def corr(x, y=None, method=None):
"""
Compute the correlation (matrix) for the input RDD(s) using the
specified method.
Methods currently supported: I{pearson (default), spearman}.
If a single RDD of Vectors is passed in, a correlation matrix
comparing the columns in the input RDD is returned. Use C{method=}
to specify the method to be used for single RDD inout.
If two RDDs of floats are passed in, a single float is returned.
>>> x = sc.parallelize([1.0, 0.0, -2.0], 2)
>>> y = sc.parallelize([4.0, 5.0, 3.0], 2)
>>> zeros = sc.parallelize([0.0, 0.0, 0.0], 2)
>>> abs(Statistics.corr(x, y) - 0.6546537) < 1e-7
True
>>> Statistics.corr(x, y) == Statistics.corr(x, y, "pearson")
True
>>> Statistics.corr(x, y, "spearman")
0.5
>>> from math import isnan
>>> isnan(Statistics.corr(x, zeros))
True
>>> from pyspark.mllib.linalg import Vectors
>>> rdd = sc.parallelize([Vectors.dense([1, 0, 0, -2]), Vectors.dense([4, 5, 0, 3]),
... Vectors.dense([6, 7, 0, 8]), Vectors.dense([9, 0, 0, 1])])
>>> pearsonCorr = Statistics.corr(rdd)
>>> print str(pearsonCorr).replace('nan', 'NaN')
[[ 1. 0.05564149 NaN 0.40047142]
[ 0.05564149 1. NaN 0.91359586]
[ NaN NaN 1. NaN]
[ 0.40047142 0.91359586 NaN 1. ]]
>>> spearmanCorr = Statistics.corr(rdd, method="spearman")
>>> print str(spearmanCorr).replace('nan', 'NaN')
[[ 1. 0.10540926 NaN 0.4 ]
[ 0.10540926 1. NaN 0.9486833 ]
[ NaN NaN 1. NaN]
[ 0.4 0.9486833 NaN 1. ]]
>>> try:
... Statistics.corr(rdd, "spearman")
... print "Method name as second argument without 'method=' shouldn't be allowed."
... except TypeError:
... pass
"""
sc = x.ctx
# Check inputs to determine whether a single value or a matrix is needed for output.
# Since it's legal for users to use the method name as the second argument, we need to
# check if y is used to specify the method name instead.
if type(y) == str:
raise TypeError("Use 'method=' to specify method name.")
jx = _to_java_object_rdd(x)
if not y:
resultMat = sc._jvm.PythonMLLibAPI().corr(jx, method)
bytes = sc._jvm.SerDe.dumps(resultMat)
ser = PickleSerializer()
return ser.loads(str(bytes)).toArray()
else:
jy = _to_java_object_rdd(y)
return sc._jvm.PythonMLLibAPI().corr(jx, jy, method)
def corr(x, y=None, method=None):
"""
Compute the correlation (matrix) for the input RDD(s) using the
specified method.
Methods currently supported: I{pearson (default), spearman}.
If a single RDD of Vectors is passed in, a correlation matrix
comparing the columns in the input RDD is returned. Use C{method=}
to specify the method to be used for single RDD inout.
If two RDDs of floats are passed in, a single float is returned.
>>> x = sc.parallelize([1.0, 0.0, -2.0], 2)
>>> y = sc.parallelize([4.0, 5.0, 3.0], 2)
>>> zeros = sc.parallelize([0.0, 0.0, 0.0], 2)
>>> abs(Statistics.corr(x, y) - 0.6546537) < 1e-7
True
>>> Statistics.corr(x, y) == Statistics.corr(x, y, "pearson")
True
>>> Statistics.corr(x, y, "spearman")
0.5
>>> from math import isnan
>>> isnan(Statistics.corr(x, zeros))
True
>>> from pyspark.mllib.linalg import Vectors
>>> rdd = sc.parallelize([Vectors.dense([1, 0, 0, -2]), Vectors.dense([4, 5, 0, 3]),
... Vectors.dense([6, 7, 0, 8]), Vectors.dense([9, 0, 0, 1])])
>>> pearsonCorr = Statistics.corr(rdd)
>>> print str(pearsonCorr).replace('nan', 'NaN')
[[ 1. 0.05564149 NaN 0.40047142]
[ 0.05564149 1. NaN 0.91359586]
[ NaN NaN 1. NaN]
[ 0.40047142 0.91359586 NaN 1. ]]
>>> spearmanCorr = Statistics.corr(rdd, method="spearman")
>>> print str(spearmanCorr).replace('nan', 'NaN')
[[ 1. 0.10540926 NaN 0.4 ]
[ 0.10540926 1. NaN 0.9486833 ]
[ NaN NaN 1. NaN]
[ 0.4 0.9486833 NaN 1. ]]
>>> try:
... Statistics.corr(rdd, "spearman")
... print "Method name as second argument without 'method=' shouldn't be allowed."
... except TypeError:
... pass
"""
sc = x.ctx
# Check inputs to determine whether a single value or a matrix is needed for output.
# Since it's legal for users to use the method name as the second argument, we need to
# check if y is used to specify the method name instead.
if type(y) == str:
raise TypeError("Use 'method=' to specify method name.")
jx = _to_java_object_rdd(x)
if not y:
resultMat = sc._jvm.PythonMLLibAPI().corr(jx, method)
bytes = sc._jvm.SerDe.dumps(resultMat)
ser = PickleSerializer()
return ser.loads(str(bytes)).toArray()
else:
jy = _to_java_object_rdd(y)
return sc._jvm.PythonMLLibAPI().corr(jx, jy, method)
def predict(self, x):
"""
Predict the label of one or more examples.
:param x: Data point (feature vector),
or an RDD of data points (feature vectors).
"""
SerDe = self._sc._jvm.SerDe
ser = PickleSerializer()
if isinstance(x, RDD):
# Bulk prediction
first = x.take(1)
if not first:
return self._sc.parallelize([])
if not isinstance(first[0], Vector):
x = x.map(_convert_to_vector)
jPred = self._java_model.predict(_to_java_object_rdd(x)).toJavaRDD()
jpyrdd = self._sc._jvm.SerDe.javaToPython(jPred)
return RDD(jpyrdd, self._sc, BatchedSerializer(ser, 1024))
else:
# Assume x is a single data point.
bytes = bytearray(ser.dumps(_convert_to_vector(x)))
vec = self._sc._jvm.SerDe.loads(bytes)
return self._java_model.predict(vec)
def colStats(rdd):
"""
Computes column-wise summary statistics for the input RDD[Vector].
>>> from pyspark.mllib.linalg import Vectors
>>> rdd = sc.parallelize([Vectors.dense([2, 0, 0, -2]),
... Vectors.dense([4, 5, 0, 3]),
... Vectors.dense([6, 7, 0, 8])])
>>> cStats = Statistics.colStats(rdd)
>>> cStats.mean()
array([ 4., 4., 0., 3.])
>>> cStats.variance()
array([ 4., 13., 0., 25.])
>>> cStats.count()
3L
>>> cStats.numNonzeros()
array([ 3., 2., 0., 3.])
>>> cStats.max()
array([ 6., 7., 0., 8.])
>>> cStats.min()
array([ 2., 0., 0., -2.])
"""
sc = rdd.ctx
jrdd = _to_java_object_rdd(rdd)
cStats = sc._jvm.PythonMLLibAPI().colStats(jrdd)
return MultivariateStatisticalSummary(sc, cStats)
def colStats(rdd):
"""
Computes column-wise summary statistics for the input RDD[Vector].
>>> from pyspark.mllib.linalg import Vectors
>>> rdd = sc.parallelize([Vectors.dense([2, 0, 0, -2]),
... Vectors.dense([4, 5, 0, 3]),
... Vectors.dense([6, 7, 0, 8])])
>>> cStats = Statistics.colStats(rdd)
>>> cStats.mean()
array([ 4., 4., 0., 3.])
>>> cStats.variance()
array([ 4., 13., 0., 25.])
>>> cStats.count()
3L
>>> cStats.numNonzeros()
array([ 3., 2., 0., 3.])
>>> cStats.max()
array([ 6., 7., 0., 8.])
>>> cStats.min()
array([ 2., 0., 0., -2.])
"""
sc = rdd.ctx
jrdd = _to_java_object_rdd(rdd)
cStats = sc._jvm.PythonMLLibAPI().colStats(jrdd)
return MultivariateStatisticalSummary(sc, cStats)
def _py2java(sc, a):
""" Convert Python object into Java """
if isinstance(a, RDD):
a = _to_java_object_rdd(a)
elif not isinstance(a, (int, long, float, bool, basestring)):
bytes = bytearray(PickleSerializer().dumps(a))
a = sc._jvm.SerDe.loads(bytes)
return a
def _py2java(sc, a):
""" Convert Python object into Java """
if isinstance(a, RDD):
a = _to_java_object_rdd(a)
elif not isinstance(a, (int, long, float, bool, basestring)):
bytes = bytearray(PickleSerializer().dumps(a))
a = sc._jvm.SerDe.loads(bytes)
return a
def _regression_train_wrapper(sc, train_func, modelClass, data, initial_weights):
initial_weights = initial_weights or [0.0] * len(data.first().features)
ser = PickleSerializer()
initial_bytes = bytearray(ser.dumps(_convert_to_vector(initial_weights)))
# use AutoBatchedSerializer before cache to reduce the memory
# overhead in JVM
cached = data._reserialize(AutoBatchedSerializer(ser)).cache()
ans = train_func(_to_java_object_rdd(cached), initial_bytes)
assert len(ans) == 2, "JVM call result had unexpected length"
weights = ser.loads(str(ans[0]))
return modelClass(weights, ans[1])
def train(cls, rdd, k, maxIterations=100, runs=1, initializationMode="k-means||"):
"""Train a k-means clustering model."""
sc = rdd.context
ser = PickleSerializer()
# cache serialized data to avoid objects over head in JVM
cached = rdd.map(_convert_to_vector)._reserialize(AutoBatchedSerializer(ser)).cache()
model = sc._jvm.PythonMLLibAPI().trainKMeansModel(
_to_java_object_rdd(cached), k, maxIterations, runs, initializationMode
)
bytes = sc._jvm.SerDe.dumps(model.clusterCenters())
centers = ser.loads(str(bytes))
return KMeansModel([c.toArray() for c in centers])
def _prepare(cls, ratings):
assert isinstance(ratings, RDD), "ratings should be RDD"
first = ratings.first()
if not isinstance(first, Rating):
if isinstance(first, (tuple, list)):
ratings = ratings.map(lambda x: Rating(*x))
else:
raise ValueError("rating should be RDD of Rating or tuple/list")
# serialize them by AutoBatchedSerializer before cache to reduce the
# objects overhead in JVM
cached = ratings._reserialize(AutoBatchedSerializer(PickleSerializer())).cache()
return _to_java_object_rdd(cached)
def _train(data, type, numClasses, categoricalFeaturesInfo,
impurity="gini", maxDepth=5, maxBins=32, minInstancesPerNode=1,
minInfoGain=0.0):
first = data.first()
assert isinstance(first, LabeledPoint), "the data should be RDD of LabeledPoint"
sc = data.context
jrdd = _to_java_object_rdd(data)
cfiMap = MapConverter().convert(categoricalFeaturesInfo,
sc._gateway._gateway_client)
model = sc._jvm.PythonMLLibAPI().trainDecisionTreeModel(
jrdd, type, numClasses, cfiMap,
impurity, maxDepth, maxBins, minInstancesPerNode, minInfoGain)
return DecisionTreeModel(sc, model)
def _prepare(cls, ratings):
assert isinstance(ratings, RDD), "ratings should be RDD"
first = ratings.first()
if not isinstance(first, Rating):
if isinstance(first, (tuple, list)):
ratings = ratings.map(lambda x: Rating(*x))
else:
raise ValueError(
"rating should be RDD of Rating or tuple/list")
# serialize them by AutoBatchedSerializer before cache to reduce the
# objects overhead in JVM
cached = ratings._reserialize(AutoBatchedSerializer(
PickleSerializer())).cache()
return _to_java_object_rdd(cached)
def predictAll(self, user_product):
assert isinstance(user_product, RDD), "user_product should be RDD of (user, product)"
first = user_product.first()
if isinstance(first, list):
user_product = user_product.map(tuple)
first = tuple(first)
assert type(first) is tuple and len(first) == 2, \
"user_product should be RDD of (user, product)"
if any(isinstance(x, str) for x in first):
user_product = user_product.map(lambda (u, p): (int(x), int(p)))
first = tuple(map(int, first))
assert all(type(x) is int for x in first), "user and product in user_product shoul be int"
sc = self._context
tuplerdd = sc._jvm.SerDe.asTupleRDD(_to_java_object_rdd(user_product).rdd())
jresult = self._java_model.predict(tuplerdd).toJavaRDD()
return RDD(sc._jvm.SerDe.javaToPython(jresult), sc,
AutoBatchedSerializer(PickleSerializer()))
def train(cls,
rdd,
k,
maxIterations=100,
runs=1,
initializationMode="k-means||"):
"""Train a k-means clustering model."""
sc = rdd.context
ser = PickleSerializer()
# cache serialized data to avoid objects over head in JVM
cached = rdd.map(_convert_to_vector)._reserialize(
AutoBatchedSerializer(ser)).cache()
model = sc._jvm.PythonMLLibAPI().trainKMeansModel(
_to_java_object_rdd(cached), k, maxIterations, runs,
initializationMode)
bytes = sc._jvm.SerDe.dumps(model.clusterCenters())
centers = ser.loads(str(bytes))
return KMeansModel([c.toArray() for c in centers])
def train(cls, data, lambda_=1.0):
"""
Train a Naive Bayes model given an RDD of (label, features) vectors.
This is the Multinomial NB (U{http://tinyurl.com/lsdw6p}) which can
handle all kinds of discrete data. For example, by converting
documents into TF-IDF vectors, it can be used for document
classification. By making every vector a 0-1 vector, it can also be
used as Bernoulli NB (U{http://tinyurl.com/p7c96j6}).
:param data: RDD of NumPy vectors, one per element, where the first
coordinate is the label and the rest is the feature vector
(e.g. a count vector).
:param lambda_: The smoothing parameter
"""
sc = data.context
jlist = sc._jvm.PythonMLLibAPI().trainNaiveBayes(_to_java_object_rdd(data), lambda_)
labels, pi, theta = PickleSerializer().loads(str(sc._jvm.SerDe.dumps(jlist)))
return NaiveBayesModel(labels.toArray(), pi.toArray(), numpy.array(theta))
def fit(self, data):
"""
Computes the vector representation of each word in vocabulary.
:param data: training data. RDD of subtype of Iterable[String]
:return: python Word2VecModel instance
"""
sc = data.context
ser = PickleSerializer()
vectorSize = self.vectorSize
learningRate = self.learningRate
numPartitions = self.numPartitions
numIterations = self.numIterations
seed = self.seed
model = sc._jvm.PythonMLLibAPI().trainWord2Vec(
_to_java_object_rdd(data), vectorSize, learningRate, numPartitions,
numIterations, seed)
return Word2VecModel(sc, model)
def fit(self, data):
"""
Computes the vector representation of each word in vocabulary.
:param data: training data. RDD of subtype of Iterable[String]
:return: python Word2VecModel instance
"""
sc = data.context
ser = PickleSerializer()
vectorSize = self.vectorSize
learningRate = self.learningRate
numPartitions = self.numPartitions
numIterations = self.numIterations
seed = self.seed
model = sc._jvm.PythonMLLibAPI().trainWord2Vec(
_to_java_object_rdd(data), vectorSize,
learningRate, numPartitions, numIterations, seed)
return Word2VecModel(sc, model)
def predictAll(self, user_product):
assert isinstance(user_product,
RDD), "user_product should be RDD of (user, product)"
first = user_product.first()
if isinstance(first, list):
user_product = user_product.map(tuple)
first = tuple(first)
assert type(first) is tuple and len(first) == 2, \
"user_product should be RDD of (user, product)"
if any(isinstance(x, str) for x in first):
user_product = user_product.map(lambda (u, p): (int(x), int(p)))
first = tuple(map(int, first))
assert all(
type(x) is int
for x in first), "user and product in user_product shoul be int"
sc = self._context
tuplerdd = sc._jvm.SerDe.asTupleRDD(
_to_java_object_rdd(user_product).rdd())
jresult = self._java_model.predict(tuplerdd).toJavaRDD()
return RDD(sc._jvm.SerDe.javaToPython(jresult), sc,
AutoBatchedSerializer(PickleSerializer()))
def train(cls, data, lambda_=1.0):
"""
Train a Naive Bayes model given an RDD of (label, features) vectors.
This is the Multinomial NB (U{http://tinyurl.com/lsdw6p}) which can
handle all kinds of discrete data. For example, by converting
documents into TF-IDF vectors, it can be used for document
classification. By making every vector a 0-1 vector, it can also be
used as Bernoulli NB (U{http://tinyurl.com/p7c96j6}).
:param data: RDD of NumPy vectors, one per element, where the first
coordinate is the label and the rest is the feature vector
(e.g. a count vector).
:param lambda_: The smoothing parameter
"""
sc = data.context
jlist = sc._jvm.PythonMLLibAPI().trainNaiveBayes(
_to_java_object_rdd(data), lambda_)
labels, pi, theta = PickleSerializer().loads(
str(sc._jvm.SerDe.dumps(jlist)))
return NaiveBayesModel(labels.toArray(), pi.toArray(),
numpy.array(theta))
