257cde7c36
Weight parameters must be initialized correctly even when numpy array is passed as initial weights. Author: lewuathe <lewuathe@me.com> Closes #5101 from Lewuathe/SPARK-6421 and squashes the following commits: 7795201 [lewuathe] Fix lint-python errors 21d4fe3 [lewuathe] Fix init logic of weights
629 lines
26 KiB
Python
629 lines
26 KiB
Python
#
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# Licensed to the Apache Software Foundation (ASF) under one or more
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# contributor license agreements. See the NOTICE file distributed with
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# this work for additional information regarding copyright ownership.
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# The ASF licenses this file to You under the Apache License, Version 2.0
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# (the "License"); you may not use this file except in compliance with
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# the License. You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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"""
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Fuller unit tests for Python MLlib.
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"""
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import os
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import sys
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import tempfile
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import array as pyarray
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from numpy import array, array_equal
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from py4j.protocol import Py4JJavaError
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if sys.version_info[:2] <= (2, 6):
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try:
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import unittest2 as unittest
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except ImportError:
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sys.stderr.write('Please install unittest2 to test with Python 2.6 or earlier')
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sys.exit(1)
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else:
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import unittest
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from pyspark.mllib.linalg import Vector, SparseVector, DenseVector, VectorUDT, _convert_to_vector,\
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DenseMatrix, Vectors, Matrices
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from pyspark.mllib.regression import LabeledPoint
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from pyspark.mllib.random import RandomRDDs
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from pyspark.mllib.stat import Statistics
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from pyspark.serializers import PickleSerializer
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from pyspark.sql import SQLContext
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from pyspark.tests import ReusedPySparkTestCase as PySparkTestCase
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_have_scipy = False
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try:
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import scipy.sparse
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_have_scipy = True
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except:
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# No SciPy, but that's okay, we'll skip those tests
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pass
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ser = PickleSerializer()
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def _squared_distance(a, b):
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if isinstance(a, Vector):
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return a.squared_distance(b)
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else:
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return b.squared_distance(a)
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class VectorTests(PySparkTestCase):
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def _test_serialize(self, v):
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self.assertEqual(v, ser.loads(ser.dumps(v)))
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jvec = self.sc._jvm.SerDe.loads(bytearray(ser.dumps(v)))
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nv = ser.loads(str(self.sc._jvm.SerDe.dumps(jvec)))
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self.assertEqual(v, nv)
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vs = [v] * 100
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jvecs = self.sc._jvm.SerDe.loads(bytearray(ser.dumps(vs)))
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nvs = ser.loads(str(self.sc._jvm.SerDe.dumps(jvecs)))
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self.assertEqual(vs, nvs)
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def test_serialize(self):
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self._test_serialize(DenseVector(range(10)))
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self._test_serialize(DenseVector(array([1., 2., 3., 4.])))
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self._test_serialize(DenseVector(pyarray.array('d', range(10))))
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self._test_serialize(SparseVector(4, {1: 1, 3: 2}))
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self._test_serialize(SparseVector(3, {}))
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self._test_serialize(DenseMatrix(2, 3, range(6)))
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def test_dot(self):
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sv = SparseVector(4, {1: 1, 3: 2})
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dv = DenseVector(array([1., 2., 3., 4.]))
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lst = DenseVector([1, 2, 3, 4])
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mat = array([[1., 2., 3., 4.],
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[1., 2., 3., 4.],
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[1., 2., 3., 4.],
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[1., 2., 3., 4.]])
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self.assertEquals(10.0, sv.dot(dv))
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self.assertTrue(array_equal(array([3., 6., 9., 12.]), sv.dot(mat)))
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self.assertEquals(30.0, dv.dot(dv))
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self.assertTrue(array_equal(array([10., 20., 30., 40.]), dv.dot(mat)))
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self.assertEquals(30.0, lst.dot(dv))
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self.assertTrue(array_equal(array([10., 20., 30., 40.]), lst.dot(mat)))
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def test_squared_distance(self):
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sv = SparseVector(4, {1: 1, 3: 2})
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dv = DenseVector(array([1., 2., 3., 4.]))
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lst = DenseVector([4, 3, 2, 1])
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self.assertEquals(15.0, _squared_distance(sv, dv))
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self.assertEquals(25.0, _squared_distance(sv, lst))
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self.assertEquals(20.0, _squared_distance(dv, lst))
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self.assertEquals(15.0, _squared_distance(dv, sv))
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self.assertEquals(25.0, _squared_distance(lst, sv))
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self.assertEquals(20.0, _squared_distance(lst, dv))
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self.assertEquals(0.0, _squared_distance(sv, sv))
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self.assertEquals(0.0, _squared_distance(dv, dv))
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self.assertEquals(0.0, _squared_distance(lst, lst))
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def test_conversion(self):
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# numpy arrays should be automatically upcast to float64
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# tests for fix of [SPARK-5089]
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v = array([1, 2, 3, 4], dtype='float64')
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dv = DenseVector(v)
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self.assertTrue(dv.array.dtype == 'float64')
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v = array([1, 2, 3, 4], dtype='float32')
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dv = DenseVector(v)
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self.assertTrue(dv.array.dtype == 'float64')
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def test_sparse_vector_indexing(self):
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sv = SparseVector(4, {1: 1, 3: 2})
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self.assertEquals(sv[0], 0.)
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self.assertEquals(sv[3], 2.)
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self.assertEquals(sv[1], 1.)
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self.assertEquals(sv[2], 0.)
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self.assertEquals(sv[-1], 2)
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self.assertEquals(sv[-2], 0)
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self.assertEquals(sv[-4], 0)
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for ind in [4, -5, 7.8]:
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self.assertRaises(ValueError, sv.__getitem__, ind)
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class ListTests(PySparkTestCase):
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"""
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Test MLlib algorithms on plain lists, to make sure they're passed through
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as NumPy arrays.
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"""
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def test_kmeans(self):
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from pyspark.mllib.clustering import KMeans
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data = [
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[0, 1.1],
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[0, 1.2],
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[1.1, 0],
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[1.2, 0],
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]
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clusters = KMeans.train(self.sc.parallelize(data), 2, initializationMode="k-means||")
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self.assertEquals(clusters.predict(data[0]), clusters.predict(data[1]))
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self.assertEquals(clusters.predict(data[2]), clusters.predict(data[3]))
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def test_kmeans_deterministic(self):
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from pyspark.mllib.clustering import KMeans
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X = range(0, 100, 10)
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Y = range(0, 100, 10)
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data = [[x, y] for x, y in zip(X, Y)]
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clusters1 = KMeans.train(self.sc.parallelize(data),
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3, initializationMode="k-means||", seed=42)
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clusters2 = KMeans.train(self.sc.parallelize(data),
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3, initializationMode="k-means||", seed=42)
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centers1 = clusters1.centers
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centers2 = clusters2.centers
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for c1, c2 in zip(centers1, centers2):
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# TODO: Allow small numeric difference.
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self.assertTrue(array_equal(c1, c2))
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def test_gmm(self):
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from pyspark.mllib.clustering import GaussianMixture
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data = self.sc.parallelize([
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[1, 2],
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[8, 9],
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[-4, -3],
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[-6, -7],
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])
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clusters = GaussianMixture.train(data, 2, convergenceTol=0.001,
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maxIterations=100, seed=56)
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labels = clusters.predict(data).collect()
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self.assertEquals(labels[0], labels[1])
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self.assertEquals(labels[2], labels[3])
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def test_gmm_deterministic(self):
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from pyspark.mllib.clustering import GaussianMixture
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x = range(0, 100, 10)
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y = range(0, 100, 10)
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data = self.sc.parallelize([[a, b] for a, b in zip(x, y)])
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clusters1 = GaussianMixture.train(data, 5, convergenceTol=0.001,
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maxIterations=100, seed=63)
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clusters2 = GaussianMixture.train(data, 5, convergenceTol=0.001,
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maxIterations=100, seed=63)
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for c1, c2 in zip(clusters1.weights, clusters2.weights):
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self.assertEquals(round(c1, 7), round(c2, 7))
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def test_classification(self):
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from pyspark.mllib.classification import LogisticRegressionWithSGD, SVMWithSGD, NaiveBayes
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from pyspark.mllib.tree import DecisionTree, DecisionTreeModel, RandomForest,\
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RandomForestModel, GradientBoostedTrees, GradientBoostedTreesModel
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data = [
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LabeledPoint(0.0, [1, 0, 0]),
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LabeledPoint(1.0, [0, 1, 1]),
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LabeledPoint(0.0, [2, 0, 0]),
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LabeledPoint(1.0, [0, 2, 1])
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]
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rdd = self.sc.parallelize(data)
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features = [p.features.tolist() for p in data]
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temp_dir = tempfile.mkdtemp()
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lr_model = LogisticRegressionWithSGD.train(rdd)
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self.assertTrue(lr_model.predict(features[0]) <= 0)
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self.assertTrue(lr_model.predict(features[1]) > 0)
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self.assertTrue(lr_model.predict(features[2]) <= 0)
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self.assertTrue(lr_model.predict(features[3]) > 0)
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svm_model = SVMWithSGD.train(rdd)
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self.assertTrue(svm_model.predict(features[0]) <= 0)
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self.assertTrue(svm_model.predict(features[1]) > 0)
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self.assertTrue(svm_model.predict(features[2]) <= 0)
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self.assertTrue(svm_model.predict(features[3]) > 0)
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nb_model = NaiveBayes.train(rdd)
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self.assertTrue(nb_model.predict(features[0]) <= 0)
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self.assertTrue(nb_model.predict(features[1]) > 0)
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self.assertTrue(nb_model.predict(features[2]) <= 0)
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self.assertTrue(nb_model.predict(features[3]) > 0)
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categoricalFeaturesInfo = {0: 3} # feature 0 has 3 categories
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dt_model = DecisionTree.trainClassifier(
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rdd, numClasses=2, categoricalFeaturesInfo=categoricalFeaturesInfo)
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self.assertTrue(dt_model.predict(features[0]) <= 0)
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self.assertTrue(dt_model.predict(features[1]) > 0)
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self.assertTrue(dt_model.predict(features[2]) <= 0)
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self.assertTrue(dt_model.predict(features[3]) > 0)
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dt_model_dir = os.path.join(temp_dir, "dt")
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dt_model.save(self.sc, dt_model_dir)
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same_dt_model = DecisionTreeModel.load(self.sc, dt_model_dir)
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self.assertEqual(same_dt_model.toDebugString(), dt_model.toDebugString())
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rf_model = RandomForest.trainClassifier(
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rdd, numClasses=2, categoricalFeaturesInfo=categoricalFeaturesInfo, numTrees=100)
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self.assertTrue(rf_model.predict(features[0]) <= 0)
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self.assertTrue(rf_model.predict(features[1]) > 0)
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self.assertTrue(rf_model.predict(features[2]) <= 0)
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self.assertTrue(rf_model.predict(features[3]) > 0)
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rf_model_dir = os.path.join(temp_dir, "rf")
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rf_model.save(self.sc, rf_model_dir)
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same_rf_model = RandomForestModel.load(self.sc, rf_model_dir)
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self.assertEqual(same_rf_model.toDebugString(), rf_model.toDebugString())
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gbt_model = GradientBoostedTrees.trainClassifier(
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rdd, categoricalFeaturesInfo=categoricalFeaturesInfo)
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self.assertTrue(gbt_model.predict(features[0]) <= 0)
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self.assertTrue(gbt_model.predict(features[1]) > 0)
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self.assertTrue(gbt_model.predict(features[2]) <= 0)
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self.assertTrue(gbt_model.predict(features[3]) > 0)
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gbt_model_dir = os.path.join(temp_dir, "gbt")
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gbt_model.save(self.sc, gbt_model_dir)
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same_gbt_model = GradientBoostedTreesModel.load(self.sc, gbt_model_dir)
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self.assertEqual(same_gbt_model.toDebugString(), gbt_model.toDebugString())
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try:
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os.removedirs(temp_dir)
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except OSError:
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pass
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def test_regression(self):
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from pyspark.mllib.regression import LinearRegressionWithSGD, LassoWithSGD, \
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RidgeRegressionWithSGD
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from pyspark.mllib.tree import DecisionTree, RandomForest, GradientBoostedTrees
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data = [
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LabeledPoint(-1.0, [0, -1]),
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LabeledPoint(1.0, [0, 1]),
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LabeledPoint(-1.0, [0, -2]),
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LabeledPoint(1.0, [0, 2])
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]
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rdd = self.sc.parallelize(data)
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features = [p.features.tolist() for p in data]
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lr_model = LinearRegressionWithSGD.train(rdd)
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self.assertTrue(lr_model.predict(features[0]) <= 0)
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self.assertTrue(lr_model.predict(features[1]) > 0)
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self.assertTrue(lr_model.predict(features[2]) <= 0)
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self.assertTrue(lr_model.predict(features[3]) > 0)
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lasso_model = LassoWithSGD.train(rdd)
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self.assertTrue(lasso_model.predict(features[0]) <= 0)
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self.assertTrue(lasso_model.predict(features[1]) > 0)
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self.assertTrue(lasso_model.predict(features[2]) <= 0)
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self.assertTrue(lasso_model.predict(features[3]) > 0)
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rr_model = RidgeRegressionWithSGD.train(rdd)
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self.assertTrue(rr_model.predict(features[0]) <= 0)
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self.assertTrue(rr_model.predict(features[1]) > 0)
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self.assertTrue(rr_model.predict(features[2]) <= 0)
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self.assertTrue(rr_model.predict(features[3]) > 0)
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categoricalFeaturesInfo = {0: 2} # feature 0 has 2 categories
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dt_model = DecisionTree.trainRegressor(
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rdd, categoricalFeaturesInfo=categoricalFeaturesInfo)
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self.assertTrue(dt_model.predict(features[0]) <= 0)
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self.assertTrue(dt_model.predict(features[1]) > 0)
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self.assertTrue(dt_model.predict(features[2]) <= 0)
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self.assertTrue(dt_model.predict(features[3]) > 0)
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rf_model = RandomForest.trainRegressor(
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rdd, categoricalFeaturesInfo=categoricalFeaturesInfo, numTrees=100, seed=1)
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self.assertTrue(rf_model.predict(features[0]) <= 0)
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self.assertTrue(rf_model.predict(features[1]) > 0)
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self.assertTrue(rf_model.predict(features[2]) <= 0)
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self.assertTrue(rf_model.predict(features[3]) > 0)
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gbt_model = GradientBoostedTrees.trainRegressor(
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rdd, categoricalFeaturesInfo=categoricalFeaturesInfo)
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self.assertTrue(gbt_model.predict(features[0]) <= 0)
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self.assertTrue(gbt_model.predict(features[1]) > 0)
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self.assertTrue(gbt_model.predict(features[2]) <= 0)
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self.assertTrue(gbt_model.predict(features[3]) > 0)
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try:
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LinearRegressionWithSGD.train(rdd, initialWeights=array([1.0, 1.0]))
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LassoWithSGD.train(rdd, initialWeights=array([1.0, 1.0]))
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RidgeRegressionWithSGD.train(rdd, initialWeights=array([1.0, 1.0]))
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except ValueError:
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self.fail()
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class StatTests(PySparkTestCase):
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# SPARK-4023
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def test_col_with_different_rdds(self):
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# numpy
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data = RandomRDDs.normalVectorRDD(self.sc, 1000, 10, 10)
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summary = Statistics.colStats(data)
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self.assertEqual(1000, summary.count())
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# array
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data = self.sc.parallelize([range(10)] * 10)
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summary = Statistics.colStats(data)
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self.assertEqual(10, summary.count())
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# array
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data = self.sc.parallelize([pyarray.array("d", range(10))] * 10)
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summary = Statistics.colStats(data)
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self.assertEqual(10, summary.count())
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class VectorUDTTests(PySparkTestCase):
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dv0 = DenseVector([])
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dv1 = DenseVector([1.0, 2.0])
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sv0 = SparseVector(2, [], [])
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sv1 = SparseVector(2, [1], [2.0])
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udt = VectorUDT()
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def test_json_schema(self):
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self.assertEqual(VectorUDT.fromJson(self.udt.jsonValue()), self.udt)
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def test_serialization(self):
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for v in [self.dv0, self.dv1, self.sv0, self.sv1]:
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self.assertEqual(v, self.udt.deserialize(self.udt.serialize(v)))
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def test_infer_schema(self):
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sqlCtx = SQLContext(self.sc)
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rdd = self.sc.parallelize([LabeledPoint(1.0, self.dv1), LabeledPoint(0.0, self.sv1)])
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srdd = sqlCtx.inferSchema(rdd)
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schema = srdd.schema
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field = [f for f in schema.fields if f.name == "features"][0]
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self.assertEqual(field.dataType, self.udt)
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vectors = srdd.map(lambda p: p.features).collect()
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self.assertEqual(len(vectors), 2)
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for v in vectors:
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if isinstance(v, SparseVector):
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self.assertEqual(v, self.sv1)
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elif isinstance(v, DenseVector):
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self.assertEqual(v, self.dv1)
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else:
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raise ValueError("expecting a vector but got %r of type %r" % (v, type(v)))
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@unittest.skipIf(not _have_scipy, "SciPy not installed")
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class SciPyTests(PySparkTestCase):
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"""
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Test both vector operations and MLlib algorithms with SciPy sparse matrices,
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if SciPy is available.
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"""
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def test_serialize(self):
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from scipy.sparse import lil_matrix
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lil = lil_matrix((4, 1))
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lil[1, 0] = 1
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lil[3, 0] = 2
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sv = SparseVector(4, {1: 1, 3: 2})
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self.assertEquals(sv, _convert_to_vector(lil))
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self.assertEquals(sv, _convert_to_vector(lil.tocsc()))
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self.assertEquals(sv, _convert_to_vector(lil.tocoo()))
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self.assertEquals(sv, _convert_to_vector(lil.tocsr()))
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self.assertEquals(sv, _convert_to_vector(lil.todok()))
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def serialize(l):
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return ser.loads(ser.dumps(_convert_to_vector(l)))
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self.assertEquals(sv, serialize(lil))
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self.assertEquals(sv, serialize(lil.tocsc()))
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self.assertEquals(sv, serialize(lil.tocsr()))
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self.assertEquals(sv, serialize(lil.todok()))
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def test_dot(self):
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from scipy.sparse import lil_matrix
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lil = lil_matrix((4, 1))
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lil[1, 0] = 1
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lil[3, 0] = 2
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dv = DenseVector(array([1., 2., 3., 4.]))
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self.assertEquals(10.0, dv.dot(lil))
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|
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def test_squared_distance(self):
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from scipy.sparse import lil_matrix
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lil = lil_matrix((4, 1))
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lil[1, 0] = 3
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lil[3, 0] = 2
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dv = DenseVector(array([1., 2., 3., 4.]))
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sv = SparseVector(4, {0: 1, 1: 2, 2: 3, 3: 4})
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self.assertEquals(15.0, dv.squared_distance(lil))
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self.assertEquals(15.0, sv.squared_distance(lil))
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|
|
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def scipy_matrix(self, size, values):
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"""Create a column SciPy matrix from a dictionary of values"""
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|
from scipy.sparse import lil_matrix
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lil = lil_matrix((size, 1))
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for key, value in values.items():
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lil[key, 0] = value
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return lil
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|
|
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def test_clustering(self):
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from pyspark.mllib.clustering import KMeans
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data = [
|
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self.scipy_matrix(3, {1: 1.0}),
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self.scipy_matrix(3, {1: 1.1}),
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self.scipy_matrix(3, {2: 1.0}),
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|
self.scipy_matrix(3, {2: 1.1})
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]
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clusters = KMeans.train(self.sc.parallelize(data), 2, initializationMode="k-means||")
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self.assertEquals(clusters.predict(data[0]), clusters.predict(data[1]))
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self.assertEquals(clusters.predict(data[2]), clusters.predict(data[3]))
|
|
|
|
def test_classification(self):
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|
from pyspark.mllib.classification import LogisticRegressionWithSGD, SVMWithSGD, NaiveBayes
|
|
from pyspark.mllib.tree import DecisionTree
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|
data = [
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|
LabeledPoint(0.0, self.scipy_matrix(2, {0: 1.0})),
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|
LabeledPoint(1.0, self.scipy_matrix(2, {1: 1.0})),
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|
LabeledPoint(0.0, self.scipy_matrix(2, {0: 2.0})),
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|
LabeledPoint(1.0, self.scipy_matrix(2, {1: 2.0}))
|
|
]
|
|
rdd = self.sc.parallelize(data)
|
|
features = [p.features for p in data]
|
|
|
|
lr_model = LogisticRegressionWithSGD.train(rdd)
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|
self.assertTrue(lr_model.predict(features[0]) <= 0)
|
|
self.assertTrue(lr_model.predict(features[1]) > 0)
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|
self.assertTrue(lr_model.predict(features[2]) <= 0)
|
|
self.assertTrue(lr_model.predict(features[3]) > 0)
|
|
|
|
svm_model = SVMWithSGD.train(rdd)
|
|
self.assertTrue(svm_model.predict(features[0]) <= 0)
|
|
self.assertTrue(svm_model.predict(features[1]) > 0)
|
|
self.assertTrue(svm_model.predict(features[2]) <= 0)
|
|
self.assertTrue(svm_model.predict(features[3]) > 0)
|
|
|
|
nb_model = NaiveBayes.train(rdd)
|
|
self.assertTrue(nb_model.predict(features[0]) <= 0)
|
|
self.assertTrue(nb_model.predict(features[1]) > 0)
|
|
self.assertTrue(nb_model.predict(features[2]) <= 0)
|
|
self.assertTrue(nb_model.predict(features[3]) > 0)
|
|
|
|
categoricalFeaturesInfo = {0: 3} # feature 0 has 3 categories
|
|
dt_model = DecisionTree.trainClassifier(rdd, numClasses=2,
|
|
categoricalFeaturesInfo=categoricalFeaturesInfo)
|
|
self.assertTrue(dt_model.predict(features[0]) <= 0)
|
|
self.assertTrue(dt_model.predict(features[1]) > 0)
|
|
self.assertTrue(dt_model.predict(features[2]) <= 0)
|
|
self.assertTrue(dt_model.predict(features[3]) > 0)
|
|
|
|
def test_regression(self):
|
|
from pyspark.mllib.regression import LinearRegressionWithSGD, LassoWithSGD, \
|
|
RidgeRegressionWithSGD
|
|
from pyspark.mllib.tree import DecisionTree
|
|
data = [
|
|
LabeledPoint(-1.0, self.scipy_matrix(2, {1: -1.0})),
|
|
LabeledPoint(1.0, self.scipy_matrix(2, {1: 1.0})),
|
|
LabeledPoint(-1.0, self.scipy_matrix(2, {1: -2.0})),
|
|
LabeledPoint(1.0, self.scipy_matrix(2, {1: 2.0}))
|
|
]
|
|
rdd = self.sc.parallelize(data)
|
|
features = [p.features for p in data]
|
|
|
|
lr_model = LinearRegressionWithSGD.train(rdd)
|
|
self.assertTrue(lr_model.predict(features[0]) <= 0)
|
|
self.assertTrue(lr_model.predict(features[1]) > 0)
|
|
self.assertTrue(lr_model.predict(features[2]) <= 0)
|
|
self.assertTrue(lr_model.predict(features[3]) > 0)
|
|
|
|
lasso_model = LassoWithSGD.train(rdd)
|
|
self.assertTrue(lasso_model.predict(features[0]) <= 0)
|
|
self.assertTrue(lasso_model.predict(features[1]) > 0)
|
|
self.assertTrue(lasso_model.predict(features[2]) <= 0)
|
|
self.assertTrue(lasso_model.predict(features[3]) > 0)
|
|
|
|
rr_model = RidgeRegressionWithSGD.train(rdd)
|
|
self.assertTrue(rr_model.predict(features[0]) <= 0)
|
|
self.assertTrue(rr_model.predict(features[1]) > 0)
|
|
self.assertTrue(rr_model.predict(features[2]) <= 0)
|
|
self.assertTrue(rr_model.predict(features[3]) > 0)
|
|
|
|
categoricalFeaturesInfo = {0: 2} # feature 0 has 2 categories
|
|
dt_model = DecisionTree.trainRegressor(rdd, categoricalFeaturesInfo=categoricalFeaturesInfo)
|
|
self.assertTrue(dt_model.predict(features[0]) <= 0)
|
|
self.assertTrue(dt_model.predict(features[1]) > 0)
|
|
self.assertTrue(dt_model.predict(features[2]) <= 0)
|
|
self.assertTrue(dt_model.predict(features[3]) > 0)
|
|
|
|
|
|
class ChiSqTestTests(PySparkTestCase):
|
|
def test_goodness_of_fit(self):
|
|
from numpy import inf
|
|
|
|
observed = Vectors.dense([4, 6, 5])
|
|
pearson = Statistics.chiSqTest(observed)
|
|
|
|
# Validated against the R command `chisq.test(c(4, 6, 5), p=c(1/3, 1/3, 1/3))`
|
|
self.assertEqual(pearson.statistic, 0.4)
|
|
self.assertEqual(pearson.degreesOfFreedom, 2)
|
|
self.assertAlmostEqual(pearson.pValue, 0.8187, 4)
|
|
|
|
# Different expected and observed sum
|
|
observed1 = Vectors.dense([21, 38, 43, 80])
|
|
expected1 = Vectors.dense([3, 5, 7, 20])
|
|
pearson1 = Statistics.chiSqTest(observed1, expected1)
|
|
|
|
# Results validated against the R command
|
|
# `chisq.test(c(21, 38, 43, 80), p=c(3/35, 1/7, 1/5, 4/7))`
|
|
self.assertAlmostEqual(pearson1.statistic, 14.1429, 4)
|
|
self.assertEqual(pearson1.degreesOfFreedom, 3)
|
|
self.assertAlmostEqual(pearson1.pValue, 0.002717, 4)
|
|
|
|
# Vectors with different sizes
|
|
observed3 = Vectors.dense([1.0, 2.0, 3.0])
|
|
expected3 = Vectors.dense([1.0, 2.0, 3.0, 4.0])
|
|
self.assertRaises(ValueError, Statistics.chiSqTest, observed3, expected3)
|
|
|
|
# Negative counts in observed
|
|
neg_obs = Vectors.dense([1.0, 2.0, 3.0, -4.0])
|
|
self.assertRaises(Py4JJavaError, Statistics.chiSqTest, neg_obs, expected1)
|
|
|
|
# Count = 0.0 in expected but not observed
|
|
zero_expected = Vectors.dense([1.0, 0.0, 3.0])
|
|
pearson_inf = Statistics.chiSqTest(observed, zero_expected)
|
|
self.assertEqual(pearson_inf.statistic, inf)
|
|
self.assertEqual(pearson_inf.degreesOfFreedom, 2)
|
|
self.assertEqual(pearson_inf.pValue, 0.0)
|
|
|
|
# 0.0 in expected and observed simultaneously
|
|
zero_observed = Vectors.dense([2.0, 0.0, 1.0])
|
|
self.assertRaises(Py4JJavaError, Statistics.chiSqTest, zero_observed, zero_expected)
|
|
|
|
def test_matrix_independence(self):
|
|
data = [40.0, 24.0, 29.0, 56.0, 32.0, 42.0, 31.0, 10.0, 0.0, 30.0, 15.0, 12.0]
|
|
chi = Statistics.chiSqTest(Matrices.dense(3, 4, data))
|
|
|
|
# Results validated against R command
|
|
# `chisq.test(rbind(c(40, 56, 31, 30),c(24, 32, 10, 15), c(29, 42, 0, 12)))`
|
|
self.assertAlmostEqual(chi.statistic, 21.9958, 4)
|
|
self.assertEqual(chi.degreesOfFreedom, 6)
|
|
self.assertAlmostEqual(chi.pValue, 0.001213, 4)
|
|
|
|
# Negative counts
|
|
neg_counts = Matrices.dense(2, 2, [4.0, 5.0, 3.0, -3.0])
|
|
self.assertRaises(Py4JJavaError, Statistics.chiSqTest, neg_counts)
|
|
|
|
# Row sum = 0.0
|
|
row_zero = Matrices.dense(2, 2, [0.0, 1.0, 0.0, 2.0])
|
|
self.assertRaises(Py4JJavaError, Statistics.chiSqTest, row_zero)
|
|
|
|
# Column sum = 0.0
|
|
col_zero = Matrices.dense(2, 2, [0.0, 0.0, 2.0, 2.0])
|
|
self.assertRaises(Py4JJavaError, Statistics.chiSqTest, col_zero)
|
|
|
|
def test_chi_sq_pearson(self):
|
|
data = [
|
|
LabeledPoint(0.0, Vectors.dense([0.5, 10.0])),
|
|
LabeledPoint(0.0, Vectors.dense([1.5, 20.0])),
|
|
LabeledPoint(1.0, Vectors.dense([1.5, 30.0])),
|
|
LabeledPoint(0.0, Vectors.dense([3.5, 30.0])),
|
|
LabeledPoint(0.0, Vectors.dense([3.5, 40.0])),
|
|
LabeledPoint(1.0, Vectors.dense([3.5, 40.0]))
|
|
]
|
|
|
|
for numParts in [2, 4, 6, 8]:
|
|
chi = Statistics.chiSqTest(self.sc.parallelize(data, numParts))
|
|
feature1 = chi[0]
|
|
self.assertEqual(feature1.statistic, 0.75)
|
|
self.assertEqual(feature1.degreesOfFreedom, 2)
|
|
self.assertAlmostEqual(feature1.pValue, 0.6873, 4)
|
|
|
|
feature2 = chi[1]
|
|
self.assertEqual(feature2.statistic, 1.5)
|
|
self.assertEqual(feature2.degreesOfFreedom, 3)
|
|
self.assertAlmostEqual(feature2.pValue, 0.6823, 4)
|
|
|
|
def test_right_number_of_results(self):
|
|
num_cols = 1001
|
|
sparse_data = [
|
|
LabeledPoint(0.0, Vectors.sparse(num_cols, [(100, 2.0)])),
|
|
LabeledPoint(0.1, Vectors.sparse(num_cols, [(200, 1.0)]))
|
|
]
|
|
chi = Statistics.chiSqTest(self.sc.parallelize(sparse_data))
|
|
self.assertEqual(len(chi), num_cols)
|
|
self.assertIsNotNone(chi[1000])
|
|
|
|
if __name__ == "__main__":
|
|
if not _have_scipy:
|
|
print "NOTE: Skipping SciPy tests as it does not seem to be installed"
|
|
unittest.main()
|
|
if not _have_scipy:
|
|
print "NOTE: SciPy tests were skipped as it does not seem to be installed"
|