I have started experimenting with the Jenetics library, however I am having some issues with trying to make a very easy "custom" set of gene/chromosomes. What I tried to do was to create a custom chromosome with a different (random) number of custom genes inside. The genes simply contain an integer value, just for the sake of simplicity. For the same simplicity, the contents of a gene can only be numbers ranging from 0 to 9 and a Gene is considered valid only if it does NOT contain the number 9 (again, retardedly simple, but I just wanted to make them custom)
Here is my code:
CustomGene:
public class CustomGene implements Gene<Integer, CustomGene> {
private Integer value;
private CustomGene(Integer value) {
this.value = value;
}
public static CustomGene of(Integer value) {
return new CustomGene(value);
}
public static ISeq<CustomGene> seq(Integer min, Integer max, int length) {
Random r = RandomRegistry.getRandom();
return MSeq.<CustomGene>ofLength(length).fill(() ->
new CustomGene(random.nextInt(r, min, max))
).toISeq();
}
@Override
public Integer getAllele() {
return value;
}
@Override
public CustomGene newInstance() {
final Random random = RandomRegistry.getRandom();
return new CustomGene(Math.abs(random.nextInt(9)));
}
@Override
public CustomGene newInstance(Integer integer) {
return new CustomGene(integer);
}
@Override
public boolean isValid() {
return value != 9;
}
}
CustomChromosome:
import org.jenetics.Chromosome;
import org.jenetics.util.ISeq;
import org.jenetics.util.RandomRegistry;
import java.util.Iterator;
import java.util.Random;
public class CustomChromosome implements Chromosome<CustomGene> {
private ISeq<CustomGene> iSeq;
private final int length;
public CustomChromosome(ISeq<CustomGene> genes) {
this.iSeq = genes;
this.length = iSeq.length();
}
public static CustomChromosome of(ISeq<CustomGene> genes) {
return new CustomChromosome(genes);
}
@Override
public Chromosome<CustomGene> newInstance(ISeq<CustomGene> iSeq) {
this.iSeq = iSeq;
return this;
}
@Override
public CustomGene getGene(int i) {
return iSeq.get(i);
}
@Override
public int length() {
return iSeq.length();
}
@Override
public ISeq<CustomGene> toSeq() {
return iSeq;
}
@Override
public Chromosome<CustomGene> newInstance() {
final Random random = RandomRegistry.getRandom();
ISeq<CustomGene> genes = ISeq.empty();
for (int i = 0; i < length; i++) {
genes = genes.append(CustomGene.of(Math.abs(random.nextInt(9))));
}
return new CustomChromosome(genes);
}
@Override
public Iterator<CustomGene> iterator() {
return iSeq.iterator();
}
@Override
public boolean isValid() {
return iSeq.stream().allMatch(CustomGene::isValid);
}
}
Main:
import org.jenetics.Genotype;
import org.jenetics.Optimize;
import org.jenetics.engine.Engine;
import org.jenetics.engine.EvolutionResult;
import org.jenetics.util.Factory;
import org.jenetics.util.RandomRegistry;
import java.util.Random;
public class Main {
private static int maxSum = - 100;
private static Integer eval(Genotype<CustomGene> gt) {
final int sum = gt.getChromosome().stream().mapToInt(CustomGene::getAllele).sum();
if(sum > maxSum)
maxSum = sum;
return sum;
}
public static void main(String[] args) {
final Random random = RandomRegistry.getRandom();
Factory<Genotype<CustomGene>> g =
Genotype.of(CustomChromosome.of(CustomGene.seq(0, 9, Math.abs(random.nextInt(9)) + 1)));
Engine<CustomGene, Integer> engine = Engine
.builder(Main::eval, g)
.optimize(Optimize.MAXIMUM)
.populationSize(100)
.build();
Genotype<CustomGene> result = engine.stream().limit(10000)
.collect(EvolutionResult.toBestGenotype());
System.out.println(eval(result));
result.getChromosome().stream().forEach(i -> {
System.out.print(i.getAllele() + " ");
});
System.out.println();
System.out.println(maxSum);
}
}
I do not understand why I get this output:
13 (evaluated result)
1 8 0 4 (all the alleles form the genes of the chosen chromosome)
32 (the actual maximum fitness found)
We can clearly see a difference between the genotype which had the biggest fitness function and the chosen genotype. Why? I know I'm doing something wrong and it's probably a silly mistake, but I really can't seem to understand what I am doing wrong. Could you please help me out?
Lots of thanks!
As posted by the creator of the library here, the answer was:
you violated the contract of the Chromosome.newInstance(ISeq) method. This method must return a new chromosome instance. After fixing this
@Override
public Chromosome<CustomGene> newInstance(ISeq<CustomGene> iSeq) {
return new CustomChromosome(iSeq);
}