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From Al Chou <hotfusion...@yahoo.com>
Subject Re: [math] Genetic Algorithms
Date Sun, 30 Mar 2008 01:15:05 GMT
----- Original Message ----
> From: Phil Steitz <phil.steitz@gmail.com>
> To: Jakarta Commons Developers List <dev@commons.apache.org>
> Sent: Saturday, March 29, 2008 5:53:47 PM
> Subject: [math] Genetic Algorithms
> 
> I would like to start work on a GA framework.  This has been on the
> WishList for some time and I now have a TLS type problem that I am
> working on that is enough motivation for me personally to get things
> rolling.  Here are some rough ideas on what I have in mind.  As
> always, feedback / suggestions / patches appreciated.

Resurfacing for a moment, I wonder if it would make sense to approach an existing project
that is open source but not GPL'ed to see if if could be folded into Commons-Math.  I've found
two candidates that meet these two criteria (and another that was under LGPL I believe, which
I haven't copied here):

http://jgap.sourceforge.net/

http://cs.gmu.edu/~eclab/projects/ecj/ (university project, no license explicitly mentioned)


Al


> 0) Scope - a framework for implementing genetic algorithms, as
> described in e.g. [1], [2].
> 1) Usage / what the framework provides - user classes should implement
> minimally encoding and objective functions.  Stock mutation, crossover
> and selection functions operating on binary encodings should be
> provided by the framework, as well as execution of the algorithm, but
> user classes should be able to plug in custom encoding, mutation,
> crossover, and selection.  Objective and other functions should also
> be allowed to have parameters, which the framework will somehow gather
> and pass in to them.
> 2) Other - the framework should not require that populations be stored
> in memory and it should support parallelization of population
> processing functions
> 3) Package - o.a.c.math.genetic  (I am open to putting this inside
> optimization, but think flatter might be better here).
> 4) Structure straw man:
> Chromosomes - Chromosome interface includes mutate(),
> crossover(Chromosome) and fitness().  AbstractBinaryChromosome
> includes stock implementations of mutate and crossover for binary
> encodings.
> Populations - Population interface provides a Chromosome Iterator,
> select(long), add(Chromosome), delete(Chromosome).  Abstract classes
> provide Roulette, Tournament, other select implementations for
> Populations backed / not backed by in memory collections and I/O /
> storage management.
> GeneticAlgorithm - implements GA (following "canonical algorithm" as
> described in [2]) given initial Population and configured sampling
> rate and stopping criteria (maximum iterations, convergence criteria).
>  Population and Chromosome classes determine the heuristics.  Should
> (eventually at least) support parallel execution by worker threads of
> breeding operations.
> 
> This may be naive and I may find that out as I start playing with real
> code.  As I said, feedback / patches welcome. One thing I don't have a
> clean idea for is how to make optional parameters available to all
> methods mentioned above.
> 
> Phil
> 
> [1] http://en.wikipedia.org/wiki/Genetic_algorithm
> [2] http://samizdat.mines.edu/ga_tutorial/ga_tutorial.ps





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