Merge remote-tracking branch 'rubixml/2.5'

RubixML · Jan 15, 2024 · 50d00bf · 50d00bf
2 parents 703404b + 865e54a
commit 50d00bf
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Showing 543 changed files with 2,521 additions and 1,654 deletions.
diff --git a/.php-cs-fixer.dist.php b/.php-cs-fixer.dist.php
@@ -27,7 +27,7 @@
     'class_attributes_separation' => true,
     'combine_consecutive_issets' => true,
     'combine_consecutive_unsets' => true,
-    'compact_nullable_typehint' => true,
+    'compact_nullable_type_declaration' => true,
     'concat_space' => ['spacing' => 'one'],
     'fully_qualified_strict_types' => true,
     'increment_style' => ['style' => 'pre'],
@@ -42,8 +42,8 @@
         'strategy' => 'no_multi_line',
     ],
     'native_function_casing' => true,
-    'native_function_type_declaration_casing' => true,
-    'new_with_braces' => true,
+    'native_type_declaration_casing' => true,
+    'new_with_parentheses' => true,
     'no_alternative_syntax' => true,
     'no_blank_lines_after_class_opening' => true,
     'no_blank_lines_after_phpdoc' => true,
@@ -60,7 +60,7 @@
     'no_superfluous_elseif' => true,
     'no_trailing_comma_in_singleline' => true,
     'no_unneeded_control_parentheses' => true,
-    'no_unneeded_curly_braces' => true,
+    'no_unneeded_braces' => true,
     'no_unset_cast' => true,
     'no_unused_imports' => true,
     'no_useless_else' => true,

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,7 @@
+- 2.5.0
+    - Added Vantage Point Spatial tree
+    - Blob Generator can now `simulate()` a Dataset object
+
 - 2.4.1
     - Sentence Tokenizer fix Arabic and Farsi language support
     - Optimize online variance updating

diff --git a/benchmarks/AnomalyDetectors/GaussianMLEBench.php b/benchmarks/AnomalyDetectors/GaussianMLEBench.php
@@ -27,7 +27,7 @@ class GaussianMLEBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\AnomalyDetectors\GaussianMLE
+     * @var GaussianMLE
      */
     protected $estimator;
 

diff --git a/benchmarks/AnomalyDetectors/IsolationForestBench.php b/benchmarks/AnomalyDetectors/IsolationForestBench.php
@@ -27,7 +27,7 @@ class IsolationForestBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\AnomalyDetectors\IsolationForest
+     * @var IsolationForest
      */
     protected $estimator;
 

diff --git a/benchmarks/AnomalyDetectors/LocalOutlierFactorBench.php b/benchmarks/AnomalyDetectors/LocalOutlierFactorBench.php
@@ -27,7 +27,7 @@ class LocalOutlierFactorBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\AnomalyDetectors\LocalOutlierFactor
+     * @var LocalOutlierFactor
      */
     protected $estimator;
 

diff --git a/benchmarks/AnomalyDetectors/LodaBench.php b/benchmarks/AnomalyDetectors/LodaBench.php
@@ -27,7 +27,7 @@ class LodaBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\AnomalyDetectors\Loda
+     * @var Loda
      */
     protected $estimator;
 

diff --git a/benchmarks/AnomalyDetectors/OneClassSVMBench.php b/benchmarks/AnomalyDetectors/OneClassSVMBench.php
@@ -27,7 +27,7 @@ class OneClassSVMBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\AnomalyDetectors\OneClassSVM
+     * @var OneClassSVM
      */
     protected $estimator;
 

diff --git a/benchmarks/AnomalyDetectors/RobustZScoreBench.php b/benchmarks/AnomalyDetectors/RobustZScoreBench.php
@@ -27,7 +27,7 @@ class RobustZScoreBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\AnomalyDetectors\RobustZScore
+     * @var RobustZScore
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/AdaBoostBench.php b/benchmarks/Classifiers/AdaBoostBench.php
@@ -28,7 +28,7 @@ class AdaBoostBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\AdaBoost
+     * @var AdaBoost
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/ClassificationTreeBench.php b/benchmarks/Classifiers/ClassificationTreeBench.php
@@ -27,7 +27,7 @@ class ClassificationTreeBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\ClassificationTree
+     * @var ClassificationTree
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/ExtraTreeClassifierBench.php b/benchmarks/Classifiers/ExtraTreeClassifierBench.php
@@ -27,7 +27,7 @@ class ExtraTreeClassifierBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\ExtraTreeClassifier
+     * @var ExtraTreeClassifier
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/GaussianNBBench.php b/benchmarks/Classifiers/GaussianNBBench.php
@@ -27,7 +27,7 @@ class GaussianNBBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\GaussianNB
+     * @var GaussianNB
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/KDNeighborsBench.php b/benchmarks/Classifiers/KDNeighborsBench.php
@@ -27,7 +27,7 @@ class KDNeighborsBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\KDNeighbors
+     * @var KDNeighbors
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/KNearestNeighborsBench.php b/benchmarks/Classifiers/KNearestNeighborsBench.php
@@ -27,7 +27,7 @@ class KNearestNeighborsBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\KNearestNeighbors
+     * @var KNearestNeighbors
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/LogisticRegressionBench.php b/benchmarks/Classifiers/LogisticRegressionBench.php
@@ -27,7 +27,7 @@ class LogisticRegressionBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\LogisticRegression
+     * @var LogisticRegression
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/LogitBoostBench.php b/benchmarks/Classifiers/LogitBoostBench.php
@@ -27,7 +27,7 @@ class LogitBoostBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\LogitBoost
+     * @var LogitBoost
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/MultilayerPerceptronBench.php b/benchmarks/Classifiers/MultilayerPerceptronBench.php
@@ -30,7 +30,7 @@ class MultilayerPerceptronBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\MultilayerPerceptron
+     * @var MultilayerPerceptron
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/NaiveBayesBench.php b/benchmarks/Classifiers/NaiveBayesBench.php
@@ -28,7 +28,7 @@ class NaiveBayesBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\NaiveBayes
+     * @var NaiveBayes
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/OneVsRestBench.php b/benchmarks/Classifiers/OneVsRestBench.php
@@ -33,7 +33,7 @@ class OneVsRestBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\OneVsRest
+     * @var OneVsRest
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/RadiusNeighborsBench.php b/benchmarks/Classifiers/RadiusNeighborsBench.php
@@ -27,7 +27,7 @@ class RadiusNeighborsBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\RadiusNeighbors
+     * @var RadiusNeighbors
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/RandomForestBench.php b/benchmarks/Classifiers/RandomForestBench.php
@@ -32,7 +32,7 @@ class RandomForestBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\RandomForest
+     * @var RandomForest
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/SVCBench.php b/benchmarks/Classifiers/SVCBench.php
@@ -28,7 +28,7 @@ class SVCBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\SVC
+     * @var SVC
      */
     protected $estimator;
 

diff --git a/benchmarks/Classifiers/SoftmaxClassifierBench.php b/benchmarks/Classifiers/SoftmaxClassifierBench.php
@@ -27,7 +27,7 @@ class SoftmaxClassifierBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Classifiers\SoftmaxClassifier
+     * @var SoftmaxClassifier
      */
     protected $estimator;
 

diff --git a/benchmarks/Clusterers/DBSCANBench.php b/benchmarks/Clusterers/DBSCANBench.php
@@ -20,7 +20,7 @@ class DBSCANBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Clusterers\DBSCAN
+     * @var DBSCAN
      */
     protected $estimator;
 

diff --git a/benchmarks/Clusterers/FuzzyCMeansBench.php b/benchmarks/Clusterers/FuzzyCMeansBench.php
@@ -27,7 +27,7 @@ class FuzzyCMeansBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Clusterers\FuzzyCMeans
+     * @var FuzzyCMeans
      */
     protected $estimator;
 

diff --git a/benchmarks/Clusterers/GaussianMixtureBench.php b/benchmarks/Clusterers/GaussianMixtureBench.php
@@ -27,7 +27,7 @@ class GaussianMixtureBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Clusterers\GaussianMixture
+     * @var GaussianMixture
      */
     protected $estimator;
 

diff --git a/benchmarks/Clusterers/KMeansBench.php b/benchmarks/Clusterers/KMeansBench.php
@@ -27,7 +27,7 @@ class KMeansBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Clusterers\KMeans
+     * @var KMeans
      */
     protected $estimator;
 

diff --git a/benchmarks/Clusterers/MeanShiftBench.php b/benchmarks/Clusterers/MeanShiftBench.php
@@ -27,7 +27,7 @@ class MeanShiftBench
     protected $testing;
 
     /**
-     * @var \Rubix\ML\Clusterers\MeanShift
+     * @var MeanShift
      */
     protected $estimator;
 

diff --git a/benchmarks/Graph/Trees/BallTreeBench.php b/benchmarks/Graph/Trees/BallTreeBench.php
@@ -20,7 +20,7 @@ class BallTreeBench
     protected $dataset;
 
     /**
-     * @var \Rubix\ML\Graph\Trees\BallTree
+     * @var BallTree
      */
     protected $tree;
 

diff --git a/benchmarks/Graph/Trees/KDTreeBench.php b/benchmarks/Graph/Trees/KDTreeBench.php
@@ -20,7 +20,7 @@ class KDTreeBench
     protected $dataset;
 
     /**
-     * @var \Rubix\ML\Graph\Trees\KDTree
+     * @var KDTree
      */
     protected $tree;
 

diff --git a/benchmarks/Graph/Trees/VantageTreeBench.php b/benchmarks/Graph/Trees/VantageTreeBench.php
@@ -0,0 +1,49 @@
+<?php
+
+namespace Rubix\ML\Benchmarks\Graph\Trees;
+
+use Rubix\ML\Graph\Trees\VantageTree;
+use Rubix\ML\Datasets\Generators\Blob;
+use Rubix\ML\Datasets\Generators\Agglomerate;
+
+/**
+ * @Groups({"Trees"})
+ * @BeforeMethods({"setUp"})
+ */
+class VantageTreeBench
+{
+    protected const DATASET_SIZE = 10000;
+
+    /**
+     * @var \Rubix\ML\Datasets\Labeled;
+     */
+    protected $dataset;
+
+    /**
+     * @var VantageTree
+     */
+    protected $tree;
+
+    public function setUp() : void
+    {
+        $generator = new Agglomerate([
+            'Iris-setosa' => new Blob([5.0, 3.42, 1.46, 0.24], [0.35, 0.38, 0.17, 0.1]),
+            'Iris-versicolor' => new Blob([5.94, 2.77, 4.26, 1.33], [0.51, 0.31, 0.47, 0.2]),
+            'Iris-virginica' => new Blob([6.59, 2.97, 5.55, 2.03], [0.63, 0.32, 0.55, 0.27]),
+        ]);
+
+        $this->dataset = $generator->generate(self::DATASET_SIZE);
+
+        $this->tree = new VantageTree(30);
+    }
+
+    /**
+     * @Subject
+     * @Iterations(3)
+     * @OutputTimeUnit("seconds", precision=3)
+     */
+    public function grow() : void
+    {
+        $this->tree->grow($this->dataset);
+    }
+}
diff --git a/benchmarks/Kernels/Distance/CanberraBench.php b/benchmarks/Kernels/Distance/CanberraBench.php
@@ -24,7 +24,7 @@ class CanberraBench
     protected $bSamples;
 
     /**
-     * @var \Rubix\ML\Kernels\Distance\Canberra
+     * @var Canberra
      */
     protected $kernel;
 

diff --git a/benchmarks/Kernels/Distance/CosineBench.php b/benchmarks/Kernels/Distance/CosineBench.php
@@ -23,7 +23,7 @@ class CosineBench
     protected $bSamples;
 
     /**
-     * @var \Rubix\ML\Kernels\Distance\Cosine
+     * @var Cosine
      */
     protected $kernel;
 

diff --git a/benchmarks/Kernels/Distance/DiagonalBench.php b/benchmarks/Kernels/Distance/DiagonalBench.php
@@ -24,7 +24,7 @@ class DiagonalBench
     protected $bSamples;
 
     /**
-     * @var \Rubix\ML\Kernels\Distance\Diagonal
+     * @var Diagonal
      */
     protected $kernel;
 

diff --git a/benchmarks/Kernels/Distance/EuclideanBench.php b/benchmarks/Kernels/Distance/EuclideanBench.php
@@ -24,7 +24,7 @@ class EuclideanBench
     protected $bSamples;
 
     /**
-     * @var \Rubix\ML\Kernels\Distance\Euclidean
+     * @var Euclidean
      */
     protected $kernel;
 

diff --git a/benchmarks/Kernels/Distance/GowerBench.php b/benchmarks/Kernels/Distance/GowerBench.php
@@ -25,7 +25,7 @@ class GowerBench
     protected $bSamples;
 
     /**
-     * @var \Rubix\ML\Kernels\Distance\Gower
+     * @var Gower
      */
     protected $kernel;
 

diff --git a/benchmarks/Kernels/Distance/JaccardBench.php b/benchmarks/Kernels/Distance/JaccardBench.php
@@ -24,7 +24,7 @@ class JaccardBench
     protected $bSamples;
 
     /**
-     * @var \Rubix\ML\Kernels\Distance\Jaccard
+     * @var Jaccard
      */
     protected $kernel;