APPENDIX A – Public class and method listing

This appendix lists all public classes and methods needed to make full use of the algorithms provided. It is not a full listing of all classes or the methods they provide.

1. networkPackage

public class AllButOne extends ConnectivityPattern implements Serializable

public AllButOne(int _numNodeToBeLeftOut)

public ConnectivityPattern copy()

public class BackPropagation extends FFLNTrainingAlgorithm implements Serializable

public BackPropagation(double _constant, DoubleFunction _function)

public BackPropagation(DoubleFunction _function)

public BackPropagation(double _constant)

public BackPropagation()

public void setConstant(double _constant)

public double getConstant()

public void setFunction(DoubleFunction _function)

public DoubleFunction getFunction()

public void trainNetwork(FeedForwardLayeredNetwork _network, double [][] _inputs, double [][] _desiredOutputs, int _numEpochs)

public void setMonitor(BackPropagationMonitor _monitor)

public BackPropagationMonitor getMonitor()

public FFLNTrainingAlgorithm copy()

public class DifferentiatedSigmoid extends DoubleFunction implements Serializable

public DifferentiatedSigmoid()

public DifferentiatedSigmoid(double _scalingConstant)

public DoubleFunction copy()

public class DivideFunction extends Function implements Serializable

public Function copy()

public class ErrorAdjust extends MNTrainingAlgorithm implements Serializable

public ErrorAdjust(double _constant)

public ErrorAdjust()

public void setConstant(double _constant)

public void trainNetwork(ModularNetwork _network, double [][] _inputs, double [][] _desiredOutputs, int _numEpochs)

public MNTrainingAlgorithm copy()

public void setMonitor(ErrorAdjustMonitor _monitor)

public ErrorAdjustMonitor getMonitor()

public class ExponentialFunction extends Function implements Serializable

public Function copy()

public class FeedForwardLayeredNetwork extends Network implements Serializable

public FeedForwardLayeredNetwork(int _numInputs, int [] _numNodesPerHiddenLayer, Function [][] _nodesFunction, ConnectivityPattern [][] _nodesConnectivityPattern, int _numOutputs, Function [] _outputsFunction, ConnectivityPattern [] _outputsConnectivityPattern, FFLNTrainingAlgorithm _trainingAlgorithm)

public FeedForwardLayeredNetwork(int _numInputs, int [] _numNodesPerHiddenLayer, Function [] _nodesFunction, ConnectivityPattern [] _nodesConnectivityPattern, int _numOutputs, Function _outputsFunction, ConnectivityPattern _outputsConnectivityPattern, FFLNTrainingAlgorithm _trainingAlgorithm)

public FeedForwardLayeredNetwork(int _numInputs, int [] _numNodesPerHiddenLayer, int _numOutputs, Function _function, ConnectivityPattern _connectivityPattern, FFLNTrainingAlgorithm _trainingAlgorithm)

public FeedForwardLayeredNetwork(int _numInputs, int [] _numNodesPerHiddenLayer, int _numOutputs, ConnectivityPattern _connectivityPattern)

public FeedForwardLayeredNetwork(int _numInputs, int _numOutputs)

public int getNumberOfInputs()

public int getNumberOfOutputs()

public int getNumberOfLayers()

public int getNumberOfNodes()

public int getNumberOfActiveNodes()

public int getNumberOfNodesInLayer(int _layerNumber)

public int getNumberOfActiveNodesInLayer(int _layerNumber)

public double [] getNetworkOutput(double [] inputValues)

public double [] getOutputActivations()

public double getOutputActivation(int _outputNumber)

public double getNodeActivation(int _layerNumber, int _nodeNumber)

public void insertLayerAt(int _insertPosition)

public void addLayer()

public void removeLayer(int _layerNumber)

public int [] getInputConnectionsToLayerAbove(int _inputNumber)

public boolean nodeActive(int _layerNumber, int _nodeNumber)

public void activateNode(int _layerNumber, int _nodeNumber)

public void deactivateNode(int _layerNumber, int _nodeNumber)

public void addNode(int layerNumber, Function function, ConnectivityPattern _connectivityPattern)

public void addNode(int layerNumber, ConnectivityPattern _connectivityPattern)

public void addNode(int layerNumber, Function function)

public void addNode(int layerNumber)

public void addNode(Function function, ConnectivityPattern _connectivityPattern)

public void addNode(Function function)

public void removeNode(int _layerNumber, int _nodeNumber)

public Function copyHiddenNodeFunction(int _layerNumber, int _nodeNumber)

public int [] getHiddenNodeConnectionsToLayerAbove(int _layerNumber, int _nodeNumber)

public ConnectivityPattern copyHiddenNodeConnectivityPattern(int _layerNumber, int _nodeNumber)

void setHiddenNodeConnectivityPattern(int _layerNumber, int _nodeNumber, ConnectivityPattern _pattern)

public int getNumberOfHiddenNodeConnections(int _layerNumber, int _nodeNumber)

public int [] getHiddenNodeConnections(int _layerNumber, int _nodeNumber)

public void setHiddenNodeConnections(int _layerNumber, int _nodeNumber, int [] connections)

public int getHiddenNodeConnection(int _layerNumber, int _nodeNumber, int _connectionNumber)

public void addConnectionToHiddenNode(int _layerNumber, int _nodeNumber, int connection)

public boolean removeConnectionFromHiddenNode(int _layerNumber, int _nodeNumber, int _connectionNumber)

public double [] getHiddenNodeWeights(int _layerNumber, int _nodeNumber)

public boolean setHiddenNodeWeights(int _layerNumber, int _nodeNumber, double [] weights)

public double getHiddenNodeWeight(int _layerNumber, int _nodeNumber, int _connectionNumber)

public boolean setHiddenNodeWeight(int _layerNumber, int _nodeNumber, int _connectionNumber, double _weight)

public double getHiddenNodeThreshold(int _layerNumber, int _nodeNumber)

public void setHiddenNodeThreshold(int _layerNumber, int _nodeNumber, double _threshold)

public Function copyOutputFunction(int _outputNumber)

public ConnectivityPattern copyOutputConnectivityPattern(int _outputNumber)

public void setOutputConnectivityPattern(int _outputNumber, ConnectivityPattern _pattern)

public int getNumberOfOutputConnections(int _outputNumber)

public int [] getOutputConnections(int _outputNumber)

public void setOutputConnections(int _outputNumber, int [] _connections)

public int getOutputConnection(int _outputNumber, int _connectionNumber)

public void addConnectionToOutputNode(int _outputNumber, int _connection)

public boolean removeConnectionFromOutputNode(int _outputNumber, int _connectionNumber)

public double [] getOutputWeights(int _outputNumber)

public boolean setOutputWeights(int _outputNumber, double [] _weights)

public double getOutputWeight(int _outputNumber, int _connectionNumber)

public double getOutputThreshold(int _outputNumber)

public void setOutputThreshold(int _outputNumber, double _threshold)

public void train(double [][] _inputs, double [][] _desiredOutputs, int _numEpochs)

public void setTrainingAlgorithm(FFLNTrainingAlgorithm algorithm)

public FFLNTrainingAlgorithm copyTrainingAlgorithm()

public void setMonitor(FeedForwardLayeredNetworkMonitor _monitor)

public FeedForwardLayeredNetworkMonitor getMonitor()

public class FullConnectivity extends ConnectivityPattern implements Serializable

public ConnectivityPattern copy()

public class ModularNetwork extends Network implements Serializable

public ModularNetwork(int _numInputs, int _numOutputs, Network [] _networks, MNTrainingAlgorithm _trainingAlgorithm)

public ModularNetwork(int _numInputs, int _numOutputs, Network [] _networks)

public double [] getNetworkOutput(double [] _inputs)

public int getNumberOfInputs()

public int getNumberOfOutputs()

public int getNumberOfNetworkModules()

public Network getNetworkModule(int _networkNumber)

public Network [] getNetworkModules()

public void addNetworkModule(Network network)

public void removeNetworkModule(int _networkNumber)

public double [] getWeightsOfSoftmaxNode(int _nodeNumber)

public void setWeightsOfSoftmaxNode(int _nodeNumber, double [] _weights)

public double [] getModuleWeights(double [] _inputs)

public double [] getModuleWeights()

public double getModuleWeight(int _numModule, double [] _inputs)

public double getModuleWeight(int _numModule)

public void setTrainingAlgorithm(MNTrainingAlgorithm algorithm)

public MNTrainingAlgorithm getTrainingAlgorithm()

public void train(double [][] _inputs, double [][] _desiredOutputs, int _numEpochs)

public void setMonitor(ModularNetworkMonitor _monitor)

public ModularNetworkMonitor getMonitor()

public class NullFunction extends Function implements Serializable

public Function copy()

public class OnlyOne extends ConnectivityPattern implements Serializable

public OnlyOne(int _numOfOnlyNode)

public ConnectivityPattern copy()

public class OnlySome extends ConnectivityPattern implements Serializable

public OnlySome(int [] theOnes)

public ConnectivityPattern copy()

public class PatternFileReader

public double [][] convertFile(int _numPatterns, int _numElements, String _filename) throws FileNotFoundException, IOException

public double [][] convertFile(int _numPatterns, int _numElements, File _file) throws FileNotFoundException, IOException

public class SigmoidFunction extends Function implements Serializable

public SigmoidFunction(double _scalingConstant)

public SigmoidFunction()

public Function copy()

public class SoftMaxFunction extends Function implements Serializable

public Function copy()

public class SumFunction extends Function implements Serializable

public Function copy()

public class UserDefinedConnectivity extends ConnectivityPattern implements Serializable

public UserDefinedConnectivity()

public ConnectivityPattern copy()

public class WinnerTakesAll extends MNTrainingAlgorithm implements Serializable

public WinnerTakesAll(double _memoryConstant, double _improvConstant, double _adjustConstant)

public WinnerTakesAll()

public void setConstants(double _memoryConstant, double _improvConstant, double _adjustConstant)

public void trainNetwork(ModularNetwork _network, double [][] _inputs, double [][] _desiredOutputs, int _numEpochs)

public MNTrainingAlgorithm copy()

public void setMonitor(WinnerTakesAllMonitor _monitor)

public WinnerTakesAllMonitor getMonitor()

2. breederPackage

public class CrossoverOperation1 extends CrossoverOperation

public void setMonitor(CrossoverOperation1Monitor _monitor)

public CrossoverOperation1Monitor getMonitor()

public class FFLNBreeder

public FFLNBreeder(FeedForwardLayeredNetwork [] _initialPopulation, CrossoverOperation _crossoverOp, FitnessEvaluator _fitnessOp, SelectionAlgorithm _selectionOp, MutationAlgorithm _mutationOp)

public FFLNBreeder(int _numInputs, int _numOutputs, int _size, int _maxNumLayers, int _maxNumNodesPerLayer, CrossoverOperation _crossoverOp, FitnessEvaluator _fitnessOp, SelectionAlgorithm _selectionOp, MutationAlgorithm _mutationOp)

public int getNumberOfInputs()

public int getNumberOfOutputs()

public int getPopulationSize()

public FeedForwardLayeredNetwork breed(int _numEpochs, double _fitnessThreshold, int _percentageReplaced, int _mutationRate, double [][] _evaluationInputs, double [][] _evaluationOutputs)

public FeedForwardLayeredNetwork [] getPopulation()

public FeedForwardLayeredNetwork getMember(int _networkNumber)

public FeedForwardLayeredNetwork getBestNetwork()

public int bestMember()

public double getMembersFitness(int _networkNumber)

public double [] getMembersFitnesses()

public MutationAlgorithm getMutationAlgorithm()

public void setMutationAlgorithm(MutationAlgorithm _op)

public CrossoverOperation getCrossoverOperation()

public void setCrossoverOperation(CrossoverOperation _op)

public FitnessEvaluator getFitnessEvaluator()

public void setFitnessEvaluator(FitnessEvaluator _evaluator)

public SelectionAlgorithm getSelectionAlgorithm()

public void setSelectionAlgorithm(SelectionAlgorithm _algorithm)

public void setMonitor(FFLNBreederMonitor _monitor)

public FFLNBreederMonitor getMonitor()

public class FitnessProportionate extends SelectionAlgorithm

public void setMonitor(FitnessProportionateMonitor _monitor)

public FitnessProportionateMonitor getMonitor()

public class InverseErrorEvaluator extends FitnessEvaluator

public InverseErrorEvaluator(double _power)

public void setMonitor(InverseErrorEvaluatorMonitor _monitor)

InverseErrorEvaluatorMonitor getMonitor()

public class LinearEvaluator extends InverseErrorEvaluator

public LinearEvaluator()

public class ModularBreeder

public ModularBreeder(int _numInputs, int _numOutputs, int _numModNets, int _initialNumModules, int _maxNumLayers, int _maxNumNodesPerLayer)

public ModularNetwork breedModularNetwork(double [][] _inputs, double [][] _desiredOutputs, int _numModularEpochs, int _numBreederEpochs, double _desiredError, int _percentageImprovement, double _backpropStepConstant, double _memoryConstant, double _stepConstant, double _improvementConstant, int _percentageReplaced, int _percentageMutated)

public void setMonitor(ModularBreederMonitor _monitor)

public ModularBreederMonitor getMonitor()

public class MutateAll extends MutationAlgorithm

public void setMonitor(MutateAllMonitor _monitor)

public MutateAllMonitor getMonitor()

public class MutateAllButConnections extends MutationAlgorithm

public void setMonitor(MutateAllMonitor _monitor)

public MutateAllMonitor getMonitor()

public class MutateConnections extends MutationAlgorithm

public void setMonitor(MutateConnectionsMonitor _monitor)

public MutateConnectionsMonitor getMonitor()

public class MutateNodes extends MutationAlgorithm

public void setMonitor(MutateNodesMonitor _monitor)

public MutateNodesMonitor getMonitor()

public class NodeDeactivationMutation extends MutationAlgorithm

public void setMonitor(NodeDeactivationMutationMonitor _monitor)

public NodeDeactivationMutationMonitor getMonitor()

3. monitorPackage

public class BackPropagationMonitor extends ActivityMonitor

public BackPropagationMonitor(String _pathname) throws IOException

public BackPropagationMonitor()

public boolean monitorAll(boolean bool)

public boolean monitorEpochs(String _pathname) throws IOException

public boolean monitorEpochs(boolean bool)

public boolean monitorInputs(String _pathname) throws IOException

public boolean monitorInputs(boolean bool)

public boolean monitorOutputs(String _pathname) throws IOException

public boolean monitorOutputs(boolean bool)

public boolean monitorErrors(String _pathname) throws IOException

public boolean monitorErrors(boolean bool)

public boolean monitorWeights(String _pathname) throws IOException

public boolean monitorWeights(boolean bool)

public boolean monitorThresholds(String _pathname) throws IOException

public boolean monitorThresholds(boolean bool)

public boolean monitorNetworkErrors(String _pathname) throws IOException

public boolean monitorNetworkErrors(boolean bool)

public class CrossoverOperation1Monitor extends ActivityMonitor

public CrossoverOperation1Monitor(String _pathname) throws IOException

public CrossoverOperation1Monitor()

public boolean monitorAll(boolean bool)

public boolean monitorLayers(String _pathname) throws IOException

public boolean monitorLayers(boolean bool)

public boolean monitorCuts(String _pathname) throws IOException

public boolean monitorCuts(boolean bool)

public boolean monitorChildren(String _pathname) throws IOException

public boolean monitorChildren(boolean bool)

public class ErrorAdjustMonitor extends ModularTrainingMonitor

public ErrorAdjustMonitor(String _pathname) throws IOException

public ErrorAdjustMonitor()

public class FeedForwardLayeredNetworkMonitor extends ActivityMonitor

public FeedForwardLayeredNetworkMonitor(String _pathname) throws IOException

public FeedForwardLayeredNetworkMonitor()

public boolean monitorAll(boolean bool)

public boolean monitorLayers(String _pathname) throws IOException

public boolean monitorLayers(boolean bool)

public boolean monitorNodes(String _pathname) throws IOException

public boolean monitorNodes(boolean bool)

public boolean monitorWeights(String _pathname) throws IOException

public boolean monitorWeights(boolean bool)

public boolean monitorThresholds(String _pathname) throws IOException

public boolean monitorThresholds(boolean bool)

public class FFLNBreederMonitor extends ActivityMonitor

public FFLNBreederMonitor(String _pathname) throws IOException

public FFLNBreederMonitor()

public boolean monitorAll(boolean bool)

public boolean monitorGenerations(String _pathname) throws IOException

public boolean monitorGenerations(boolean bool)

public boolean monitorBest(String _pathname) throws IOException

public boolean monitorBest(boolean bool)

public boolean monitorFitness(String _pathname) throws IOException

public boolean monitorFitness(boolean bool)

public boolean monitorPopulation(String _pathname) throws IOException

public boolean monitorPopulation(boolean bool)

public boolean monitorNetworks(String _pathname) throws IOException

public boolean monitorNetworks(boolean bool)

public class FitnessProportionateMonitor extends ActivityMonitor

public FitnessProportionateMonitor(String _pathname) throws IOException

public FitnessProportionateMonitor()

public boolean monitorAll(boolean bool)

public class InverseErrorEvaluatorMonitor extends ActivityMonitor

public InverseErrorEvaluatorMonitor(String _pathname) throws IOException

public InverseErrorEvaluatorMonitor()

public boolean monitorAll(boolean bool)

public class ModularBreederMonitor extends ActivityMonitor

public ModularBreederMonitor(String _pathname) throws IOException

public ModularBreederMonitor()

public boolean monitorAll(boolean bool)

public boolean monitorCycles(String _pathname) throws IOException

public boolean monitorCycles(boolean bool)

public boolean monitorErrors(String _pathname) throws IOException

public boolean monitorErrors(boolean bool)

public class ModularNetworkMonitor extends ActivityMonitor

public ModularNetworkMonitor(String _pathname) throws IOException

public ModularNetworkMonitor()

public boolean monitorAll(boolean bool)

public boolean monitorModules(String _pathname) throws IOException

public boolean monitorModules(boolean bool)

public boolean monitorModuleWeights(String _pathname) throws IOException

public boolean monitorModuleWeights(boolean bool)

public boolean monitorWeights(String _pathname) throws IOException

public boolean monitorWeights(boolean bool)

public class ModularTrainingMonitor extends ActivityMonitor

public ModularTrainingMonitor(String _pathname) throws IOException

public boolean monitorAll(boolean bool)

public boolean monitorEpochs(String _pathname) throws IOException

public boolean monitorEpochs(boolean bool)

public boolean monitorInputs(String _pathname) throws IOException

public boolean monitorInputs(boolean bool)

public boolean monitorErrors(String _pathname) throws IOException

public boolean monitorErrors(boolean bool)

public boolean monitorSoftmaxWeights(String _pathname) throws IOException

public boolean monitorSoftmaxWeights(boolean bool)

public boolean monitorWinningNetworks(String _pathname) throws IOException

public boolean monitorWinningNetworks(boolean bool)

public boolean monitorAverageErrors(String _pathname) throws IOException

public boolean monitorAverageErrors(boolean bool)

public boolean monitorAverageWeights(String _pathname) throws IOException

public boolean monitorAverageWeights(boolean bool)

public class MutateAllMonitor extends ActivityMonitor

public MutateAllMonitor(String _pathname) throws IOException

public MutateAllMonitor()

public boolean monitorAll(boolean bool)

public boolean monitorLayers(String _pathname) throws IOException

public boolean monitorLayers(boolean bool)

public boolean monitorNodes(String _pathname) throws IOException

public boolean monitorNodes(boolean bool)

public boolean monitorConnections(String _pathname) throws IOException

public boolean monitorConnections(boolean bool)

public class MutateConnectionsMonitor extends ActivityMonitor

public MutateConnectionsMonitor(String _pathname) throws IOException

public MutateConnectionsMonitor()

public boolean monitorAll(boolean bool)

public class MutateNodesMonitor extends ActivityMonitor

public MutateNodesMonitor(String _pathname) throws IOException

public MutateNodesMonitor()

public boolean monitorAll(boolean bool)

public class NodeDeactivationMutationMonitor extends ActivityMonitor

public NodeDeactivationMutationMonitor(String _pathname) throws IOException

public NodeDeactivationMutationMonitor()

public boolean monitorAll(boolean bool)

public class WinnerTakesAllMonitor extends ModularTrainingMonitor

public WinnerTakesAllMonitor(String _pathname) throws IOException

public WinnerTakesAllMonitor()

public boolean monitorAll(boolean bool)

public boolean monitorImprovement(String _pathname) throws IOException

public boolean monitorImprovement(boolean bool)

3. interfacePackage

public class Interface

public static void main(String [] args)

public class NetSys

public static void main(String [] args)