Optimization API optimization-33 (20130530172738)

edu.cornell.med.icb.optimization
Class OptimizeSubSet

java.lang.Object
  extended by edu.cornell.med.icb.optimization.OptimizeSubSet

public class OptimizeSubSet
extends Object

Optimize a subset of elements according to some convergenceCriterion. Given a set S of N elements, determines the subset Sk of S with k elements which maximizes a configurable convergenceCriterion.

Author:
Fabien Campagne Date: Oct 10, 2007 Time: 12:38:14 PM

Constructor Summary
OptimizeSubSet(IntSet set, int k, SubSetFitnessFunction convergenceCriterion)
           
OptimizeSubSet(IntSet set, int k, SubSetFitnessFunction convergenceCriterion, int populationSize, String... params)
           
OptimizeSubSet(IntSet set, int k, SubSetFitnessFunction convergenceCriterion, String... params)
           
 
Method Summary
 void configure()
           
 double getFitestFunctionValue()
           
 double[] getFitestParameterValues()
           
 IntSet getFitestSubset()
          Get the fittest subset of elements.
 int getNumberOfIterationsPerformed()
           
 int getNumberOfParameters()
           
 boolean optimize(int numSteps, double convergenceDelta)
          Find an optimal subset, given the convergenceCriterion.
 void setLog(Logger log)
           
 void setModuloProgressReport(int moduloProgressReport)
           
 void setPopulationSize(int populationSize)
          Set the number of individuals in the population used by the genetic algorithm.
 void setRandomSeed(int randomSeed)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

OptimizeSubSet

public OptimizeSubSet(IntSet set,
                      int k,
                      SubSetFitnessFunction convergenceCriterion)
               throws org.jgap.InvalidConfigurationException
Throws:
org.jgap.InvalidConfigurationException

OptimizeSubSet

public OptimizeSubSet(IntSet set,
                      int k,
                      SubSetFitnessFunction convergenceCriterion,
                      String... params)
               throws org.jgap.InvalidConfigurationException
Throws:
org.jgap.InvalidConfigurationException

OptimizeSubSet

public OptimizeSubSet(IntSet set,
                      int k,
                      SubSetFitnessFunction convergenceCriterion,
                      int populationSize,
                      String... params)
               throws org.jgap.InvalidConfigurationException
Throws:
org.jgap.InvalidConfigurationException
Method Detail

setModuloProgressReport

public void setModuloProgressReport(int moduloProgressReport)

setPopulationSize

public void setPopulationSize(int populationSize)
Set the number of individuals in the population used by the genetic algorithm.

Parameters:
populationSize -

setRandomSeed

public void setRandomSeed(int randomSeed)

configure

public void configure()
               throws org.jgap.InvalidConfigurationException
Throws:
org.jgap.InvalidConfigurationException

setLog

public void setLog(Logger log)

getNumberOfIterationsPerformed

public int getNumberOfIterationsPerformed()

optimize

public boolean optimize(int numSteps,
                        double convergenceDelta)
                 throws org.jgap.InvalidConfigurationException
Find an optimal subset, given the convergenceCriterion. Optimization will proceed for at most numSteps. If convergence of the convergenceCriterion cost function occurs becore maxSteps, the optimization terminates. Formally, the optimization terminates if cost(step i+1) - cost(step i) < abs(convergenceDelta) for more than deltaNumSteps contiguous steps.

Parameters:
numSteps - Maximum number of steps before stopping.
convergenceDelta - convergence cost function convergenceCriterion
Returns:
True when the optimization has converged, False otherwise.
Throws:
org.jgap.InvalidConfigurationException - If an error occurs configuring the optimization solver.

getFitestSubset

public IntSet getFitestSubset()
Get the fittest subset of elements. The subset with the elements that maximize the fitness function.

Returns:
The subset with the elements that maximize the fitness function.

getFitestParameterValues

public double[] getFitestParameterValues()

getNumberOfParameters

public int getNumberOfParameters()

getFitestFunctionValue

public double getFitestFunctionValue()

Optimization API optimization-33 (20130530172738)

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