ec.gp.koza
Class MutationPipeline

java.lang.Object
  extended by ec.BreedingSource
      extended by ec.BreedingPipeline
          extended by ec.gp.GPBreedingPipeline
              extended by ec.gp.koza.MutationPipeline
All Implemented Interfaces:
Prototype, Setup, SteadyStateBSourceForm, RandomChoiceChooser, java.io.Serializable, java.lang.Cloneable

public class MutationPipeline
extends GPBreedingPipeline

MutationPipeline is a GPBreedingPipeline which implements a strongly-typed version of the "Point Mutation" operator as described in Koza I. Actually, that's not quite true. Koza doesn't have any tree depth restrictions on his mutation operator. This one does -- if the tree gets deeper than the maximum tree depth, then the new subtree is rejected and another one is tried. Similar to how the Crosssover operator is implemented.

Mutated trees are restricted to being maxdepth depth at most. If in tries attemptes, the pipeline cannot come up with a mutated tree within the depth limit, then it simply copies the original individual wholesale with no mutation.

One additional feature: if equal is true, then MutationPipeline will attempt to replace the subtree with a tree of approximately equal size. How this is done exactly, and how close it is, is entirely up to the pipeline's tree builder -- for example, Grow/Full/HalfBuilder don't support this at all, while RandomBranch will replace it with a tree of the same size or "slightly smaller" as described in the algorithm.

Typical Number of Individuals Produced Per produce(...) call
...as many as the child produces

Number of Sources
1

Parameters

base.tries
int >= 1
(number of times to try finding valid pairs of nodes)
base.maxdepth
int >= 1
(maximum valid depth of a crossed-over subtree)
base.ns
classname, inherits and != GPNodeSelector
(GPNodeSelector for tree)
base.build.0
classname, inherits and != GPNodeBuilder
(GPNodeBuilder for new subtree)
equal
bool = true or false (default)
(do we attempt to replace the subtree with a new one of roughly the same size?)
base.tree.0
0 < int < (num trees in individuals), if exists
(tree chosen for mutation; if parameter doesn't exist, tree is picked at random)

Default Base
gp.koza.mutate

Parameter bases

base.ns
nodeselect
base.build
builder

Version:
1.0
Author:
Sean Luke
See Also:
Serialized Form

Field Summary
 GPNodeBuilder builder
          How the pipeline builds a new subtree
static int INDS_PRODUCED
           
 GPNodeSelector nodeselect
          How the pipeline chooses a subtree to mutate
static int NUM_SOURCES
           
static java.lang.String P_BUILDER
           
static java.lang.String P_EQUALSIZE
           
static java.lang.String P_MAXDEPTH
           
static java.lang.String P_MUTATION
           
static java.lang.String P_NUM_TRIES
           
 
Fields inherited from class ec.gp.GPBreedingPipeline
P_NODESELECTOR, P_TREE, TREE_UNFIXED
 
Fields inherited from class ec.BreedingPipeline
DYNAMIC_SOURCES, mybase, P_NUMSOURCES, P_SOURCE, sources, V_SAME
 
Fields inherited from class ec.BreedingSource
CHECKBOUNDARY, DEFAULT_PRODUCED, NO_PROBABILITY, P_PROB, probability, UNUSED
 
Constructor Summary
MutationPipeline()
           
 
Method Summary
 java.lang.Object clone()
          Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context.
 Parameter defaultBase()
          Returns the default base for this prototype.
 int numSources()
          Returns the number of sources to this pipeline.
 int produce(int min, int max, int start, int subpopulation, Individual[] inds, EvolutionState state, int thread)
          Produces n individuals from the given subpopulation and puts them into inds[start...start+n-1], where n = Min(Max(q,min),max), where q is the "typical" number of individuals the BreedingSource produces in one shot, and returns n.
 void setup(EvolutionState state, Parameter base)
          Sets up the BreedingPipeline.
 
Methods inherited from class ec.gp.GPBreedingPipeline
produces
 
Methods inherited from class ec.BreedingPipeline
finishProducing, individualReplaced, maxChildProduction, minChildProduction, preparePipeline, prepareToProduce, sourcesAreProperForm, typicalIndsProduced
 
Methods inherited from class ec.BreedingSource
getProbability, pickRandom, setProbability, setupProbabilities
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

P_NUM_TRIES

public static final java.lang.String P_NUM_TRIES
See Also:
Constant Field Values

P_MAXDEPTH

public static final java.lang.String P_MAXDEPTH
See Also:
Constant Field Values

P_MUTATION

public static final java.lang.String P_MUTATION
See Also:
Constant Field Values

P_BUILDER

public static final java.lang.String P_BUILDER
See Also:
Constant Field Values

P_EQUALSIZE

public static final java.lang.String P_EQUALSIZE
See Also:
Constant Field Values

INDS_PRODUCED

public static final int INDS_PRODUCED
See Also:
Constant Field Values

NUM_SOURCES

public static final int NUM_SOURCES
See Also:
Constant Field Values

nodeselect

public GPNodeSelector nodeselect
How the pipeline chooses a subtree to mutate


builder

public GPNodeBuilder builder
How the pipeline builds a new subtree

Constructor Detail

MutationPipeline

public MutationPipeline()
Method Detail

defaultBase

public Parameter defaultBase()
Description copied from interface: Prototype
Returns the default base for this prototype. This should generally be implemented by building off of the static base() method on the DefaultsForm object for the prototype's package. This should be callable during setup(...).


numSources

public int numSources()
Description copied from class: BreedingPipeline
Returns the number of sources to this pipeline. Called during BreedingPipeline's setup. Be sure to return a value > 0, or DYNAMIC_SOURCES which indicates that setup should check the parameter file for the parameter "num-sources" to make its determination.

Specified by:
numSources in class BreedingPipeline

clone

public java.lang.Object clone()
Description copied from interface: Prototype
Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context.

Typically this should be a full "deep" clone. However, you may share certain elements with other objects rather than clone hem, depending on the situation:

Implementations.

Specified by:
clone in interface Prototype
Overrides:
clone in class BreedingPipeline

setup

public void setup(EvolutionState state,
                  Parameter base)
Description copied from class: BreedingSource
Sets up the BreedingPipeline. You can use state.output.error here because the top-level caller promises to call exitIfErrors() after calling setup. Note that probability might get modified again by an external source if it doesn't normalize right.

The most common modification is to normalize it with some other set of probabilities, then set all of them up in increasing summation; this allows the use of the fast static BreedingSource-picking utility method, BreedingSource.pickRandom(...). In order to use this method, for example, if four breeding source probabilities are {0.3, 0.2, 0.1, 0.4}, then they should get normalized and summed by the outside owners as: {0.3, 0.5, 0.6, 1.0}.

Specified by:
setup in interface Prototype
Specified by:
setup in interface Setup
Overrides:
setup in class BreedingPipeline
See Also:
Prototype.setup(EvolutionState,Parameter)

produce

public int produce(int min,
                   int max,
                   int start,
                   int subpopulation,
                   Individual[] inds,
                   EvolutionState state,
                   int thread)
Description copied from class: BreedingSource
Produces n individuals from the given subpopulation and puts them into inds[start...start+n-1], where n = Min(Max(q,min),max), where q is the "typical" number of individuals the BreedingSource produces in one shot, and returns n. max must be >= min, and min must be >= 1. For example, crossover might typically produce two individuals, tournament selection might typically produce a single individual, etc.

Specified by:
produce in class BreedingSource