Parameter mybase
double likelihood
BreedingSource[] sources
double probability
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}.
Problem p_problem
MasterProblem masterproblem
java.lang.String runComplete
ParameterDatabase parameters
MersenneTwisterFast[] random
java.util.HashMap<K,V>[] data
Output output
int breedthreads
int evalthreads
boolean checkpoint
java.io.File checkpointDirectory
java.lang.String checkpointPrefix
int checkpointModulo
int randomSeedOffset
boolean quitOnRunComplete
java.lang.Object[] job
java.lang.String[] runtimeArguments
int generation
int evaluations
int numGenerations
long numEvaluations
Population population
Initializer initializer
Finisher finisher
Breeder breeder
Evaluator evaluator
Statistics statistics
Exchanger exchanger
long innovationNumber
java.lang.Object[] lock
java.util.ArrayList<E> trials
Individual[] context
java.util.ArrayList<E> subpops
boolean loadInds
Parameter file
Individual i_prototype
BreedingSource pipe_prototype
Fitness f_prototype
Statistics[] children
boolean silentFile
boolean silentPrint
boolean loadInds
Parameter file
Species species
IntBag[] parents
java.util.ArrayList<E> individuals
int initialSize
int numDuplicateRetries
int extraBehavior
boolean warned
java.util.ArrayList<E> buffer
int bufSize
int numTimes
boolean firstTime
int numInds
int maxGeneratable
boolean generateMax
int generationSwitch
int maxGeneratable
boolean generateMax
Individual individual
IntBag parents
BreedingSource stubPipeline
java.util.HashSet<E> set
boolean resetEachGeneration
int numDuplicateRetries
boolean generateMax
int style
int groupSize
boolean allowOverEvaluation
int whereToPutInformation
int numCurrent
int numShuffled
int numGuru
Individual[][] guruIndividuals
int numPrev
Population previousPopulation
SelectionMethod[] selectionMethodPrev
SelectionMethod[] selectionMethodCurrent
Individual[] inds
boolean[] updates
double F_NOISE
double F
double Cr
int retries
Population previousPopulation
int[] bestSoFarIndex
double PF
ParameterDatabase parameters
EvolutionState state
java.lang.Thread playThread
boolean playing
boolean paused
java.lang.Object buttonLock
java.lang.Object cleanupLock
int currentJob
java.lang.String[] clArgs
javax.swing.JPanel jContentPane
javax.swing.JMenuBar jJMenuBar
javax.swing.JMenu fileMenu
javax.swing.JMenu helpMenu
javax.swing.JMenuItem exitMenuItem
javax.swing.JMenuItem aboutMenuItem
javax.swing.JTabbedPane jTabbedPane
javax.swing.JToolBar jToolBar
javax.swing.JButton playButton
javax.swing.JButton pauseButton
javax.swing.JButton stopButton
javax.swing.JButton stepButton
javax.swing.JMenuItem loadParametersMenuItem
ParametersPanel paramPanel
ControlPanel conPanel
javax.swing.JFrame aboutFrame
boolean threadIsToStop
boolean _step
int result
javax.swing.JMenuItem loadCheckpointMenuItem
javax.swing.JTabbedPane statisticsPane
javax.swing.JTabbedPane inspectionPane
javax.swing.JPanel statusPane
javax.swing.JTextField statusField
Console console
javax.swing.JLabel jLabel
javax.swing.JTextField numGensField
javax.swing.JCheckBox quitOnRunCompleteCheckbox
javax.swing.JLabel jLabel1
javax.swing.JTextField numJobsField
javax.swing.JLabel jLabel2
javax.swing.JLabel jLabel3
javax.swing.JTextField evalThreadsField
javax.swing.JTextField breedThreadsField
javax.swing.JPanel jPanel
javax.swing.JRadioButton seedFileRadioButton
javax.swing.JTextField seedFileField
javax.swing.JButton seedFileButton
javax.swing.JRadioButton randomSeedsRadioButton
javax.swing.JTable seedsTable
javax.swing.JScrollPane jScrollPane
javax.swing.JLabel jLabel6
javax.swing.JCheckBox checkpointCheckBox
javax.swing.JPanel checkpointPanel
javax.swing.JLabel jLabel7
javax.swing.JTextField checkpointModuloField
javax.swing.JLabel jLabel8
javax.swing.JTextField prefixField
javax.swing.JLabel jLabel10
javax.swing.ButtonGroup seedButtonGroup
javax.swing.JButton generateSeedsButton
javax.swing.JRadioButton sequentialSeedsRadioButton
javax.swing.JLabel jLabel5
javax.swing.JTextField jobFilePrefixField
Console console
javax.swing.JScrollPane parameterTreeScrollPane
javax.swing.JTree parameterTree
javax.swing.JScrollPane parameterTableScrollPane
javax.swing.JTable parameterTable
javax.swing.JSplitPane jSplitPane
int numCharts
Console console
int subPopNum
javax.swing.JList<E> individualsList
javax.swing.JScrollPane individualListPane
javax.swing.JSplitPane subpopPane
javax.swing.JSplitPane individualDisplayPane
IndividualPortrayal portrayal
javax.swing.JScrollPane inspectionPane
javax.swing.JTree inspectionTree
org.jfree.data.category.DefaultCategoryDataset dataset
java.lang.String title
java.lang.String xlabel
java.lang.String ylabel
javax.swing.JPanel jPanel
javax.swing.JButton printButton
javax.swing.JButton closeButton
org.jfree.chart.ChartPanel chartPane
org.jfree.data.xy.XYSeriesCollection seriesCollection
javax.swing.JTextPane textPane
java.io.CharArrayWriter printIndividualWriter
boolean useAltTermination
double tau
double fitnessVarianceTolerance
int maximumNoImprovementStretch
int noImprovementStretch
double alphaAMS
double userAlphaAMS
double deltaAMS
double etaP
double userEtaP
double etaS
double userEtaS
double distributionMultiplierDecrease
double distributionMultiplierIncrease
double distributionMultiplier
double stDevRatioThresh
org.ejml.data.DenseMatrix64F mean
org.ejml.data.DenseMatrix64F prevMean
org.ejml.data.DenseMatrix64F xAvgImp
org.ejml.data.DenseMatrix64F meanShift
org.ejml.data.DenseMatrix64F genCovarMatrix
org.ejml.data.DenseMatrix64F aggCovarMatrix
org.ejml.data.DenseMatrix64F covarMatrix
org.ejml.data.DenseMatrix64F choleskyLower
org.ejml.data.DenseMatrix64F temp
org.ejml.data.DenseMatrix64F temp2
org.ejml.data.DenseMatrix64F temp3
org.ejml.data.DenseMatrix64F tempMatrix
java.util.IdentityHashMap<K,V> constraintViolations
boolean firstGeneration
int lambda
int mu
double[] weights
double mueff
double cmu
double c1
double cc
double cs
double damps
double sigma
org.ejml.simple.SimpleMatrix xmean
org.ejml.simple.SimpleMatrix c
org.ejml.simple.SimpleMatrix b
org.ejml.simple.SimpleMatrix d
org.ejml.data.DenseMatrix64F bd
org.ejml.data.DenseMatrix64F sbd
org.ejml.simple.SimpleMatrix invsqrtC
org.ejml.simple.SimpleMatrix ps
org.ejml.simple.SimpleMatrix pc
double chiN
int lastEigenDecompositionGeneration
boolean useAltTermination
boolean useAltGenerator
int altGeneratorTries
double sumSquared
double sum
double mean
int numOfObservations
double variance
int optimalIndex
int warmUp
java.util.ArrayList<E> visited
java.util.HashMap<K,V> visitedIndexMap
java.util.ArrayList<E> corners
java.util.ArrayList<E> activeSolutions
java.util.ArrayList<E> Ek
boolean stochastic
int initialReps
int repetition
long numOfTotalSamples
java.util.ArrayList<E> A
double[] b
java.util.ArrayList<E> boxA
java.util.ArrayList<E> boxB
double alpha
int b
java.util.List<E> distributions
int[] mu
int[] lambda
Population parentPopulation
byte[] comparison
java.util.ArrayList<E>[][] newIndividuals
int[] count
int[] children
int[] parents
int jobSize
boolean showDebugInfo
boolean batchMode
Problem problem
java.util.ArrayList<E> queue
Parameter base
ParameterDatabase p_database
ParameterDatabase currentDatabase
int runs
boolean reevaluateIndividuals
Individual[] bestUnderlyingIndividual
java.lang.Object lock
java.lang.Object[] domain
boolean setRandom
int countdown
int upperbound
int start
java.lang.String restartType
Parameter base
ec.exchange.InterPopulationExchange.IPEInformation[] exchangeInformation
Individual[][] immigrants
int[] nImmigrants
int nrSources
boolean chatty
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
boolean chatty
java.lang.Thread serverThread
Parameter base
java.lang.String serverAddress
int serverPort
int clientPort
boolean iAmServer
java.lang.String ownId
boolean compressedCommunication
SelectionMethod immigrantsSelectionMethod
SelectionMethod indsToDieSelectionMethod
ec.exchange.IslandExchangeMailbox mailbox
java.lang.Thread mailboxThread
int number_of_destination_islands
boolean synchronous
int modulo
int offset
int size
java.net.Socket[] outSockets
java.io.DataOutputStream[] outWriters
java.lang.String[] outgoingIds
boolean[] running
java.net.Socket serverSocket
java.io.DataOutputStream toServer
java.io.DataInputStream fromServer
boolean alreadyReadGoodBye
java.lang.String message
int associatedTree
java.lang.String name
int argument
java.lang.String name
ADFContext context_proto
int onStack
int onSubstack
int inReserve
ADFContext[] stack
ADFContext[] substack
ADFContext[] reserve
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
java.lang.String name
java.util.Hashtable<K,V> nodes_h
GPNode[][] nodes
java.util.Hashtable<K,V> nonterminals_h
GPNode[][] nonterminals
java.util.Hashtable<K,V> terminals_h
GPNode[][] terminals
java.util.Hashtable<K,V> nodesByName
GPNode[][][] nodesByArity
GPNode[][][] nonterminalsUnderArity
GPNode[][][] nonterminalsOverArity
GPTree[] trees
java.util.Hashtable<K,V> typeRepository
GPType[] types
int numAtomicTypes
int numSetTypes
java.util.Hashtable<K,V> nodeConstraintRepository
GPNodeConstraints[] nodeConstraints
byte numNodeConstraints
java.util.Hashtable<K,V> functionSetRepository
java.util.Hashtable<K,V> treeConstraintRepository
GPTreeConstraints[] treeConstraints
byte numTreeConstraints
GPNodeParent parent
GPNode[] children
byte argposition
byte constraints
int minSize
int maxSize
double[] sizeDistribution
double probabilityOfSelection
byte constraintNumber
GPType returntype
GPType[] childtypes
java.lang.String name
GPNode[] zeroChildren
GPNode node
int[] types_packed
boolean[] types_sparse
java.util.Hashtable<K,V> types_h
GPNode child
GPIndividual owner
byte constraints
int printStyle
boolean printTerminalsAsVariablesInC
boolean printTwoArgumentNonterminalsAsOperatorsInC
java.lang.String name
byte constraintNumber
GPNodeBuilder init
GPType treetype
GPFunctionSet functionset
java.lang.String name
int type
GPNodeSelector nodeselect0
GPNodeSelector nodeselect1
int numTries
int maxDepth
int tree1
int tree2
GPNodeSelector nodeselect
int tree
int numTries
int maxDepth
int tree
GPNode demotableNode
GPNodeSelector nodeselect
int tree
GPNodeSelector nodeselect
int tree
int tree
int numTries
GPNode promotableNode
int numTries
int tree
GPNode swappableNode
int numTries
int tree
GPNode rehangableNode
GPNodeSelector nodeselect1
GPNodeSelector nodeselect2
int tree1
int tree2
int numTries
int maxDepth
boolean tossSecondParent
java.util.ArrayList<E> parents
boolean homologous
int maxDepth
int expectedSize
double[][] q_ty
double[][] q_ny
double[][] p_y
int[] arities
boolean aritySetupDone
java.util.LinkedList<E> permutations
GPFunctionSet[] functionsets
java.util.Hashtable<K,V> _functionsets
java.util.Hashtable<K,V> funcnodes
int numfuncnodes
int maxarity
int maxtreesize
java.math.BigInteger[][][] _truesizes
double[][][] truesizes
boolean useTrueDistribution
java.math.BigInteger[][][] NUMTREESOFTYPE
java.math.BigInteger[][][] NUMTREESROOTEDBYNODE
java.math.BigInteger[][][][][] NUMCHILDPERMUTATIONS
ec.gp.build.UniformGPNodeStorage[][][][] ROOT_D
boolean[][][] ROOT_D_ZERO
double[][][][][] CHILD_D
GPProblem problem
GPSpecies gpspecies
java.util.HashMap<K,V> ERCBank
GrammarRuleNode[] grammar
int passes
java.lang.String initScheme
GrammarParser parser_prototype
GrammarParser[] grammarParser
GPNode prototype
java.lang.String head
java.util.ArrayList<E> children
java.util.HashMap<K,V> rules
GrammarRuleNode root
java.util.ArrayList<E> productionRuleList
java.util.HashMap<K,V> indexToRule
java.util.HashMap<K,V> ruleToIndex
java.util.HashMap<K,V> functionHeadToIndex
java.util.HashMap<K,V> ruleHeadToIndex
java.util.HashMap<K,V> absIndexToRelIndex
java.util.HashMap<K,V> ruleToFirstSet
java.util.HashMap<K,V> ruleToFollowSet
java.util.HashMap<K,V> ruleToPredictSet
int[][] predictiveParseTable
GPNodeSelector nodeselect1
GPNodeSelector nodeselect2
int tree1
int tree2
int numTries
int maxDepth
int maxSize
boolean tossSecondParent
java.util.ArrayList<E> parents
double pickGrowProbability
int maxDepth
int minDepth
double standardizedFitness
int hits
double rootProbability
double terminalProbability
double nonterminalProbability
int nonterminals
int terminals
int nodes
boolean doDepth
long[][] totalDepthSoFarTree
long[][] totalSizeSoFarTree
long[][] totalSizeThisGenTree
long[][] totalDepthThisGenTree
GPNodeSelector nodeselect
GPNodeBuilder builder
int numTries
int maxDepth
int maxSize
boolean equalSize
int tree
GPNode[] dummy
java.lang.StringBuilder buffer
java.lang.String[] instructions
PushInstruction[] customInstructions
int[] indices
java.lang.String value
double[] referencePoint
double[] maxObjective
double[] minObjective
boolean[] maximize
double[] objectives
boolean silentFront
boolean doHypervolume
double[] referencePoint
int frontLog
boolean warned
NSGA2Breeder.BreedingState breedingState
int[] numElites
Population oldPopulation
int rank
double sparsity
int k
boolean normalize
SPEA2Breeder.BreedingState breedingState
Population oldPopulation
double strength
double kthNNDistance
double fitness
double weight
NEATNode inNode
NEATNode outNode
int inNodeId
int outNodeId
boolean isRecurrent
boolean timeDelay
int innovationNumber
double mutationNumber
boolean enable
boolean frozen
double adjustedFitness
NEATSubspecies subspecies
double expectedOffspring
int generation
boolean eliminate
boolean champion
int superChampionOffspring
boolean popChampion
boolean popChampionChild
double highFit
int timeAlive
java.util.ArrayList<E> nodes
int innovationType
int inNodeId
int outNodeId
int innovationNum1
int innovationNum2
double newWeight
int newNodeId
int oldInnovationNum
boolean recurFlag
NEATIndividual individual
java.util.ArrayList<E> nodes
java.util.ArrayList<E> inputs
java.util.ArrayList<E> outputs
int activationCount
double lastActivation
double previousLastActivation
boolean override
double overrideValue
boolean frozen
NEATNode.FunctionType functionType
NEATNode.NodeType type
NEATNode.NodePlace geneticNodeLabel
double activeSum
double activation
boolean activeFlag
java.util.ArrayList<E> incomingGenes
int nodeId
int innerLevel
boolean isTraversed
NEATNode nodePrototype
NEATNetwork networkPrototype
NEATSubspecies subspeciesPrototype
NEATInnovation innovationPrototype
int currNodeId
int currInnovNum
double highestFitness
int highestLastChanged
double weightMutationPower
double disjointCoeff
double excessCoeff
double mutDiffCoeff
double compatThreshold
double ageSignificance
double survivalThreshold
double mutateOnlyProb
double mutateLinkWeightsProb
double mutateToggleEnableProb
double mutateGeneReenableProb
double mutateAddNodeProb
double mutateAddLinkProb
double interspeciesMateRate
double mateMultipointProb
double mateMultipointAvgProb
double mateSinglepointProb
double mateOnlyProb
double recurOnlyProb
int dropoffAge
int newLinkTries
int newNodeTries
int babiesStolen
int maxNetworkDepth
int addNodeMaxGenomeLength
Parameter base
java.util.ArrayList<E> subspecies
java.util.HashMap<K,V> innovations
java.lang.Object innoLock
int age
int ageOfLastImprovement
double maxFitnessEver
java.util.ArrayList<E> individuals
java.util.ArrayList<E> newGenIndividuals
int expectedOffspring
int size
boolean pickWorst
int nBuckets
int[] bucketValues
int size
int size2
double probabilityOfSelection
double probabilityOfSelection2
boolean pickWorst
boolean pickWorst2
boolean doLengthFirst
double fitnessPressureProb
int size
boolean pickWorst
double ratio
int[] bucketValues
double killProportion
int neighborhood
double velCoeff
double personalCoeff
double informantCoeff
double globalCoeff
int neighborhoodSize
boolean includeSelf
double[][] globalBest
Fitness[] globalBestFitness
byte constraints
byte constraintNumber
java.lang.String name
RuleSet[] rulesets
java.util.Hashtable<K,V> ruleConstraintRepository
RuleConstraints[] ruleConstraints
byte numRuleConstraints
java.util.Hashtable<K,V> ruleSetConstraintRepository
RuleSetConstraints[] ruleSetConstraints
byte numRuleSetConstraints
byte constraints
Rule[] rules
int numRules
int minSize
int maxSize
int resetMinSize
int resetMaxSize
double[] sizeDistribution
double p_add
double p_del
double p_randorder
Rule rulePrototype
byte constraintNumber
java.lang.String name
boolean tossSecondParent
double ruleCrossProbability
java.util.ArrayList<E> parents
boolean cache
int best
double temperature
double t
double cutdown
int size
double probabilityOfPickingSizePlusOne
boolean pickWorst
int[] sortedPop
int bestn
double bestnFrac
double startingTemperature
double coolingRate
double[] fitnesses
double[] sortedFitOver
double[] sortedFitUnder
int[] sortedPop
double top_n_percent
double gets_n_percent
SelectionMethod[] selects
double fitnessFloor
int[] indices
double[] fitnesses
boolean shuffle
double offset
int lastIndex
int steps
boolean cache
int best
int size
double probabilityOfPickingSizePlusOne
boolean pickWorst
int[] elite
double[] eliteFrac
boolean[] reevaluateElites
boolean sequentialBreeding
boolean clonePipelineAndPopulation
Population backupPopulation
java.util.ArrayList<E>[][] newIndividuals
ThreadPool pool
int numTests
int mergeForm
boolean cloneProblem
java.lang.Object[] lock
int individualCounter
int subPopCounter
int chunkSize
ThreadPool pool
Population oldpop
double fitness
boolean isIdeal
int statisticslog
int modulus
java.lang.String delimiter
boolean doSize
boolean doTime
boolean doSubpops
boolean doHeader
Individual[] bestSoFar
long[] totalSizeSoFar
long[] totalIndsSoFar
long[] totalIndsThisGen
long[] totalSizeThisGen
double[] totalFitnessThisGen
Individual[] bestOfGeneration
long lastTime
int statisticslog
Individual[] best_of_run
boolean compress
boolean doFinal
boolean doGeneration
boolean doMessage
boolean doDescription
boolean doPerGenerationDescription
boolean warned
boolean toroidal
int[] indexes
int neighborhoodSize
boolean indCompetes
int type
Individual ind
int subpop
BreedingSource[] bp
SelectionMethod[] deselectors
java.util.LinkedList<E> queue
int subpopulationBeingEvaluated
SimpleProblemForm problem
boolean generationBoundary
int generationSize
double replacementProbability
boolean emptyAtGenerationBoundary
java.util.HashMap<K,V>[] individualHash
int whichSubpop
boolean firstTime
int[] objs
int numObjs
boolean silent
java.io.File filename
boolean postAnnouncements
LogRestarter restarter
boolean repostAnnouncementsOnRestart
boolean appendOnRestart
boolean isLoggingToSystemOut
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
int[] mt
int mti
int[] mag01
double __nextNextGaussian
boolean __haveNextNextGaussian
int[] mt
int mti
int[] mag01
double __nextNextGaussian
boolean __haveNextNextGaussian
boolean errors
java.util.Vector<E> logs
java.util.Vector<E> announcements
boolean store
java.lang.String filePrefix
boolean throwsErrors
java.lang.StringBuilder error
java.util.HashSet<E> oneTimeWarnings
java.lang.String param
int printState
java.lang.String label
java.util.Vector<E> parents
java.io.File directory
boolean checked
java.util.Hashtable<K,V> gotten
java.util.Hashtable<K,V> accessed
java.lang.Class<T> relativeClass
java.lang.String relativePath
java.util.Properties properties
Parameter parameter
java.lang.String value
int type
boolean visibleLeaves
private void readObject(java.io.ObjectInputStream stream) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream stream) throws java.io.IOException
java.io.IOException
java.util.LinkedList<E> workers
java.lang.Object workersLock
int totalWorkers
boolean[] genome
int[] mutationType
byte[] genome
double[] genome
float[] genome
double[] minGene
double[] maxGene
int[] mutationType
double[] gaussMutationStdev
boolean[] mutationIsBounded
boolean mutationIsBoundedDefined
int[] mutationDistributionIndex
boolean[] polynomialIsAlternative
boolean polynomialIsAlternativeDefined
double[] randomWalkProbability
int outOfBoundsRetries
Gene[] genome
Gene genePrototype
int[] genome
long[] minGene
long[] maxGene
int[] mutationType
double[] randomWalkProbability
boolean[] mutationIsBounded
boolean mutationIsBoundedDefined
long[] genome
short[] genome
int[] duplicateRetries
double[] mutationProbability
double crossoverProbability
int crossoverType
int genomeSize
int crossoverDistributionIndex
int genomeResizeAlgorithm
int minInitialSize
int maxInitialSize
double genomeIncreaseProbability
int chunksize
double lineDistance
boolean dynamicInitialSize
boolean tossSecondParent
int crossoverType
int minChildSize
int numTries
double minCrossoverPercentage
double maxCrossoverPercentage
java.util.ArrayList<E> parents
java.util.ArrayList<E> parents
boolean tossSecondParent
java.util.ArrayList<E> parents