/*
* 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.
*/
/*
* GeneticSearch.java
* Copyright (C) 1999 University of Waikato, Hamilton, New Zealand
*
*/
package weka.attributeSelection;
import weka.core.Instances;
import weka.core.Option;
import weka.core.OptionHandler;
import weka.core.Range;
import weka.core.RevisionHandler;
import weka.core.RevisionUtils;
import weka.core.TechnicalInformation;
import weka.core.TechnicalInformationHandler;
import weka.core.Utils;
import weka.core.TechnicalInformation.Field;
import weka.core.TechnicalInformation.Type;
import java.io.Serializable;
import java.util.BitSet;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Random;
import java.util.Vector;
/**
<!-- globalinfo-start -->
* GeneticSearch:<br/>
* <br/>
* Performs a search using the simple genetic algorithm described in Goldberg (1989).<br/>
* <br/>
* For more information see:<br/>
* <br/>
* David E. Goldberg (1989). Genetic algorithms in search, optimization and machine learning. Addison-Wesley.
* <p/>
<!-- globalinfo-end -->
*
<!-- technical-bibtex-start -->
* BibTeX:
* <pre>
* @book{Goldberg1989,
* author = {David E. Goldberg},
* publisher = {Addison-Wesley},
* title = {Genetic algorithms in search, optimization and machine learning},
* year = {1989},
* ISBN = {0201157675}
* }
* </pre>
* <p/>
<!-- technical-bibtex-end -->
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -P <start set>
* Specify a starting set of attributes.
* Eg. 1,3,5-7.If supplied, the starting set becomes
* one member of the initial random
* population.</pre>
*
* <pre> -Z <population size>
* Set the size of the population.
* (default = 10).</pre>
*
* <pre> -G <number of generations>
* Set the number of generations.
* (default = 20)</pre>
*
* <pre> -C <probability of crossover>
* Set the probability of crossover.
* (default = 0.6)</pre>
*
* <pre> -M <probability of mutation>
* Set the probability of mutation.
* (default = 0.033)</pre>
*
* <pre> -R <report frequency>
* Set frequency of generation reports.
* e.g, setting the value to 5 will
* report every 5th generation
* (default = number of generations)</pre>
*
* <pre> -S <seed>
* Set the random number seed.
* (default = 1)</pre>
*
<!-- options-end -->
*
* @author Mark Hall (mhall@cs.waikato.ac.nz)
* @version $Revision: 1.19 $
*/
public class GeneticSearch
extends ASSearch
implements StartSetHandler, OptionHandler, TechnicalInformationHandler {
/** for serialization */
static final long serialVersionUID = -1618264232838472679L;
/**
* holds a starting set as an array of attributes. Becomes one member of the
* initial random population
*/
private int[] m_starting;
/** holds the start set for the search as a Range */
private Range m_startRange;
/** does the data have a class */
private boolean m_hasClass;
/** holds the class index */
private int m_classIndex;
/** number of attributes in the data */
private int m_numAttribs;
/** the current population */
private GABitSet [] m_population;
/** the number of individual solutions */
private int m_popSize;
/** the best population member found during the search */
private GABitSet m_best;
/** the number of features in the best population member */
private int m_bestFeatureCount;
/** the number of entries to cache for lookup */
private int m_lookupTableSize;
/** the lookup table */
private Hashtable m_lookupTable;
/** random number generation */
private Random m_random;
/** seed for random number generation */
private int m_seed;
/** the probability of crossover occuring */
private double m_pCrossover;
/** the probability of mutation occuring */
private double m_pMutation;
/** sum of the current population fitness */
private double m_sumFitness;
private double m_maxFitness;
private double m_minFitness;
private double m_avgFitness;
/** the maximum number of generations to evaluate */
private int m_maxGenerations;
/** how often reports are generated */
private int m_reportFrequency;
/** holds the generation reports */
private StringBuffer m_generationReports;
// Inner class
/**
* A bitset for the genetic algorithm
*/
protected class GABitSet
implements Cloneable, Serializable, RevisionHandler {
/** for serialization */
static final long serialVersionUID = -2930607837482622224L;
/** the bitset */
private BitSet m_chromosome;
/** holds raw merit */
private double m_objective = -Double.MAX_VALUE;
/** the fitness */
private double m_fitness;
/**
* Constructor
*/
public GABitSet () {
m_chromosome = new BitSet();
}
/**
* makes a copy of this GABitSet
* @return a copy of the object
* @throws CloneNotSupportedException if something goes wrong
*/
public Object clone() throws CloneNotSupportedException {
GABitSet temp = new GABitSet();
temp.setObjective(this.getObjective());
temp.setFitness(this.getFitness());
temp.setChromosome((BitSet)(this.m_chromosome.clone()));
return temp;
//return super.clone();
}
/**
* sets the objective merit value
* @param objective the objective value of this population member
*/
public void setObjective(double objective) {
m_objective = objective;
}
/**
* gets the objective merit
* @return the objective merit of this population member
*/
public double getObjective() {
return m_objective;
}
/**
* sets the scaled fitness
* @param fitness the scaled fitness of this population member
*/
public void setFitness(double fitness) {
m_fitness = fitness;
}
/**
* gets the scaled fitness
* @return the scaled fitness of this population member
*/
public double getFitness() {
return m_fitness;
}
/**
* get the chromosome
* @return the chromosome of this population member
*/
public BitSet getChromosome() {
return m_chromosome;
}
/**
* set the chromosome
* @param c the chromosome to be set for this population member
*/
public void setChromosome(BitSet c) {
m_chromosome = c;
}
/**
* unset a bit in the chromosome
* @param bit the bit to be cleared
*/
public void clear(int bit) {
m_chromosome.clear(bit);
}
/**
* set a bit in the chromosome
* @param bit the bit to be set
*/
public void set(int bit) {
m_chromosome.set(bit);
}
/**
* get the value of a bit in the chromosome
* @param bit the bit to query
* @return the value of the bit
*/
public boolean get(int bit) {
return m_chromosome.get(bit);
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.19 $");
}
}
/**
* Returns an enumeration describing the available options.
* @return an enumeration of all the available options.
**/
public Enumeration listOptions () {
Vector newVector = new Vector(6);
newVector.addElement(new Option("\tSpecify a starting set of attributes."
+ "\n\tEg. 1,3,5-7."
+"If supplied, the starting set becomes"
+"\n\tone member of the initial random"
+"\n\tpopulation."
,"P",1
, "-P <start set>"));
newVector.addElement(new Option("\tSet the size of the population."
+"\n\t(default = 10)."
, "Z", 1
, "-Z <population size>"));
newVector.addElement(new Option("\tSet the number of generations."
+"\n\t(default = 20)"
, "G", 1, "-G <number of generations>"));
newVector.addElement(new Option("\tSet the probability of crossover."
+"\n\t(default = 0.6)"
, "C", 1, "-C <probability of"
+" crossover>"));
newVector.addElement(new Option("\tSet the probability of mutation."
+"\n\t(default = 0.033)"
, "M", 1, "-M <probability of mutation>"));
newVector.addElement(new Option("\tSet frequency of generation reports."
+"\n\te.g, setting the value to 5 will "
+"\n\treport every 5th generation"
+"\n\t(default = number of generations)"
, "R", 1, "-R <report frequency>"));
newVector.addElement(new Option("\tSet the random number seed."
+"\n\t(default = 1)"
, "S", 1, "-S <seed>"));
return newVector.elements();
}
/**
* Parses a given list of options. <p/>
*
<!-- options-start -->
* Valid options are: <p/>
*
* <pre> -P <start set>
* Specify a starting set of attributes.
* Eg. 1,3,5-7.If supplied, the starting set becomes
* one member of the initial random
* population.</pre>
*
* <pre> -Z <population size>
* Set the size of the population.
* (default = 10).</pre>
*
* <pre> -G <number of generations>
* Set the number of generations.
* (default = 20)</pre>
*
* <pre> -C <probability of crossover>
* Set the probability of crossover.
* (default = 0.6)</pre>
*
* <pre> -M <probability of mutation>
* Set the probability of mutation.
* (default = 0.033)</pre>
*
* <pre> -R <report frequency>
* Set frequency of generation reports.
* e.g, setting the value to 5 will
* report every 5th generation
* (default = number of generations)</pre>
*
* <pre> -S <seed>
* Set the random number seed.
* (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 {
String optionString;
resetOptions();
optionString = Utils.getOption('P', options);
if (optionString.length() != 0) {
setStartSet(optionString);
}
optionString = Utils.getOption('Z', options);
if (optionString.length() != 0) {
setPopulationSize(Integer.parseInt(optionString));
}
optionString = Utils.getOption('G', options);
if (optionString.length() != 0) {
setMaxGenerations(Integer.parseInt(optionString));
setReportFrequency(Integer.parseInt(optionString));
}
optionString = Utils.getOption('C', options);
if (optionString.length() != 0) {
setCrossoverProb((new Double(optionString)).doubleValue());
}
optionString = Utils.getOption('M', options);
if (optionString.length() != 0) {
setMutationProb((new Double(optionString)).doubleValue());
}
optionString = Utils.getOption('R', options);
if (optionString.length() != 0) {
setReportFrequency(Integer.parseInt(optionString));
}
optionString = Utils.getOption('S', options);
if (optionString.length() != 0) {
setSeed(Integer.parseInt(optionString));
}
}
/**
* Gets the current settings of ReliefFAttributeEval.
*
* @return an array of strings suitable for passing to setOptions()
*/
public String[] getOptions () {
String[] options = new String[14];
int current = 0;
if (!(getStartSet().equals(""))) {
options[current++] = "-P";
options[current++] = ""+startSetToString();
}
options[current++] = "-Z";
options[current++] = "" + getPopulationSize();
options[current++] = "-G";
options[current++] = "" + getMaxGenerations();
options[current++] = "-C";
options[current++] = "" + getCrossoverProb();
options[current++] = "-M";
options[current++] = "" + getMutationProb();
options[current++] = "-R";
options[current++] = "" + getReportFrequency();
options[current++] = "-S";
options[current++] = "" + getSeed();
while (current < options.length) {
options[current++] = "";
}
return options;
}
/**
* Returns the tip text for this property
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String startSetTipText() {
return "Set a start point for the search. This is specified as a comma "
+"seperated list off attribute indexes starting at 1. It can include "
+"ranges. Eg. 1,2,5-9,17. The start set becomes one of the population "
+"members of the initial population.";
}
/**
* Sets a starting set of attributes for the search. It is the
* search method's responsibility to report this start set (if any)
* in its toString() method.
* @param startSet a string containing a list of attributes (and or ranges),
* eg. 1,2,6,10-15.
* @throws Exception if start set can't be set.
*/
public void setStartSet (String startSet) throws Exception {
m_startRange.setRanges(startSet);
}
/**
* Returns a list of attributes (and or attribute ranges) as a String
* @return a list of attributes (and or attribute ranges)
*/
public String getStartSet () {
return m_startRange.getRanges();
}
/**
* Returns the tip text for this property
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String seedTipText() {
return "Set the random seed.";
}
/**
* set the seed for random number generation
* @param s seed value
*/
public void setSeed(int s) {
m_seed = s;
}
/**
* get the value of the random number generator's seed
* @return the seed for random number generation
*/
public int getSeed() {
return m_seed;
}
/**
* Returns the tip text for this property
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String reportFrequencyTipText() {
return "Set how frequently reports are generated. Default is equal to "
+"the number of generations meaning that a report will be printed for "
+"initial and final generations. Setting the value to 5 will result in "
+"a report being printed every 5 generations.";
}
/**
* set how often reports are generated
* @param f generate reports every f generations
*/
public void setReportFrequency(int f) {
m_reportFrequency = f;
}
/**
* get how often repports are generated
* @return how often reports are generated
*/
public int getReportFrequency() {
return m_reportFrequency;
}
/**
* Returns the tip text for this property
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String mutationProbTipText() {
return "Set the probability of mutation occuring.";
}
/**
* set the probability of mutation
* @param m the probability for mutation occuring
*/
public void setMutationProb(double m) {
m_pMutation = m;
}
/**
* get the probability of mutation
* @return the probability of mutation occuring
*/
public double getMutationProb() {
return m_pMutation;
}
/**
* Returns the tip text for this property
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String crossoverProbTipText() {
return "Set the probability of crossover. This is the probability that "
+"two population members will exchange genetic material.";
}
/**
* set the probability of crossover
* @param c the probability that two population members will exchange
* genetic material
*/
public void setCrossoverProb(double c) {
m_pCrossover = c;
}
/**
* get the probability of crossover
* @return the probability of crossover
*/
public double getCrossoverProb() {
return m_pCrossover;
}
/**
* Returns the tip text for this property
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String maxGenerationsTipText() {
return "Set the number of generations to evaluate.";
}
/**
* set the number of generations to evaluate
* @param m the number of generations
*/
public void setMaxGenerations(int m) {
m_maxGenerations = m;
}
/**
* get the number of generations
* @return the maximum number of generations
*/
public int getMaxGenerations() {
return m_maxGenerations;
}
/**
* Returns the tip text for this property
* @return tip text for this property suitable for
* displaying in the explorer/experimenter gui
*/
public String populationSizeTipText() {
return "Set the population size. This is the number of individuals "
+"(attribute sets) in the population.";
}
/**
* set the population size
* @param p the size of the population
*/
public void setPopulationSize(int p) {
m_popSize = p;
}
/**
* get the size of the population
* @return the population size
*/
public int getPopulationSize() {
return m_popSize;
}
/**
* Returns a string describing this search method
* @return a description of the search suitable for
* displaying in the explorer/experimenter gui
*/
public String globalInfo() {
return
"GeneticSearch:\n\nPerforms a search using the simple genetic "
+ "algorithm described in Goldberg (1989).\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.BOOK);
result.setValue(Field.AUTHOR, "David E. Goldberg");
result.setValue(Field.YEAR, "1989");
result.setValue(Field.TITLE, "Genetic algorithms in search, optimization and machine learning");
result.setValue(Field.ISBN, "0201157675");
result.setValue(Field.PUBLISHER, "Addison-Wesley");
return result;
}
/**
* Constructor. Make a new GeneticSearch object
*/
public GeneticSearch() {
resetOptions();
}
/**
* converts the array of starting attributes to a string. This is
* used by getOptions to return the actual attributes specified
* as the starting set. This is better than using m_startRanges.getRanges()
* as the same start set can be specified in different ways from the
* command line---eg 1,2,3 == 1-3. This is to ensure that stuff that
* is stored in a database is comparable.
* @return a comma seperated list of individual attribute numbers as a String
*/
private String startSetToString() {
StringBuffer FString = new StringBuffer();
boolean didPrint;
if (m_starting == null) {
return getStartSet();
}
for (int i = 0; i < m_starting.length; i++) {
didPrint = false;
if ((m_hasClass == false) ||
(m_hasClass == true && i != m_classIndex)) {
FString.append((m_starting[i] + 1));
didPrint = true;
}
if (i == (m_starting.length - 1)) {
FString.append("");
}
else {
if (didPrint) {
FString.append(",");
}
}
}
return FString.toString();
}
/**
* returns a description of the search
* @return a description of the search as a String
*/
public String toString() {
StringBuffer GAString = new StringBuffer();
GAString.append("\tGenetic search.\n\tStart set: ");
if (m_starting == null) {
GAString.append("no attributes\n");
}
else {
GAString.append(startSetToString()+"\n");
}
GAString.append("\tPopulation size: "+m_popSize);
GAString.append("\n\tNumber of generations: "+m_maxGenerations);
GAString.append("\n\tProbability of crossover: "
+Utils.doubleToString(m_pCrossover,6,3));
GAString.append("\n\tProbability of mutation: "
+Utils.doubleToString(m_pMutation,6,3));
GAString.append("\n\tReport frequency: "+m_reportFrequency);
GAString.append("\n\tRandom number seed: "+m_seed+"\n");
GAString.append(m_generationReports.toString());
return GAString.toString();
}
/**
* Searches the attribute subset space using a genetic algorithm.
*
* @param ASEval the attribute evaluator to guide the search
* @param data the training instances.
* @return an array (not necessarily ordered) of selected attribute indexes
* @throws Exception if the search can't be completed
*/
public int[] search (ASEvaluation ASEval, Instances data)
throws Exception {
m_best = null;
m_generationReports = new StringBuffer();
if (!(ASEval instanceof SubsetEvaluator)) {
throw new Exception(ASEval.getClass().getName()
+ " is not a "
+ "Subset evaluator!");
}
if (ASEval instanceof UnsupervisedSubsetEvaluator) {
m_hasClass = false;
}
else {
m_hasClass = true;
m_classIndex = data.classIndex();
}
SubsetEvaluator ASEvaluator = (SubsetEvaluator)ASEval;
m_numAttribs = data.numAttributes();
m_startRange.setUpper(m_numAttribs-1);
if (!(getStartSet().equals(""))) {
m_starting = m_startRange.getSelection();
}
// initial random population
m_lookupTable = new Hashtable(m_lookupTableSize);
m_random = new Random(m_seed);
m_population = new GABitSet [m_popSize];
// set up random initial population
initPopulation();
evaluatePopulation(ASEvaluator);
populationStatistics();
scalePopulation();
checkBest();
m_generationReports.append(populationReport(0));
boolean converged;
for (int i=1;i<=m_maxGenerations;i++) {
generation();
evaluatePopulation(ASEvaluator);
populationStatistics();
scalePopulation();
// find the best pop member and check for convergence
converged = checkBest();
if ((i == m_maxGenerations) ||
((i % m_reportFrequency) == 0) ||
(converged == true)) {
m_generationReports.append(populationReport(i));
if (converged == true) {
break;
}
}
}
return attributeList(m_best.getChromosome());
}
/**
* converts a BitSet into a list of attribute indexes
* @param group the BitSet to convert
* @return an array of attribute indexes
**/
private int[] attributeList (BitSet group) {
int count = 0;
// count how many were selected
for (int i = 0; i < m_numAttribs; i++) {
if (group.get(i)) {
count++;
}
}
int[] list = new int[count];
count = 0;
for (int i = 0; i < m_numAttribs; i++) {
if (group.get(i)) {
list[count++] = i;
}
}
return list;
}
/**
* checks to see if any population members in the current
* population are better than the best found so far. Also checks
* to see if the search has converged---that is there is no difference
* in fitness between the best and worse population member
* @return true is the search has converged
* @throws Exception if something goes wrong
*/
private boolean checkBest() throws Exception {
int i,count,lowestCount = m_numAttribs;
double b = -Double.MAX_VALUE;
GABitSet localbest = null;
BitSet temp;
boolean converged = false;
int oldcount = Integer.MAX_VALUE;
if (m_maxFitness - m_minFitness > 0) {
// find the best in this population
for (i=0;i<m_popSize;i++) {
if (m_population[i].getObjective() > b) {
b = m_population[i].getObjective();
localbest = m_population[i];
oldcount = countFeatures(localbest.getChromosome());
} else if (Utils.eq(m_population[i].getObjective(), b)) {
// see if it contains fewer features
count = countFeatures(m_population[i].getChromosome());
if (count < oldcount) {
b = m_population[i].getObjective();
localbest = m_population[i];
oldcount = count;
}
}
}
} else {
// look for the smallest subset
for (i=0;i<m_popSize;i++) {
temp = m_population[i].getChromosome();
count = countFeatures(temp);;
if (count < lowestCount) {
lowestCount = count;
localbest = m_population[i];
b = localbest.getObjective();
}
}
converged = true;
}
// count the number of features in localbest
count = 0;
temp = localbest.getChromosome();
count = countFeatures(temp);
// compare to the best found so far
if (m_best == null) {
m_best = (GABitSet)localbest.clone();
m_bestFeatureCount = count;
} else if (b > m_best.getObjective()) {
m_best = (GABitSet)localbest.clone();
m_bestFeatureCount = count;
} else if (Utils.eq(m_best.getObjective(), b)) {
// see if the localbest has fewer features than the best so far
if (count < m_bestFeatureCount) {
m_best = (GABitSet)localbest.clone();
m_bestFeatureCount = count;
}
}
return converged;
}
/**
* counts the number of features in a subset
* @param featureSet the feature set for which to count the features
* @return the number of features in the subset
*/
private int countFeatures(BitSet featureSet) {
int count = 0;
for (int i=0;i<m_numAttribs;i++) {
if (featureSet.get(i)) {
count++;
}
}
return count;
}
/**
* performs a single generation---selection, crossover, and mutation
* @throws Exception if an error occurs
*/
private void generation () throws Exception {
int i,j=0;
double best_fit = -Double.MAX_VALUE;
int old_count = 0;
int count;
GABitSet [] newPop = new GABitSet [m_popSize];
int parent1,parent2;
/** first ensure that the population best is propogated into the new
generation */
for (i=0;i<m_popSize;i++) {
if (m_population[i].getFitness() > best_fit) {
j = i;
best_fit = m_population[i].getFitness();
old_count = countFeatures(m_population[i].getChromosome());
} else if (Utils.eq(m_population[i].getFitness(), best_fit)) {
count = countFeatures(m_population[i].getChromosome());
if (count < old_count) {
j = i;
best_fit = m_population[i].getFitness();
old_count = count;
}
}
}
newPop[0] = (GABitSet)(m_population[j].clone());
newPop[1] = newPop[0];
for (j=2;j<m_popSize;j+=2) {
parent1 = select();
parent2 = select();
newPop[j] = (GABitSet)(m_population[parent1].clone());
newPop[j+1] = (GABitSet)(m_population[parent2].clone());
// if parents are equal mutate one bit
if (parent1 == parent2) {
int r;
if (m_hasClass) {
while ((r = (Math.abs(m_random.nextInt()) % m_numAttribs)) == m_classIndex);
}
else {
r = m_random.nextInt() % m_numAttribs;
}
if (newPop[j].get(r)) {
newPop[j].clear(r);
}
else {
newPop[j].set(r);
}
} else {
// crossover
double r = m_random.nextDouble();
if (m_numAttribs >= 3) {
if (r < m_pCrossover) {
// cross point
int cp = Math.abs(m_random.nextInt());
cp %= (m_numAttribs-2);
cp ++;
for (i=0;i<cp;i++) {
if (m_population[parent1].get(i)) {
newPop[j+1].set(i);
}
else {
newPop[j+1].clear(i);
}
if (m_population[parent2].get(i)) {
newPop[j].set(i);
}
else {
newPop[j].clear(i);
}
}
}
}
// mutate
for (int k=0;k<2;k++) {
for (i=0;i<m_numAttribs;i++) {
r = m_random.nextDouble();
if (r < m_pMutation) {
if (m_hasClass && (i == m_classIndex)) {
// ignore class attribute
}
else {
if (newPop[j+k].get(i)) {
newPop[j+k].clear(i);
}
else {
newPop[j+k].set(i);
}
}
}
}
}
}
}
m_population = newPop;
}
/**
* selects a population member to be considered for crossover
* @return the index of the selected population member
*/
private int select() {
int i;
double r,partsum;
partsum = 0;
r = m_random.nextDouble() * m_sumFitness;
for (i=0;i<m_popSize;i++) {
partsum += m_population[i].getFitness();
if (partsum >= r) {
break;
}
}
// if none was found, take first
if (i == m_popSize)
i = 0;
return i;
}
/**
* evaluates an entire population. Population members are looked up in
* a hash table and if they are not found then they are evaluated using
* ASEvaluator.
* @param ASEvaluator the subset evaluator to use for evaluating population
* members
* @throws Exception if something goes wrong during evaluation
*/
private void evaluatePopulation (SubsetEvaluator ASEvaluator)
throws Exception {
int i;
double merit;
for (i=0;i<m_popSize;i++) {
// if its not in the lookup table then evaluate and insert
if (m_lookupTable.containsKey(m_population[i]
.getChromosome()) == false) {
merit = ASEvaluator.evaluateSubset(m_population[i].getChromosome());
m_population[i].setObjective(merit);
m_lookupTable.put(m_population[i].getChromosome(),m_population[i]);
} else {
GABitSet temp = (GABitSet)m_lookupTable.
get(m_population[i].getChromosome());
m_population[i].setObjective(temp.getObjective());
}
}
}
/**
* creates random population members for the initial population. Also
* sets the first population member to be a start set (if any)
* provided by the user
* @throws Exception if the population can't be created
*/
private void initPopulation () throws Exception {
int i,j,bit;
int num_bits;
boolean ok;
int start = 0;
// add the start set as the first population member (if specified)
if (m_starting != null) {
m_population[0] = new GABitSet();
for (i=0;i<m_starting.length;i++) {
if ((m_starting[i]) != m_classIndex) {
m_population[0].set(m_starting[i]);
}
}
start = 1;
}
for (i=start;i<m_popSize;i++) {
m_population[i] = new GABitSet();
num_bits = m_random.nextInt();
num_bits = num_bits % m_numAttribs-1;
if (num_bits < 0) {
num_bits *= -1;
}
if (num_bits == 0) {
num_bits = 1;
}
for (j=0;j<num_bits;j++) {
ok = false;
do {
bit = m_random.nextInt();
if (bit < 0) {
bit *= -1;
}
bit = bit % m_numAttribs;
if (m_hasClass) {
if (bit != m_classIndex) {
ok = true;
}
}
else {
ok = true;
}
} while (!ok);
if (bit > m_numAttribs) {
throw new Exception("Problem in population init");
}
m_population[i].set(bit);
}
}
}
/**
* calculates summary statistics for the current population
*/
private void populationStatistics() {
int i;
m_sumFitness = m_minFitness = m_maxFitness =
m_population[0].getObjective();
for (i=1;i<m_popSize;i++) {
m_sumFitness += m_population[i].getObjective();
if (m_population[i].getObjective() > m_maxFitness) {
m_maxFitness = m_population[i].getObjective();
}
else if (m_population[i].getObjective() < m_minFitness) {
m_minFitness = m_population[i].getObjective();
}
}
m_avgFitness = (m_sumFitness / m_popSize);
}
/**
* scales the raw (objective) merit of the population members
*/
private void scalePopulation() {
int j;
double a = 0;
double b = 0;
double fmultiple = 2.0;
double delta;
// prescale
if (m_minFitness > ((fmultiple * m_avgFitness - m_maxFitness) /
(fmultiple - 1.0))) {
delta = m_maxFitness - m_avgFitness;
a = ((fmultiple - 1.0) * m_avgFitness / delta);
b = m_avgFitness * (m_maxFitness - fmultiple * m_avgFitness) / delta;
}
else {
delta = m_avgFitness - m_minFitness;
a = m_avgFitness / delta;
b = -m_minFitness * m_avgFitness / delta;
}
// scalepop
m_sumFitness = 0;
for (j=0;j<m_popSize;j++) {
if (a == Double.POSITIVE_INFINITY || a == Double.NEGATIVE_INFINITY ||
b == Double.POSITIVE_INFINITY || b == Double.NEGATIVE_INFINITY) {
m_population[j].setFitness(m_population[j].getObjective());
} else {
m_population[j].
setFitness(Math.abs((a * m_population[j].getObjective() + b)));
}
m_sumFitness += m_population[j].getFitness();
}
}
/**
* generates a report on the current population
* @return a report as a String
*/
private String populationReport (int genNum) {
int i;
StringBuffer temp = new StringBuffer();
if (genNum == 0) {
temp.append("\nInitial population\n");
}
else {
temp.append("\nGeneration: "+genNum+"\n");
}
temp.append("merit \tscaled \tsubset\n");
for (i=0;i<m_popSize;i++) {
temp.append(Utils.doubleToString(Math.
abs(m_population[i].getObjective()),
8,5)
+"\t"
+Utils.doubleToString(m_population[i].getFitness(),
8,5)
+"\t");
temp.append(printPopMember(m_population[i].getChromosome())+"\n");
}
return temp.toString();
}
/**
* prints a population member as a series of attribute numbers
* @param temp the chromosome of a population member
* @return a population member as a String of attribute numbers
*/
private String printPopMember(BitSet temp) {
StringBuffer text = new StringBuffer();
for (int j=0;j<m_numAttribs;j++) {
if (temp.get(j)) {
text.append((j+1)+" ");
}
}
return text.toString();
}
/**
* prints a population member's chromosome
* @param temp the chromosome of a population member
* @return a population member's chromosome as a String
*/
private String printPopChrom(BitSet temp) {
StringBuffer text = new StringBuffer();
for (int j=0;j<m_numAttribs;j++) {
if (temp.get(j)) {
text.append("1");
} else {
text.append("0");
}
}
return text.toString();
}
/**
* reset to default values for options
*/
private void resetOptions () {
m_population = null;
m_popSize = 20;
m_lookupTableSize = 1001;
m_pCrossover = 0.6;
m_pMutation = 0.033;
m_maxGenerations = 20;
m_reportFrequency = m_maxGenerations;
m_starting = null;
m_startRange = new Range();
m_seed = 1;
}
/**
* Returns the revision string.
*
* @return the revision
*/
public String getRevision() {
return RevisionUtils.extract("$Revision: 1.19 $");
}
}