├── .gitattributes ├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── NOTICE.txt ├── README.md ├── classes ├── production │ └── encog-java-core │ │ └── org │ │ └── encog │ │ └── data │ │ ├── analyst.csv │ │ ├── blank.xlsx │ │ ├── classes.txt │ │ ├── mt4.mql4 │ │ └── ninja.cs └── test │ └── encog-java-core │ └── org │ └── encog │ └── data │ ├── analyst.csv │ ├── blank.xlsx │ ├── classes.txt │ ├── encodernet.eg │ ├── encog25.xml │ ├── img │ ├── a.png │ ├── b.png │ └── c.png │ ├── iris-euro.csv │ ├── iris.csv │ ├── mt4.mql4 │ ├── networks.eg │ ├── ninja.cs │ ├── simple-c.ega │ ├── simple-r.ega │ ├── simple.csv │ └── testresource ├── dependencies ├── UmlGraph.jar └── hsqldb.jar ├── gradle.properties ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat └── src ├── .gitignore ├── main ├── assembly │ └── release.xml ├── java │ └── org │ │ └── encog │ │ ├── ConsoleStatusReportable.java │ │ ├── Encog.java │ │ ├── EncogError.java │ │ ├── EncogShutdownTask.java │ │ ├── NullStatusReportable.java │ │ ├── StatusReportable.java │ │ ├── Test.java │ │ ├── app │ │ ├── analyst │ │ │ ├── AnalystError.java │ │ │ ├── AnalystFileFormat.java │ │ │ ├── AnalystGoal.java │ │ │ ├── AnalystListener.java │ │ │ ├── ConsoleAnalystListener.java │ │ │ ├── EncogAnalyst.java │ │ │ ├── analyze │ │ │ │ ├── AnalyzedField.java │ │ │ │ ├── PerformAnalysis.java │ │ │ │ └── package-info.java │ │ │ ├── commands │ │ │ │ ├── Cmd.java │ │ │ │ ├── CmdBalance.java │ │ │ │ ├── CmdCluster.java │ │ │ │ ├── CmdCode.java │ │ │ │ ├── CmdCreate.java │ │ │ │ ├── CmdEvaluate.java │ │ │ │ ├── CmdEvaluateRaw.java │ │ │ │ ├── CmdGenerate.java │ │ │ │ ├── CmdNormalize.java │ │ │ │ ├── CmdProcess.java │ │ │ │ ├── CmdRandomize.java │ │ │ │ ├── CmdReset.java │ │ │ │ ├── CmdSegregate.java │ │ │ │ ├── CmdSet.java │ │ │ │ ├── CmdTrain.java │ │ │ │ └── package-info.java │ │ │ ├── csv │ │ │ │ ├── AnalystClusterCSV.java │ │ │ │ ├── AnalystEvaluateCSV.java │ │ │ │ ├── AnalystEvaluateRawCSV.java │ │ │ │ ├── TimeSeriesUtil.java │ │ │ │ ├── balance │ │ │ │ │ ├── BalanceCSV.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── basic │ │ │ │ │ ├── BaseCachedColumn.java │ │ │ │ │ ├── BasicCachedFile.java │ │ │ │ │ ├── BasicFile.java │ │ │ │ │ ├── FileData.java │ │ │ │ │ ├── LoadedRow.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── filter │ │ │ │ │ ├── ExcludedField.java │ │ │ │ │ ├── FilterCSV.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── normalize │ │ │ │ │ ├── AnalystNormalizeCSV.java │ │ │ │ │ ├── AnalystNormalizeToEGB.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── package-info.java │ │ │ │ ├── process │ │ │ │ │ ├── AnalystProcess.java │ │ │ │ │ └── ProcessExtension.java │ │ │ │ ├── segregate │ │ │ │ │ ├── SegregateCSV.java │ │ │ │ │ ├── SegregateTargetPercent.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── shuffle │ │ │ │ │ ├── ShuffleCSV.java │ │ │ │ │ └── package-info.java │ │ │ │ └── sort │ │ │ │ │ ├── RowComparator.java │ │ │ │ │ ├── SortCSV.java │ │ │ │ │ ├── SortType.java │ │ │ │ │ ├── SortedField.java │ │ │ │ │ └── package-info.java │ │ │ ├── missing │ │ │ │ ├── DiscardMissing.java │ │ │ │ ├── HandleMissingValues.java │ │ │ │ ├── MeanAndModeMissing.java │ │ │ │ └── NegateMissing.java │ │ │ ├── package-info.java │ │ │ ├── report │ │ │ │ ├── AnalystReport.java │ │ │ │ └── package-info.java │ │ │ ├── script │ │ │ │ ├── AnalystClassItem.java │ │ │ │ ├── AnalystScript.java │ │ │ │ ├── DataField.java │ │ │ │ ├── ScriptLoad.java │ │ │ │ ├── ScriptSave.java │ │ │ │ ├── ml │ │ │ │ │ └── ScriptOpcode.java │ │ │ │ ├── normalize │ │ │ │ │ ├── AnalystField.java │ │ │ │ │ ├── AnalystNormalize.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── package-info.java │ │ │ │ ├── preprocess │ │ │ │ │ ├── AnalystPreprocess.java │ │ │ │ │ ├── FieldPreprocess.java │ │ │ │ │ └── PreprocessAction.java │ │ │ │ ├── process │ │ │ │ │ ├── AnalystProcess.java │ │ │ │ │ └── ProcessField.java │ │ │ │ ├── prop │ │ │ │ │ ├── PropertyConstraints.java │ │ │ │ │ ├── PropertyEntry.java │ │ │ │ │ ├── PropertyType.java │ │ │ │ │ ├── ScriptProperties.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── segregate │ │ │ │ │ ├── AnalystSegregate.java │ │ │ │ │ ├── AnalystSegregateTarget.java │ │ │ │ │ └── package-info.java │ │ │ │ └── task │ │ │ │ │ ├── AnalystTask.java │ │ │ │ │ └── package-info.java │ │ │ ├── util │ │ │ │ ├── AnalystReportBridge.java │ │ │ │ ├── AnalystUtility.java │ │ │ │ ├── CSVHeaders.java │ │ │ │ ├── ConvertStringConst.java │ │ │ │ ├── FieldDirection.java │ │ │ │ └── package-info.java │ │ │ └── wizard │ │ │ │ ├── AnalystWizard.java │ │ │ │ ├── NormalizeRange.java │ │ │ │ ├── PredictionType.java │ │ │ │ ├── SourceElement.java │ │ │ │ ├── WizardMethodType.java │ │ │ │ └── package-info.java │ │ ├── generate │ │ │ ├── AnalystCodeGenerationError.java │ │ │ ├── EncogCodeGeneration.java │ │ │ ├── TargetLanguage.java │ │ │ ├── generators │ │ │ │ ├── AbstractGenerator.java │ │ │ │ ├── AbstractTemplateGenerator.java │ │ │ │ ├── LanguageSpecificGenerator.java │ │ │ │ ├── ProgramGenerator.java │ │ │ │ ├── TemplateGenerator.java │ │ │ │ ├── cs │ │ │ │ │ └── GenerateCS.java │ │ │ │ ├── java │ │ │ │ │ └── GenerateEncogJava.java │ │ │ │ ├── js │ │ │ │ │ └── GenerateEncogJavaScript.java │ │ │ │ ├── mql4 │ │ │ │ │ └── GenerateMQL4.java │ │ │ │ └── ninja │ │ │ │ │ └── GenerateNinjaScript.java │ │ │ └── program │ │ │ │ ├── EncogArgType.java │ │ │ │ ├── EncogGenProgram.java │ │ │ │ ├── EncogProgramArg.java │ │ │ │ ├── EncogProgramNode.java │ │ │ │ ├── EncogTreeNode.java │ │ │ │ └── NodeType.java │ │ └── quant │ │ │ ├── QuantError.java │ │ │ ├── QuantTask.java │ │ │ ├── indicators │ │ │ ├── Indicator.java │ │ │ ├── MovingAverage.java │ │ │ ├── ProcessIndicators.java │ │ │ ├── package-info.java │ │ │ └── predictive │ │ │ │ ├── BestClose.java │ │ │ │ ├── BestReturn.java │ │ │ │ └── package-info.java │ │ │ ├── loader │ │ │ ├── LoaderError.java │ │ │ ├── MarketLoader.java │ │ │ ├── package-info.java │ │ │ └── yahoo │ │ │ │ ├── YahooDownload.java │ │ │ │ └── package-info.java │ │ │ ├── ninja │ │ │ ├── NinjaFileConvert.java │ │ │ ├── NinjaStreamWriter.java │ │ │ └── package-info.java │ │ │ ├── package-info.java │ │ │ └── util │ │ │ ├── BarBuffer.java │ │ │ └── package-info.java │ │ ├── bot │ │ ├── BotError.java │ │ ├── BotUtil.java │ │ ├── browse │ │ │ ├── Address.java │ │ │ ├── BrowseError.java │ │ │ ├── Browser.java │ │ │ ├── LoadWebPage.java │ │ │ ├── WebPage.java │ │ │ ├── package-info.java │ │ │ └── range │ │ │ │ ├── Div.java │ │ │ │ ├── DocumentRange.java │ │ │ │ ├── Form.java │ │ │ │ ├── FormElement.java │ │ │ │ ├── Input.java │ │ │ │ ├── Link.java │ │ │ │ ├── Span.java │ │ │ │ └── package-info.java │ │ ├── dataunit │ │ │ ├── CodeDataUnit.java │ │ │ ├── DataUnit.java │ │ │ ├── TagDataUnit.java │ │ │ ├── TextDataUnit.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ └── rss │ │ │ ├── RSS.java │ │ │ ├── RSSItem.java │ │ │ └── package-info.java │ │ ├── ca │ │ ├── CellularAutomataError.java │ │ ├── program │ │ │ ├── CAProgram.java │ │ │ ├── basic │ │ │ │ ├── BasicProgram.java │ │ │ │ └── Movement.java │ │ │ ├── conway │ │ │ │ └── ConwayProgram.java │ │ │ ├── elementary │ │ │ │ └── ElementaryCA.java │ │ │ └── generic │ │ │ │ ├── GenericCA.java │ │ │ │ ├── GenericIO.java │ │ │ │ └── Trans.java │ │ ├── runner │ │ │ ├── BasicCARunner.java │ │ │ └── CARunner.java │ │ ├── universe │ │ │ ├── ContinuousCell.java │ │ │ ├── DiscreteCell.java │ │ │ ├── Universe.java │ │ │ ├── UniverseCell.java │ │ │ ├── UniverseCellFactory.java │ │ │ ├── UniverseListener.java │ │ │ └── basic │ │ │ │ ├── BasicCellFactory.java │ │ │ │ ├── BasicContinuousCell.java │ │ │ │ ├── BasicDiscreteCell.java │ │ │ │ ├── BasicUniverse.java │ │ │ │ └── PersistBasicUniverse.java │ │ └── visualize │ │ │ ├── CAVisualizer.java │ │ │ └── basic │ │ │ └── BasicCAVisualizer.java │ │ ├── engine │ │ └── network │ │ │ └── activation │ │ │ ├── ActivationBiPolar.java │ │ │ ├── ActivationBipolarSteepenedSigmoid.java │ │ │ ├── ActivationClippedLinear.java │ │ │ ├── ActivationCompetitive.java │ │ │ ├── ActivationElliott.java │ │ │ ├── ActivationElliottSymmetric.java │ │ │ ├── ActivationFunction.java │ │ │ ├── ActivationGaussian.java │ │ │ ├── ActivationLOG.java │ │ │ ├── ActivationLinear.java │ │ │ ├── ActivationRamp.java │ │ │ ├── ActivationReLU.java │ │ │ ├── ActivationSIN.java │ │ │ ├── ActivationSigmoid.java │ │ │ ├── ActivationSoftMax.java │ │ │ ├── ActivationSteepenedSigmoid.java │ │ │ ├── ActivationStep.java │ │ │ ├── ActivationTANH.java │ │ │ └── package-info.java │ │ ├── ensemble │ │ ├── Ensemble.java │ │ ├── EnsembleAggregator.java │ │ ├── EnsembleML.java │ │ ├── EnsembleMLMethodFactory.java │ │ ├── EnsembleTrainFactory.java │ │ ├── EnsembleTypes.java │ │ ├── EnsembleWeightedAggregator.java │ │ ├── GenericEnsembleML.java │ │ ├── adaboost │ │ │ └── AdaBoost.java │ │ ├── aggregator │ │ │ ├── Averaging.java │ │ │ ├── MajorityVoting.java │ │ │ ├── MetaClassifier.java │ │ │ └── WeightedAveraging.java │ │ ├── bagging │ │ │ └── Bagging.java │ │ ├── data │ │ │ ├── EnsembleDataSet.java │ │ │ └── factories │ │ │ │ ├── EnsembleDataSetFactory.java │ │ │ │ ├── NonResamplingDataSetFactory.java │ │ │ │ ├── ResamplingDataSetFactory.java │ │ │ │ ├── WeightedResamplingDataSetFactory.java │ │ │ │ └── WrappingNonResamplingDataSetFactory.java │ │ ├── dropout │ │ │ └── Dropout.java │ │ ├── ml │ │ │ └── mlp │ │ │ │ └── factory │ │ │ │ └── MultiLayerPerceptronFactory.java │ │ ├── stacking │ │ │ └── Stacking.java │ │ └── training │ │ │ ├── BackpropagationFactory.java │ │ │ ├── LevenbergMarquardtFactory.java │ │ │ ├── ManhattanPropagationFactory.java │ │ │ ├── ResilientPropagationFactory.java │ │ │ └── ScaledConjugateGradientFactory.java │ │ ├── mathutil │ │ ├── BoundMath.java │ │ ├── BoundNumbers.java │ │ ├── ComplexNumber.java │ │ ├── Convert.java │ │ ├── EncogFunction.java │ │ ├── EncogMath.java │ │ ├── EncogMathError.java │ │ ├── Equilateral.java │ │ ├── IntPair.java │ │ ├── IntRange.java │ │ ├── MathConst.java │ │ ├── NumericRange.java │ │ ├── VectorAlgebra.java │ │ ├── dimension │ │ │ ├── DimensionConstraint.java │ │ │ └── MultiDimension.java │ │ ├── error │ │ │ ├── ErrorCalculation.java │ │ │ ├── ErrorCalculationMode.java │ │ │ ├── NormalizedError.java │ │ │ └── package-info.java │ │ ├── libsvm │ │ │ ├── svm.java │ │ │ ├── svm_model.java │ │ │ ├── svm_node.java │ │ │ ├── svm_parameter.java │ │ │ ├── svm_print_interface.java │ │ │ └── svm_problem.java │ │ ├── matrices │ │ │ ├── BiPolarUtil.java │ │ │ ├── Matrix.java │ │ │ ├── MatrixError.java │ │ │ ├── MatrixMath.java │ │ │ ├── decomposition │ │ │ │ ├── CholeskyDecomposition.java │ │ │ │ ├── EigenvalueDecomposition.java │ │ │ │ ├── LUDecomposition.java │ │ │ │ ├── QRDecomposition.java │ │ │ │ ├── SingularValueDecomposition.java │ │ │ │ └── package-info.java │ │ │ ├── hessian │ │ │ │ ├── BasicHessian.java │ │ │ │ ├── ChainRuleWorker.java │ │ │ │ ├── ComputeHessian.java │ │ │ │ ├── HessianCR.java │ │ │ │ └── HessianFD.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ ├── probability │ │ │ ├── CalcProbability.java │ │ │ └── vars │ │ │ │ ├── RandomVariable.java │ │ │ │ └── VariableList.java │ │ ├── randomize │ │ │ ├── BasicRandomizer.java │ │ │ ├── ConsistentRandomizer.java │ │ │ ├── ConstRandomizer.java │ │ │ ├── Distort.java │ │ │ ├── FanInRandomizer.java │ │ │ ├── GaussianRandomizer.java │ │ │ ├── NguyenWidrowRandomizer.java │ │ │ ├── RandomChoice.java │ │ │ ├── Randomizer.java │ │ │ ├── RangeRandomizer.java │ │ │ ├── XaiverRandomizer.java │ │ │ ├── factory │ │ │ │ ├── BasicRandomFactory.java │ │ │ │ └── RandomFactory.java │ │ │ ├── generate │ │ │ │ ├── AbstractBoxMuller.java │ │ │ │ ├── AbstractGenerateRandom.java │ │ │ │ ├── BasicGenerateRandom.java │ │ │ │ ├── GenerateRandom.java │ │ │ │ ├── LinearCongruentialRandom.java │ │ │ │ ├── MersenneTwisterGenerateRandom.java │ │ │ │ ├── MultiplyWithCarryGenerateRandom.java │ │ │ │ └── SecureGenerateRandom.java │ │ │ └── package-info.java │ │ └── rbf │ │ │ ├── BasicRBF.java │ │ │ ├── GaussianFunction.java │ │ │ ├── InverseMultiquadricFunction.java │ │ │ ├── MexicanHatFunction.java │ │ │ ├── MultiquadricFunction.java │ │ │ ├── RBFEnum.java │ │ │ ├── RadialBasisFunction.java │ │ │ └── package-info.java │ │ ├── ml │ │ ├── BasicML.java │ │ ├── CalculateScore.java │ │ ├── MLAutoAssocation.java │ │ ├── MLClassification.java │ │ ├── MLCluster.java │ │ ├── MLClustering.java │ │ ├── MLContext.java │ │ ├── MLEncodable.java │ │ ├── MLError.java │ │ ├── MLFactory.java │ │ ├── MLInput.java │ │ ├── MLInputOutput.java │ │ ├── MLMethod.java │ │ ├── MLOutput.java │ │ ├── MLProperties.java │ │ ├── MLRegression.java │ │ ├── MLResettable.java │ │ ├── MLStateSequence.java │ │ ├── MethodFactory.java │ │ ├── TrainingImplementationType.java │ │ ├── anneal │ │ │ ├── SimulatedAnnealing.java │ │ │ └── package-info.java │ │ ├── bayesian │ │ │ ├── BayesianChoice.java │ │ │ ├── BayesianError.java │ │ │ ├── BayesianEvent.java │ │ │ ├── BayesianNetwork.java │ │ │ ├── EventType.java │ │ │ ├── PersistBayes.java │ │ │ ├── bif │ │ │ │ ├── BIFDefinition.java │ │ │ │ ├── BIFHandler.java │ │ │ │ ├── BIFUtil.java │ │ │ │ ├── BIFVariable.java │ │ │ │ └── FileSection.java │ │ │ ├── parse │ │ │ │ ├── ParseProbability.java │ │ │ │ ├── ParsedChoice.java │ │ │ │ ├── ParsedEvent.java │ │ │ │ └── ParsedProbability.java │ │ │ ├── query │ │ │ │ ├── BasicQuery.java │ │ │ │ ├── BayesianQuery.java │ │ │ │ ├── enumerate │ │ │ │ │ └── EnumerationQuery.java │ │ │ │ └── sample │ │ │ │ │ ├── EventState.java │ │ │ │ │ └── SamplingQuery.java │ │ │ ├── table │ │ │ │ ├── BayesianTable.java │ │ │ │ └── TableLine.java │ │ │ └── training │ │ │ │ ├── BayesianInit.java │ │ │ │ ├── TrainBayesian.java │ │ │ │ ├── estimator │ │ │ │ ├── BayesEstimator.java │ │ │ │ ├── EstimatorNone.java │ │ │ │ └── SimpleEstimator.java │ │ │ │ └── search │ │ │ │ ├── SearchNone.java │ │ │ │ └── k2 │ │ │ │ ├── BayesSearch.java │ │ │ │ └── SearchK2.java │ │ ├── data │ │ │ ├── MLComplexData.java │ │ │ ├── MLData.java │ │ │ ├── MLDataError.java │ │ │ ├── MLDataPair.java │ │ │ ├── MLDataSet.java │ │ │ ├── MLSequenceSet.java │ │ │ ├── auto │ │ │ │ ├── AutoFloatColumn.java │ │ │ │ └── AutoFloatDataSet.java │ │ │ ├── basic │ │ │ │ ├── BasicMLComplexData.java │ │ │ │ ├── BasicMLData.java │ │ │ │ ├── BasicMLDataCentroid.java │ │ │ │ ├── BasicMLDataPair.java │ │ │ │ ├── BasicMLDataPairCentroid.java │ │ │ │ ├── BasicMLDataSet.java │ │ │ │ ├── BasicMLSequenceSet.java │ │ │ │ └── package-info.java │ │ │ ├── buffer │ │ │ │ ├── BinaryDataLoader.java │ │ │ │ ├── BufferedDataError.java │ │ │ │ ├── BufferedDataSetIterator.java │ │ │ │ ├── BufferedMLDataSet.java │ │ │ │ ├── EncogEGBFile.java │ │ │ │ ├── MemoryDataLoader.java │ │ │ │ ├── codec │ │ │ │ │ ├── ArrayDataCODEC.java │ │ │ │ │ ├── CSVDataCODEC.java │ │ │ │ │ ├── DataSetCODEC.java │ │ │ │ │ ├── ExcelCODEC.java │ │ │ │ │ ├── NeuralDataSetCODEC.java │ │ │ │ │ ├── SQLCODEC.java │ │ │ │ │ └── package-info.java │ │ │ │ └── package-info.java │ │ │ ├── cross │ │ │ │ ├── DataFold.java │ │ │ │ ├── KFoldCrossvalidation.java │ │ │ │ └── package-info.java │ │ │ ├── folded │ │ │ │ ├── FoldedDataSet.java │ │ │ │ ├── FoldedIterator.java │ │ │ │ └── package-info.java │ │ │ ├── market │ │ │ │ ├── MarketDataDescription.java │ │ │ │ ├── MarketDataType.java │ │ │ │ ├── MarketError.java │ │ │ │ ├── MarketMLDataSet.java │ │ │ │ ├── MarketPoint.java │ │ │ │ ├── TickerSymbol.java │ │ │ │ └── loader │ │ │ │ │ ├── LoadedMarketData.java │ │ │ │ │ ├── LoaderError.java │ │ │ │ │ ├── MarketLoader.java │ │ │ │ │ └── YahooFinanceLoader.java │ │ │ ├── package-info.java │ │ │ ├── sparse │ │ │ │ └── SparseMLData.java │ │ │ ├── specific │ │ │ │ ├── BiPolarNeuralData.java │ │ │ │ ├── CSVNeuralDataSet.java │ │ │ │ └── package-info.java │ │ │ ├── temporal │ │ │ │ ├── TemporalDataDescription.java │ │ │ │ ├── TemporalError.java │ │ │ │ ├── TemporalMLDataSet.java │ │ │ │ └── TemporalPoint.java │ │ │ └── versatile │ │ │ │ ├── MatrixMLDataSet.java │ │ │ │ ├── NormalizationHelper.java │ │ │ │ ├── VersatileMLDataSet.java │ │ │ │ ├── columns │ │ │ │ ├── ColumnDefinition.java │ │ │ │ ├── ColumnType.java │ │ │ │ └── package-info.java │ │ │ │ ├── division │ │ │ │ ├── DataDivision.java │ │ │ │ ├── PerformDataDivision.java │ │ │ │ └── package-info.java │ │ │ │ ├── missing │ │ │ │ ├── MeanMissingHandler.java │ │ │ │ ├── MissingHandler.java │ │ │ │ └── package-info.java │ │ │ │ ├── normalizers │ │ │ │ ├── IndexedNormalizer.java │ │ │ │ ├── Normalizer.java │ │ │ │ ├── OneOfNNormalizer.java │ │ │ │ ├── PassThroughNormalizer.java │ │ │ │ ├── RangeNormalizer.java │ │ │ │ ├── RangeOrdinal.java │ │ │ │ ├── package-info.java │ │ │ │ └── strategies │ │ │ │ │ ├── BasicNormalizationStrategy.java │ │ │ │ │ ├── NormalizationStrategy.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── package-info.java │ │ │ │ └── sources │ │ │ │ ├── CSVDataSource.java │ │ │ │ ├── VersatileDataSource.java │ │ │ │ └── package-info.java │ │ ├── ea │ │ │ ├── codec │ │ │ │ ├── GeneticCODEC.java │ │ │ │ └── GenomeAsPhenomeCODEC.java │ │ │ ├── exception │ │ │ │ ├── EACompileError.java │ │ │ │ ├── EAError.java │ │ │ │ └── EARuntimeError.java │ │ │ ├── genome │ │ │ │ ├── BasicGenome.java │ │ │ │ ├── Genome.java │ │ │ │ └── GenomeFactory.java │ │ │ ├── opp │ │ │ │ ├── CompoundOperator.java │ │ │ │ ├── EvolutionaryOperator.java │ │ │ │ ├── OperationList.java │ │ │ │ └── selection │ │ │ │ │ ├── SelectionOperator.java │ │ │ │ │ ├── TournamentSelection.java │ │ │ │ │ └── TruncationSelection.java │ │ │ ├── population │ │ │ │ ├── BasicPopulation.java │ │ │ │ ├── Population.java │ │ │ │ ├── PopulationGenerator.java │ │ │ │ └── package-info.java │ │ │ ├── rules │ │ │ │ ├── BasicRuleHolder.java │ │ │ │ ├── ConstraintRule.java │ │ │ │ ├── RewriteRule.java │ │ │ │ └── RuleHolder.java │ │ │ ├── score │ │ │ │ ├── AdjustScore.java │ │ │ │ ├── EmptyScoreFunction.java │ │ │ │ ├── adjust │ │ │ │ │ └── ComplexityAdjustedScore.java │ │ │ │ └── parallel │ │ │ │ │ ├── ParallelScore.java │ │ │ │ │ └── ParallelScoreTask.java │ │ │ ├── sort │ │ │ │ ├── AbstractGenomeComparator.java │ │ │ │ ├── GenomeComparator.java │ │ │ │ ├── MaximizeAdjustedScoreComp.java │ │ │ │ ├── MaximizeScoreComp.java │ │ │ │ ├── MinimizeAdjustedScoreComp.java │ │ │ │ ├── MinimizeScoreComp.java │ │ │ │ ├── SortGenomesForSpecies.java │ │ │ │ └── SpeciesComparator.java │ │ │ ├── species │ │ │ │ ├── BasicSpecies.java │ │ │ │ ├── SingleSpeciation.java │ │ │ │ ├── Speciation.java │ │ │ │ ├── Species.java │ │ │ │ └── ThresholdSpeciation.java │ │ │ └── train │ │ │ │ ├── EvolutionaryAlgorithm.java │ │ │ │ └── basic │ │ │ │ ├── BasicEA.java │ │ │ │ ├── EAWorker.java │ │ │ │ └── TrainEA.java │ │ ├── factory │ │ │ ├── MLActivationFactory.java │ │ │ ├── MLMethodFactory.java │ │ │ ├── MLTrainFactory.java │ │ │ ├── method │ │ │ │ ├── BayesianFactory.java │ │ │ │ ├── EPLFactory.java │ │ │ │ ├── FeedforwardFactory.java │ │ │ │ ├── NEATFactory.java │ │ │ │ ├── PNNFactory.java │ │ │ │ ├── RBFNetworkFactory.java │ │ │ │ ├── SOMFactory.java │ │ │ │ ├── SRNFactory.java │ │ │ │ ├── SVMFactory.java │ │ │ │ └── package-info.java │ │ │ ├── package-info.java │ │ │ ├── parse │ │ │ │ ├── ArchitectureLayer.java │ │ │ │ ├── ArchitectureParse.java │ │ │ │ └── package-info.java │ │ │ └── train │ │ │ │ ├── AnnealFactory.java │ │ │ │ ├── BackPropFactory.java │ │ │ │ ├── ClusterSOMFactory.java │ │ │ │ ├── EPLGAFactory.java │ │ │ │ ├── GeneticFactory.java │ │ │ │ ├── LMAFactory.java │ │ │ │ ├── ManhattanFactory.java │ │ │ │ ├── NEATGAFactory.java │ │ │ │ ├── NeighborhoodSOMFactory.java │ │ │ │ ├── NelderMeadFactory.java │ │ │ │ ├── PNNTrainFactory.java │ │ │ │ ├── PSOFactory.java │ │ │ │ ├── QuickPropFactory.java │ │ │ │ ├── RBFSVDFactory.java │ │ │ │ ├── RPROPFactory.java │ │ │ │ ├── SCGFactory.java │ │ │ │ ├── SVMFactory.java │ │ │ │ ├── SVMSearchFactory.java │ │ │ │ ├── TrainBayesianFactory.java │ │ │ │ └── package-info.java │ │ ├── fitness │ │ │ ├── FitnessObjective.java │ │ │ └── MultiObjectiveFitness.java │ │ ├── fitting │ │ │ ├── gaussian │ │ │ │ ├── GaussianFitting.java │ │ │ │ └── TrainGaussian.java │ │ │ └── linear │ │ │ │ ├── LinearRegression.java │ │ │ │ └── TrainLinearRegression.java │ │ ├── genetic │ │ │ ├── GeneticError.java │ │ │ ├── MLEncodableCODEC.java │ │ │ ├── MLMethodGeneticAlgorithm.java │ │ │ ├── MLMethodGenome.java │ │ │ ├── MLMethodGenomeFactory.java │ │ │ ├── crossover │ │ │ │ ├── Splice.java │ │ │ │ ├── SpliceNoRepeat.java │ │ │ │ └── package-info.java │ │ │ ├── genome │ │ │ │ ├── ArrayGenome.java │ │ │ │ ├── DoubleArrayGenome.java │ │ │ │ ├── DoubleArrayGenomeFactory.java │ │ │ │ ├── IntegerArrayGenome.java │ │ │ │ ├── IntegerArrayGenomeFactory.java │ │ │ │ └── package-info.java │ │ │ ├── mutate │ │ │ │ ├── MutatePerturb.java │ │ │ │ ├── MutateShuffle.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── graph │ │ │ ├── BasicEdge.java │ │ │ ├── BasicGraph.java │ │ │ ├── BasicNode.java │ │ │ ├── BasicPath.java │ │ │ ├── EuclideanNode.java │ │ │ └── search │ │ │ │ ├── AStarSearch.java │ │ │ │ ├── AbstractGraphSearch.java │ │ │ │ ├── BreadthFirstSearch.java │ │ │ │ ├── CostEstimator.java │ │ │ │ ├── DepthFirstSearch.java │ │ │ │ ├── EuclideanCostEstimator.java │ │ │ │ ├── FrontierHolder.java │ │ │ │ ├── GraphSearch.java │ │ │ │ ├── Prioritizer.java │ │ │ │ ├── SearchGoal.java │ │ │ │ └── SimpleDestinationGoal.java │ │ ├── hmm │ │ │ ├── HiddenMarkovModel.java │ │ │ ├── PersistHMM.java │ │ │ ├── alog │ │ │ │ ├── ForwardBackwardCalculator.java │ │ │ │ ├── ForwardBackwardScaledCalculator.java │ │ │ │ ├── KullbackLeiblerDistanceCalculator.java │ │ │ │ ├── MarkovGenerator.java │ │ │ │ └── ViterbiCalculator.java │ │ │ ├── distributions │ │ │ │ ├── ContinousDistribution.java │ │ │ │ ├── DiscreteDistribution.java │ │ │ │ └── StateDistribution.java │ │ │ └── train │ │ │ │ ├── bw │ │ │ │ ├── BaseBaumWelch.java │ │ │ │ ├── TrainBaumWelch.java │ │ │ │ └── TrainBaumWelchScaled.java │ │ │ │ └── kmeans │ │ │ │ ├── Clusters.java │ │ │ │ └── TrainKMeans.java │ │ ├── importance │ │ │ ├── AbstractFeatureImportance.java │ │ │ ├── CorrelationFeatureImportanceCalc.java │ │ │ ├── FeatureImportance.java │ │ │ ├── FeatureRank.java │ │ │ ├── NeuralFeatureImportanceCalc.java │ │ │ └── PerturbationFeatureImportanceCalc.java │ │ ├── kmeans │ │ │ ├── BasicCluster.java │ │ │ ├── KMeansClustering.java │ │ │ └── package-info.java │ │ ├── model │ │ │ ├── EncogModel.java │ │ │ ├── config │ │ │ │ ├── FeedforwardConfig.java │ │ │ │ ├── MethodConfig.java │ │ │ │ ├── NEATConfig.java │ │ │ │ ├── PNNConfig.java │ │ │ │ ├── RBFNetworkConfig.java │ │ │ │ ├── SVMConfig.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── package-info.java │ │ ├── prg │ │ │ ├── EncogProgram.java │ │ │ ├── EncogProgramContext.java │ │ │ ├── EncogProgramVariables.java │ │ │ ├── PersistPrgPopulation.java │ │ │ ├── PrgCODEC.java │ │ │ ├── ProgramNode.java │ │ │ ├── VariableMapping.java │ │ │ ├── expvalue │ │ │ │ ├── DivisionByZeroError.java │ │ │ │ ├── EvaluateExpr.java │ │ │ │ ├── ExpressionValue.java │ │ │ │ └── ValueType.java │ │ │ ├── extension │ │ │ │ ├── BasicTemplate.java │ │ │ │ ├── ConstantPool.java │ │ │ │ ├── EncogOpcodeRegistry.java │ │ │ │ ├── FunctionFactory.java │ │ │ │ ├── NodeType.java │ │ │ │ ├── ParamTemplate.java │ │ │ │ ├── ProgramExtensionTemplate.java │ │ │ │ └── StandardExtensions.java │ │ │ ├── generator │ │ │ │ ├── AbstractPrgGenerator.java │ │ │ │ ├── GenerateWorker.java │ │ │ │ ├── PrgFullGenerator.java │ │ │ │ ├── PrgGenerator.java │ │ │ │ ├── PrgGrowGenerator.java │ │ │ │ └── RampedHalfAndHalf.java │ │ │ ├── opp │ │ │ │ ├── ConstMutation.java │ │ │ │ ├── LevelHolder.java │ │ │ │ ├── SubtreeCrossover.java │ │ │ │ └── SubtreeMutation.java │ │ │ ├── species │ │ │ │ ├── CompareEncogProgram.java │ │ │ │ └── PrgSpeciation.java │ │ │ └── train │ │ │ │ ├── PrgGenomeFactory.java │ │ │ │ ├── PrgPopulation.java │ │ │ │ ├── ZeroEvalScoreFunction.java │ │ │ │ └── rewrite │ │ │ │ ├── RewriteAlgebraic.java │ │ │ │ ├── RewriteBoolean.java │ │ │ │ └── RewriteConstants.java │ │ ├── schedule │ │ │ ├── ActionNode.java │ │ │ ├── CalculateScheduleTimes.java │ │ │ └── ScheduleGraph.java │ │ ├── svm │ │ │ ├── KernelType.java │ │ │ ├── PersistSVM.java │ │ │ ├── SVM.java │ │ │ ├── SVMType.java │ │ │ ├── package-info.java │ │ │ └── training │ │ │ │ ├── EncodeSVMProblem.java │ │ │ │ ├── SVMSearchTrain.java │ │ │ │ ├── SVMTrain.java │ │ │ │ └── package-info.java │ │ ├── train │ │ │ ├── BasicTraining.java │ │ │ ├── MLTrain.java │ │ │ └── strategy │ │ │ │ ├── Greedy.java │ │ │ │ ├── HybridStrategy.java │ │ │ │ ├── RequiredImprovementStrategy.java │ │ │ │ ├── ResetStrategy.java │ │ │ │ ├── StopTrainingStrategy.java │ │ │ │ ├── Strategy.java │ │ │ │ └── end │ │ │ │ ├── EarlyStoppingStrategy.java │ │ │ │ ├── EndIterationsStrategy.java │ │ │ │ ├── EndMaxErrorStrategy.java │ │ │ │ ├── EndMinutesStrategy.java │ │ │ │ ├── EndTrainingStrategy.java │ │ │ │ └── StoppingStrategy.java │ │ ├── tree │ │ │ ├── TreeNode.java │ │ │ ├── basic │ │ │ │ └── BasicTreeNode.java │ │ │ └── traverse │ │ │ │ ├── DepthFirstTraversal.java │ │ │ │ ├── TreeTraversal.java │ │ │ │ ├── TreeTraversalTask.java │ │ │ │ └── tasks │ │ │ │ ├── TaskCountNodes.java │ │ │ │ ├── TaskGetNodeIndex.java │ │ │ │ └── TaskReplaceNode.java │ │ └── world │ │ │ ├── Action.java │ │ │ ├── ActionProbability.java │ │ │ ├── AgentPolicy.java │ │ │ ├── PerformAction.java │ │ │ ├── State.java │ │ │ ├── SuccessorState.java │ │ │ ├── World.java │ │ │ ├── WorldAgent.java │ │ │ ├── WorldError.java │ │ │ ├── basic │ │ │ ├── BasicAction.java │ │ │ ├── BasicAgent.java │ │ │ ├── BasicState.java │ │ │ └── BasicWorld.java │ │ │ ├── grid │ │ │ ├── GridState.java │ │ │ ├── GridWorld.java │ │ │ └── probability │ │ │ │ ├── GridAbstractProbability.java │ │ │ │ ├── GridDeterministicProbability.java │ │ │ │ └── GridStochasticProbability.java │ │ │ └── learning │ │ │ ├── mdp │ │ │ ├── MarkovDecisionProcess.java │ │ │ └── ValueIteration.java │ │ │ └── q │ │ │ └── QLearning.java │ │ ├── neural │ │ ├── NeuralNetworkError.java │ │ ├── art │ │ │ ├── ART.java │ │ │ ├── ART1.java │ │ │ ├── PersistART1.java │ │ │ └── package-info.java │ │ ├── bam │ │ │ ├── BAM.java │ │ │ ├── PersistBAM.java │ │ │ └── package-info.java │ │ ├── cpn │ │ │ ├── CPN.java │ │ │ ├── PersistCPN.java │ │ │ ├── package-info.java │ │ │ └── training │ │ │ │ ├── TrainInstar.java │ │ │ │ ├── TrainOutstar.java │ │ │ │ └── package-info.java │ │ ├── data │ │ │ ├── NeuralData.java │ │ │ ├── NeuralDataPair.java │ │ │ ├── NeuralDataSet.java │ │ │ ├── basic │ │ │ │ ├── BasicNeuralData.java │ │ │ │ ├── BasicNeuralDataPair.java │ │ │ │ ├── BasicNeuralDataSet.java │ │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── error │ │ │ ├── ATanErrorFunction.java │ │ │ ├── CrossEntropyErrorFunction.java │ │ │ ├── ErrorFunction.java │ │ │ ├── LinearErrorFunction.java │ │ │ └── OutputErrorFunction.java │ │ ├── flat │ │ │ ├── FlatLayer.java │ │ │ ├── FlatNetwork.java │ │ │ ├── FlatNetworkRBF.java │ │ │ └── package-info.java │ │ ├── freeform │ │ │ ├── FreeformConnection.java │ │ │ ├── FreeformContextNeuron.java │ │ │ ├── FreeformLayer.java │ │ │ ├── FreeformNetwork.java │ │ │ ├── FreeformNetworkError.java │ │ │ ├── FreeformNeuron.java │ │ │ ├── InputSummation.java │ │ │ ├── TempTrainingData.java │ │ │ ├── basic │ │ │ │ ├── BasicActivationSummation.java │ │ │ │ ├── BasicActivationSummationFactory.java │ │ │ │ ├── BasicFreeformConnection.java │ │ │ │ ├── BasicFreeformConnectionFactory.java │ │ │ │ ├── BasicFreeformLayer.java │ │ │ │ ├── BasicFreeformLayerFactory.java │ │ │ │ ├── BasicFreeformNeuron.java │ │ │ │ └── BasicFreeformNeuronFactory.java │ │ │ ├── factory │ │ │ │ ├── FreeformConnectionFactory.java │ │ │ │ ├── FreeformLayerFactory.java │ │ │ │ ├── FreeformNeuronFactory.java │ │ │ │ └── InputSummationFactory.java │ │ │ ├── task │ │ │ │ ├── ConnectionTask.java │ │ │ │ └── NeuronTask.java │ │ │ └── training │ │ │ │ ├── FreeformBackPropagation.java │ │ │ │ ├── FreeformPropagationTraining.java │ │ │ │ └── FreeformResilientPropagation.java │ │ ├── hyperneat │ │ │ ├── FactorHyperNEATGenome.java │ │ │ ├── HyperNEATCODEC.java │ │ │ ├── HyperNEATGenome.java │ │ │ └── substrate │ │ │ │ ├── Substrate.java │ │ │ │ ├── SubstrateFactory.java │ │ │ │ ├── SubstrateLink.java │ │ │ │ └── SubstrateNode.java │ │ ├── neat │ │ │ ├── FactorNEATGenome.java │ │ │ ├── NEATCODEC.java │ │ │ ├── NEATGenomeFactory.java │ │ │ ├── NEATLink.java │ │ │ ├── NEATNetwork.java │ │ │ ├── NEATNeuronType.java │ │ │ ├── NEATPopulation.java │ │ │ ├── NEATUtil.java │ │ │ ├── PersistNEATPopulation.java │ │ │ └── training │ │ │ │ ├── NEATBaseGene.java │ │ │ │ ├── NEATGenome.java │ │ │ │ ├── NEATInnovation.java │ │ │ │ ├── NEATInnovationList.java │ │ │ │ ├── NEATInnovationType.java │ │ │ │ ├── NEATLinkGene.java │ │ │ │ ├── NEATNeuronGene.java │ │ │ │ ├── opp │ │ │ │ ├── NEATCrossover.java │ │ │ │ ├── NEATMutateAddLink.java │ │ │ │ ├── NEATMutateAddNode.java │ │ │ │ ├── NEATMutateRemoveLink.java │ │ │ │ ├── NEATMutateWeights.java │ │ │ │ ├── NEATMutation.java │ │ │ │ └── links │ │ │ │ │ ├── MutateLinkWeight.java │ │ │ │ │ ├── MutatePerturbLinkWeight.java │ │ │ │ │ ├── MutateResetLinkWeight.java │ │ │ │ │ ├── SelectFixed.java │ │ │ │ │ ├── SelectLinks.java │ │ │ │ │ └── SelectProportion.java │ │ │ │ └── species │ │ │ │ └── OriginalNEATSpeciation.java │ │ ├── networks │ │ │ ├── BasicNetwork.java │ │ │ ├── ContainsFlat.java │ │ │ ├── NeuralDataMapping.java │ │ │ ├── PersistBasicNetwork.java │ │ │ ├── layers │ │ │ │ ├── BasicLayer.java │ │ │ │ └── Layer.java │ │ │ ├── package-info.java │ │ │ ├── structure │ │ │ │ ├── AnalyzeNetwork.java │ │ │ │ ├── NetworkCODEC.java │ │ │ │ ├── NeuralStructure.java │ │ │ │ └── package-info.java │ │ │ └── training │ │ │ │ ├── BatchSize.java │ │ │ │ ├── LearningRate.java │ │ │ │ ├── Momentum.java │ │ │ │ ├── StochasticTrainingSetScore.java │ │ │ │ ├── Train.java │ │ │ │ ├── TrainingError.java │ │ │ │ ├── TrainingSetScore.java │ │ │ │ ├── anneal │ │ │ │ ├── NeuralSimulatedAnnealing.java │ │ │ │ ├── NeuralSimulatedAnnealingHelper.java │ │ │ │ └── package-info.java │ │ │ │ ├── concurrent │ │ │ │ ├── ConcurrentTrainingManager.java │ │ │ │ ├── jobs │ │ │ │ │ ├── BPROPJob.java │ │ │ │ │ ├── RPROPJob.java │ │ │ │ │ ├── TrainingJob.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── package-info.java │ │ │ │ └── performers │ │ │ │ │ ├── ConcurrentTrainingPerformer.java │ │ │ │ │ ├── ConcurrentTrainingPerformerCPU.java │ │ │ │ │ ├── PerformerTask.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── cross │ │ │ │ ├── CrossTraining.java │ │ │ │ ├── CrossValidationKFold.java │ │ │ │ ├── NetworkFold.java │ │ │ │ └── package-info.java │ │ │ │ ├── lma │ │ │ │ ├── LevenbergMarquardtTraining.java │ │ │ │ └── package-info.java │ │ │ │ ├── nm │ │ │ │ └── NelderMeadTraining.java │ │ │ │ ├── package-info.java │ │ │ │ ├── pnn │ │ │ │ ├── CalculationCriteria.java │ │ │ │ ├── DeriveMinimum.java │ │ │ │ ├── GlobalMinimumSearch.java │ │ │ │ ├── TrainBasicPNN.java │ │ │ │ └── package-info.java │ │ │ │ ├── propagation │ │ │ │ ├── GradientWorker.java │ │ │ │ ├── GradientWorkerOwner.java │ │ │ │ ├── PersistTrainingContinuation.java │ │ │ │ ├── Propagation.java │ │ │ │ ├── TrainingContinuation.java │ │ │ │ ├── back │ │ │ │ │ ├── Backpropagation.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── manhattan │ │ │ │ │ ├── ManhattanPropagation.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── package-info.java │ │ │ │ ├── quick │ │ │ │ │ ├── QuickPropagation.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── resilient │ │ │ │ │ ├── RPROPConst.java │ │ │ │ │ ├── RPROPType.java │ │ │ │ │ ├── ResilientPropagation.java │ │ │ │ │ └── package-info.java │ │ │ │ ├── scg │ │ │ │ │ ├── ScaledConjugateGradient.java │ │ │ │ │ └── package-info.java │ │ │ │ └── sgd │ │ │ │ │ ├── BatchDataSet.java │ │ │ │ │ ├── StochasticGradientDescent.java │ │ │ │ │ └── update │ │ │ │ │ ├── AdaGradUpdate.java │ │ │ │ │ ├── AdamUpdate.java │ │ │ │ │ ├── MomentumUpdate.java │ │ │ │ │ ├── NesterovUpdate.java │ │ │ │ │ ├── RMSPropUpdate.java │ │ │ │ │ └── UpdateRule.java │ │ │ │ ├── pso │ │ │ │ ├── NeuralPSO.java │ │ │ │ └── NeuralPSOWorker.java │ │ │ │ ├── simple │ │ │ │ ├── TrainAdaline.java │ │ │ │ └── package-info.java │ │ │ │ └── strategy │ │ │ │ ├── RegularizationStrategy.java │ │ │ │ ├── SmartLearningRate.java │ │ │ │ ├── SmartMomentum.java │ │ │ │ └── package-info.java │ │ ├── pattern │ │ │ ├── ADALINEPattern.java │ │ │ ├── ART1Pattern.java │ │ │ ├── BAMPattern.java │ │ │ ├── BoltzmannPattern.java │ │ │ ├── CPNPattern.java │ │ │ ├── ElmanPattern.java │ │ │ ├── FeedForwardPattern.java │ │ │ ├── HopfieldPattern.java │ │ │ ├── JordanPattern.java │ │ │ ├── NeuralNetworkPattern.java │ │ │ ├── PNNPattern.java │ │ │ ├── PatternError.java │ │ │ ├── RadialBasisPattern.java │ │ │ ├── SOMPattern.java │ │ │ ├── SVMPattern.java │ │ │ └── package-info.java │ │ ├── pnn │ │ │ ├── AbstractPNN.java │ │ │ ├── BasicPNN.java │ │ │ ├── PNNKernelType.java │ │ │ ├── PNNOutputMode.java │ │ │ ├── PersistBasicPNN.java │ │ │ └── package-info.java │ │ ├── prune │ │ │ ├── HiddenLayerParams.java │ │ │ ├── NetworkPattern.java │ │ │ ├── PruneIncremental.java │ │ │ ├── PruneSelective.java │ │ │ └── package-info.java │ │ ├── rbf │ │ │ ├── PersistRBFNetwork.java │ │ │ ├── RBFNetwork.java │ │ │ ├── package-info.java │ │ │ └── training │ │ │ │ ├── SVD.java │ │ │ │ ├── SVDTraining.java │ │ │ │ └── package-info.java │ │ ├── som │ │ │ ├── PersistSOM.java │ │ │ ├── SOM.java │ │ │ ├── package-info.java │ │ │ └── training │ │ │ │ ├── basic │ │ │ │ ├── BasicTrainSOM.java │ │ │ │ ├── BestMatchingUnit.java │ │ │ │ ├── neighborhood │ │ │ │ │ ├── NeighborhoodBubble.java │ │ │ │ │ ├── NeighborhoodFunction.java │ │ │ │ │ ├── NeighborhoodRBF.java │ │ │ │ │ ├── NeighborhoodRBF1D.java │ │ │ │ │ ├── NeighborhoodSingle.java │ │ │ │ │ └── package-info.java │ │ │ │ └── package-info.java │ │ │ │ ├── clustercopy │ │ │ │ ├── SOMClusterCopyTraining.java │ │ │ │ └── package-info.java │ │ │ │ └── package-info.java │ │ └── thermal │ │ │ ├── BoltzmannMachine.java │ │ │ ├── HopfieldNetwork.java │ │ │ ├── PersistBoltzmann.java │ │ │ ├── PersistHopfield.java │ │ │ ├── ThermalNetwork.java │ │ │ └── package-info.java │ │ ├── parse │ │ ├── ParseError.java │ │ ├── PeekableInputStream.java │ │ ├── expression │ │ │ ├── CommonRender.java │ │ │ ├── ExpressionNodeType.java │ │ │ ├── common │ │ │ │ ├── ParseCommonExpression.java │ │ │ │ └── RenderCommonExpression.java │ │ │ ├── epl │ │ │ │ ├── ParseEPL.java │ │ │ │ └── RenderEPL.java │ │ │ ├── latex │ │ │ │ └── RenderLatexExpression.java │ │ │ └── rpn │ │ │ │ └── RenderRPN.java │ │ └── tags │ │ │ ├── Tag.java │ │ │ ├── TagConst.java │ │ │ ├── read │ │ │ ├── ReadHTML.java │ │ │ ├── ReadTags.java │ │ │ └── ReadXML.java │ │ │ └── write │ │ │ ├── WriteTags.java │ │ │ └── WriteXML.java │ │ ├── persist │ │ ├── EncogDirectoryPersistence.java │ │ ├── EncogFileSection.java │ │ ├── EncogPersistor.java │ │ ├── EncogReadHelper.java │ │ ├── EncogWriteHelper.java │ │ ├── PersistConst.java │ │ ├── PersistError.java │ │ ├── PersistorRegistry.java │ │ ├── package-info.java │ │ └── source │ │ │ ├── ObtainFallbackStream.java │ │ │ ├── ObtainFileInputStream.java │ │ │ ├── ObtainInputStream.java │ │ │ └── ObtainResourceInputStream.java │ │ ├── platformspecific │ │ └── j2se │ │ │ ├── EncogPlatformSpecific.java │ │ │ ├── TrainingDialog.java │ │ │ └── data │ │ │ ├── SQLNeuralDataSet.java │ │ │ └── image │ │ │ ├── ImageMLData.java │ │ │ ├── ImageMLDataSet.java │ │ │ └── package-info.java │ │ ├── plugin │ │ ├── EncogPluginBase.java │ │ ├── EncogPluginLogging1.java │ │ ├── EncogPluginService1.java │ │ ├── package-info.java │ │ └── system │ │ │ ├── SystemActivationPlugin.java │ │ │ ├── SystemLoggingPlugin.java │ │ │ ├── SystemMethodsPlugin.java │ │ │ ├── SystemTrainingPlugin.java │ │ │ └── package-info.java │ │ └── util │ │ ├── EncogValidate.java │ │ ├── EngineArray.java │ │ ├── Format.java │ │ ├── HTMLReport.java │ │ ├── ImageSize.java │ │ ├── ObjectPair.java │ │ ├── ParamsHolder.java │ │ ├── ResourceLoader.java │ │ ├── SimpleParser.java │ │ ├── Stopwatch.java │ │ ├── YahooSearch.java │ │ ├── arrayutil │ │ ├── Array.java │ │ ├── ClassItem.java │ │ ├── NormalizationAction.java │ │ ├── NormalizeArray.java │ │ ├── NormalizedField.java │ │ ├── TemporalType.java │ │ ├── TemporalWindowArray.java │ │ ├── TemporalWindowField.java │ │ ├── VectorWindow.java │ │ └── WindowDouble.java │ │ ├── benchmark │ │ ├── EncoderTrainingFactory.java │ │ ├── EncogBenchmark.java │ │ ├── Evaluate.java │ │ └── RandomTrainingFactory.java │ │ ├── concurrency │ │ ├── DetermineWorkload.java │ │ ├── EngineConcurrency.java │ │ ├── EngineTask.java │ │ ├── MultiThreadable.java │ │ ├── PoolItem.java │ │ ├── TaskGroup.java │ │ └── job │ │ │ ├── ConcurrentJob.java │ │ │ ├── JobUnitContext.java │ │ │ └── JobUnitWorker.java │ │ ├── csv │ │ ├── CSVError.java │ │ ├── CSVFormat.java │ │ ├── NumberList.java │ │ ├── ParseCSVLine.java │ │ └── ReadCSV.java │ │ ├── data │ │ ├── GenerationUtil.java │ │ └── MNISTReader.java │ │ ├── datastruct │ │ ├── StackInt.java │ │ ├── StackObject.java │ │ ├── StackString.java │ │ └── WindowInt.java │ │ ├── downsample │ │ ├── Downsample.java │ │ ├── RGBDownsample.java │ │ └── SimpleIntensityDownsample.java │ │ ├── error │ │ └── CalculateRegressionError.java │ │ ├── file │ │ ├── Directory.java │ │ ├── FileUtil.java │ │ └── ResourceInputStream.java │ │ ├── http │ │ ├── CookieUtility.java │ │ ├── FormUtility.java │ │ └── URLUtility.java │ │ ├── identity │ │ ├── BasicGenerateID.java │ │ └── GenerateID.java │ │ ├── kmeans │ │ ├── Centroid.java │ │ ├── CentroidFactory.java │ │ ├── Cluster.java │ │ └── KMeansUtil.java │ │ ├── logging │ │ ├── DumpMatrix.java │ │ ├── EncogFormatter.java │ │ └── EncogLogging.java │ │ ├── normalize │ │ ├── DataNormalization.java │ │ ├── NormalizationError.java │ │ ├── input │ │ │ ├── BasicInputField.java │ │ │ ├── HasFixedLength.java │ │ │ ├── InputField.java │ │ │ ├── InputFieldArray1D.java │ │ │ ├── InputFieldArray2D.java │ │ │ ├── InputFieldCSV.java │ │ │ ├── InputFieldCSVText.java │ │ │ ├── InputFieldEncogCollection.java │ │ │ ├── InputFieldMLDataSet.java │ │ │ └── MLDataFieldHolder.java │ │ ├── output │ │ │ ├── BasicOutputField.java │ │ │ ├── BasicOutputFieldGroup.java │ │ │ ├── OutputField.java │ │ │ ├── OutputFieldDirect.java │ │ │ ├── OutputFieldGroup.java │ │ │ ├── OutputFieldGrouped.java │ │ │ ├── OutputFieldRangeMapped.java │ │ │ ├── RequireTwoPass.java │ │ │ ├── mapped │ │ │ │ ├── MappedRange.java │ │ │ │ └── OutputFieldEncode.java │ │ │ ├── multiplicative │ │ │ │ ├── MultiplicativeGroup.java │ │ │ │ └── OutputFieldMultiplicative.java │ │ │ ├── nominal │ │ │ │ ├── NominalItem.java │ │ │ │ ├── OutputEquilateral.java │ │ │ │ └── OutputOneOf.java │ │ │ └── zaxis │ │ │ │ ├── OutputFieldZAxis.java │ │ │ │ ├── OutputFieldZAxisSynthetic.java │ │ │ │ └── ZAxisGroup.java │ │ ├── segregate │ │ │ ├── IntegerBalanceSegregator.java │ │ │ ├── RangeSegregator.java │ │ │ ├── SegregationRange.java │ │ │ ├── Segregator.java │ │ │ └── index │ │ │ │ ├── IndexRangeSegregator.java │ │ │ │ ├── IndexSampleSegregator.java │ │ │ │ └── IndexSegregator.java │ │ └── target │ │ │ ├── NormalizationStorage.java │ │ │ ├── NormalizationStorageArray1D.java │ │ │ ├── NormalizationStorageArray2D.java │ │ │ ├── NormalizationStorageCSV.java │ │ │ ├── NormalizationStorageEncogCollection.java │ │ │ └── NormalizationStorageNeuralDataSet.java │ │ ├── obj │ │ ├── ActivationUtil.java │ │ ├── ChooseObject.java │ │ ├── ObjectCloner.java │ │ ├── ObjectHolder.java │ │ ├── ReflectionUtil.java │ │ └── SerializeObject.java │ │ ├── simple │ │ ├── EncogUtility.java │ │ └── TrainingSetUtil.java │ │ ├── text │ │ ├── BagOfWords.java │ │ ├── Base64.java │ │ ├── DoubleString.java │ │ └── LevenshteinDistance.java │ │ ├── time │ │ ├── DateUtil.java │ │ ├── EnglishTimeUnitNames.java │ │ ├── NumericDateUtil.java │ │ ├── TimeSpan.java │ │ ├── TimeUnit.java │ │ └── TimeUnitNames.java │ │ └── validate │ │ └── ValidateNetwork.java └── resources │ └── org │ └── encog │ └── data │ ├── analyst.csv │ ├── blank.xlsx │ ├── classes.txt │ ├── mt4.mql4 │ └── ninja.cs └── test ├── java └── org │ └── encog │ ├── TestEncog.java │ ├── app │ ├── analyst │ │ ├── AnalystTestingUtility.java │ │ ├── TestAnalystClassification.java │ │ ├── TestAnalystRegression.java │ │ └── TestEncogAnalyst.java │ └── quant │ │ ├── TestBalanceCSV.java │ │ ├── TestFilter.java │ │ ├── TestNinjaFileConvert.java │ │ ├── TestNinjaStreamWriter.java │ │ ├── TestNormalizeArray.java │ │ ├── TestProcessIndicators.java │ │ ├── TestSegregateCSV.java │ │ ├── TestShuffle.java │ │ └── TestSort.java │ ├── bot │ ├── browse │ │ ├── TestAddress.java │ │ ├── TestBrowse.java │ │ └── TestWebPageData.java │ └── html │ │ ├── TestParseHTML.java │ │ └── TestPeekableInputStream.java │ ├── ensemble │ ├── aggregator │ │ └── TestMajorityVoting.java │ └── bagging │ │ └── TestBagging.java │ ├── mathutil │ ├── TestErrorCalculation.java │ ├── matrices │ │ └── decomposition │ │ │ └── EigenvalueDecompositionTest.java │ └── matrixes │ │ └── hessian │ │ └── TestHessian.java │ ├── matrix │ ├── TestBiPolarUtil.java │ ├── TestDecomp.java │ ├── TestMatrix.java │ └── TestMatrixMath.java │ ├── ml │ ├── bayesian │ │ ├── TestBayesNet.java │ │ ├── TestEnumerationQuery.java │ │ ├── TestK2.java │ │ └── TestSamplingQuery.java │ ├── data │ │ ├── auto │ │ │ ├── TestAutoFloatColumn.java │ │ │ └── TestAutoFloatDataSet.java │ │ ├── basic │ │ │ └── TestBasicMLSequenceSet.java │ │ ├── folded │ │ │ └── TestFoldedDataSet.java │ │ ├── temporal │ │ │ └── TestTemporal.java │ │ └── versatile │ │ │ ├── TestMatrixMLDataSet.java │ │ │ └── TestNormalizationHelper.java │ ├── factory │ │ └── TestMLMethodFactory.java │ ├── genetic │ │ └── sort │ │ │ ├── TestMaximizeAdjustedScoreComp.java │ │ │ ├── TestMaximizeScoreComp.java │ │ │ ├── TestMinimizeAdjustedScoreComp.java │ │ │ └── TestMinimizeScoreComp.java │ ├── graph │ │ └── TestSearch.java │ ├── hmm │ │ └── TestHMM.java │ ├── kmeans │ │ └── TestKMeans.java │ ├── linear │ │ ├── TestGaussian.java │ │ └── TestLinearRegression.java │ └── prg │ │ ├── TestEncogProgram.java │ │ ├── TestProgramClone.java │ │ ├── species │ │ └── TestCompareEncogProgram.java │ │ └── train │ │ ├── TestGenerate.java │ │ ├── crossover │ │ └── TestSubtreeCrossover.java │ │ └── rewrite │ │ ├── TestRewriteAlgebraic.java │ │ └── TestRewriteConstants.java │ ├── neural │ ├── activation │ │ ├── TestActivationBiPolar.java │ │ ├── TestActivationGaussian.java │ │ ├── TestActivationLOG.java │ │ ├── TestActivationLinear.java │ │ ├── TestActivationSIN.java │ │ ├── TestActivationSigmoid.java │ │ ├── TestActivationSoftMax.java │ │ └── TestActivationTANH.java │ ├── data │ │ ├── TestNeuralDataError.java │ │ ├── bipolar │ │ │ └── TestBiPolarNeuralData.java │ │ ├── buffer │ │ │ ├── TestBinaryData.java │ │ │ ├── TestBufferedNeuralDataSet.java │ │ │ └── TestExcel.java │ │ ├── csv │ │ │ └── TestCSVNeuralData.java │ │ └── image │ │ │ └── TestImageDataSet.java │ ├── flat │ │ └── FlatNetworkTest.java │ ├── freeform │ │ ├── TestFreeform.java │ │ └── TestFreeformTraining.java │ ├── networks │ │ ├── NetworkUtil.java │ │ ├── TestBiasActivation.java │ │ ├── TestConsistency.java │ │ ├── TestLimited.java │ │ ├── TestSRN.java │ │ ├── TestWeightAccess.java │ │ ├── XOR.java │ │ ├── layers │ │ │ └── TestClone.java │ │ ├── logic │ │ │ └── TestADALINE.java │ │ ├── neat │ │ │ └── training │ │ │ │ └── species │ │ │ │ └── TestSortGenomesForSpecies.java │ │ ├── structure │ │ │ └── TestAnalyzeNetwork.java │ │ └── training │ │ │ ├── MockTrain.java │ │ │ ├── TestFolded.java │ │ │ ├── TestNEAT.java │ │ │ ├── TestStrategy.java │ │ │ ├── TestTraining.java │ │ │ ├── TestTrainingContinuation.java │ │ │ ├── TrainComplete.java │ │ │ ├── competitive │ │ │ ├── TestCompetitive.java │ │ │ └── neighborhood │ │ │ │ └── TestNeighborhood.java │ │ │ └── concurrent │ │ │ └── TestConcurrent.java │ └── prune │ │ └── TestPruneSelective.java │ ├── parse │ ├── expression │ │ ├── common │ │ │ ├── TestBoolean.java │ │ │ ├── TestExpression.java │ │ │ ├── TestExpressionVar.java │ │ │ ├── TestFunctions.java │ │ │ ├── TestRenderCommon.java │ │ │ └── TestString.java │ │ ├── epl │ │ │ └── TestRenderEPL.java │ │ └── rpn │ │ │ └── TestRenderRPN.java │ └── tags │ │ ├── read │ │ └── TestXMLRead.java │ │ └── write │ │ └── TestXMLWrite.java │ ├── persist │ ├── TestPersistART.java │ ├── TestPersistBAM.java │ ├── TestPersistBasicNetwork.java │ ├── TestPersistBayes.java │ ├── TestPersistBoltzmann.java │ ├── TestPersistCPN.java │ ├── TestPersistEPLPopulation.java │ ├── TestPersistFreeform.java │ ├── TestPersistHMM.java │ ├── TestPersistHopfield.java │ ├── TestPersistLargeHopfield.java │ ├── TestPersistNEAT.java │ ├── TestPersistPNN.java │ ├── TestPersistPopulation.java │ ├── TestPersistPopulationNPE.java │ ├── TestPersistRBF.java │ ├── TestPersistSOM.java │ ├── TestPersistSVM.java │ └── TestPersistTrainingContinuation.java │ ├── platformspecific │ └── j2se │ │ └── data │ │ └── image │ │ └── TestImageMLDataSet.java │ └── util │ ├── HSQLUtil.java │ ├── SerializeRoundTrip.java │ ├── StatusCounter.java │ ├── TempDir.java │ ├── TestEngineArray.java │ ├── TestErrorCalculation.java │ ├── TestTimeSpan.java │ ├── arrayutil │ ├── ArrayTest.java │ ├── TestNorm.java │ └── TestVectorWindow.java │ ├── csv │ ├── TestNumberList.java │ └── TestReadCSV.java │ ├── datastruct │ ├── TestStackInt.java │ └── TestWindowInt.java │ ├── downsample │ └── TestRGBDownsample.java │ ├── normalize │ ├── TestMapped.java │ ├── TestMultiplicative.java │ ├── TestNormArray.java │ ├── TestNormCSV.java │ ├── TestNormDataSet.java │ ├── TestSegregate.java │ └── TestZAxis.java │ ├── obj │ └── TestReflectionUtil.java │ └── text │ └── TestBagOfWords.java └── resources └── org └── encog └── data ├── analyst.csv ├── blank.xlsx ├── 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