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A method for JIT'ing algorithms and data structures with LLVMA method for JIT'ing algorithms and data structures... Hello folks, I always post about Python and EvoComp (Pyevolve), but this time it's about C, LLVM, search algorithms and data structures. This post describes the efforts to implement an idea: to JIT...

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Send Subversion commit messages to TwitterSend Subversion commit messages to Twitter Hello, this is a bridge between Subversion (svn) and Twitter, the intent of this tool is to update a Twitter account when new commit messages arrives in a Subversion repository. We almost never have access...

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An analysis of Benford's law applied to TwitterAn analysis of Benford's law applied to Twitter Benford's law is one of those very weird things that we can't explain, and when we discovery more and more events which obeys the law, we became astonished. Two men (Simon Newcomb - 1881 and Frank Benford...

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TSP on Nokia N73 using PyS60 and PyevolveTSP on Nokia N73 using PyS60 and Pyevolve As I promised on the post about Pyevolve on N73, I've ported the TSP problem to run on the cellphone. The script will draw the best individual of every generation on the screen using the PyS60 Canvas API....

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Python: acessing near real-time MODIS images and fire data from NASA's Aqua and Terra satellitesPython: acessing near real-time MODIS images and fire... From Modis Rapid Response System site: The MODIS Rapid Response System was developed to provide daily satellite images of the Earth's landmasses in near real time. True-color, photo-like imagery and...

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Pyevolve on SIGEVOlution

Posted on : 09-11-2009 | By : Perone | In : News, Pyevolve, Python, Science

3

SIGEVOlution200901WebCover

I’m proud to announce that Pyevolve is featuring on the last issue of SIGEVOlution (Volume 4, Issue 1), a newsletter from the ACM Special Interest Group on Evolutionary Computation. I would like to thank the newsletter editor Pier Luca Lanzi and the board for the corrections in the article and for the well done reformatted version of the paper.

Pyevolve is currently in version 0.5, in a few months I’ll be releasing the new 0.6 release with the new major features that are currently implemented in the development version only (you can check it at the subversion repository in sourceforge.net).

I hope you enjoy the article !

Yours,
- Christian S. Perone

Pyevolve benchmark on different Python flavors

Posted on : 19-10-2009 | By : Perone | In : Pyevolve, Python

14

So I did a comparative of Pyevolve GP/GA core in different Python interpreters. I’ve used my Pentium Core 2 Duo (E4500 @ 2.20GHz, 1GB RAM), using Ubuntu 9.04 and Windows XP SP3 just for IronPython 2.6.1 (IronPython doesn’t run with Mono, so I used the win xp with .net 2.0).

The interpreters used were:

Unladen Swallow 2009Q2

I tried using 2009Q3 (the currently main trunk), but I think it’s unstable yet, cause it was more slow than 2009Q2, so I used 2009Q2; I compiled it with GCC 4.3.3 just using the default configure parameters (./configure).

CPython 2.6.2

I used the default CPython package of Ubuntu 9.04.

CPython 2.5.4

I used the default CPython package of Ubuntu 9.04 too, the python2.5 package.

PyPy 1.1.0 (svn:r68612)

I used the last svn version of the repository, the release 68612. My Pentium Core 2 Duo had only 1GB of RAM, and the PyPy translation process eats more RAM than Java (sorry for the joke), so I used a notebook with 3GB of RAM to create the pypy-c, what took 1 hour (I used –opt=3) and a beautiful ascii Mandelbrot fractal !

Jython 2.5.1

I used the default installer from the Jython project site. I used the Sun JRE 1.6.0_16.

IronPython 2.6.10920.0

I’ve used the 2.6 RC1 available at IronPython project site with MS .NET 2.0.

To test the GA core I’ve used this source-code (a simple sphere function):

?View Code PYTHON
from pyevolve import G1DList
from pyevolve import Mutators, Initializators
from pyevolve import GSimpleGA, Consts
 
# This is the Sphere Function
def sphere(xlist):
   total = 0
   for i in xlist:
      total += i**2
   return total
 
def run_main():
   genome = G1DList.G1DList(140)
   genome.setParams(rangemin=-5.12, rangemax=5.13)
   genome.initializator.set(Initializators.G1DListInitializatorReal)
   genome.mutator.set(Mutators.G1DListMutatorRealGaussian)
   genome.evaluator.set(sphere)
 
   ga = GSimpleGA.GSimpleGA(genome, seed=666)
   ga.setMinimax(Consts.minimaxType["minimize"])
   ga.setGenerations(1500)
   ga.setMutationRate(0.01)
   ga.evolve(freq_stats=500)
 
   best = ga.bestIndividual()
 
if __name__ == "__main__":
   run_main()

And to test the GP core, I’ve used this source-code (a simple symbolic regression):

?View Code PYTHON
from pyevolve import GTree
from pyevolve import Mutators
from pyevolve import GSimpleGA, Consts, Util
import math
 
rmse_accum = Util.ErrorAccumulator()
 
def gp_add(a, b): return a+b
def gp_sub(a, b): return a-b
def gp_mul(a, b): return a*b
def gp_sqrt(a):   return math.sqrt(abs(a))
 
def eval_func(chromosome):
   global rmse_accum
   rmse_accum.reset()
   code_comp = chromosome.getCompiledCode()
 
   for a in xrange(0, 10):
      for b in xrange(0, 10):
         evaluated     = eval(code_comp)
         target        = math.sqrt((a*a)+(b*b))
         rmse_accum   += (target, evaluated)
   return rmse_accum.getRMSE()
 
def main_run():
   genome = GTree.GTreeGP()
   genome.setParams(max_depth=4, method="ramped")
   genome.evaluator += eval_func
   genome.mutator.set(Mutators.GTreeGPMutatorSubtree)
 
   ga = GSimpleGA.GSimpleGA(genome, seed=666)
   ga.setParams(gp_terminals       = ['a', 'b'],
                gp_function_prefix = "gp")
 
   ga.setMinimax(Consts.minimaxType["minimize"])
   ga.setGenerations(40)
   ga.setCrossoverRate(1.0)
   ga.setMutationRate(0.08)
   ga.setPopulationSize(800)
 
   ga(freq_stats=10)
   best = ga.bestIndividual()
 
if __name__ == "__main__":
   main_run()

UPDATE 19/08: the x-axis is measured in “seconds“, and the y-axis is the python flavor;

The results are are described in the graph below:

pyevolve_pyvmsAs we can see, Unladen Swallow 2009Q2 did a little better performance than CPython 2.6.2, but Jython and PyPy (experimental) were left behind in that scenario, even behind IronPython 2.6.1.

Successful pyevolve multiprocessing speedup for Genetic Programming

Posted on : 11-10-2009 | By : Perone | In : Pyevolve, Python, genetic programming

0

As we know, Genetic Programming usually requires intensive processing power for the fitness functions and tree manipulations (in crossover operations), and this fact can be a huge problem when using a pure Python approach like Pyevolve. So, to overcome this situation, I’ve used the Python multiprocessing features to implement a parallel fitness evaluation approach in Pyevolve and I was surprised by the super linear speedup I got for a cpu bound fitness function used to do the symbolic regression of the Pythagoras theorem: c = \sqrt{a^2 + b^2}. I’ve used the same seed for the GP, so it has consumed nearly the same cpu resources for both test categories. Here are the results I obtained:

pyevolve_multiprocessing

The first fitness landscape I’ve used had 2.500 points and the later had a fitness landscape of 6.400 points, here is the source code I’ve used (you just need to turn on the multiprocessing option using the setMultiProcessing method, so Pyevolve will use multiprocessing when you have more than one single core, you can enable the logging feature to check what’s going on behind the scenes):

?View Code PYTHON
from pyevolve import *
import math
 
rmse_accum = Util.ErrorAccumulator()
 
def gp_add(a, b): return a+b
def gp_sub(a, b): return a-b
def gp_mul(a, b): return a*b
def gp_sqrt(a):   return math.sqrt(abs(a))
 
def eval_func(chromosome):
   global rmse_accum
   rmse_accum.reset()
   code_comp = chromosome.getCompiledCode()
 
   for a in xrange(0, 80):
      for b in xrange(0, 80):
         evaluated     = eval(code_comp)
         target        = math.sqrt((a*a)+(b*b))
         rmse_accum   += (target, evaluated)
   return rmse_accum.getRMSE()
 
def main_run():
   genome = GTree.GTreeGP()
   genome.setParams(max_depth=4, method="ramped")
   genome.evaluator += eval_func
   genome.mutator.set(Mutators.GTreeGPMutatorSubtree)
 
   ga = GSimpleGA.GSimpleGA(genome, seed=666)
   ga.setParams(gp_terminals       = ['a', 'b'],
                gp_function_prefix = "gp")
 
   ga.setMinimax(Consts.minimaxType["minimize"])
   ga.setGenerations(20)
   ga.setCrossoverRate(1.0)
   ga.setMutationRate(0.08)
   ga.setPopulationSize(800)
   ga.setMultiProcessing(True)
 
   ga(freq_stats=5)
   best = ga.bestIndividual()
 
if __name__ == "__main__":
   main_run()

As you can see, the population size was 800 individuals with a 8% mutation rate and a 100% crossover rate for a simple 20 generations evolution. Of course you don’t need so many points in the fitness landscape, I’ve used 2.500+ points to create a cpu intensive fitness function, otherwise, the speedup can be less than 1.0 due the communication overhead between the processes. For the first case (2.500 points fitness landscape) I’ve got a 3.33x speedup and for the last case (6.400 points fitness landscape) I’ve got a 3.28x speedup. The tests were executed in a 2 cores pc (Intel Core 2 Duo).

n-queens problem using Pyevolve

Posted on : 19-09-2009 | By : Perone | In : Genetic Algorithms, Pyevolve, Python

4

Last night I’ve read a post on Reddit written by Matthew Rollings showing a code in Python to solve Eight Queens puzzle using EA. So I decided to implement it in Python again but this time using Pyevolve, here is the code:

?View Code PYTHON
from pyevolve import *
from random import shuffle
 
BOARD_SIZE = 64
 
def queens_eval(genome):
   collisions = 0
   for i in xrange(0, BOARD_SIZE):
      if i not in genome: return 0
   for i in xrange(0, BOARD_SIZE):
      col = False
      for j in xrange(0, BOARD_SIZE):
         if (i != j) and (abs(i-j) == abs(genome[j]-genome[i])):
            col = True
      if col == True: collisions +=1
   return BOARD_SIZE-collisions
 
def queens_init(genome, **args):
   genome.genomeList = range(0, BOARD_SIZE)
   shuffle(genome.genomeList)
 
def run_main():
   genome = G1DList.G1DList(BOARD_SIZE)
   genome.setParams(bestrawscore=BOARD_SIZE, rounddecimal=2)
   genome.initializator.set(queens_init)
   genome.mutator.set(Mutators.G1DListMutatorSwap)
   genome.crossover.set(Crossovers.G1DListCrossoverCutCrossfill)
   genome.evaluator.set(queens_eval)
 
   ga = GSimpleGA.GSimpleGA(genome)
   ga.terminationCriteria.set(GSimpleGA.RawScoreCriteria)
   ga.setMinimax(Consts.minimaxType["maximize"])
 
   ga.setPopulationSize(100)
   ga.setGenerations(5000)
   ga.setMutationRate(0.02)
   ga.setCrossoverRate(1.0)
 
   # This DBAdapter is to create graphs later, it'll store statistics in
   # a SQLite db file
   sqlite_adapter = DBAdapters.DBSQLite(identify="queens")
   ga.setDBAdapter(sqlite_adapter)
 
   ga.evolve(freq_stats=10)
 
   best = ga.bestIndividual()
   print best
   print "\nBest individual score: %.2f\n" % (best.score,)
 
if __name__ == "__main__":
   run_main()

It tooks 49 generations to solve a 64×64 (4.096 chess squares) chessboard, here is the output:

Gen. 0 (0.00%): Max/Min/Avg Fitness(Raw) [20.83(27.00)/13.63(7.00)/17.36(17.36)]
Gen. 10 (0.20%): Max/Min/Avg Fitness(Raw) [55.10(50.00)/39.35(43.00)/45.92(45.92)]
Gen. 20 (0.40%): Max/Min/Avg Fitness(Raw) [52.51(55.00)/28.37(24.00)/43.76(43.76)]
Gen. 30 (0.60%): Max/Min/Avg Fitness(Raw) [67.45(62.00)/51.92(54.00)/56.21(56.21)]
Gen. 40 (0.80%): Max/Min/Avg Fitness(Raw) [65.50(62.00)/19.89(31.00)/54.58(54.58)]

        Evolution stopped by Termination Criteria function !

Gen. 49 (0.98%): Max/Min/Avg Fitness(Raw) [69.67(64.00)/54.03(56.00)/58.06(58.06)]
Total time elapsed: 39.141 seconds.

And here is the plots generated by the Graph Plot Tool of Pyevolve:

fig1

fig3

fig5

fig8

Pyevolve: announce of the user group

Posted on : 04-08-2009 | By : Perone | In : Pyevolve, Python

0

image5

This post is to announce the Pyevolve user group I’ve created, since some users are requesting it and I think it’s important to exchange experiences and help users, here is the group (it’s hosted on google groups).

Cya !

Approximating Pi number using Genetic Programming

Posted on : 22-07-2009 | By : Perone | In : News, Pyevolve, Python, Time Waste, genetic programming

9

pi

As many (or very few in the real life haha) people know, today is the Pi Approximation Day ! So it’s time to make a contribution to celebrate this funny day =)

My contribution is to use Python and Pyevolve to approximate Pi number using Genetic Programming approach. I’ve created the functions gp_add(+), gp_sub(-), gp_div(/), gp_mul(*) and gp_sqrt (square root) to use as non-terminals of the GP. The fitness function is very simple too, it simple returns the absolute difference between the Python math.pi and the evaluated individual. I’ve used also a population size of 1k individuals with max tree depth of 8 and the random ephemeral constants as random integers. The best approximation I’ve got while running the GP for about 8 minutes (40 generations) was 3.1416185511, best for 3 digits, you can improve it and let it run for more time to get better approximations.

Here is the formulae I’ve got with the GP (click to enlarge):

tree_pi

And here is the output of the script:

Best (0): 3.1577998365
        Error: 0.0162071829
Best (10): 3.1417973679
        Error: 0.0002047143
Best (20): 3.1417973679
        Error: 0.0002047143
Best (30): 3.1417973679
        Error: 0.0002047143
Best (40): 3.1416185511
        Error: 0.0000258975

- GenomeBase
        Score:                   0.000026
        Fitness:                 15751.020831

        Params:          {'max_depth': 8, 'method': 'ramped'}

        Slot [Evaluator] (Count: 1)
        Slot [Initializator] (Count: 1)
                Name: GTreeGPInitializator - Weight: 0.50
                Doc: This initializator accepts the follow parameters:

   *max_depth*
      The max depth of the tree

   *method*
      The method, accepts "grow" or "full"

   .. versionadded:: 0.6
      The *GTreeGPInitializator* function.

        Slot [Mutator] (Count: 1)
                Name: GTreeGPMutatorSubtree - Weight: 0.50
                Doc:  The mutator of GTreeGP, Subtree Mutator

   .. versionadded:: 0.6
      The *GTreeGPMutatorSubtree* function

        Slot [Crossover] (Count: 1)
                Name: GTreeGPCrossoverSinglePoint - Weight: 0.50

- GTree
        Height:                 8
        Nodes:                  21

GTreeNodeBase [Childs=1] - [gp_sqrt]
  GTreeNodeBase [Childs=2] - [gp_div]
    GTreeNodeBase [Childs=2] - [gp_add]
      GTreeNodeBase [Childs=0] - [26]
      GTreeNodeBase [Childs=2] - [gp_div]
        GTreeNodeBase [Childs=2] - [gp_mul]
          GTreeNodeBase [Childs=2] - [gp_add]
            GTreeNodeBase [Childs=2] - [gp_sub]
              GTreeNodeBase [Childs=0] - [34]
              GTreeNodeBase [Childs=2] - [gp_sub]
                GTreeNodeBase [Childs=0] - [44]
                GTreeNodeBase [Childs=0] - [1]
            GTreeNodeBase [Childs=2] - [gp_mul]
              GTreeNodeBase [Childs=0] - [49]
              GTreeNodeBase [Childs=0] - [43]
          GTreeNodeBase [Childs=1] - [gp_sqrt]
            GTreeNodeBase [Childs=0] - [18]
        GTreeNodeBase [Childs=0] - [16]
    GTreeNodeBase [Childs=2] - [gp_add]
      GTreeNodeBase [Childs=0] - [24]
      GTreeNodeBase [Childs=0] - [35]

- GTreeGP
        Expression: gp_sqrt(gp_div(gp_add(26,
gp_div(gp_mul(gp_add(gp_sub(34,
gp_sub(44, 1)), gp_mul(49, 43)), gp_sqrt(18)),
16)), gp_add(24, 35)))

And finally, here is the source code:

?View Code PYTHON
from __future__ import division
from pyevolve import *
import math
 
def gp_add(a, b): return a+b
def gp_sub(a, b): return a-b
def gp_div(a, b): return 1 if b==0 else a/b
def gp_mul(a, b): return a*b
def gp_sqrt(a):   return math.sqrt(abs(a))
 
def eval_func(chromosome):
   code_comp = chromosome.getCompiledCode()
   ret = eval(code_comp)
   return abs(math.pi - ret)
 
def step_callback(engine):
   gen = engine.getCurrentGeneration()
   if gen % 10 == 0:
      best = engine.bestIndividual()
      best_pi = eval(best.getCompiledCode())
      print "Best (%d): %.10f" % (gen, best_pi)
      print "\tError: %.10f" % (abs(math.pi - best_pi))
 
   return False
 
def main_run():
   genome = GTree.GTreeGP()
 
   genome.setParams(max_depth=8, method="ramped")
   genome.evaluator += eval_func
 
   ga = GSimpleGA.GSimpleGA(genome)
   ga.setParams(gp_terminals       = ['ephemeral:random.randint(1, 50)'],
                gp_function_prefix = "gp")
 
   ga.setMinimax(Consts.minimaxType["minimize"])
   ga.setGenerations(50000)
   ga.setCrossoverRate(1.0)
   ga.setMutationRate(0.09)
   ga.setPopulationSize(1000)
   ga.stepCallback.set(step_callback)
 
   ga.evolve()
   best = ga.bestIndividual()
   best.writeDotImage("tree_pi.png")
 
   print best
 
if __name__ == "__main__":
   main_run()

If you are interested why today is the Pi Approximation day, see some resources:

Little Cartoon

Some Background History

Some Pi Approximations

Genetic Programming and Flex layouts

Posted on : 29-06-2009 | By : Perone | In : Pyevolve, Python, genetic programming

0

To show how Genetic Programming of Pyevolve can be flexible, I’ve done a simple example using Adobe Flex and Pyevolve, the example is just to show how to evolve some kind of Flex layouts, I’ve not implemented the fitness function, this example will just create a random Flex layout using MXML. So, here is the Pyevolve code of the example:

?View Code PYTHON
import random
from pyevolve import *
 
def gp_hbox(x, y):
   return "%s %s" % (x,y)
 
def gp_vbox(x, y):
   return "%s %s" % (x,y)
 
def gp_panel(x, y):
   return "%s %s" % (x,y)
 
def eval_func(chromosome):
   code_comp = chromosome.getCompiledCode()
 
   for a in xrange(0, 5):
      for b in xrange(0, 5):
         evaluated     = eval(code_comp)
   return random.randint(1,100)
 
def main_run():
   genome = GTree.GTreeGP()
   genome.setParams(max_depth=5, method="ramped")
   genome.evaluator += eval_func
 
   ga = GSimpleGA.GSimpleGA(genome)
 
   button     = repr("<mx:Button label='Button'/>")
   label      = repr("<mx:Label text='Label'/>")
   text_input = repr("<mx:TextInput width='50'/>")
 
   ga.setParams(gp_terminals       = [button, label, text_input],
                gp_function_prefix = "gp")
   ga.setMinimax(Consts.minimaxType["minimize"])
   ga.evolve(freq_stats=5)
   print ga.bestIndividual()
 
if __name__ == "__main__":
   main_run()

As you can see, I’ve created the layout tags like HBox, VBox and Panel as functions of GP and the Button, Labe, TextInput as terminals of the GP, the result is very funny, it’s just a random layout, but you can use your imagination to create some nice and interesting fitness functions.

Here is the SWF generated from a random individual of the population:

I hope you enjoyed =)

Genetic Programming meets Python

Posted on : 08-06-2009 | By : Perone | In : Pyevolve, Python, genetic programming

12

I’m proud to announce that the new versions of Pyevolve will have Genetic Programming support; after some time fighting with these evil syntax trees, I think I have a very easy and flexible implementation of GP in Python. I was tired to see people giving up and trying to learn how to implement a simple GP using the hermetic libraries for C/C++ and Java (unfortunatelly I’m a Java web developer hehe).

The implementation is still under some tests and optimization, but it’s working nice, here is some details about it:

The implementation has been done in pure Python, so we still have many bonus from this, but unfortunatelly we lost some performance.

The GP core is very very flexible, because it compiles the GP Trees in Python bytecodes to speed the execution of the function. So, you can use even Python objects as terminals, or any possible Python expression. Any Python function can be used too, and you can use all power of Python to create those functions, which will be automatic detected by the framework using the name prefix =)

As you can see in the source-code, you don’t need to bind variables when calling the syntax tree of the individual, you simple use the “getCompiledCode” method which returns the Python compiled function ready to be executed.

Here is a source-code example:

?View Code PYTHON
from pyevolve import *
import math
 
error_accum = Util.ErrorAccumulator()
 
# This is the functions used by the GP core,
# Pyevolve will automatically detect them
# and the they number of arguments
def gp_add(a, b): return a+b
def gp_sub(a, b): return a-b
def gp_mul(a, b): return a*b
def gp_sqrt(a):   return math.sqrt(abs(a))
 
def eval_func(chromosome):
   global error_accum
   error_accum.reset()
   code_comp = chromosome.getCompiledCode()
 
   for a in xrange(0, 5):
      for b in xrange(0, 5):
         # The eval will execute a pre-compiled syntax tree
         # as a Python expression, and will automatically use
         # the "a" and "b" variables (the terminals defined)
         evaluated     = eval(code_comp)
         target        = math.sqrt((a*a)+(b*b))
         error_accum += (target, evaluated)
   return error_accum.getRMSE()
 
def main_run():
   genome = GTree.GTreeGP()
   genome.setParams(max_depth=5, method="ramped")
   genome.evaluator.set(eval_func)
 
   ga = GSimpleGA.GSimpleGA(genome)
   # This method will catch and use every function that
   # begins with "gp", but you can also add them manually.
   # The terminals are Python variables, you can use the
   # ephemeral random consts too, using ephemeral:random.randint(0,2)
   # for example.
   ga.setParams(gp_terminals       = ['a', 'b'],
                gp_function_prefix = "gp")
   # You can even use a function call as terminal, like "func()"
   # and Pyevolve will use the result of the call as terminal
   ga.setMinimax(Consts.minimaxType["minimize"])
   ga.setGenerations(1000)
   ga.setMutationRate(0.08)
   ga.setCrossoverRate(1.0)
   ga.setPopulationSize(2000)
   ga.evolve(freq_stats=5)
 
   print ga.bestIndividual()
 
if __name__ == "__main__":
   main_run()

I’m very happy and testing the possibilities of this GP implementation in Python.

And of course, everything in Pyevolve can be visualized any time you want (click to enlarge):

ramped_small

ramped_big

The visualization is very flexible too, if you use Python decorators to set how functions will be graphical represented, you can have many interesting visualization patterns. If I change the function “gp_add” to:

?View Code PYTHON
@GTree.gpdec(representation="+", color="red")
def gp_add(a, b): return a+b

We’ll got the follow visualization (click to enlarge):

full

I hope you enjoyed it, I’m currently fixing some bugs, implementing new features, docs and preparing the next release of Pyevolve, which will take some time yet =)

Pyevolve: Sourceforge.net Nomination

Posted on : 06-05-2009 | By : Perone | In : Pyevolve

2

Pyevolve is a free (as in freedom), free (as in free beer) and open-source project. If you use it and like it, you can help us by nominating it for the Sourceforge Community Choice Awards ! Here is the link for the nomination.

nomination

Pyevolve: Genetic Algorithms + Interactive Mode

Posted on : 27-04-2009 | By : Perone | In : Pyevolve, Python

0

I’ve made a video of an example using the Pyevolve’s Interactive Mode in the middle of the evolution of a Genetic Algorithm. The video is in high resolution, so you can see it here or clicking on the image below:

vid_pyevolve

Pyevolve: LaTeX documentation

Posted on : 31-03-2009 | By : Perone | In : Pyevolve

0

I created the LaTeX documentation for the 0.5 release of Pyevolve, the link is now on the front page of the documentation site.

You can download the PDF documentation here.

TSP on Nokia N73 using PyS60 and Pyevolve

Posted on : 25-03-2009 | By : Perone | In : Genetic Algorithms, Pyevolve, Python, pys60

4

As I promised on the post about Pyevolve on N73, I’ve ported the TSP problem to run on the cellphone. The script will draw the best individual of every generation on the screen using the PyS60 Canvas API. The quality of the video is very low, I’m using another cellphone with VGA only recording.

When I have time, I’ll release the source-code here in the same post. The TSP code is the same used in PSP, but ported to use the Canvas API of PyS60.

I hope you enjoy.

UPDATE 24/04: the source-code can be downloaded here.

Genetic Algorithms on cellphones ! Pyevolve on Nokia N73 (Symbian + PyS60)

Posted on : 21-03-2009 | By : Perone | In : Genetic Algorithms, News, Pyevolve, Python, Time Waste, genetic programming

5

Hello ! This is the 2nd post related to the Pyevolve on portable devices, the first was in the Sony PSP here and the PoC of Pyevolve solving the TSP problem with a graphical output of best individuals on the Sony PSP screen. Now, it’s time to go further and run Pyevolve into the most portable device used by us, the cellphone.

Using the new version of the PyS60, the release 1.9.1, which comes with the new amazing 2.5.1 Python core, I’ve executed the Pyevolve with no problem, and I was very surprised by the performance of the GA on the Nokia N73, the GA I’ve ran is the minimization of one of the De Jogn’s test suite functions, the Sphere function, the function is very simple and I’ve used 5 real variables between the interval of [-5.12, 5.12], the Gaussian Real Mutator and the Single Point Crossover of the Pyevolve framework. Also I’ve set a population size of 80 individuals and the mutation rate of 2% and crossover rate of 90%.

After 18 generations (about 8 seconds), the GA ended with the best score of 0.0, representing the optimal minimization of the De Jong’s Sphere function.

Follow some screenshots of the adventure (click on the pictures to enlarge):

How to install Pyevolve on the PyS60 ?

1) First, you need to install the PyS60 for your Symbian platform. Here is the installation manual. The order of the installation is: Python Runtime for S60, Python Script Shell and PIPS Library.

2) Then, you must create a directory on your Memory Card, inside the “Python” directory, named “Lib”, and inside this directory, you copy the “pyevolve” folder. The absolute folder structure will be like this:

MemoryCard:\Python\Lib\pyevolve

Some features of the framework will not work, like the some DB Adapters, however, the GA core is working really good. I’ve used the Pyevolve subversion release r157, but it should works with the 0.5 release too. I’ve not finished the documentation of the new release, I’m working on some features yet.

Here is the source code I’ve used to minimize the De Jong’s Sphere function:

?View Code PYTHON
import e32
print "Loading Pyevolve modules...",
e32.ao_yield()
 
from pyevolve import G1DList, GSimpleGA
from pyevolve import Initializators, Mutators, Consts
 
print " done !"
e32.ao_yield()
 
def sphere(xlist):
   n = len(xlist)
   total = 0
   for i in range(n):
      total += (xlist[i]**2)
   return total
 
def ga_callback(ga_engine):
   gen = ga_engine.getCurrentGeneration()
   best = ga.bestIndividual()
   print "Generation %d - Best Score: %.2f" % (gen, best.score)
   e32.ao_yield()
 
   return False
 
if __name__ == "__main__":
 
   genome = G1DList.G1DList(5)
   genome.setParams(rangemin=-5.12, rangemax=5.13, bestRawScore=0.00, roundDecimal=2)
   genome.initializator.set(Initializators.G1DListInitializatorReal)
   genome.mutator.set(Mutators.G1DListMutatorRealGaussian)
 
   genome.evaluator.set(sphere)
 
   ga = GSimpleGA.GSimpleGA(genome)
   ga.setMinimax(Consts.minimaxType["minimize"])
   ga.setGenerations(100)
   ga.setMutationRate(0.02)
   ga.terminationCriteria.set(GSimpleGA.RawScoreCriteria)
   ga.stepCallback.set(ga_callback)
 
   ga.evolve()
 
   best = ga.bestIndividual()
   print "\nBest individual score: %.2f" % (best.score,)

You can note the use of the module “e32″ of the PyS60, this is used to process pending events, so we can follow the statistics of current generation while it evolves.

I hope you enjoyed this work, the next step is to port the TSP problem to cellphone =)

Some time ago I’ve asked Guido van Rossum on the Google Moderator about the future of Python for mobile phones (aka PyS60), and here is the full answer from him:

I’m hopeful, but concerned that Java has cornered this market. For example, the Android development kit is extremely slick but only supports Java at the moment. There’s no doubt about which is the dominant app development language on most mobile platforms, including S60 and anything Symbian-based. In the long run I expect Python to just happen on mobile devices, as increases in disk space will allow the set of pre-installed tools to grow. In the mean time I see a bigger role for Python server-side, for example there are iPhone apps backed by services written in Python running on App Engine (and probably also apps backed by Python running on other server platforms).
Guido van Rossum, San Francisco Bay Area

Well, I think that with this new version of PyS60, with the 2.5.1 core, the Python on mobiles can be very useful and productive. Recently, Nokia have signed a loan agreement with the European Investment Bank (EIB) to the tune of €500 million ($623.9 million). According to Reuters, the five-year loan will be used in part to “finance software research and development (R&D) projects Nokia is undertaking during 2009-2011 to make Symbian-based smartphones more competitive.” So I’m with great expectations with this new investment on Symbian smartphones and with the future possibilities of the PyS60.

Travelling Salesman on Sony PSP using Stackless Python + Pyevolve

Posted on : 10-03-2009 | By : Perone | In : Genetic Algorithms, News, Pyevolve, Time Waste

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This is my first PoC of the Travelling Salesman Problem on PSP, since I’ve installed the Pyevolve on the Sony PSP,  I can optimize any problem while using the graphical interface of PSP (in that problem I’m using the 2D functions to plot the cities and the path) to show results in real-time. Here is the video, the quality is very low, I’ve used my cellphone :)

Here is the source code I’ve used, the Pyevolve version of this example is the development version r166, which in the future will be the 0.6 final release (I’m working on many new features yet, so it will take time to release), however, this PoC should work on 0.5 release too:

?View Code PYTHON
import psp2d, pspos
 
WHITE_COLOR = psp2d.Color(255,255,255)
CLEAR_COLOR = psp2d.Color(0,0,0,255)
RED_COLOR   = psp2d.Color(255, 0, 0)
 
cm     = []
coords = []
CITIES = 20
 
pspos.setclocks(333,166)
psp_scr  = psp2d.Screen()
psp_font = psp2d.Font('font.png')
psp_scr.clear(CLEAR_COLOR)
psp_font.drawText(psp_scr, 0, 5, "Loading Pyevolve modules...")
psp_scr.swap()
 
from pyevolve import G1DList
from pyevolve import GSimpleGA
from pyevolve import GAllele
from pyevolve import Mutators
from pyevolve import Crossovers
from pyevolve import Consts
 
from random import shuffle as rand_shuffle, randint as rand_randint
from math import sqrt
 
def cartesian_matrix(coords):
   """ A distance matrix """
   matrix={}
   for i,(x1,y1) in enumerate(coords):
      for j,(x2,y2) in enumerate(coords):
         dx, dy = x1-x2, y1-y2
         dist=sqrt(dx*dx + dy*dy)
         matrix[i,j] = dist
   return matrix
 
def tour_length(matrix, tour):
   """ Returns the total length of the tour """
   total = 0
   for i in range(CITIES):
      j      = (i+1)%CITIES
      total += matrix[tour[i], tour[j]]
   return total
 
def write_tour_to_img(coords, tour):
   """ The function to plot the graph """
   psp_scr.clear(CLEAR_COLOR)
   for i in range(CITIES):
      j      = (i+1)%CITIES
      city_i = tour[i]
      city_j = tour[j]
      x1, y1 = coords[city_i]
      x2, y2 = coords[city_j]
      psp_scr.drawLine(int(x1), int(y1), int(x2), int(y2), WHITE_COLOR)
      psp_font.drawText(psp_scr, int(x1)+7, int(y1)-5, str(i))
      psp_scr.fillRect(int(x1), int(y1), 6, 6, RED_COLOR)
 
   psp_scr.swap()
 
def G1DListTSPInitializator(genome, **args):
   """ The initializator for the TSP """
   lst = [i for i in xrange(genome.getListSize())]
   rand_shuffle(lst)
   genome.genomeList = lst
 
def evolve_callback(ga_engine):
   """ Callback called every generation by Pyevolve """
   write_tour_to_img(coords, ga_engine.bestIndividual())
   return False
 
def main_run():
   global cm, coords
 
   width, height = psp_scr.size
   coords = [(rand_randint(0, width),rand_randint(0, height))
                 for i in xrange(CITIES)]
   cm     = cartesian_matrix(coords)
 
   setOfAlleles = GAllele.GAlleles(homogeneous=True)
   range_allele = GAllele.GAlleleRange(0, len(coords)-1)
   setOfAlleles.add(range_allele)
 
   genome = G1DList.G1DList(len(coords))
   genome.setParams(allele=setOfAlleles)
 
   genome.evaluator.set(lambda chromosome: tour_length(cm, chromosome))
   genome.mutator.set(Mutators.G1DListMutatorSwap)
   genome.crossover.set(Crossovers.G1DListCrossoverOX)
   genome.initializator.set(G1DListTSPInitializator)
 
   ga = GSimpleGA.GSimpleGA(genome)
   ga.setMinimax(Consts.minimaxType["minimize"])
   ga.setGenerations(300)
   ga.setPopulationSize(200)
   ga.setCrossoverRate(1.0)
   ga.setMutationRate(0.1)
   ga.stepCallback.set(evolve_callback)
 
   ga.evolve()
 
if __name__ == "__main__":
   main_run()

Rosenbrock’s banana function and friends

Posted on : 06-03-2009 | By : Perone | In : Genetic Algorithms, Pyevolve, Python

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This post is a report of an optimization test suite applied to Pyevolve GA Core.

I’m writing a paper about Pyevolve and I’ve done some tests on the GA quality of Pyevolve with must common optimization test functions: Schaffer, Rastringin, Sphere, Ackley and the absolute GA-hard Rosenbrock. Follows in the end of the post, the results of the trials, I’ve exported the latex formulae as images.

The only function that the GA had some trouble (it failed to find the global minima in 3 of 10 trials, the “fail” term means that it had not found an optimal solution for 5.000 generations) was the Rosenbrock’s function with 20 variables, also known as Rosenbrock’s banana function due the dinstinctive shape of the contour lines, here is the 3D plot with 2 variables.

As Wikipedia says,

This function is often used to test performance of optimization algorithms. The global minimum is inside a long, narrow, parabolic shaped flat valley. To find the valley is trivial, however to converge to the global minimum is difficult.

However, this behavior was not unexpected, since we can note the same on the research of [1], [2], [3] and [4], among other many papers.

I think this trial results brings more reliability to the framework, when the Pyevolve paper was published, I’ll post it here.

[1] Seredynski, Franciszek, et. al. (2003). “Function Optimization with Coevolutionary Algorithms”, in International Intelligent Information Processing and Web Mining Conference.

[2] Hiroyasu, Tomoyuki, et. al. (1999). “Distributed Genetic Algorithms with Randomized Migration Rate”, IEEE Proceedings of Systems, Man and Cybernetics Conference SMC’99, Vol. 1, pp. 689-694.

[3] Bouvry, Pascal, et. al. (1997). “Distributed evolutionary optimization in Manifold: the Rosenbrock’s function case study”, Duke University.

[4] Panait, Liviu (2002). “A comparison of two competitive fitness functions”, in GECCO 2002: Proceedings of the Genetic and Evolutionary Computation Conference.

Pyevolve on Sony PSP ! (genetic algorithms on PSP)

Posted on : 03-03-2009 | By : Perone | In : Genetic Algorithms, Pyevolve, Python

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Sony PSP can be more interesting than funny sometimes. Few people know about the potential of the PSP port of Stackless Python 2.5.2. This great port of python was done by Carlos E. and you can find more information about the progress of the port on his blog.

Well, I’ve tested the Pyevolve GA framework on the Stackless Python for PSP and for my surprise, it worked without changing one single line of code on the framework due the fact of Pyevolve has been written in pure Python (except the platform specific issue like the Interactive Mode, but this issue is automaticly disabled on unsupported platforms).

So now, we have Genetic Algorithms on PSP.

Follow some screenshots (click to enlarge):

psp2psp1

The GA running on the PSP screenshot is the minimization of the Sphere function.

Here is the steps to install Pyevolve on PSP:

PSP Stackless Python Installation

1) First, create a directory called “python” on your PSP under the “/PSP/GAME” and the directory structure “/python/site-packages/” on the root of your memory stick (this last directory will be used to put Pyevolve later).
2) Copy the EBOOT.PBP and the python.zip files to this created directory;

Pyevolve Installation

3) Download the Pyevolve source and copy the directory called “pyevolve” to the created directory “/python/site-packages/”, the final directory structure will be: “/python/site-packages/pyevolve”

Ready ! Now you can import Pyevolve modules inside scripts on your PSP, of course you can’t use the graphical plotting tool or some DB Adapters of Pyevolve, but the GA Core it’s working very well.

Here is some basic usage of PSP Stackless Python port. I’ve used the psp2d module to show the information on screen. When I got more time, I’ll port the visualization of the TSP problem to use the psp2d, it will be nice to see Traveling Salesperson Problem running with real-time visualization on PSP =)

Related Links

Google Code Project of PSP Stackless Python

Pyevolve: the effect of Linear Scaling

Posted on : 02-03-2009 | By : Perone | In : Genetic Algorithms, Pyevolve, Python

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There’s an interesting graph in Pyevolve which is a heat-like graph of the population raw and fitness scores. In this graph you can note the effect of Linear Scaling over the scores, the raw scores graph is in left and the fitness scaled scores is in the right, this plot uses the Gaussian interpolation method.

linear

This graph feature is very interesting to study the effects of selections and scaling schemes and even to see the propagation of best individuals on the population while evolving, I think this graph should be more explored.

Good news: IronPython and Jython compatibility !

Posted on : 16-02-2009 | By : Perone | In : Pyevolve, Python

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Good news, I’ve tested Pyevolve 0.5 with the IronPython 2.0.1 and Jython 2.5b1, and the framework is working perfect (besides the performance loss when comparing with CPython 2.5 and 2.6). The only feature that do not worked is the dump of statistics with the sqlite3, sine there is no sqlite3 on the default install of Jython and IronPython. To Pyevolve work on IronPython, you must install the zlib module for IronPython and import your Python modules like this:

?View Code PYTHON
import sys
sys.path.append(r"c:\python25\lib")

With this compatibility issue, you can use Pyevolve on your .NET platform or in your Java applications.

Pyevolve profiling dot graph

Posted on : 14-02-2009 | By : Perone | In : Pyevolve, Python

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I’ve created a profiling dot graph of the pyevolve_example15_rosenbrock.py with the Gprof2Dot, this Pyevolve example is the minimization of the Rosenbrock function with 20 variables.

stat

I’ve created that graph to show the call structure of Pyevolve, as you can see, the accumulation in FunctionSlot applyFunctions method is the effect of the use of FunctionSlot use in many operations like scaling,  selection, evaluation, crossover and mutation.

The Pyevolve Interactive Mode on Mac OS

Posted on : 12-02-2009 | By : Perone | In : Genetic Algorithms, Pyevolve, Python

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The Interactive Mode of Pyevolve is the only part of Pyevolve which is platform dependant, I’ve created the platform dependant code for Win and Linux, but not yet for Mac, I’m working on that issue for the next release 0.6 of Pyevolve, but there is a way to enter in the Interactive Mode on the Mac, it’s a workaround for a while, this is the code: