Merge pull request #4338 from VesnaT/outlier_detection

[RFC][ENH] Outliers: Widget upgrade

Orange/classification/__init__.py

@@ -15,7 +15,7 @@
 from .tree import *
 from .simple_tree import *
 from .simple_random_forest import *
-from .elliptic_envelope import *
+from .outlier_detection import *
 from .rules import *
 from .sgd import *
 from .neural_network import *

Orange/classification/outlier_detection.py

@@ -0,0 +1,73 @@
+# pylint: disable=unused-argument
+from sklearn.covariance import EllipticEnvelope
+from sklearn.ensemble import IsolationForest
+from sklearn.neighbors import LocalOutlierFactor
+from Orange.base import SklLearner, SklModel
+from Orange.data import Table, Domain
+
+__all__ = ["LocalOutlierFactorLearner", "IsolationForestLearner",
+           "EllipticEnvelopeLearner"]
+
+
+class _OutlierDetector(SklLearner):
+    def __call__(self, data: Table):
+        data = data.transform(Domain(data.domain.attributes))
+        return super().__call__(data)
+
+
+class LocalOutlierFactorLearner(_OutlierDetector):
+    __wraps__ = LocalOutlierFactor
+    name = "Local Outlier Factor"
+
+    def __init__(self, n_neighbors=20, algorithm="auto", leaf_size=30,
+                 metric="minkowski", p=2, metric_params=None,
+                 contamination="auto", novelty=True, n_jobs=None,
+                 preprocessors=None):
+        super().__init__(preprocessors=preprocessors)
+        self.params = vars()
+
+
+class IsolationForestLearner(_OutlierDetector):
+    __wraps__ = IsolationForest
+    name = "Isolation Forest"
+
+    def __init__(self, n_estimators=100, max_samples='auto',
+                 contamination='auto', max_features=1.0, bootstrap=False,
+                 n_jobs=None, behaviour='deprecated', random_state=None,
+                 verbose=0, warm_start=False, preprocessors=None):
+        super().__init__(preprocessors=preprocessors)
+        self.params = vars()
+
+
+class EllipticEnvelopeClassifier(SklModel):
+    def mahalanobis(self, observations):
+        """Computes squared Mahalanobis distances of given observations.
+
+        Parameters
+        ----------
+        observations : ndarray (n_samples, n_features) or Orange Table
+
+        Returns
+        -------
+        distances : ndarray (n_samples,)
+            Squared Mahalanobis distances given observations.
+        """
+        if isinstance(observations, Table):
+            observations = observations.X
+        return self.skl_model.mahalanobis(observations)
+
+
+class EllipticEnvelopeLearner(_OutlierDetector):
+    __wraps__ = EllipticEnvelope
+    __returns__ = EllipticEnvelopeClassifier
+    name = "Covariance Estimator"
+
+    def __init__(self, store_precision=True, assume_centered=False,
+                 support_fraction=None, contamination=0.1,
+                 random_state=None, preprocessors=None):
+        super().__init__(preprocessors=preprocessors)
+        self.params = vars()
+
+    def __call__(self, data: Table):
+        data = data.transform(Domain(data.domain.attributes))
+        return super().__call__(data)

Orange/classification/svm.py

@@ -69,6 +69,7 @@ def __init__(self, nu=0.5, kernel='rbf', degree=3, gamma="auto", coef0=0.0,
 
 
 class OneClassSVMLearner(SklLearnerBase):
+    name = "One class SVM"
     __wraps__ = skl_svm.OneClassSVM
     preprocessors = svm_pps
 

Orange/tests/test_elliptic_envelope.py → Orange/classification/tests/test_outlier_detection.py

@@ -5,7 +5,8 @@
 
 import numpy as np
 from Orange.data import Table, Domain, ContinuousVariable
-from Orange.classification import EllipticEnvelopeLearner
+from Orange.classification import EllipticEnvelopeLearner, \
+    IsolationForestLearner, LocalOutlierFactorLearner
 
 
 class TestEllipticEnvelopeLearner(unittest.TestCase):
@@ -44,7 +45,7 @@ def test_mahalanobis(self):
 
     def test_EllipticEnvelope_ignores_y(self):
         domain = Domain((ContinuousVariable("x1"), ContinuousVariable("x2")),
-                        class_vars=(ContinuousVariable("y1"), ContinuousVariable("y2")))
+                        (ContinuousVariable("y1"), ContinuousVariable("y2")))
         X = np.random.random((40, 2))
         Y = np.random.random((40, 2))
         table = Table(domain, X, Y)
@@ -60,3 +61,25 @@ def test_EllipticEnvelope_ignores_y(self):
         np.testing.assert_array_equal(pred1, pred2)
         np.testing.assert_array_equal(pred2, pred3)
         np.testing.assert_array_equal(pred3, pred4)
+
+
+class TestOutlierDetection(unittest.TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls.iris = Table("iris")
+
+    def test_LocalOutlierFactorDetector(self):
+        detector = LocalOutlierFactorLearner(contamination=0.1)
+        detect = detector(self.iris)
+        is_inlier = detect(self.iris)
+        self.assertEqual(len(np.where(is_inlier == -1)[0]), 14)
+
+    def test_IsolationForestDetector(self):
+        detector = IsolationForestLearner(contamination=0.1)
+        detect = detector(self.iris)
+        is_inlier = detect(self.iris)
+        self.assertEqual(len(np.where(is_inlier == -1)[0]), 15)
+
+
+if __name__ == "__main__":
+    unittest.main()