Adding the Lesson5 - how to create your own genotype
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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
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<html>
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
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<meta name="GENERATOR" content="Mozilla/4.78 [en] (X11; U; Linux 2.4.7-10 i686) [Netscape]">
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<title>Tutorial: Lesson 5</title>
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</head>
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<body text="#000000" link="#0000EE" vlink="#551A8B" alink="#FF0000" background="beige009.jpg">
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<a href="eoLesson4.html">Lesson 4</a> -
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<a href="eoLesson6.html">Lesson
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6</a> -
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<a href="eoTutorial.html">Main page</a> -
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<a href="eoTopDown.html">Algorithm-Based</a>
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- <a href="eoBottomUp.html">Component-Based</a> - <a href="eoProgramming.html">Hints</a>
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- <b><font face="Arial,Helvetica"><font size=+1><a href="../../doc/html/index.html">EO
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documentation</a></font></font></b>
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<br>
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<hr WIDTH="100%"><!-- -------------- End of header ------------------ --><!-- ----------------------------------------------- -->
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<center>
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<h1>
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<font color="#FF0000">Tutorial Lesson 5: using your own genotype</font></h1></center>
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In this lesson, you will learn how to design and evolve <b><font color="#FF0000">your
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own genotype structure</font></b>. Note that at the moment, only algorithms
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involving a scalar fitness (double) are implemented (see test dir for Pareto
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optimization of multiple-objective fitness - or be patient :-)
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<p>The minimum code you'll have to write is first, of course, the code
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for the <a href="genotype">genotype structure</a>. Then, the representation-dependent
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code: <a href="#initialization">intialization procedure(s)</a>,
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<a href="#variation">variation
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operators</a> (quadratic crossover, mutation operator), ... and <a href="evaluation">evaluation
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function</a> - and that's it : we have prepared some template files and
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the script create.sh that will take care of generating a few other files
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to make your application complete.
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<p>In what follows, we will suppose that you want to evolve some data structure,
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and that you have enough programming skills to be able to write C code
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for its random initilialization, its crossover, its mutation and the computation
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of its fitness.
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<br>The examples will be described supposing you want to evolve ... bitstings
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to solve the OneMax problem (oh no!!!).
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<p>
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<hr WIDTH="100%"><a NAME="using"></a><b><font color="#000099"><font size=+2>Using
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template files</font></font></b>
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<br>Follow this very simple procedure:
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<ul>
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<li>
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choose a <b><font color="#FF6600">name</font></b> for you application -
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here <b><font color="#FF6600">OneMax</font></b> will be used</li>
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<li>
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go to the <b><tt><font color="#993300">tutorial/Templates</font></tt></b>
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dir</li>
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<br><tt><font color="#FF6666"> <b>cd
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pathWhereEOisInstalled/tutorial/Templates</b></font></tt>
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<li>
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run the <b><tt><font color="#993300">create.sh</font></tt></b> script with
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argument OneMax and second optional argument a directory name (suppose
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it's called APPLICATION here)</li>
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<br><b><tt><font color="#FF6666">
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./create.sh OneMax APPLICATION</font></tt></b>
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<br>This will create a directory <b><tt><font color="#993300">tutorial/APPLICATION</font></tt></b>
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<li>
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Go to the APPLICATION directory</li>
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<br><b><tt><font color="#FF6666">
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cd ../APPLICATION</font></tt></b>
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<br>You should see the following files:
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<br> <b><tt><font color="#993300">OneMaxEA.cpp
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</font></tt></b>the main main file, includes all other, to be compiled
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<br> <b><tt><font color="#993300">Makefile
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</font></tt></b>with default target eoOneMaxEA
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<br> <b><tt><font color="#993300">eoOneMax.h
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</font></tt></b>class eoOneMax, the genotype
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<br> <b><tt><font color="#993300">eoOneMaxEvalFunc.h
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</font></tt></b>class for the computation of fitness
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<br> <b><tt><font color="#993300">eoOneMaxInit.h
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</font></tt></b>class for genotype initlialization
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<br> <b><tt><font color="#993300">eoOneMaxMutation.h
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</font></tt></b>class for mutation
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<br> <b><tt><font color="#993300">eoOneMaxQuadCrossover.h
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</font></tt></b>class
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for (quadratic) crossover
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<br> <b><tt><font color="#993300">make_genotype_OneMax.h
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</font></tt></b>helper function that create the initializer
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<br> <b><tt><font color="#993300">make_op_OneMax.h
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</font></tt></b>helper function that handles the rates of application of
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the variation operators<br>
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<b><tt><font color="#993300">OneMaxLibEA.cpp
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</font></tt></b>another main file, for separate compilation of representation-independent
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stuff
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<br> <b><tt><font color="#993300">make_OneMaxEA.cpp
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</font></tt></b>the source for the representation-independent stuff
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<br>
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<li>
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Compile the whole application</li>
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<br><b><tt><font color="#FF6666">
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make</font></tt></b>
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<br>and you should have no error there and see a new executable file named
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<b><tt><font color="#FF6666">OneMaxEA</font></tt></b>.
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You can run it and ... it will do nothing (what did you expect???).<br>
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<BR>
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<li>
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Now you should go and edit the files. The minimal changes that you
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will need are</li>
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<br> in <b><tt><font color="#993300">eoOneMax.h
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</font></tt></b>define your genotype
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<br> in <b><tt><font color="#993300">eoOneMaxInit.h
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</font></tt></b>define the initialization of one genotype
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<br> in <b><tt><font color="#993300">eoOneMaxMutation.h
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</font></tt></b>define the mutation of one genotype
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<br> in <b><tt><font color="#993300">eoOneMaxQuadCrossover.h
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</font></tt></b>define the crossover of 2 genotypes</ul>
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<font color="#FF0000"><font size=+1>Smooth application building:</font></font>
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<ul>
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<li>
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After editing a particular file, <b><font color="#FF6600">compile</font></b>
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the whole thing immediately (by running make) <b><font color="#FF6600">and
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run</font></b> the algorithm, to validate your code</li>
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<li>
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In each file, start by only adding code between keyword-pairs <b><tt><font color="#993300">START</font></tt></b>
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and <b><font color="#993300">END</font></b></li>
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</ul>
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We shall now take a look in turn at the 4 files mentionned above, then
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describe rapidly the other files, especially the main files.
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<br>
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<hr WIDTH="100%"><a NAME="genotype"></a><b><font color="#000099"><font size=+2>Genotype
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- and its pre-requisites: </font></font><tt><font color="#993300"><font size=+1>eoOneMax.h</font></font></tt></b>
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<p>First thing is to write the code for <font color="#999900"><b>the structure
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of the genotype</b>.</font> This is done by filling in the template file
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<a href="eoOneMax.html">eoOneMax.h</a>.
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There are 4 places that you should consider filling in:
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<ul>
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<li>
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Of course, <a href="eoOneMax.html#data">the data</a> that will build up
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the genotype. The convention in EO is to have it at the end of the class
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definition, and as private data.</li>
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<li>
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The <a href="eoOneMax.html#constructor">default constructor</a> of an instance.
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Note that <b><font color="#FF6600">you must provide a default constructor</font></b>,
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and that no other constructor will be called within EO code. you might
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think you need some other constructor to initialize problem-specific data.
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This should be rather done in the eoInit object used to randomly initialize
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all individuals, or in the eoEvalFunc object, used to compute the fitness.</li>
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<li>
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The <a href="eoOneMax.html#print">printOn</a> method, that writes the object
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to a stream. You<font color="#000000"> must</font><b><font color="#FF6600">
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call the EO::printOn</font></b> method that will take care of the fitness,
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and then write the specific code for your data structure.</li>
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<li>
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The <a href="eoOneMax.html#read">readFrom</a> method, that will read an
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object from a stream. Again, you should <b><font color="#FF6600">call the
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EO::readFrom</font></b> method first to take care of the fitness.</li>
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<br>Also note that readFrom will be generally called from an object that
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will have been constructed through the default constructor. This is why
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the EO objects that we provide always start printing structures with their
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length...</ul>
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You can of course also add <a href="eoOneMax.html#destructor">a destructor</a>
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if needed, and any other helper method. For instance, you will probably
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consider adding <b><font color="#FF6600">accessors and setters</font></b>
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for the private data - unless you prefer to make everything public :-(
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<br>See now an example of <a href="eoOneMax_complete.html">a comple eoOneMax.h</a>
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file. Note that this is the only "colored" completed file we will show,
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you will have to go to the <b><tt><font color="#993300">.../tutorial/OneMax</font></tt></b>
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dir to <a href="../OneMax">browse all files at once</a>.
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<br>
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<hr WIDTH="100%"><a NAME="initialization"></a><b><font color="#000099"><font size=+2>Initialization:</font></font></b>
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<p><font size=+1><font color="#FF0000">Initializer: </font><b><tt><font color="#993300">eoOneMaxInit.h</font></tt></b></font>
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<br>You must provide an <b><tt><font color="#CC33CC">eoInit</font></tt></b>
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object for your genotype, that is an object that will <b><font color="#FF6600">randomize
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a genotype built by the default constructor</font></b> of the EO class
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(here, an eoOneMax object) . Here you must at least fill <a href="eoOneMaxInit.html#operator">the
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code for such randomization.</a>
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<br>But you might also need some parameters (e.g. the size of the bitstring
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in eoOneMax): you should then <a href="eoOneMaxInit.html#constructor">pass
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them through the constructor</a> of the eoOneMaxInit class, and <a href="eoOneMaxInit.html#data">store
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it in its private data</a>.
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<br>And of course you might need to add a destructor (no example here)
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if you use complex data type in the object.
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<p><font size=+1><font color="#FF0000">Parameters: </font><b><tt><font color="#993300">make_genotype_OneMax.h</font></tt></b></font>
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<br>There is another file you will probably want to modify as far as initialization
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is concerned, that is <a href="make_genotype_OneMax.html">make_genotype_OneMax.h.</a>
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Such helper files are used for all components of advanced EO programs (see
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Lesson 4). The main reason for that is to allow separate compilation of
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such sub-components for known EO types, as this is done in the directories
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src/ga and src/es. But a useful consequence is to make your code modular.
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For instance, the <a href="make_genotype_OneMax.html#representation">make_genotype_OneMax.h</a>
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file takes care of all the preparation of all data regarding the eoInit
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object - and returns to the main fonction a reference to an eoInit that
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will later be used to <a href="OneMaxEA.html#initPop">initialize the whole
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population</a> in a representation-independent way.
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<br>What you have to do in that file is to set values for all parameters
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needed by the eoOneMaxInit class, for instance by reading them from the
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parser: this allows later to modify them easily from the command-line.
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Note however that an alternative could be to pass the parser to the constructor
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of the eoOneMaxInit class, and to read all parameters there...
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<br><b><font color="#FF0000">Note</font></b>: Remember that the make_xxx
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files were first introduced to allow the user to compile sepearately most
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of the code of standard Evolutionary Algorithm written in EO for bitstring
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and real vector representations (
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<br>
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<hr WIDTH="100%"><a NAME="evaluation"></a><b><font color="#000099"><font size=+2>Evaluation:
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</font></font><tt><font color="#993300"><font size=+1>eoOneMaxEvalFunc.h</font></font></tt></b>
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<p>The <b><tt><font color="#CC0000">eoOneMaxEvalFunc</font></tt></b> is
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the object that will <b><font color="#FF6600">compute the fitness of an
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eoOneMax object</font></b>. You have to fill in the <a href="eoOneMaxEvalFunc.html#operator">code
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for the computation of the fitness value</a> (there is no way that this
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can be done automatically :-) Note that this code must be run <b><font color="#FF6600">only
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if</font></b> the <b><tt><font color="#993300">_eo.invalid() </font></tt></b>test
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returns true, to avoid computing the fitness of an object that has not
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been modified and thus still holds a valid fitness value. After computing
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the fitness, store it into the object by calling the <b><tt><font color="#993300">fitness(FitnessType)</font></tt></b>
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method.
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<br>Should you need some specific data for that, the <a href="eoOneMaxEvalFunc.html#constructor">constructor
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of the object</a> is the place to get such data, and you should, again,
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store it in some <a href="eoOneMaxEvalFunc.html#data">private data</a>
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of the class.
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<br>
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<hr WIDTH="100%"><a NAME="variation"></a><b><font color="#000099"><font size=+2>Variation
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Operators</font></font></b>
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<br>You can write as many crossover and mutation operators as you like.
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However, we only provide the template files for <a href="eoOperators.html#crossover">quadratic
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crossover </a>and <a href="eoOperators.html#mutation">mutation</a>, but
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you could then easily write the equivalent code for binary crossover, or
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general variation operator.
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<p><font size=+1><font color="#FF0000">Crossover: </font><b><tt><font color="#993300">eoOneMaxQuadCrossover.h</font></tt></b></font>
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<br>As usual, you must go and write the <a href="eoOneMaxQuadCrossover.html#operator">code
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for the operator()</a> that will perform the crossover, possibly modifying
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both arguments. Don't forget to <b><font color="#FF6600">update the boolean
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parameter</font></b> that will report whether the genotypes have been modified
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- allowing to recompute the fitness only of the ones that have actually
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been modified. You can also have <b><font color="#FF6600">parameters</font></b>
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to the crossover by <a href="eoOneMaxQuadCrossover.html#constructor">passing
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them to the constructor</a>, ans storing them in the <a href="eoOneMaxQuadCrossover.html#data">private
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data of the crossover object</a>.
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<p><font size=+1><font color="#FF0000">Mutation: </font><b><tt><font color="#993300">eoOneMaxMutation.h</font></tt></b></font>
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<br>Here again, you must go and write the code for the operator() that
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will perform the mutation, eventually modifying its arguments. Don't forget
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to <b><font color="#FF6600">update the boolean parameter</font></b> that
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will report whether the genotype has been modified - allowing to recompute
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the fitness only of the ones that have actually been modified. You can
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also have <b><font color="#FF6600">parameters</font></b> to the mutation
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by <a href="eoOneMaxMutation.html#constructor">passing them to the constructor</a>,
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ans storing them in the <a href="eoOneMaxMutation.html#data">private data
|
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of the mutation object</a>.
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<p><font size=+1><font color="#FF0000">Parameters: </font><b><tt><font color="#993300">make_op_OneMax.h</font></tt></b></font>
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<br>First of all, if you intend to use <b><font color="#FF6600">only one
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crossover</font></b> operator and <b><font color="#FF6600">one mutation</font></b>
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operator, you have <b><font color="#FF6600">nothing to modify</font></b>
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in <a href="make_op_OneMax.html">make_op_OneMax function</a>, except maybe
|
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reading user-defined parameters (copy the code from <a href="make_genotype_OneMax.html#representation">make_genotype_OneMax</a>)
|
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and passing them to <a href="make_op_OneMax.html#cross_ctor">the appropriate
|
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operator constructor</a>.
|
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<br>As it is written now, it allows you enter a crossover probability <b><tt><font color="#CC33CC">Pcross</font></tt></b>
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and a mutation probability <b><tt><font color="#CC33CC">Pmut</font></tt></b>,
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and to build an eoGeneralOp that will call in sequence the <b><tt><font color="#CC33CC">eoOneMaxQuadCrossover</font></tt></b>
|
||||
that is defined above with probability <b><tt><font color="#CC33CC">Pcross</font></tt></b>
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and the <b><tt><font color="#CC33CC">eoOneMaxMutation</font></tt></b> also
|
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defined above with probability <b><tt><font color="#CC33CC">Pmut</font></tt></b>.
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Beware that all allocated objects must be stored in the eoState otherwise
|
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you will run into trouble (see <a href="eoProgramming.html#memory">EO Memory
|
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Management explanations</a>).
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<p>However, everything is there (commented out) to allow you to use <a href="make_op_OneMax.html#crossover">more
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than one crossover</a> and <a href="make_op_OneMax.html#mutation">one mutation</a>
|
||||
- provided you write the code for them , of course.
|
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<p>The code starts by defining an <b><tt><font color="#CC33CC">eoOneMaxQuadCrossover</font></tt></b>object,
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then reads some application rate that is totally useless if you have only
|
||||
one crossover, then creates an <b><tt><font color="#CC33CC"><a href="eoLesson2.html#combined_operators">eoPropCombinedQuadOp</a></font></tt></b>
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with this simple oeprator. The same story repeats for the mutation. <a href="make_op_OneMax.html#donottouch">Finally</a>,
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the <b><tt><font color="#CC33CC"><a href="eoOperators.html#general_combination">eoGeneralOp</a></font></tt></b>
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is created from those combined operators and the individulal level probabilities
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<b><tt><font color="#CC33CC">Pcross</font></tt></b>
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and <b><tt><font color="#CC33CC">Pmut</font></tt></b>.
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<p>In order to add a second crossover operator for instance (called <b><tt><font color="#CC33CC">eoOneMaxSecondCrossover</font></tt></b>
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in the commented code) all you need to is
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<ul>
|
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<li>
|
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Create the code for the new class <b><tt><font color="#CC33CC">eoOneMaxSecondCrossover</font></tt></b>:
|
||||
simply copy the <b><tt><font color="#993300">eoOneMaxQuadCrossover.h</font></tt></b>
|
||||
file into <b><tt><font color="#993300">eoOneMaxSecondCrossover.h</font></tt></b>
|
||||
and change all names <b><tt><font color="#CC33CC">eoOneMaxQuadCrossover</font></tt></b>
|
||||
to <b><tt><font color="#CC33CC">eoOneMaxSecondCrossover </font></tt></b>(inlcluding
|
||||
after the #ifdef statement!!!);</li>
|
||||
|
||||
<li>
|
||||
Uncomment the <a href="make_op_OneMax.html#crossover">corresponding lines
|
||||
in make_op_OneMax.h</a>, possibly adding user-defined parameter reading</li>
|
||||
|
||||
<li>
|
||||
Repeat as many times as you have operators, using of course different names!
|
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The same recommendations hold for mutations.</li>
|
||||
</ul>
|
||||
In case you have more than one operator of a kind, then of course the relative
|
||||
weights of application do make sense, allowing you to tune with command-line
|
||||
parameters the proportion with which each operator that will be applied.
|
||||
<p>
|
||||
<hr WIDTH="100%"><a NAME="main"></a><b><font color="#000099"><font size=+2>Main
|
||||
files: </font></font><tt><font color="#993300"><font size=+1>OneMaxEA.cpp
|
||||
</font></font></tt></b>and<b><tt><font color="#993300"><font size=+1> OneMaxLibEA.cpp</font></font></tt></b><font color="#FF0000"><font size=+1></font></font>
|
||||
<p>As a start, you should only (eventually) modify in <b><tt><font color="#993300">OneMaxEA.cpp
|
||||
</font></tt></b>the <a href="OneMax.cpp#fitness">type of fitness</a> you
|
||||
will be handling, namely <b><tt><font color="#CC0000">double</font></tt></b>
|
||||
if you are <b><font color="#FF6600">maximizing</font></b>, or <b><tt><font color="#CC0000">eoMinimizingFitness</font></tt></b>
|
||||
if you are <b><font color="#FF6600">minimizing</font></b>. Then running
|
||||
<b><tt><font color="#FF6666">make</font></tt></b> will result in a perfectly
|
||||
valid executable named <b><tt><font color="#FF6666">OneMaxEA</font></tt></b>.
|
||||
<p>The skeleton of the main file here mimics that of the main file in
|
||||
<a href="eoLesson4.html">Lesson4</a>,
|
||||
and <a href="eoLesson4.html#programmerguide">uses the make_xxx separate
|
||||
files construct</a>: the part of an Evolutionary Algorithm related to the
|
||||
<b><font color="#009900">evolution
|
||||
engine</font></b> is <b><font color="#FF6600">indepenent of the representation</font></b>,
|
||||
and can be directly used ... provided it is compiled with the right template
|
||||
(remember everything in EO is <a href="eoProgramming.html#templates">templatized
|
||||
over the EO objects it handles</a>. Main file <b><tt><font color="#993300">OneMaxEA.cpp</font></tt></b>
|
||||
is written so that it includes eveything - and thus everytime you run <b><tt><font color="#FF6666">make</font></tt></b>
|
||||
(or <b><tt><font color="#FF6666">make OneMaxEA</font></tt></b>), you compile
|
||||
the code for make_pop, make_continue and make_checkpoint that is defined
|
||||
in the .../src/do directory.
|
||||
<p>The basic construct is (for instance to build the evolution engine)
|
||||
<br>
|
||||
<table BORDER=0 CELLSPACING=0 COLS=1 WIDTH="100%" BGCOLOR="#CCCCCC" NOSAVE >
|
||||
<tr>
|
||||
<td><b><tt><font color="#009900">#include <do/make_algo_scalar.h></font></tt></b>
|
||||
<br><b><tt><font color="#009900">eoAlgo<Indi>& make_algo_scalar(eoParser&
|
||||
_parser, eoState& _state, eoEvalFunc<Indi>& _eval, eoContinue<Indi>&
|
||||
_continue, eoGenOp<Indi>& _op)</font></tt></b>
|
||||
<br><b><tt><font color="#009900">{</font></tt></b>
|
||||
<br><b><tt><font color="#009900"> return do_make_algo_scalar(_parser,
|
||||
_state, _eval, _continue, _op);</font></tt></b>
|
||||
<br><b><tt><font color="#009900">}</font></tt></b></td>
|
||||
</tr>
|
||||
</table>
|
||||
First, include the code (from the do directory). Then define the make_xxx
|
||||
function from the do_make_xxx function.
|
||||
<br>Of course, such construct is stupid here, as you could perfectly call
|
||||
directly the do_make_xxx function in the main. However, if you ever want
|
||||
to do separate compilation of some parts, you will need such construct
|
||||
(see <a href="eoLesson4.html">Lesson4</a>) so we have kept it here for
|
||||
consistency reasons.
|
||||
<p>Go in your application directory, and look at the differences between
|
||||
both files and you'll see how this is handled in both cases.
|
||||
<p><b><font color="#FF0000">Reducing compilation time:</font></b>
|
||||
<br>However, we also provide another main file (<b><tt><font color="#993300">OneMaxLibEA.cpp</font></tt></b>)that
|
||||
only includes the code that is specific to your application, and is supposed
|
||||
to be linked with another object file that will contain the code that is
|
||||
representation independent (<b><tt><font color="#993300">make_OneMax.cpp</font></tt></b>).
|
||||
This is done by running <b><tt><font color="#FF6666">make OneMaxLibEA</font></tt></b>
|
||||
on the command-line.
|
||||
<br>For example, on a PentiumIII 400MHz with g++ 2.96, compiling <b><tt><font color="#FF6666">OneMaxEA</font></tt></b>
|
||||
takes about <b><font color="#FF6600">33s</font></b>, compiling both <b><tt><font color="#FF6666">make_OneMax.o</font></tt></b>
|
||||
and <b><tt><font color="#FF6666">OneMaxLibEA</font></tt></b> takes about
|
||||
<b><font color="#FF6600">54s</font></b> but compiling only <b><tt><font color="#FF6666">OneMaxLibEA</font></tt></b>
|
||||
takes only <b><font color="#FF6600">14s</font></b> <b><tt><font color="#FF6666">make_OneMax.o</font></tt></b>
|
||||
is up-to-date ...
|
||||
<p><b><font color="#FF0000">Hints:</font></b>
|
||||
<br>While developping the genotype structure itself in file <b><tt><font color="#993300">eoOneMax.h</font></tt></b>,
|
||||
you should use the <b><tt><font color="#993300">OneMaxEA.cpp</font></tt></b>
|
||||
file. But after the <b><tt><font color="#993300">eoOneMax.h</font></tt></b>
|
||||
file is frozen, you should use the <b><tt><font color="#993300">eoOneMaxLibEA.cpp</font></tt></b>
|
||||
file. Of course, both resulting programs are strictly identical!
|
||||
<p>
|
||||
<hr WIDTH="100%"><font color="#000000"><a href="eoLesson4.html">Lesson
|
||||
4</a> -
|
||||
<a href="eoLesson6.html">Lesson 6</a> -
|
||||
<a href="eoTutorial.html">Main
|
||||
page</a> -
|
||||
<a href="eoTopDown.html">Algorithm-Based</a> - <a href="eoBottomUp.html">Component-Based</a>
|
||||
- <a href="eoProgramming.html">Hints</a> -<b> <font face="Arial,Helvetica"><font size=+1><a href="../../doc/html/index.html">EO
|
||||
documentation</a></font></font></b></font>
|
||||
<br>
|
||||
<hr>
|
||||
<address>
|
||||
<font color="#000000"><a href="mailto:Marc.Schoenauer@inria.fr">Marc Schoenauer</a></font></address>
|
||||
|
||||
</body>
|
||||
</html>
|
||||
Reference in a new issue