/*
* 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 2 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, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*/
/*
* CitationKNN.java
* Copyright (C) 2005 Miguel Garcia Torres
*/
package weka.classifiers.mi;
import weka.classifiers.Classifier;
import weka.core.Capabilities;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.MultiInstanceCapabilitiesHandler;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.RevisionHandler;
import weka.core.RevisionUtils;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.core.Capabilities.Capability;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import java.io.Serializable;
import java.util.Enumeration;
import java.util.Vector;
/**
<!-- globalinfo-start -->
* Modified version of the Citation kNN multi instance classifier.<br/>
* <br/>
* For more information see:<br/>
* <br/>
* Jun Wang, Zucker, Jean-Daniel: Solving Multiple-Instance Problem: A Lazy Learning Approach. In: 17th International Conference on Machine Learning, 1119-1125, 2000.
* <p/>
<!-- globalinfo-end -->
*
<!-- technical-bibtex-start -->
* BibTeX:
* <pre>
* @inproceedings{Wang2000,
* author = {Jun Wang and Zucker and Jean-Daniel},
* booktitle = {17th International Conference on Machine Learning},
* editor = {Pat Langley},
* pages = {1119-1125},
* title = {Solving Multiple-Instance Problem: A Lazy Learning Approach},
* year = {2000}
* }
* </pre>
* <p/>
<!-- technical-bibtex-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -R <number of references>
* Number of Nearest References (default 1)</pre>
*
* <pre> -C <number of citers>
* Number of Nearest Citers (default 1)</pre>
*
* <pre> -H <rank>
* Rank of the Hausdorff Distance (default 1)</pre>
*
<!-- options-end -->
*
* @author Miguel Garcia Torres (mgarciat@ull.es)
* @version $Revision: 1.9 $
*/
public class CitationKNN
extends Classifier
implements OptionHandler, MultiInstanceCapabilitiesHandler,
TechnicalInformationHandler {
/** for serialization */
static final long serialVersionUID = -8435377743874094852L;
/** The index of the class attribute */
protected int m_ClassIndex;
/** The number of the class labels */
protected int m_NumClasses;
/** */
protected int m_IdIndex;
/** Debugging output */
protected boolean m_Debug;
/** Class labels for each bag */
protected int[] m_Classes;
/** attribute name structure of the relational attribute*/
protected Instances m_Attributes;
/** Number of references */
protected int m_NumReferences = 1;
/** Number of citers*/
protected int m_NumCiters = 1;
/** Training bags*/
protected Instances m_TrainBags;
/** Different debugging output */
protected boolean m_CNNDebug = false;
protected boolean m_CitersDebug = false;
protected boolean m_ReferencesDebug = false;
protected boolean m_HDistanceDebug = false;
protected boolean m_NeighborListDebug = false;
/** C nearest neighbors considering all the bags*/
protected NeighborList[] m_CNN;
/** C nearest citers */
protected int[] m_Citers;
/** R nearest references */
protected int[] m_References;
/** Rank associated to the Hausdorff distance*/
protected int m_HDRank = 1;
/** Normalization of the euclidean distance */
private double[] m_Diffs;
private double[] m_Min;
private double m_MinNorm = 0.95;
private double[] m_Max;
private double m_MaxNorm = 1.05;
/**
* Returns a string describing this filter
*
* @return a description of the filter suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return
"Modified version of the Citation kNN multi instance classifier.\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.INPROCEEDINGS);
result.setValue(Field.AUTHOR, "Jun Wang and Zucker and Jean-Daniel");
result.setValue(Field.TITLE, "Solving Multiple-Instance Problem: A Lazy Learning Approach");
result.setValue(Field.BOOKTITLE, "17th International Conference on Machine Learning");
result.setValue(Field.EDITOR, "Pat Langley");
result.setValue(Field.YEAR, "2000");
result.setValue(Field.PAGES, "1119-1125");
return result;
}
/**
* Calculates the normalization of each attribute.
*/
public void preprocessData(){
int i,j, k;
double min, max;
Instances instances;
Instance instance;
// compute the min/max of each feature
for (i=0;i<m_Attributes.numAttributes();i++) {
min=Double.POSITIVE_INFINITY ;
max=Double.NEGATIVE_INFINITY ;
for(j = 0; j < m_TrainBags.numInstances(); j++){
instances = m_TrainBags.instance(j).relationalValue(1);
for (k=0;k<instances.numInstances();k++) {
instance = instances.instance(k);
if(instance.value(i) < min)
min= instance.value(i);
if(instance.value(i) > max)
max= instance.value(i);
}
}
m_Min[i] = min * m_MinNorm;
m_Max[i] = max * m_MaxNorm;
m_Diffs[i]= max * m_MaxNorm - min * m_MinNorm;
}
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String HDRankTipText() {
return "The rank associated to the Hausdorff distance.";
}
/**
* Sets the rank associated to the Hausdorff distance
* @param hDRank the rank of the Hausdorff distance
*/
public void setHDRank(int hDRank){
m_HDRank = hDRank;
}
/**
* Returns the rank associated to the Hausdorff distance
* @return the rank number
*/
public int getHDRank(){
return m_HDRank;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String numReferencesTipText() {
return
"The number of references considered to estimate the class "
+ "prediction of tests bags.";
}
/**
* Sets the number of references considered to estimate
* the class prediction of tests bags
* @param numReferences the number of references
*/
public void setNumReferences(int numReferences){
m_NumReferences = numReferences;
}
/**
* Returns the number of references considered to estimate
* the class prediction of tests bags
* @return the number of references
*/
public int getNumReferences(){
return m_NumReferences;
}
/**
* Returns the tip text for this property
*
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String numCitersTipText() {
return
"The number of citers considered to estimate the class "
+ "prediction of test bags.";
}
/**
* Sets the number of citers considered to estimate
* the class prediction of tests bags
* @param numCiters the number of citers
*/
public void setNumCiters(int numCiters){
m_NumCiters = numCiters;
}
/**
* Returns the number of citers considered to estimate
* the class prediction of tests bags
* @return the number of citers
*/
public int getNumCiters(){
return m_NumCiters;
}
/**
* Returns default capabilities of the classifier.
*
* @return the capabilities of this classifier
*/
public Capabilities getCapabilities() {
Capabilities result = super.getCapabilities();
// attributes
result.enable(Capability.NOMINAL_ATTRIBUTES);
result.enable(Capability.NUMERIC_ATTRIBUTES);
result.enable(Capability.DATE_ATTRIBUTES);
result.enable(Capability.RELATIONAL_ATTRIBUTES);
result.enable(Capability.MISSING_VALUES);
// class
result.enable(Capability.NOMINAL_CLASS);
result.enable(Capability.MISSING_CLASS_VALUES);
// other
result.enable(Capability.ONLY_MULTIINSTANCE);
return result;
}
/**
* Returns the capabilities of this multi-instance classifier for the
* relational data.
*
* @return the capabilities of this object
* @see Capabilities
*/
public Capabilities getMultiInstanceCapabilities() {
Capabilities result = super.getCapabilities();
// attributes
result.enable(Capability.NOMINAL_ATTRIBUTES);
result.enable(Capability.NUMERIC_ATTRIBUTES);
result.enable(Capability.DATE_ATTRIBUTES);
result.enable(Capability.MISSING_VALUES);
// class
result.disableAllClasses();
result.enable(Capability.NO_CLASS);
return result;
}
/**
* Builds the classifier
*
* @param train the training data to be used for generating the
* boosted classifier.
* @throws Exception if the classifier could not be built successfully
*/
public void buildClassifier(Instances train) throws Exception {
// can classifier handle the data?
getCapabilities().testWithFail(train);
// remove instances with missing class
train = new Instances(train);
train.deleteWithMissingClass();
m_TrainBags = train;
m_ClassIndex = train.classIndex();
m_IdIndex = 0;
m_NumClasses = train.numClasses();
m_Classes = new int [train.numInstances()]; // Class values
m_Attributes = train.instance(0).relationalValue(1).stringFreeStructure();
m_Citers = new int[train.numClasses()];
m_References = new int[train.numClasses()];
m_Diffs = new double[m_Attributes.numAttributes()];
m_Min = new double[m_Attributes.numAttributes()];
m_Max = new double[m_Attributes.numAttributes()];
preprocessData();
buildCNN();
if(m_CNNDebug){
System.out.println("########################################### ");
System.out.println("###########CITATION######################## ");
System.out.println("########################################### ");
for(int i = 0; i < m_CNN.length; i++){
System.out.println("Bag: " + i);
m_CNN[i].printReducedList();
}
}
}
/**
* generates all the variables associated to the citation
* classifier
*
* @throws Exception if generation fails
*/
public void buildCNN() throws Exception {
int numCiters = 0;
if((m_NumCiters >= m_TrainBags.numInstances()) ||
(m_NumCiters < 0))
throw new Exception("Number of citers is out of the range [0, numInstances)");
else
numCiters = m_NumCiters;
m_CNN = new NeighborList[m_TrainBags.numInstances()];
Instance bag;
for(int i = 0; i< m_TrainBags.numInstances(); i++){
bag = m_TrainBags.instance(i);
//first we find its neighbors
NeighborList neighborList = findNeighbors(bag, numCiters, m_TrainBags);
m_CNN[i] = neighborList;
}
}
/**
* calculates the citers associated to a bag
* @param bag the bag cited
*/
public void countBagCiters(Instance bag){
//Initialization of the vector
for(int i = 0; i < m_TrainBags.numClasses(); i++)
m_Citers[i] = 0;
//
if(m_CitersDebug == true)
System.out.println("-------CITERS--------");
NeighborList neighborList;
NeighborNode current;
boolean stopSearch = false;
int index;
// compute the distance between the test bag and each training bag. Update
// the bagCiter count in case it be a neighbour
double bagDistance = 0;
for(int i = 0; i < m_TrainBags.numInstances(); i++){
//measure the distance
bagDistance = distanceSet(bag, m_TrainBags.instance(i));
if(m_CitersDebug == true){
System.out.print("bag - bag(" + i + "): " + bagDistance);
System.out.println(" <" + m_TrainBags.instance(i).classValue() + ">");
}
//compare the distance to see if it would belong to the
// neighborhood of each training exemplar
neighborList = m_CNN[i];
current = neighborList.mFirst;
while((current != null) && (!stopSearch)) {
if(m_CitersDebug == true)
System.out.println("\t\tciter Distance: " + current.mDistance);
if(current.mDistance < bagDistance){
current = current.mNext;
} else{
stopSearch = true;
if(m_CitersDebug == true){
System.out.println("\t***");
}
}
}
if(stopSearch == true){
stopSearch = false;
index = (int)(m_TrainBags.instance(i)).classValue();
m_Citers[index] += 1;
}
}
if(m_CitersDebug == true){
for(int i= 0; i < m_Citers.length; i++){
System.out.println("[" + i + "]: " + m_Citers[i]);
}
}
}
/**
* Calculates the references of the exemplar bag
* @param bag the exemplar to which the nearest references
* will be calculated
*/
public void countBagReferences(Instance bag){
int index = 0, referencesIndex = 0;
if(m_TrainBags.numInstances() < m_NumReferences)
referencesIndex = m_TrainBags.numInstances() - 1;
else
referencesIndex = m_NumReferences;
if(m_CitersDebug == true){
System.out.println("-------References (" + referencesIndex+ ")--------");
}
//Initialization of the vector
for(int i = 0; i < m_References.length; i++)
m_References[i] = 0;
if(referencesIndex > 0){
//first we find its neighbors
NeighborList neighborList = findNeighbors(bag, referencesIndex, m_TrainBags);
if(m_ReferencesDebug == true){
System.out.println("Bag: " + bag + " Neighbors: ");
neighborList.printReducedList();
}
NeighborNode current = neighborList.mFirst;
while(current != null){
index = (int) current.mBag.classValue();
m_References[index] += 1;
current = current.mNext;
}
}
if(m_ReferencesDebug == true){
System.out.println("References:");
for(int j = 0; j < m_References.length; j++)
System.out.println("[" + j + "]: " + m_References[j]);
}
}
/**
* Build the list of nearest k neighbors to the given test instance.
* @param bag the bag to search for neighbors of
* @param kNN the number of nearest neighbors
* @param bags the data
* @return a list of neighbors
*/
protected NeighborList findNeighbors(Instance bag, int kNN, Instances bags){
double distance;
int index = 0;
if(kNN > bags.numInstances())
kNN = bags.numInstances() - 1;
NeighborList neighborList = new NeighborList(kNN);
for(int i = 0; i < bags.numInstances(); i++){
if(bag != bags.instance(i)){ // for hold-one-out cross-validation
distance = distanceSet(bag, bags.instance(i)) ; //mDistanceSet.distance(bag, mInstances, bags.exemplar(i), mInstances);
if(m_NeighborListDebug)
System.out.println("distance(bag, " + i + "): " + distance);
if(neighborList.isEmpty() || (index < kNN) || (distance <= neighborList.mLast.mDistance))
neighborList.insertSorted(distance, bags.instance(i), i);
index++;
}
}
if(m_NeighborListDebug){
System.out.println("bag neighbors:");
neighborList.printReducedList();
}
return neighborList;
}
/**
* Calculates the distance between two instances
* @param first instance
* @param second instance
* @return the distance value
*/
public double distanceSet(Instance first, Instance second){
double[] h_f = new double[first.relationalValue(1).numInstances()];
double distance;
//initilization
for(int i = 0; i < h_f.length; i++)
h_f[i] = Double.MAX_VALUE;
int rank;
if(m_HDRank >= first.relationalValue(1).numInstances())
rank = first.relationalValue(1).numInstances();
else if(m_HDRank < 1)
rank = 1;
else
rank = m_HDRank;
if(m_HDistanceDebug){
System.out.println("-------HAUSDORFF DISTANCE--------");
System.out.println("rank: " + rank + "\nset of instances:");
System.out.println("\tset 1:");
for(int i = 0; i < first.relationalValue(1).numInstances(); i++)
System.out.println(first.relationalValue(1).instance(i));
System.out.println("\n\tset 2:");
for(int i = 0; i < second.relationalValue(1).numInstances(); i++)
System.out.println(second.relationalValue(1).instance(i));
System.out.println("\n");
}
//for each instance in bag first
for(int i = 0; i < first.relationalValue(1).numInstances(); i++){
// calculate the distance to each instance in
// bag second
if(m_HDistanceDebug){
System.out.println("\nDistances:");
}
for(int j = 0; j < second.relationalValue(1).numInstances(); j++){
distance = distance(first.relationalValue(1).instance(i), second.relationalValue(1).instance(j));
if(distance < h_f[i])
h_f[i] = distance;
if(m_HDistanceDebug){
System.out.println("\tdist(" + i + ", "+ j + "): " + distance + " --> h_f[" + i + "]: " + h_f[i]);
}
}
}
int[] index_f = Utils.stableSort(h_f);
if(m_HDistanceDebug){
System.out.println("\nRanks:\n");
for(int i = 0; i < index_f.length; i++)
System.out.println("\trank " + (i + 1) + ": " + h_f[index_f[i]]);
System.out.println("\n\t\t>>>>> rank " + rank + ": " + h_f[index_f[rank - 1]] + " <<<<<");
}
return h_f[index_f[rank - 1]];
}
/**
* distance between two instances
* @param first the first instance
* @param second the other instance
* @return the distance in double precision
*/
public double distance(Instance first, Instance second){
double sum = 0, diff;
for(int i = 0; i < m_Attributes.numAttributes(); i++){
diff = (first.value(i) - m_Min[i])/ m_Diffs[i] -
(second.value(i) - m_Min[i])/ m_Diffs[i];
sum += diff * diff;
}
return sum = Math.sqrt(sum);
}
/**
* Computes the distribution for a given exemplar
*
* @param bag the exemplar for which distribution is computed
* @return the distribution
* @throws Exception if the distribution can't be computed successfully
*/
public double[] distributionForInstance(Instance bag)
throws Exception {
if(m_TrainBags.numInstances() == 0)
throw new Exception("No training bags!");
updateNormalization(bag);
//build references (R nearest neighbors)
countBagReferences(bag);
//build citers
countBagCiters(bag);
return makeDistribution();
}
/**
* Updates the normalization of each attribute.
*
* @param bag the exemplar to update the normalization for
*/
public void updateNormalization(Instance bag){
int i, k;
double min, max;
Instances instances;
Instance instance;
// compute the min/max of each feature
for (i = 0; i < m_TrainBags.attribute(1).relation().numAttributes(); i++) {
min = m_Min[i] / m_MinNorm;
max = m_Max[i] / m_MaxNorm;
instances = bag.relationalValue(1);
for (k=0;k<instances.numInstances();k++) {
instance = instances.instance(k);
if(instance.value(i) < min)
min = instance.value(i);
if(instance.value(i) > max)
max = instance.value(i);
}
m_Min[i] = min * m_MinNorm;
m_Max[i] = max * m_MaxNorm;
m_Diffs[i]= max * m_MaxNorm - min * m_MinNorm;
}
}
/**
* Wether the instances of two exemplars are or are not equal
* @param exemplar1 first exemplar
* @param exemplar2 second exemplar
* @return if the instances of the exemplars are equal or not
*/
public boolean equalExemplars(Instance exemplar1, Instance exemplar2){
if(exemplar1.relationalValue(1).numInstances() ==
exemplar2.relationalValue(1).numInstances()){
Instances instances1 = exemplar1.relationalValue(1);
Instances instances2 = exemplar2.relationalValue(1);
for(int i = 0; i < instances1.numInstances(); i++){
Instance instance1 = instances1.instance(i);
Instance instance2 = instances2.instance(i);
for(int j = 0; j < instance1.numAttributes(); j++){
if(instance1.value(j) != instance2.value(j)){
return false;
}
}
}
return true;
}
return false;
}
/**
* Turn the references and citers list into a probability distribution
*
* @return the probability distribution
* @throws Exception if computation of distribution fails
*/
protected double[] makeDistribution() throws Exception {
double total = 0;
double[] distribution = new double[m_TrainBags.numClasses()];
boolean debug = false;
total = (double)m_TrainBags.numClasses() / Math.max(1, m_TrainBags.numInstances());
for(int i = 0; i < m_TrainBags.numClasses(); i++){
distribution[i] = 1.0 / Math.max(1, m_TrainBags.numInstances());
if(debug) System.out.println("distribution[" + i + "]: " + distribution[i]);
}
if(debug)System.out.println("total: " + total);
for(int i = 0; i < m_TrainBags.numClasses(); i++){
distribution[i] += m_References[i];
distribution[i] += m_Citers[i];
}
total = 0;
//total
for(int i = 0; i < m_TrainBags.numClasses(); i++){
total += distribution[i];
if(debug)System.out.println("distribution[" + i + "]: " + distribution[i]);
}
for(int i = 0; i < m_TrainBags.numClasses(); i++){
distribution[i] = distribution[i] / total;
if(debug)System.out.println("distribution[" + i + "]: " + distribution[i]);
}
return distribution;
}
/**
* Returns an enumeration of all the available options..
*
* @return an enumeration of all available options.
*/
public Enumeration listOptions(){
Vector result = new Vector();
result.addElement(new Option(
"\tNumber of Nearest References (default 1)",
"R", 0, "-R <number of references>"));
result.addElement(new Option(
"\tNumber of Nearest Citers (default 1)",
"C", 0, "-C <number of citers>"));
result.addElement(new Option(
"\tRank of the Hausdorff Distance (default 1)",
"H", 0, "-H <rank>"));
return result.elements();
}
/**
* Sets the OptionHandler's options using the given list. All options
* will be set (or reset) during this call (i.e. incremental setting
* of options is not possible). <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -R <number of references>
* Number of Nearest References (default 1)</pre>
*
* <pre> -C <number of citers>
* Number of Nearest Citers (default 1)</pre>
*
* <pre> -H <rank>
* Rank of the Hausdorff Distance (default 1)</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{
setDebug(Utils.getFlag('D', options));
String option = Utils.getOption('R', options);
if(option.length() != 0)
setNumReferences(Integer.parseInt(option));
else
setNumReferences(1);
option = Utils.getOption('C', options);
if(option.length() != 0)
setNumCiters(Integer.parseInt(option));
else
setNumCiters(1);
option = Utils.getOption('H', options);
if(option.length() != 0)
setHDRank(Integer.parseInt(option));
else
setHDRank(1);
}
/**
* Gets the current option settings for the OptionHandler.
*
* @return the list of current option settings as an array of strings
*/
public String[] getOptions() {
Vector result;
result = new Vector();
if (getDebug())
result.add("-D");
result.add("-R");
result.add("" + getNumReferences());
result.add("-C");
result.add("" + getNumCiters());
result.add("-H");
result.add("" + getHDRank());
return (String[]) result.toArray(new String[result.size()]);
}
/**
* returns a string representation of the classifier
*
* @return the string representation
*/
public String toString() {
StringBuffer result;
int i;
result = new StringBuffer();
// title
result.append(this.getClass().getName().replaceAll(".*\\.", "") + "\n");
result.append(this.getClass().getName().replaceAll(".*\\.", "").replaceAll(".", "=") + "\n\n");
if (m_Citers == null) {
result.append("no model built yet!\n");
}
else {
// internal representation
result.append("Citers....: " + Utils.arrayToString(m_Citers) + "\n");
result.append("References: " + Utils.arrayToString(m_References) + "\n");
result.append("Min.......: ");
for (i = 0; i < m_Min.length; i++) {
if (i > 0)
result.append(",");
result.append(Utils.doubleToString(m_Min[i], 3));
}
result.append("\n");
result.append("Max.......: ");
for (i = 0; i < m_Max.length; i++) {
if (i > 0)
result.append(",");
result.append(Utils.doubleToString(m_Max[i], 3));
}
result.append("\n");
result.append("Diffs.....: ");
for (i = 0; i < m_Diffs.length; i++) {
if (i > 0)
result.append(",");
result.append(Utils.doubleToString(m_Diffs[i], 3));
}
result.append("\n");
}
return result.toString();
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.9 $");
}
/**
* Main method for testing this class.
*
* @param argv should contain the command line arguments to the
* scheme (see Evaluation)
*/
public static void main(String[] argv) {
runClassifier(new CitationKNN(), argv);
}
//########################################################################
//########################################################################
//########################################################################
//########################################################################
//########################################################################
/**
* A class for storing data about a neighboring instance
*/
private class NeighborNode
implements Serializable, RevisionHandler {
/** for serialization */
static final long serialVersionUID = -3947320761906511289L;
/** The neighbor bag */
private Instance mBag;
/** The distance from the current instance to this neighbor */
private double mDistance;
/** A link to the next neighbor instance */
private NeighborNode mNext;
/** the position in the bag */
private int mBagPosition;
/**
* Create a new neighbor node.
*
* @param distance the distance to the neighbor
* @param bag the bag instance
* @param position the position in the bag
* @param next the next neighbor node
*/
public NeighborNode(double distance, Instance bag, int position, NeighborNode next){
mDistance = distance;
mBag = bag;
mNext = next;
mBagPosition = position;
}
/**
* Create a new neighbor node that doesn't link to any other nodes.
*
* @param distance the distance to the neighbor
* @param bag the neighbor instance
* @param position the position in the bag
*/
public NeighborNode(double distance, Instance bag, int position) {
this(distance, bag, position, null);
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.9 $");
}
}
//##################################################
/**
* A class for a linked list to store the nearest k neighbours
* to an instance. We use a list so that we can take care of
* cases where multiple neighbours are the same distance away.
* i.e. the minimum length of the list is k.
*/
private class NeighborList
implements Serializable, RevisionHandler {
/** for serialization */
static final long serialVersionUID = 3432555644456217394L;
/** The first node in the list */
private NeighborNode mFirst;
/** The last node in the list */
private NeighborNode mLast;
/** The number of nodes to attempt to maintain in the list */
private int mLength = 1;
/**
* Creates the neighborlist with a desired length
*
* @param length the length of list to attempt to maintain
*/
public NeighborList(int length) {
mLength = length;
}
/**
* Gets whether the list is empty.
*
* @return true if so
*/
public boolean isEmpty() {
return (mFirst == null);
}
/**
* Gets the current length of the list.
*
* @return the current length of the list
*/
public int currentLength() {
int i = 0;
NeighborNode current = mFirst;
while (current != null) {
i++;
current = current.mNext;
}
return i;
}
/**
* Inserts an instance neighbor into the list, maintaining the list
* sorted by distance.
*
* @param distance the distance to the instance
* @param bag the neighboring instance
* @param position the position in the bag
*/
public void insertSorted(double distance, Instance bag, int position) {
if (isEmpty()) {
mFirst = mLast = new NeighborNode(distance, bag, position);
} else {
NeighborNode current = mFirst;
if (distance < mFirst.mDistance) {// Insert at head
mFirst = new NeighborNode(distance, bag, position, mFirst);
} else { // Insert further down the list
for( ;(current.mNext != null) &&
(current.mNext.mDistance < distance);
current = current.mNext);
current.mNext = new NeighborNode(distance, bag, position, current.mNext);
if (current.equals(mLast)) {
mLast = current.mNext;
}
}
// Trip down the list until we've got k list elements (or more if the
// distance to the last elements is the same).
int valcount = 0;
for(current = mFirst; current.mNext != null;
current = current.mNext) {
valcount++;
if ((valcount >= mLength) && (current.mDistance !=
current.mNext.mDistance)) {
mLast = current;
current.mNext = null;
break;
}
}
}
}
/**
* Prunes the list to contain the k nearest neighbors. If there are
* multiple neighbors at the k'th distance, all will be kept.
*
* @param k the number of neighbors to keep in the list.
*/
public void pruneToK(int k) {
if (isEmpty())
return;
if (k < 1)
k = 1;
int currentK = 0;
double currentDist = mFirst.mDistance;
NeighborNode current = mFirst;
for(; current.mNext != null; current = current.mNext) {
currentK++;
currentDist = current.mDistance;
if ((currentK >= k) && (currentDist != current.mNext.mDistance)) {
mLast = current;
current.mNext = null;
break;
}
}
}
/**
* Prints out the contents of the neighborlist
*/
public void printList() {
if (isEmpty()) {
System.out.println("Empty list");
} else {
NeighborNode current = mFirst;
while (current != null) {
System.out.print("Node: instance " + current.mBagPosition + "\n");
System.out.println(current.mBag);
System.out.println(", distance " + current.mDistance);
current = current.mNext;
}
System.out.println();
}
}
/**
* Prints out the contents of the neighborlist
*/
public void printReducedList() {
if (isEmpty()) {
System.out.println("Empty list");
} else {
NeighborNode current = mFirst;
while (current != null) {
System.out.print("Node: bag " + current.mBagPosition + " (" + current.mBag.relationalValue(1).numInstances() +"): ");
//for(int i = 0; i < current.mBag.getInstances().numInstances(); i++){
//System.out.print(" " + (current.mBag).getInstances().instance(i));
//}
System.out.print(" <" + current.mBag.classValue() + ">");
System.out.println(" (d: " + current.mDistance + ")");
current = current.mNext;
}
System.out.println();
}
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.9 $");
}
}
}