Module io.jenetics.base

Package io.jenetics

package io.jenetics
This is the base package of the Jenetics library and contains all domain classes, like Gene, Chromosome or Genotype. Most of these types are immutable data classes and don't implement any behavior. It also contains the Selector and Alterer interfaces and its implementations. The classes in this package are (almost) sufficient to implement an own GA. Introduction

Jenetics is an Genetic Algorithm, respectively an Evolutionary Algorithm, library written in Java. It is designed with a clear separation of the several concepts of the algorithm, e. g. Gene, Chromosome, Genotype, Phenotype, Population and fitness Function. Jenetics allows you to minimize and maximize the given fitness function without tweaking it. In contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java streaming API.

Getting Started

The minimum evolution Engine setup needs a genotype factory, Factory<Genotype<?>>, and a fitness Function. The Genotype implements the Factory interface and can therefore be used as prototype for creating the initial Population and for creating new random Genotypes.

import io.jenetics.BitChromosome; import io.jenetics.BitGene; import io.jenetics.Genotype; import io.jenetics.engine.Engine; import io.jenetics.engine.EvolutionResult; import io.jenetics.util.Factory; public class HelloWorld { // 2.) Definition of the fitness function. private static Integer eval(Genotype<BitGene> gt) { return ((BitChromosome)gt.chromosome()).bitCount(); } public static void main(String[] args) { // 1.) Define the genotype (factory) suitable // for the problem. Factory<Genotype<BitGene>> gtf = Genotype.of(BitChromosome.of(10, 0.5)); // 3.) Create the execution environment. Engine<BitGene, Integer> engine = Engine .builder(HelloWorld::eval, gtf) .build(); // 4.) Start the execution (evolution) and // collect the result. Genotype<BitGene> result = engine.stream() .limit(100) .collect(EvolutionResult.toBestGenotype()); System.out.println("Hello World:\n" + result); } }

In contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java streaming API. Now let's have a closer look at listing above and discuss this simple program step by step:

  1. The probably most challenging part, when setting up a new evolution Engine, is to transform the problem domain into a appropriate Genotype (factory) representation. In our example we want to count the number of ones of a BitChromosome. Since we are counting only the ones of one chromosome, we are adding only one BitChromosome to our Genotype. In general, the Genotype can be created with 1 to n chromosomes.
  2. Once this is done, the fitness function which should be maximized, can be defined. Utilizing the new language features introduced in Java 8, we simply write a private static method, which takes the genotype we defined and calculate it's fitness value. If we want to use the optimized bit-counting method, bitCount(), we have to cast the Chromosome<BitGene> class to the actual used BitChromosome class. Since we know for sure that we created the Genotype with a BitChromosome, this can be done safely. A reference to the eval method is then used as fitness function and passed to the Engine.build method.
  3. In the third step we are creating the evolution Engine, which is responsible for changing, respectively evolving, a given population. The Engine is highly configurable and takes parameters for controlling the evolutionary and the computational environment. For changing the evolutionary behavior, you can set different alterers and selectors. By changing the used Executor service, you control the number of threads, the Engine is allowed to use. An new Engine instance can only be created via its builder, which is created by calling the Engine.builder method.
  4. In the last step, we can create a new EvolutionStream from our Engine. The EvolutionStream is the model or view of the evolutionary process. It serves as a »process handle« and also allows you, among other things, to control the termination of the evolution. In our example, we simply truncate the stream after 100 generations. If you don't limit the stream, the EvolutionStream will not terminate and run forever. Since the EvolutionStream extends the java.util.stream.Stream interface, it integrates smoothly with the rest of the Java streaming API. The final result, the best Genotype in our example, is then collected with one of the predefined collectors of the EvolutionResult class.
Since:
1.0
Version:
3.1