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From Michael Heuer <heue...@acm.org>
Subject RE: [math] Genetic Algorithms
Date Sun, 30 Mar 2008 19:02:00 GMT

Here's an framework for evolutionary algorithms (EA not GA)

> http://dishevelled.org/evolve

Generic in the sense that individuals don't need be "chromosomes";
mutation, recombination, and selection are provided through functors.

LGPL version 3, but I am the only contributor.

   michael


On Sun, 30 Mar 2008, Brent Worden wrote:

> Here's a little code I've had laying around for a few years.
>
> http://people.apache.org/~brentworden/genetics.zip
>
> Feel free to use, modify, or throw away as you see fit.
>
> Brent
>
> -----Original Message-----
> From: Phil Steitz [mailto:phil.steitz@gmail.com]
> Sent: Sunday, March 30, 2008 12:31 AM
> To: Jakarta Commons Developers List
> Subject: Re: [math] Genetic Algorithms
>
> On Sat, Mar 29, 2008 at 6:15 PM, Al Chou <hotfusionman@yahoo.com> wrote:
> > ----- 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/
>
> This looks like GPL with BSD as an option in exchange for $.  Would
> have to be relicensed.
> >
> >  http://cs.gmu.edu/~eclab/projects/ecj/ (university project, no
> license explicitly mentioned)
>
> Academic Free License ("AFL") v. 3.0  - don't know if this is
> ASL-compatible or not.  Looks like the PRNG impls include some NR
> code, so all would have to be carefully vetted.  Also would have to
> get clearance from what looks like a large list of contributors.
>
> Of course we are open to any and all contributions and contributors.
> I would personally rather spend my time developing a small, clean-room
> implementation than chasing down code grants, CLAs and commitment to
> support;  but by all means if you or anyone else are interested in
> enlisting more volunteers, I am +1 for that.  We just need to make
> sure that we do not end up taking on code without volunteers to join
> our community and support it or encumbered code.
>
> In the mean time, I will keep playing with the ideas above and welcome
> input or patches.  I do not see this as a large amount of code and
> would for my personal uses like very much to have a small ASL-licensed
> framework with no dependencies outside of [math] (but all the
> capabilities of [math] available for use by the framework and client
> code).
>
> Phil
>
> >
> >
> >  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
> >
> >
> >
> >
> >
> >
> >
> ________________________________________________________________________
> ____________
> >  You rock. That's why Blockbuster's offering you one month of
> Blockbuster Total Access, No Cost.
> >  http://tc.deals.yahoo.com/tc/blockbuster/text5.com
>
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