// Compute scores for new leaf0 and leaf1, and add them to scoreList.
private void computeNewLeafScores(SelectedSet selectedSet, int i, int j) {
int NS = selectedSet.getN();
for (int a = 0; a < NS; a++) {
Individual individual = selectedSet.getIndividual(a);
IGraph iterator = decisionGraphs[i].getGraph();
while (!(iterator
instanceof Leaf)) { // Iterator is a variable because we are still traversing the DG.
int x = ((Variable) iterator).getVariable();
char alleleX = individual.getAllele(x);
if (alleleX == '0') {
iterator = ((Variable) iterator).getZero();
} else {
iterator = ((Variable) iterator).getOne();
}
}
int itrPosition = decisionGraphs[i].getLeafs().indexOf((Leaf) iterator);
if (itrPosition == j || itrPosition == j + 1) { // We've reached one of the new leafs.
int mZero = ((Leaf) iterator).getMZero();
int mOne = ((Leaf) iterator).getMOne();
if (mZero > 0 && mOne > 0) { // It's still "interesting" to split.
char alleleI = individual.getAllele(i); // Value of Xi in individual a.
for (int split : splitList[i]) {
char alleleS = individual.getAllele(split); // Value of Xsplit in individual a.
if (alleleI == '0') {
if (alleleS == '0') {
((Leaf) iterator).addPossibleSplitFrequency(0, split); // m00[split]++;
} else {
((Leaf) iterator).addPossibleSplitFrequency(1, split); // m01[split]++;
}
} else if (alleleS == '0') {
((Leaf) iterator).addPossibleSplitFrequency(2, split); // m10[split]++;
} else {
((Leaf) iterator).addPossibleSplitFrequency(3, split); // m11[split]++;
}
}
}
}
}
for (int a = 0; a <= 1; a++) {
Leaf newLeaf =
decisionGraphs[i].getLeaf(j + a); // The two new leafs are at positions 'j' and 'j+1'.
int mZero = newLeaf.getMZero();
int mOne = newLeaf.getMOne();
if (mZero > 0 && mOne > 0) {
for (int s : splitList[i]) {
int m00 = newLeaf.getPossibleSplitFrequency(0, s);
int m01 = newLeaf.getPossibleSplitFrequency(1, s);
int m10 = newLeaf.getPossibleSplitFrequency(2, s);
int m11 = newLeaf.getPossibleSplitFrequency(3, s);
double scoreGain = bayesianMetric.computeScoreGain(mZero, mOne, m00, m01, m10, m11);
newLeaf.setScoreGain(s, scoreGain);
newLeaf.updateBestSplit(
s,
scoreGain); // Responsible for updating the value of the best split score gain in this
// leaf.
}
}
} // END: for(int a = 0 ...)
} // END: computeNewLeafScores(...)
public Individual getIndividualCopy(int i) { // NOTE: Non shallow copy!
Individual indiv = new Individual();
for (int j = 0; j < Problem.n; j++) {
indiv.setAllele(j, individuals[i].getAllele(j));
}
return indiv;
}
public SimplePopulation getPopulation(BinaryString template) {
SimplePopulation pop = new SimplePopulation();
for (Individual ind : individuals) {
pop.addIndividual(ind.getSolution(template));
}
return pop;
}
public float computeFitness(Individual individual) {
int six;
float fit = 0;
for (int i = 0; i < Problem.n; ) { // Empty increment
six = Integer.parseInt(String.valueOf(individual.getAllele(i++)));
six += Integer.parseInt(String.valueOf(individual.getAllele(i++)));
six += Integer.parseInt(String.valueOf(individual.getAllele(i++)));
six += Integer.parseInt(String.valueOf(individual.getAllele(i++)));
six += Integer.parseInt(String.valueOf(individual.getAllele(i++)));
six += Integer.parseInt(String.valueOf(individual.getAllele(i++)));
six = Math.abs(six - 3);
switch (six) {
case 0:
fit += 0.9;
break;
case 1:
fit += 0.8;
break;
case 3:
fit += 1;
break;
default:
break;
}
}
return fit;
}
public float computeFitness(Individual individual) {
for (int i = 0; i < Problem.n; ) { // Empty increment
char c = individual.getAllele(i++);
for (int j = 1; j < 6; j++) if (individual.getAllele(i++) != c) return (float) 0;
}
return (float) 1;
}
public int compare(Individual individual_1, Individual individual_2) {
if (individual_1.getRate() == individual_2.getRate()) {
return 0;
} else if (individual_1.getRate() < individual_2.getRate()) {
return 1;
} else {
return -1;
}
}
// Generate chromosome using random permutations
public Individual generateRandomChromosome() {
Individual indiv = new Individual();
// Filling in the order
for (int i = 0; i < Problem.customersNumber; i++) {
indiv.getChromosome().add(i);
}
// And shuffling
Collections.shuffle(indiv.getChromosome());
return indiv;
}
// Calculate inidividuals fittness by comparing it to our candidate solution
static int getFitness(Individual individual) {
int fitness = 0;
// Loop through our individuals genes and compare them to our cadidates
for (int i = 0; i < individual.size() && i < solution.length; i++) {
if (individual.getGene(i) == solution[i]) {
fitness++;
}
}
return fitness;
}
public Individual run(
EvolutionState state,
SimpleProblemForm p,
Individual x,
int maxIter,
ClusWrapperNonStatic objectClus)
throws Exception { // talvez passe um individuo já com o genoma e score
Random rand = new Random();
// IntegerVectorIndividual mutatedX = (IntegerVectorIndividual) deepClone(x);
IntegerVectorIndividual mutatedX = (IntegerVectorIndividual) x.clone();
mutatedX.evaluated = false;
double alpha = 0.95; // cálculo do alpha, percentual de diminuição da temperatura
double t_final = 1;
double t0 = Math.pow(alpha, maxIter + Math.log(t_final)); // estimar a temperatura inicial
double temp_atual = t0; // tf = temperatura da vez
int iter = 0;
maxIter *= 2;
while (iter < maxIter) {
int[] genome = mutatedX.genome;
genome = mutate(genome, 1 - iter / maxIter); // mutar o vetor
mutatedX.setGenome(genome);
((ec.Problem) p).prepareToEvaluate(state, 0);
System.out.print("Mutated Genoma: " + mutatedX.genome[0]);
for (int i = 0; i < mutatedX.genomeLength(); i++) System.out.print("," + mutatedX.genome[i]);
System.out.println();
p.evaluate(state, mutatedX, 0, 0, objectClus);
((ec.Problem) p).finishEvaluating(state, 0);
double newF = mutatedX.fitness.fitness();
// adequar para minimizar o fitness
float delta = (float) (x.fitness.fitness() - newF);
if (delta < 0 || rand.nextDouble() < Math.exp(-(delta) / temp_atual)) {
((IntegerVectorIndividual) x).setGenome(mutatedX.getGenome());
x.evaluated = false;
((ec.Problem) p).prepareToEvaluate(state, 0);
p.evaluate(state, x, 0, 0, objectClus);
((ec.Problem) p).finishEvaluating(state, 0);
}
iter += 1;
temp_atual = temp_atual * alpha;
}
return x;
}
public Individual getFittest() {
Individual fittest = individuals[0];
// Loop through individuals to find fittest
for (int i = 0; i < size(); i++) {
if (fittest.getFitness() <= getIndividual(i).getFitness()) {
fittest = getIndividual(i);
}
}
return fittest;
}
public float computeFitness(Individual individual) {
int k;
float fit = 0;
for (int i = 0; i < Problem.n; ) { // Empty increment
k = Integer.parseInt(String.valueOf(individual.getAllele(i++)));
for (int j = 1; j < kay; j++)
k += Integer.parseInt(String.valueOf(individual.getAllele(i++)));
if (k < kay) fit += kay - 1 - k;
else fit += kay;
}
return fit;
}
public Population(int population_size, int chromosome_length, boolean initialize) {
individuals = new Individual[population_size];
this.chromosome_length = chromosome_length;
// Initialize population
if (initialize) {
for (int i = 0; i < size(); i++) {
Individual ind = new Individual();
ind.generateIndividual(chromosome_length);
saveIndividual(i, ind);
}
}
}
public List<Family> getFamiliesTDT() {
List<Family> families = new ArrayList<>();
Individual ind;
for (Map.Entry<String, Individual> entry : this.individuals.entrySet()) {
ind = entry.getValue();
if (ind.getFather() != null && ind.getMother() != null) {
addIndividualToFamily(ind, ind.getFather(), ind.getMother(), families);
}
}
return families;
}
public boolean needsToRun(Run run, int generation) {
Population pop = getPopulationFor(run, generation);
int count = run.getIntProperty(GenetikConstants.POPULATION, Integer.MAX_VALUE, true);
int scoreCount = 0;
for (int i = 0, max = pop.size(); i < max; i++) {
Individual ind = pop.get(i);
if (ind.hasFitness() && ind.hasScores()) {
scoreCount++;
}
}
return scoreCount != count;
}
@Override
public String toString() {
StringBuilder sb = new StringBuilder();
sb.append("Pedigree\n");
if (fields.size() > 0) {
sb.append("fields = " + fields.keySet().toString() + "\n");
}
for (Map.Entry<String, Set<Individual>> elem : this.families.entrySet()) {
sb.append(elem.getKey() + "\n");
for (Individual ind : elem.getValue()) {
sb.append("\t" + ind.toString() + "\n");
}
}
return sb.toString();
}
public static int getFitness(Individual gene, CityMap cm) {
int fitness = 0;
if (cm == null) {
System.out.println("CityMap is NULL. Terminate 3");
System.exit(3);
}
for (int i = 0; i < gene.length(); i++) {
int dist, city = gene.getItem(i), nextCity;
if (i + 1 >= gene.length()) nextCity = gene.getItem(0);
else nextCity = gene.getItem(i + 1);
if (city == 0 || nextCity == 0) System.out.println(gene);
dist = cm.getDist(city, nextCity);
fitness += dist;
}
return fitness;
}
public Individual(Individual individual) {
this(individual.getLociPattern());
for (int i = 0; i < individual.getGenomeSize(); i++) {
Object clonedLocus = null;
try {
clonedLocus = individual.getLocus(i).clone();
} catch (CloneNotSupportedException e) {
e.printStackTrace();
}
if (getLociPattern().getLocusType(i) == LociPattern.LocusType.Fitness) {
loci[i] = (FitnessLocus) clonedLocus;
} else if (getLociPattern().getLocusType(i) == LociPattern.LocusType.Mutator) {
loci[i] = (MutatorLocus) clonedLocus;
} else if (getLociPattern().getLocusType(i) == LociPattern.LocusType.Recombination) {
loci[i] = (RecombinationLocus) clonedLocus;
}
}
}
public float computeFitness(Individual individual) {
float fit = 0;
for (int i = 0; i < Problem.n; ) { // Empty increment
char a = individual.getAllele(i++);
char b = individual.getAllele(i++);
if (a == '1' && b == '1') fit += 0.9;
if (a == '0' && b == '0') fit += 1;
}
return fit;
}
public Individual[] generateChildren(Individual[] parents, Run run) {
Individual parent = parents[0];
Individual retVal = parent.duplicate();
retVal.setId(parent.getId());
retVal.setParentOne(parent.getId());
retVal.setParentTwo(null);
Individual[] children = {retVal};
return children;
}
// Generate chromosome using greedy procedure from 22p.
public Individual generateGreedyChromosome() {
Individual indiv = new Individual();
Random random = new Random();
List<Integer> tempChromosome = new ArrayList<Integer>(Problem.customersNumber);
for (int i = 0; i < Problem.customersNumber; i++) {
tempChromosome.add(i);
}
while (!tempChromosome.isEmpty()) {
int randIndex = (int) (random.nextInt(tempChromosome.size()));
int randCustId = tempChromosome.get(randIndex);
tempChromosome.remove(randIndex);
indiv.getChromosome().add(randCustId);
Point randCust = Problem.getCustomer(randCustId);
while (true) {
// Finding the nearest point
double dist;
double minDist =
GA.EUCLIDEAN_RADIUS; // If the distance is greater than EUCLIDEAN_RADIUS, then this
// point is not interesting anyway
int nearestId = -1;
for (Point p : Problem.customers) {
dist = randCust.distanceTo(p);
if (dist < minDist
&& dist > 0
&& // To exclude itself
!indiv.getChromosome().contains(p.getId())) { // Still not in list
minDist = dist;
nearestId = p.getId();
}
}
if (nearestId == -1) { // The nearest point is not exist
break;
}
tempChromosome.remove((Object) nearestId);
indiv.getChromosome().add(nearestId);
randCust = Problem.getCustomer(nearestId);
}
}
return indiv;
}
public int compareTo(Individual arg) {
// Compare by class name first:
String first = getClass().getSimpleName();
String argFirst = arg.getClass().getSimpleName();
int firstCompare = first.compareTo(argFirst);
if (firstCompare != 0) return firstCompare;
if (name != null && arg.name != null) {
int secondCompare = name.compareTo(arg.name);
if (secondCompare != 0) return secondCompare;
}
return (arg.id < id ? -1 : (arg.id == id ? 0 : 1));
}
public float computeFitness(Individual individual) {
int three;
float fit = 0;
for (int i = 0; i < Problem.n; ) { // Empty increment
three = Integer.parseInt(String.valueOf(individual.getAllele(i++)));
three += Integer.parseInt(String.valueOf(individual.getAllele(i++)));
three += Integer.parseInt(String.valueOf(individual.getAllele(i++)));
switch (three) {
case 0:
fit += 1;
break;
case 2:
fit += 0.8;
break;
case 3:
fit += 0.9;
break;
default:
break;
}
}
return fit;
}
public void evaluate(
final EvolutionState state,
final Individual ind,
final int subpopulation,
final int threadnum) {
if (!ind.evaluated) // don't bother reevaluating
{
// trees[0].child is the root
double score = fitness(((GPIndividual) ind).trees[0].child, state);
SimpleFitness f = ((SimpleFitness) ind.fitness);
f.setFitness(state, score, false);
ind.evaluated = true;
}
}
/** Saves an individual to disk under a given filename, in computer-readable format. */
public void storeIndividual(final EvolutionState state, String filename, Individual ind) {
try {
File file = openFile(state, filename);
// PrintWriter writer = new PrintWriter(file);
// ind.printIndividual(state, writer);
// writer.close();
int log =
state.output.addLog(
file,
Output.V_NO_GENERAL - 1,
false,
!state.parameters.getBoolean(new Parameter(P_COMPRESS), null, false),
state.parameters.getBoolean(new Parameter(P_COMPRESS), null, false));
ind.printIndividual(state, log, Output.V_NO_GENERAL);
state.output.message("Best Individual stored in " + filename);
} catch (Exception e) {
state.output.error("Exception " + e);
}
}
public static HomeFolder xmlToModel(fr.cg95.cvq.xml.common.HomeFolderType homeFolderType) {
HomeFolder homeFolder = new HomeFolder();
homeFolder.setId(new Long(homeFolderType.getId()));
homeFolder.setAdress(Address.xmlToModel(homeFolderType.getAddress()));
IndividualType[] individualsArray = homeFolderType.getIndividualsArray();
Arrays.asList(individualsArray);
List<Individual> individualsSet = new ArrayList<Individual>();
for (int i = 0; i < individualsArray.length; i++) {
individualsSet.add(Individual.xmlToModel(individualsArray[i]));
}
homeFolder.setIndividuals(individualsSet);
if (homeFolderType.getState() != null)
homeFolder.setState(ActorState.forString(homeFolderType.getState().toString()));
if (homeFolderType.getFamilyQuotient() != null)
homeFolder.setFamilyQuotient(homeFolderType.getFamilyQuotient());
return homeFolder;
}
public void evaluate(
final EvolutionState state,
final Individual ind,
final int subpopulation,
final int threadnum) {
float accuracy = (float) 0.0;
int i;
double total_correct = 0;
if (!ind.evaluated) // don't bother reevaluating
{
SVM_GP.setInd(ind);
SVM_GP.setInput(input);
SVM_GP.setProblem(this);
SVM_GP.setStack(stack);
SVM_GP.setState(state);
SVM_GP.setSubpopulation(subpopulation);
SVM_GP.setThreadnum(threadnum);
double[] target = new double[prob.l];
SVM_GP.svm_cross_validation(prob, param, nr_fold, target);
/*((GPIndividual)ind).trees[0].child.eval(
state,threadnum,input,stack,((GPIndividual)ind),this);*/
// result = Math.abs(expectedResult - input.x);
for (i = 0; i < prob.l; i++) if (target[i] == prob.y[i]) ++total_correct;
accuracy = (float) (total_correct / prob.l);
System.out.print("Cross Validation Accuracy = " + 100.0 * accuracy + "%\n");
}
SimpleFitness f = ((SimpleFitness) ind.fitness);
f.setFitness(state, accuracy, accuracy == 1.0);
// the fitness better be KozaFitness!
// KozaFitness f = ((KozaFitness)ind.fitness);
// f.setStandardizedFitness(state,(float)accuracy);
// f.hits = hits;
ind.evaluated = true;
}
public void evaluate(
final EvolutionState state,
final Individual ind,
final int subpopulation,
final int threadnum) {
if (ca == null) ca = new CA(CA_WIDTH, NEIGHBORHOOD);
// we always reevaluate
// if (!ind.evaluated) // don't bother reevaluating
{
MajorityData input = (MajorityData) (this.input);
int sum = 0;
// extract the rule
((GPIndividual) ind)
.trees[0].child.eval(state, threadnum, input, stack, ((GPIndividual) ind), this);
int[] rule = ca.getRule();
for (int i = 0; i < 64; i++) rule[i] = (int) (((input.data0) >> i) & 0x1);
for (int i = 64; i < 128; i++) rule[i] = (int) (((input.data1) >> (i - 64)) & 0x1);
ca.setRule(rule); // for good measure though it doesn't matter
for (int i = 0; i < NUM_TRIALS; i++) {
// set up and run the CA
ca.setVals(trials[i]);
ca.step(STEPS, true);
// extract the fitness
if (all(ca.getVals(), majorities[i])) sum++;
}
SimpleFitness f = ((SimpleFitness) ind.fitness);
f.setFitness(state, sum / (double) NUM_TRIALS, (sum == NUM_TRIALS));
ind.evaluated = true;
}
}
private void applyRule(int row, int column, Individual[][] a_lattice) {
/*
* TODO: clever way to do this with iteration
*
*/
// placeholder
Individual currentIndividual = a_lattice[row][column];
if (currentIndividual.state == 'I') {
// infect neighbours
Individual neighbour = getLeft(row, column, a_lattice);
if (neighbour.getDiseaseState() == 'S' && Math.random() < beta) {
// transmission happens
neighbour.infect();
if (currentIndividual.isPrimaryCase) {
this.countOfSecondaryInfections++;
}
}
// update the time spent infected
// if this time exceeds the infectious period then turn Removed ('R')
currentIndividual.updateDiseaseState();
neighbour = getRight(row, column, a_lattice);
if (neighbour.getDiseaseState() == 'S' && Math.random() < beta) {
// transmission happens
neighbour.infect();
if (currentIndividual.isPrimaryCase) {
this.countOfSecondaryInfections++;
}
}
// update the time spent infected
// if this time exceeds the infectious period then turn Removed ('R')
currentIndividual.updateDiseaseState();
neighbour = getDown(row, column, a_lattice);
if (neighbour.getDiseaseState() == 'S' && Math.random() < beta) {
// transmission happens
neighbour.infect();
if (currentIndividual.isPrimaryCase) {
this.countOfSecondaryInfections++;
}
}
// update the time spent infected
// if this time exceeds the infectious period then turn Removed ('R')
currentIndividual.updateDiseaseState();
neighbour = getUp(row, column, a_lattice);
if (neighbour.getDiseaseState() == 'S' && Math.random() < beta) {
// transmission happens
neighbour.infect();
if (currentIndividual.isPrimaryCase) {
this.countOfSecondaryInfections++;
}
}
// update the time spent infected
// if this time exceeds the infectious period then turn Removed ('R')
currentIndividual.updateDiseaseState();
neighbour = getUpLeft(row, column, a_lattice);
if (neighbour.getDiseaseState() == 'S' && Math.random() < beta) {
// transmission happens
neighbour.infect();
if (currentIndividual.isPrimaryCase) {
this.countOfSecondaryInfections++;
}
}
neighbour = getDownLeft(row, column, a_lattice);
if (neighbour.getDiseaseState() == 'S' && Math.random() < beta) {
// transmission happens
neighbour.infect();
if (currentIndividual.isPrimaryCase) {
this.countOfSecondaryInfections++;
}
}
neighbour = getUpRight(row, column, a_lattice);
if (neighbour.getDiseaseState() == 'S' && Math.random() < beta) {
// transmission happens
neighbour.infect();
if (currentIndividual.isPrimaryCase) {
this.countOfSecondaryInfections++;
}
}
neighbour = getDownRight(row, column, a_lattice);
if (neighbour.getDiseaseState() == 'S' && Math.random() < beta) {
// transmission happens
neighbour.infect();
if (currentIndividual.isPrimaryCase) {
this.countOfSecondaryInfections++;
}
}
}
}
public void addIndividual(Individual newInd) {
family.add(newInd);
numIndividuals++;
familyFitness.add(newInd.getFitness());
}
public DataPropertyStatementImpl(Individual individual) {
if (individual != null) {
this.individualURI = individual.getURI();
}
}