[jira] [Commented] (MATH-1618) Change in Existing Design

["Gilles Sadowski (Jira)" <ji...@apache.org>]

    [ https://issues.apache.org/jira/browse/MATH-1618?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17522535#comment-17522535 ] 

Gilles Sadowski commented on MATH-1618:
---------------------------------------

I've just attached a few [Java source files|https://issues.apache.org/jira/secure/attachment/13042471/ga.zip].
They are mainly interfaces; for now, they are meant to illustrate an alternative approach with maximal decoupling of the steps
that make up a "genetic algorithm" (GA).  It's not tested (beyond compilation) and I've probably cut some corners (the devil is in the details), but the question is whether this can form the basis for the refactored GA functionality.
Aside from the still missing implementations (actually the current concrete classes of the various chromosome representations, and their associated genetic operators, could probably be readily adapted).

> Change in Existing Design
> -------------------------
>
>                 Key: MATH-1618
>                 URL: https://issues.apache.org/jira/browse/MATH-1618
>             Project: Commons Math
>          Issue Type: Sub-task
>    Affects Versions: 3.6.1
>            Reporter: AVIJIT BASAK
>            Priority: Major
>         Attachments: ga.zip
>
>
> *1) Creation of abstraction for GeneticAlgorithm*: In order to have different types of implementation for Genetic Algorithm like adaptive GA along with the existing one, we need to introduce an abstraction and a hierarchy of algorithm. AbstracttGeneticAlgorithm class needs to be implemented which would be extended by all other Algorithm class. This would also ease any future extension.
> Removed Components: None
> New Components: AbstractGeneticAlgorithm
> Affected Components: GeneticAlgorithm
> *2) Delegation of fitness calculation*: As per the current design Fitness interface is implemented by chromosome class, which forces implementation of fitness() method for any concrete chromosome. However this restricts the use of same concrete chromosome implementation to be reused for different problem domain. This inheritance based implementation should be replaced by composition. A new interface FitnessCalculator would be introduced. An instance of FitnessCalculator will be provided during creation of every concrete chromosome. This will enable reuse of concrete chromosome classes in different problem domain and hence improve extensibility and re-usability. This will require addition of an argument for each factory method and constructors.
> Removed Components: Fitness 
> New Components: FitnessFunction
> Affected Components: Chromosome, AbstractListChromosome, BinaryChromosome, RandomKey 
> *3) Enable finer control for mutation and crossover probability*: Current design uses the crossover and mutation probability at the chromosome level. For finer control of mutation and crossover process the probability would be managed within MutationPolicy and CrossoverPolicy implementations. Probability would be passed as an argument to the respective operations. This way the corresponding operations will be responsible for managing probability and apply in convenient way. I have seen the controlling the mutation probability at the allele(gene) level improves the exploring capability of the optimization process and hence improves robustness.
> Removed Components: None
> New Components: None
> Affected Components: MutationPolicy, CrossoverPolicy and all other implementation classes
> *4) Addition of new Simulation Stopping conditions*: New simulation stopping conditions would be added based on population statistical characteristics. The simulation can be stopped based on variations of population average fitness or best fitness. These parameters are much better to represent nature of convergence. This will improve robustness to a considerable extent.
> Removed Components: None
> New Components: UnchangedAvgFitness, UnchangedBestFitness,
> Affected Components: SimulationStoppingCondition, GeneticAlgorithm, FixedElapsedTime, FixedGenerationCount
> *5) Introduction of Convergence listeners*: New convergence listener interface and registry would be introduced to enable tracking of convergence.
> Removed components: None
> New Components: ConvergenceListener, ListenerRegistry, PopulationStatisticalSummary
> Affected Components: AbstractGeneticAlgorithm, GeneticAlgorithm
> *6) Restructuring Elitism*: Elitism can be handled by the hierarchy of Algorithm classes. Use of a separate ElitisticListPopulation class may not be necessary. The method nextGeneration() in Population would accept the elitism rate as an argument. Any concrete instance of Population would provide the necessary implementation.
> Removed components: ElitisticListPopulation
> New Component: None
> Affected Components: AbstractGeneticAlgorithm, GeneticAlgorithm, Population, ListPopulation
> *7) Introducing Hierarchy in Crossover and Mutation Operator*: Abstract classes has been introduced for crossover and mutation operators.
> Removed components: None
> New Component: AbstractChromosomeCrossoverPolicy, AbstractListChromosomeCrossoverPolicy, AbstractListChromosomeMutationPolicy
> Affected Components: All concrete implementation classes for crossover and mutation.
> *8) Rename the method newFixedLengthChromosome() in AbstractList**Chromosome***: The method newFixedLengthChromosome would be renamed as newChromosome. As we are not considering any variable length chromosome and chromosome representation is immutable in AbstractListChromosome we don't need any explicit mention of the phrase 'FixedLength' as part of the method.
> *9) Introduction of Decoder and Phenotype:*  Phenotype has been introduced as Generic. Decoder has been also introduced to transform the chromosome genotype to phenotype. The phenotype would be used for majority of computation like calculation of fitness, chromosome comparison etc. This is major design change from the previous model. This will enable same genotype to be used for both direct and indirect encoding of chromosomes with an exchange of decoder.
> Removed Components: None
> New Components: Decoder, AbstractListChromosomeDecoder, , TransparentListChromosomeDecoder, RandomKeyDecoder.
> Affected Components: Chromosome, AbstractChromosome, FitnessFunction
> All classes were modified to incorporate phenotype <P> as Generic.
> *10) Introduction of RealValuedChromosome and IntegralValuedChromosome:* Two new genotype has been introduced as real and integral valued chromosome. These two can serve both for indirect and direct encodings.
> Removed Components: RandomKey
> New Components: RealValuedChromosome, RandomKeyDecoder, IntegralValuedChromosome
> Affected Components: BinaryChromosome
>  



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