
*/
public Enumeration enumerateMeasures() {
if (m_CrossValidate) {
Enumeration enm = m_NNSearch.enumerateMeasures();
Vector measures = new Vector();
while (enm.hasMoreElements())
measures.add(enm.nextElement());
measures.add("measureKNN");
return measures.elements();
}
else {
return m_NNSearch.enumerateMeasures();
}
}
/**
* Returns the value of the named measure from the
* neighbour search algorithm, plus the chosen K in case
* cross-validation is enabled.
*
* @param additionalMeasureName the name of the measure to query for its value
* @return the value of the named measure
* @throws IllegalArgumentException if the named measure is not supported
*/
public double getMeasure(String additionalMeasureName) {
if (additionalMeasureName.equals("measureKNN"))
return m_kNN;
else
return m_NNSearch.getMeasure(additionalMeasureName);
}
/**
* Returns a description of this classifier.
*
* @return a description of this classifier as a string.
*/
public String toString() {
if (m_Train == null) {
return "IBk: No model built yet.";
}
if (m_Train.numInstances() == 0) {
return "Warning: no training instances - ZeroR model used.";
}
if (!m_kNNValid && m_CrossValidate) {
crossValidate();
}
String result = "IB1 instance-based classifier\n" +
"using " + m_kNN;
switch (m_DistanceWeighting) {
case WEIGHT_INVERSE:
result += " inverse-distance-weighted";
break;
case WEIGHT_SIMILARITY:
result += " similarity-weighted";
break;
}
result += " nearest neighbour(s) for classification\n";
if (m_WindowSize != 0) {
result += "using a maximum of "
+ m_WindowSize + " (windowed) training instances\n";
}
return result;
}
/**
* Initialise scheme variables.
*/
protected void init() {
setKNN(1);
m_WindowSize = 0;
m_DistanceWeighting = WEIGHT_NONE;
m_CrossValidate = false;
m_MeanSquared = false;
}
/**
* Turn the list of nearest neighbors into a probability distribution.
*
* @param neighbours the list of nearest neighboring instances
* @param distances the distances of the neighbors
* @return the probability distribution
* @throws Exception if computation goes wrong or has no class attribute
*/
protected double [] makeDistribution(Instances neighbours, double[] distances)
throws Exception {
double total = 0, weight;
double [] distribution = new double [m_NumClasses];
// Set up a correction to the estimator
if (m_ClassType == Attribute.NOMINAL) {
for(int i = 0; i < m_NumClasses; i++) {
distribution[i] = 1.0 / Math.max(1,m_Train.numInstances());
}
total = (double)m_NumClasses / Math.max(1,m_Train.numInstances());
}
for(int i=0; i < neighbours.numInstances(); i++) {
// Collect class counts
Instance current = neighbours.instance(i);
distances[i] = distances[i]*distances[i];
distances[i] = Math.sqrt(distances[i]/m_NumAttributesUsed);
switch (m_DistanceWeighting) {
case WEIGHT_INVERSE:
weight = 1.0 / (distances[i] + 0.001); // to avoid div by zero
break;
case WEIGHT_SIMILARITY:
weight = 1.0 - distances[i];
break;
default: // WEIGHT_NONE:
weight = 1.0;
break;
}
weight *= current.weight();
try {
switch (m_ClassType) {
case Attribute.NOMINAL:
distribution[(int)current.classValue()] += weight;
break;
case Attribute.NUMERIC:
distribution[0] += current.classValue() * weight;
break;
}
} catch (Exception ex) {
throw new Error("Data has no class attribute!");
}
total += weight;
}
// Normalise distribution
if (total > 0) {
Utils.normalize(distribution, total);
}
return distribution;
}
/**
* Select the best value for k by hold-one-out cross-validation.
* If the class attribute is nominal, classification error is
* minimised. If the class attribute is numeric, mean absolute
* error is minimised
*/
protected void crossValidate() {
try {
if (m_NNSearch instanceof weka.core.neighboursearch.CoverTree)
throw new Exception("CoverTree doesn't support hold-one-out "+
"cross-validation. Use some other NN " +
"method.");
double [] performanceStats = new double [m_kNNUpper];
double [] performanceStatsSq = new double [m_kNNUpper];
for(int i = 0; i < m_kNNUpper; i++) {
performanceStats[i] = 0;
performanceStatsSq[i] = 0;
}
m_kNN = m_kNNUpper;
Instance instance;
Instances neighbours;
double[] origDistances, convertedDistances;
for(int i = 0; i < m_Train.numInstances(); i++) {
if (m_Debug && (i % 50 == 0)) {
System.err.print("Cross validating "
+ i + "/" + m_Train.numInstances() + "\r");
}
instance = m_Train.instance(i);
neighbours = m_NNSearch.kNearestNeighbours(instance, m_kNN);
origDistances = m_NNSearch.getDistances();
for(int j = m_kNNUpper - 1; j >= 0; j--) {
// Update the performance stats
convertedDistances = new double[origDistances.length];
System.arraycopy(origDistances, 0,
convertedDistances, 0, origDistances.length);
double [] distribution = makeDistribution(neighbours,
convertedDistances);
double thisPrediction = Utils.maxIndex(distribution);
if (m_Train.classAttribute().isNumeric()) {
thisPrediction = distribution[0];
double err = thisPrediction - instance.classValue();
performanceStatsSq[j] += err * err; // Squared error
performanceStats[j] += Math.abs(err); // Absolute error
} else {
if (thisPrediction != instance.classValue()) {
performanceStats[j] ++; // Classification error
}
}
if (j >= 1) {
neighbours = pruneToK(neighbours, convertedDistances, j);
}
}
}
// Display the results of the cross-validation
for(int i = 0; i < m_kNNUpper; i++) {
if (m_Debug) {
System.err.print("Hold-one-out performance of " + (i + 1)
+ " neighbors " );
}
if (m_Train.classAttribute().isNumeric()) {
if (m_Debug) {
if (m_MeanSquared) {
System.err.println("(RMSE) = "
+ Math.sqrt(performanceStatsSq[i]
/ m_Train.numInstances()));
} else {
System.err.println("(MAE) = "
+ performanceStats[i]
/ m_Train.numInstances());
}
}
} else {
if (m_Debug) {
System.err.println("(%ERR) = "
+ 100.0 * performanceStats[i]
/ m_Train.numInstances());
}
}
}
// Check through the performance stats and select the best
// k value (or the lowest k if more than one best)
double [] searchStats = performanceStats;
if (m_Train.classAttribute().isNumeric() && m_MeanSquared) {
searchStats = performanceStatsSq;
}
double bestPerformance = Double.NaN;
int bestK = 1;
for(int i = 0; i < m_kNNUpper; i++) {
if (Double.isNaN(bestPerformance)
|| (bestPerformance > searchStats[i])) {
bestPerformance = searchStats[i];
bestK = i + 1;
}
}
m_kNN = bestK;
if (m_Debug) {
System.err.println("Selected k = " + bestK);
}
m_kNNValid = true;
} catch (Exception ex) {
throw new Error("Couldn't optimize by cross-validation: "
+ex.getMessage());
}
}
/**
* Prunes the list to contain the k nearest neighbors. If there are
* multiple neighbors at the k'th distance, all will be kept.
*
* @param neighbours the neighbour instances.
* @param distances the distances of the neighbours from target instance.
* @param k the number of neighbors to keep.
* @return the pruned neighbours.
*/
public Instances pruneToK(Instances neighbours, double[] distances, int k) {
if(neighbours==null || distances==null || neighbours.numInstances()==0) {
return null;
}
if (k < 1) {
k = 1;
}
int currentK = 0;
double currentDist;
for(int i=0; i < neighbours.numInstances(); i++) {
currentK++;
currentDist = distances[i];
if(currentK>k && currentDist!=distances[i-1]) {
currentK--;
neighbours = new Instances(neighbours, 0, currentK);
break;
}
}
return neighbours;
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 8034 $");
}
/**
* Main method for testing this class.
*
* @param argv should contain command line options (see setOptions)
*/
public static void main(String [] argv) {
runClassifier(new IBk(), argv);
}
}