├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── README.md ├── gradle └── wrapper │ ├── gradle-wrapper.jar │ └── gradle-wrapper.properties ├── gradlew ├── gradlew.bat └── src ├── main └── java │ └── com │ └── clust4j │ ├── Clust4j.java │ ├── GlobalState.java │ ├── NamedEntity.java │ ├── algo │ ├── AbstractAutonomousClusterer.java │ ├── AbstractCentroidClusterer.java │ ├── AbstractClusterer.java │ ├── AbstractDBSCAN.java │ ├── AbstractDensityClusterer.java │ ├── AbstractPartitionalClusterer.java │ ├── AffinityPropagation.java │ ├── AffinityPropagationParameters.java │ ├── BallTree.java │ ├── BaseClassifier.java │ ├── BaseClassifierParameters.java │ ├── BaseClustererParameters.java │ ├── BaseModel.java │ ├── BaseNeighborsModel.java │ ├── BoruvkaAlgorithm.java │ ├── CentroidClustererParameters.java │ ├── CentroidLearner.java │ ├── Convergeable.java │ ├── ConvergeablePlanner.java │ ├── DBSCAN.java │ ├── DBSCANParameters.java │ ├── HDBSCAN.java │ ├── HDBSCANParameters.java │ ├── HierarchicalAgglomerative.java │ ├── HierarchicalAgglomerativeParameters.java │ ├── KDTree.java │ ├── KMeans.java │ ├── KMeansParameters.java │ ├── KMedoids.java │ ├── KMedoidsParameters.java │ ├── LabelEncoder.java │ ├── MeanShift.java │ ├── MeanShiftParameters.java │ ├── MetricValidator.java │ ├── ModelSummary.java │ ├── NearestCentroid.java │ ├── NearestCentroidParameters.java │ ├── NearestNeighborHeapSearch.java │ ├── NearestNeighbors.java │ ├── NearestNeighborsParameters.java │ ├── Neighborhood.java │ ├── NeighborsClassifierParameters.java │ ├── NoiseyClusterer.java │ ├── NoiseyLabelEncoder.java │ ├── ParallelChunkingTask.java │ ├── RadiusNeighbors.java │ ├── RadiusNeighborsParameters.java │ ├── SafeLabelEncoder.java │ ├── SupervisedClassifier.java │ ├── SupervisedClassifierParameters.java │ ├── UnsupervisedClassifier.java │ ├── UnsupervisedClassifierParameters.java │ ├── pipeline │ │ ├── NeighborsPipeline.java │ │ ├── Pipeline.java │ │ ├── SupervisedPipeline.java │ │ └── UnsupervisedPipeline.java │ └── preprocess │ │ ├── BoxCoxTransformer.java │ │ ├── MeanCenterer.java │ │ ├── MedianCenterer.java │ │ ├── MinMaxScaler.java │ │ ├── PCA.java │ │ ├── PreProcessor.java │ │ ├── RobustScaler.java │ │ ├── StandardScaler.java │ │ ├── Transformer.java │ │ ├── WeightTransformer.java │ │ ├── YeoJohnsonTransformer.java │ │ └── impute │ │ ├── BootstrapImputation.java │ │ ├── CentralTendencyMethod.java │ │ ├── MatrixImputation.java │ │ ├── MeanImputation.java │ │ ├── MedianImputation.java │ │ └── NearestNeighborImputation.java │ ├── data │ ├── BreastCancerLoader.java │ ├── BufferedMatrixReader.java │ ├── DataSet.java │ ├── ExampleDataSets.java │ ├── IrisLoader.java │ ├── ToyMoonsLoader.java │ ├── TrainTestSplit.java │ └── WineLoader.java │ ├── except │ ├── IllegalClusterStateException.java │ ├── MatrixParseException.java │ ├── ModelNotFitException.java │ ├── NaNException.java │ └── NonUniformMatrixException.java │ ├── kernel │ ├── ANOVAKernel.java │ ├── CauchyKernel.java │ ├── CircularKernel.java │ ├── ConstantKernel.java │ ├── ExponentialKernel.java │ ├── GaussianKernel.java │ ├── GeneralizedMinKernel.java │ ├── HyperbolicTangentKernel.java │ ├── InverseMultiquadricKernel.java │ ├── Kernel.java │ ├── LaplacianKernel.java │ ├── LinearKernel.java │ ├── LogKernel.java │ ├── MinKernel.java │ ├── MultiquadricKernel.java │ ├── PolynomialKernel.java │ ├── PowerKernel.java │ ├── RadialBasisKernel.java │ ├── RationalQuadraticKernel.java │ ├── SphericalKernel.java │ └── SplineKernel.java │ ├── log │ ├── Log.java │ ├── LogProperties.java │ ├── LogTimeFormatter.java │ ├── LogTimer.java │ ├── Loggable.java │ └── Timer.java │ ├── metrics │ ├── pairwise │ │ ├── BooleanSimilarity.java │ │ ├── Distance.java │ │ ├── DistanceMetric.java │ │ ├── GeometricallySeparable.java │ │ ├── MinkowskiDistance.java │ │ ├── Pairwise.java │ │ ├── Similarity.java │ │ └── SimilarityMetric.java │ └── scoring │ │ ├── EvaluationMetric.java │ │ ├── SupervisedMetric.java │ │ └── UnsupervisedMetric.java │ ├── optimize │ ├── BaseDownhillOptimizer.java │ ├── Bracket.java │ ├── BrentDownhillOptimizer.java │ └── OptimizableCaller.java │ ├── sample │ ├── Bootstrapper.java │ └── Sampler.java │ └── utils │ ├── ArrayFormatter.java │ ├── DeepCloneable.java │ ├── EntryPair.java │ ├── MatUtils.java │ ├── MatrixFormatter.java │ ├── QuadTup.java │ ├── Series.java │ ├── SimpleHeap.java │ ├── SynchronicityLock.java │ ├── TableFormatter.java │ ├── VecUtils.java │ └── parallel │ ├── MatrixMRTask.java │ └── map │ ├── DistributedMatrixMultiplication.java │ ├── DualMatrixMapTask.java │ ├── DualMatrixMapTaskOperator.java │ └── MatrixMapTask.java └── test └── java └── com └── clust4j ├── TestClust4j.java ├── TestGlobals.java ├── TestPublicAPI.java ├── TestSuite.java ├── algo ├── AffinityPropagationTests.java ├── BaseModelTest.java ├── BoruvkaTests.java ├── ClassifierTest.java ├── ClustTests.java ├── ClusterTest.java ├── ConvergeableTest.java ├── DBSCANTests.java ├── HDBSCANTests.java ├── HierarchicalTests.java ├── KMeansTests.java ├── KMedoidsTests.java ├── MeanShiftTests.java ├── NNHSTests.java ├── NearestCentroidTests.java ├── NearestNeighborsTests.java ├── ParallelTaskTests.java ├── RadiusNeighborsTests.java ├── TestLabelEncoder.java ├── pipeline │ └── PipelineTest.java └── preprocess │ ├── ImputationTests.java │ └── PreProcessorTests.java ├── data ├── BufferedMatrixReaderTests.java ├── SerializableObject.java ├── TestDataSet.java └── TrainTestSplitTests.java ├── except └── TestExcept.java ├── kernel └── KernelTestCases.java ├── load ├── LoadTests.java └── TestAll.java ├── log └── LogTest.java ├── metrics ├── pairwise │ ├── HaversineTest.java │ ├── PairwiseTests.java │ └── TestDistanceEnums.java └── scoring │ └── TestMetrics.java ├── optimize └── TestOptimizer.java ├── sample └── BootstrapTest.java └── utils ├── FormatterTests.java ├── HeapTests.java ├── MatTests.java ├── QuadTupTests.java ├── SeriesTests.java ├── TestArrayFormatter.java ├── 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