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
String runComplete
ParameterDatabase parameters
MersenneTwisterFast[] random
HashMap<K,V>[] data
Output output
int breedthreads
int evalthreads
boolean checkpoint
File checkpointDirectory
String checkpointPrefix
int checkpointModulo
int randomSeedOffset
boolean quitOnRunComplete
Object[] job
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
Object[] lock
ArrayList<E> trials
Individual[] context
Individual i_prototype
BreedingSource pipe_prototype
Fitness f_prototype
Statistics[] children
boolean silentFile
boolean silentPrint
boolean loadInds
Parameter file
Species species
IntBag[] parents
ArrayList<E> individuals
int initialSize
int numDuplicateRetries
int extraBehavior
boolean warned
int maxMoves
int food
int[][] map
int[] foodx
int[] foody
int maxx
int maxy
int posx
int posy
int sum
int orientation
int moves
int pmod
String[] problemTypes
String[] noiseTypes
int problemType
int noise
boolean reevaluateNoisyProblems
boolean zeroIsBest
double fOpt
double[] xOpt
double fAdd_Init
double f0
double[][] rotation
double[][] rot2
double[][] linearTF
double[] peaks21
double[] peaks22
int[] rperm
int[] rperm21
int[] rperm22
double[][] xLocal
double[][] xLocal21
double[][] xLocal22
double[][] arrScales
double[][] arrScales21
double[][] arrScales22
double[] aK
double[] bK
double[] peakvalues
double scales
int MAX_STEPS
double x
double x_dot
double theta
double theta_dot
int steps
int y
boolean shouldSetContext
int problemType
long seed
boolean alreadyChecked
double[][] afox10
double[] cfox10
boolean[] start
boolean[] accept
int numNodes
int[] from
int[] to
int[] reading
int numEdges
int[][] reading1
int[] reading1_l
int[][] reading0
int[] reading0_l
int[][] epsilon
int[] epsilon_l
boolean[][] posT
boolean[][] negT
boolean[][] posA
boolean[][] negA
boolean[] state1
boolean[] state2
boolean generalize
int totpos
int totneg
int edge
String problemName
int problemSize
char value
int index
int[] seriesID
int[] seriesID
int K
int P
int Rc
int[][] map
int maxx
int maxy
int posx
int posy
int sum
int orientation
int moves
int pmod
int x
int y
int maxx
int maxy
int x
int y
int maxWeight
int targetDepth
int targetTerminals
int actualDepth
int actualTerminals
int weightDepth
int weightTerminals
int[] ca
int[] ca2
int[] rule
int neighborhood
long data0
long data1
Individual best_of_run
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
IOException
ClassNotFoundException
private void writeObject(ObjectOutputStream out) throws IOException
IOException
BufferedImage original
BufferedImage image
Graphics graphics
int[] xpoints
int[] ypoints
int count
int problemType
int bits
Stack<E> tmp
long[] dat_11
long dat_6
byte dat_3
byte status
int bits
int amax
int dmax
int addressPart
int dataPart
int x
double fitness
int fitnessContributionType
boolean doEven
int numBits
int totalSize
int bits
int x
int trainingSetSize
boolean useFunction
double[] inputs
double[] outputs
int maxSteps
double[] currentValue
double[][] trainingInputs
double[] trainingOutputs
double[][] testingInputs
double[] testingOutputs
double currentValue
int trainingSetSize
boolean useFunction
double[] inputs
double[] outputs
double x
double value
char[] successors
SAT.Clause[] formula
int[] variables
boolean allowCycles
TSPGraph graph
int popLog
int infoLog
double middleProbability
double x
double currentX
double currentY
int currentIndex
int trainingSetSize
int range
double[] inputsl0
double[] inputsw0
double[] inputsh0
double[] inputsl1
double[] inputsw1
double[] inputsh1
double[] outputs
double x
int numTimes
boolean firstTime
int numInds
int maxGeneratable
boolean generateMax
int generationSwitch
int maxGeneratable
boolean generateMax
Individual individual
IntBag parents
BreedingSource stubPipeline
double rho
double minimumPheromone
ConstructionRule constructionRule
PheromoneTable pheromones
UpdateRule updateRule
UpdateRule localUpdateRule
double decayRate
AntSystemUpdateRule.DepositRule depositRule
double q
GlobalUpdateRule.BestStrategy bestStrategy
double rho
ConstructiveIndividual<T extends Component> best
double alpha
double beta
double probBest
ProportionateComponentSelector proportionateSelector
String startComponent
ComponentSelector selector
ConstructionRule constructionRule
String startComponent
ComponentSelector selector
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
Thread playThread
boolean playing
boolean paused
Object buttonLock
Object cleanupLock
int currentJob
String[] clArgs
JPanel jContentPane
JMenuBar jJMenuBar
JMenu fileMenu
JMenu helpMenu
JMenuItem exitMenuItem
JMenuItem aboutMenuItem
JTabbedPane jTabbedPane
JToolBar jToolBar
JButton playButton
JButton pauseButton
JButton stopButton
JButton stepButton
JMenuItem loadParametersMenuItem
ParametersPanel paramPanel
ControlPanel conPanel
JFrame aboutFrame
boolean threadIsToStop
boolean _step
int result
JMenuItem loadCheckpointMenuItem
JTabbedPane statisticsPane
JTabbedPane inspectionPane
JPanel statusPane
JTextField statusField
Console console
JLabel jLabel
JTextField numGensField
JCheckBox quitOnRunCompleteCheckbox
JLabel jLabel1
JTextField numJobsField
JLabel jLabel2
JLabel jLabel3
JTextField evalThreadsField
JTextField breedThreadsField
JPanel jPanel
JRadioButton seedFileRadioButton
JTextField seedFileField
JButton seedFileButton
JRadioButton randomSeedsRadioButton
JTable seedsTable
JScrollPane jScrollPane
JLabel jLabel6
JCheckBox checkpointCheckBox
JPanel checkpointPanel
JLabel jLabel7
JTextField checkpointModuloField
JLabel jLabel8
JTextField prefixField
JLabel jLabel10
ButtonGroup seedButtonGroup
JButton generateSeedsButton
JRadioButton sequentialSeedsRadioButton
JLabel jLabel5
JTextField jobFilePrefixField
Console console
JScrollPane parameterTreeScrollPane
JTree parameterTree
JScrollPane parameterTableScrollPane
JTable parameterTable
JSplitPane jSplitPane
int numCharts
Console console
int subPopNum
JList<E> individualsList
JScrollPane individualListPane
JSplitPane subpopPane
JSplitPane individualDisplayPane
IndividualPortrayal portrayal
JScrollPane inspectionPane
JTree inspectionTree
org.jfree.data.category.DefaultCategoryDataset dataset
org.jfree.data.xy.XYSeriesCollection seriesCollection
JTextPane textPane
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
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
ArrayList<E> visited
HashMap<K,V> visitedIndexMap
ArrayList<E> corners
ArrayList<E> activeSolutions
ArrayList<E> Ek
boolean stochastic
int initialReps
int repetition
long numOfTotalSamples
ArrayList<E> A
double[] b
int[] mu
int[] lambda
Population parentPopulation
byte[] comparison
ArrayList<E>[][] newIndividuals
int[] count
int[] children
int[] parents
Parameter base
ParameterDatabase p_database
ParameterDatabase currentDatabase
int runs
boolean reevaluateIndividuals
Individual[] bestUnderlyingIndividual
Object lock
Object[] domain
boolean setRandom
int countdown
int upperbound
int start
String restartType
Parameter base
InterPopulationExchange.IPEInformation[] exchangeInformation
Individual[][] immigrants
int[] nImmigrants
int nrSources
boolean chatty
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
IOException
ClassNotFoundException
private void writeObject(ObjectOutputStream out) throws IOException
IOException
boolean chatty
Thread serverThread
Parameter base
String serverAddress
int serverPort
int clientPort
boolean iAmServer
String ownId
boolean compressedCommunication
SelectionMethod immigrantsSelectionMethod
SelectionMethod indsToDieSelectionMethod
IslandExchangeMailbox mailbox
Thread mailboxThread
int number_of_destination_islands
boolean synchronous
int modulo
int offset
int size
Socket[] outSockets
DataOutputStream[] outWriters
String[] outgoingIds
boolean[] running
Socket serverSocket
DataOutputStream toServer
DataInputStream fromServer
boolean alreadyReadGoodBye
String message
int associatedTree
String name
int argument
String name
ADFContext context_proto
int onStack
int onSubstack
int inReserve
ADFContext[] stack
ADFContext[] substack
ADFContext[] reserve
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
IOException
ClassNotFoundException
private void writeObject(ObjectOutputStream out) throws IOException
IOException
String name
Hashtable<K,V> nodes_h
GPNode[][] nodes
Hashtable<K,V> nonterminals_h
GPNode[][] nonterminals
Hashtable<K,V> terminals_h
GPNode[][] terminals
Hashtable<K,V> nodesByName
GPNode[][][] nodesByArity
GPNode[][][] nonterminalsUnderArity
GPNode[][][] nonterminalsOverArity
GPTree[] trees
Hashtable<K,V> typeRepository
GPType[] types
int numAtomicTypes
int numSetTypes
Hashtable<K,V> nodeConstraintRepository
GPNodeConstraints[] nodeConstraints
byte numNodeConstraints
Hashtable<K,V> functionSetRepository
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
String name
GPNode[] zeroChildren
GPNode node
GPNode child
GPIndividual owner
byte constraints
int printStyle
boolean printTerminalsAsVariablesInC
boolean printTwoArgumentNonterminalsAsOperatorsInC
String name
byte constraintNumber
GPNodeBuilder init
GPType treetype
GPFunctionSet functionset
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
ArrayList<E> parents
boolean homologous
int maxDepth
int expectedSize
double[][] q_ty
double[][] q_ny
double[][] p_y
int[] arities
boolean aritySetupDone
LinkedList<E> permutations
GPFunctionSet[] functionsets
Hashtable<K,V> _functionsets
Hashtable<K,V> funcnodes
int numfuncnodes
int maxarity
int maxtreesize
BigInteger[][][] _truesizes
double[][][] truesizes
boolean useTrueDistribution
BigInteger[][][] NUMTREESOFTYPE
BigInteger[][][] NUMTREESROOTEDBYNODE
BigInteger[][][][][] NUMCHILDPERMUTATIONS
UniformGPNodeStorage[][][][] ROOT_D
boolean[][][] ROOT_D_ZERO
double[][][][][] CHILD_D
GPProblem problem
GPSpecies gpspecies
HashMap<K,V> ERCBank
GrammarRuleNode[] grammar
int passes
String initScheme
GrammarParser parser_prototype
GrammarParser[] grammarParser
GPNode prototype
HashMap<K,V> rules
GrammarRuleNode root
ArrayList<E> productionRuleList
HashMap<K,V> indexToRule
HashMap<K,V> ruleToIndex
HashMap<K,V> functionHeadToIndex
HashMap<K,V> ruleHeadToIndex
HashMap<K,V> absIndexToRelIndex
HashMap<K,V> ruleToFirstSet
HashMap<K,V> ruleToFollowSet
HashMap<K,V> ruleToPredictSet
int[][] predictiveParseTable
GPNodeSelector nodeselect1
GPNodeSelector nodeselect2
int tree1
int tree2
int numTries
int maxDepth
int maxSize
boolean tossSecondParent
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
StringBuilder buffer
String[] instructions
PushInstruction[] customInstructions
int[] indices
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
ArrayList<E> nodes
int innovationType
int inNodeId
int outNodeId
int innovationNum1
int innovationNum2
double newWeight
int newNodeId
int oldInnovationNum
boolean recurFlag
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
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
ArrayList<E> subspecies
HashMap<K,V> innovations
Object innoLock
int age
int ageOfLastImprovement
double maxFitnessEver
ArrayList<E> individuals
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
String name
RuleSet[] rulesets
Hashtable<K,V> ruleConstraintRepository
RuleConstraints[] ruleConstraints
byte numRuleConstraints
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
String name
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
ArrayList<E>[][] newIndividuals
ThreadPool pool
int numTests
int mergeForm
boolean cloneProblem
Object[] lock
int individualCounter
int subPopCounter
int chunkSize
ThreadPool pool
Population oldpop
double fitness
boolean isIdeal
int statisticslog
int modulus
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[] elite
int[] expandedSubpopSize
boolean[] stubsFilled
int statisticsModulo
int exchangeModulo
boolean toroidal
int[] indexes
int neighborhoodSize
boolean indCompetes
int type
Individual ind
int subpop
BreedingSource[] bp
SelectionMethod[] deselectors
LinkedList<E> queue
int subpopulationBeingEvaluated
SimpleProblemForm problem
boolean generationBoundary
int generationSize
double replacementProbability
boolean emptyAtGenerationBoundary
HashMap<K,V>[] individualHash
int whichSubpop
boolean firstTime
int[] objs
int numObjs
boolean silent
File filename
boolean postAnnouncements
LogRestarter restarter
boolean repostAnnouncementsOnRestart
boolean appendOnRestart
boolean isLoggingToSystemOut
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException
IOException
ClassNotFoundException
private void writeObject(ObjectOutputStream out) throws IOException
IOException
int[] mt
int mti
int[] mag01
double __nextNextGaussian
boolean __haveNextNextGaussian
int[] mt
int mti
int[] mag01
double __nextNextGaussian
boolean __haveNextNextGaussian
String param
boolean visibleLeaves
private void readObject(ObjectInputStream stream) throws IOException, ClassNotFoundException
IOException
ClassNotFoundException
private void writeObject(ObjectOutputStream stream) throws IOException
IOException
LinkedList<E> workers
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
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