[SPARK-4118] [MLLIB] [PYSPARK] Python bindings for StreamingKMeans

Python bindings for StreamingKMeans

Will change status to MRG once docs, tests and examples are updated.

Author: MechCoder <[email protected]>

Closes apache#6499 from MechCoder/spark-4118 and squashes the following commits:

7722d16 [MechCoder] minor style fixes
51052d3 [MechCoder] Doc fixes
2061a76 [MechCoder] Add tests for simultaneous training and prediction Minor style fixes
81482fd [MechCoder] minor
5d9fe61 [MechCoder] predictOn should take into account the latest model
8ab9e89 [MechCoder] Fix Python3 error
a9817df [MechCoder] Better tests and minor fixes
c80e451 [MechCoder] Add ignore_unicode_prefix
ee8ce16 [MechCoder] Update tests, doc and examples
4b1481f [MechCoder] Some changes and tests
d8b066a [MechCoder] [SPARK-4118] [MLlib] [PySpark] Python bindings for StreamingKMeans

Author: MechCoder

docs/mllib-clustering.md

@@ -592,15 +592,55 @@ model.predictOnValues(testData.map(lp => (lp.label, lp.features))).print()
 ssc.start()
 ssc.awaitTermination()
 
+{% endhighlight %}
+</div>
+
+<div data-lang="python" markdown="1">
+First we import the neccessary classes.
+
+{% highlight python %}
+from pyspark.mllib.linalg import Vectors
+from pyspark.mllib.regression import LabeledPoint
+from pyspark.mllib.clustering import StreamingKMeans
 {% endhighlight %}
 
+Then we make an input stream of vectors for training, as well as a stream of labeled data
+points for testing. We assume a StreamingContext `ssc` has been created, see
+[Spark Streaming Programming Guide](streaming-programming-guide.html#initializing) for more info.
+
+{% highlight python %}
+def parse(lp):
+    label = float(lp[lp.find('(') + 1: lp.find(',')])
+    vec = Vectors.dense(lp[lp.find('[') + 1: lp.find(']')].split(','))
+    return LabeledPoint(label, vec)
+
+trainingData = ssc.textFileStream("/training/data/dir").map(Vectors.parse)
+testData = ssc.textFileStream("/testing/data/dir").map(parse)
+{% endhighlight %}
+
+We create a model with random clusters and specify the number of clusters to find
+
+{% highlight python %}
+model = StreamingKMeans(k=2, decayFactor=1.0).setRandomCenters(3, 1.0, 0)
+{% endhighlight %}
+
+Now register the streams for training and testing and start the job, printing
+the predicted cluster assignments on new data points as they arrive.
+
+{% highlight python %}
+model.trainOn(trainingData)
+print(model.predictOnValues(testData.map(lambda lp: (lp.label, lp.features))))
+
+ssc.start()
+ssc.awaitTermination()
+{% endhighlight %}
+</div>
+
+</div>
+
 As you add new text files with data the cluster centers will update. Each training
 point should be formatted as `[x1, x2, x3]`, and each test data point
 should be formatted as `(y, [x1, x2, x3])`, where `y` is some useful label or identifier
 (e.g. a true category assignment). Anytime a text file is placed in `/training/data/dir`
 the model will update. Anytime a text file is placed in `/testing/data/dir`
 you will see predictions. With new data, the cluster centers will change!
-
-</div>
-
-</div>

mllib/src/main/scala/org/apache/spark/mllib/api/python/PythonMLLibAPI.scala

@@ -964,6 +964,21 @@ private[python] class PythonMLLibAPI extends Serializable {
       points.asScala.toArray)
   }
 
+  /**
+   * Java stub for the update method of StreamingKMeansModel.
+   */
+  def updateStreamingKMeansModel(
+      clusterCenters: JList[Vector],
+      clusterWeights: JList[Double],
+      data: JavaRDD[Vector],
+      decayFactor: Double,
+      timeUnit: String): JList[Object] = {
+    val model = new StreamingKMeansModel(
+      clusterCenters.asScala.toArray, clusterWeights.asScala.toArray)
+        .update(data, decayFactor, timeUnit)
+      List[AnyRef](model.clusterCenters, Vectors.dense(model.clusterWeights)).asJava
+  }
+
 }
 
 /**

python/pyspark/mllib/clustering.py

@@ -21,16 +21,20 @@
 if sys.version > '3':
     xrange = range
 
-from numpy import array
+from math import exp, log
+
+from numpy import array, random, tile
 
-from pyspark import RDD
 from pyspark import SparkContext
+from pyspark.rdd import RDD, ignore_unicode_prefix
 from pyspark.mllib.common import callMLlibFunc, callJavaFunc, _py2java, _java2py
-from pyspark.mllib.linalg import SparseVector, _convert_to_vector
+from pyspark.mllib.linalg import SparseVector, _convert_to_vector, DenseVector
 from pyspark.mllib.stat.distribution import MultivariateGaussian
 from pyspark.mllib.util import Saveable, Loader, inherit_doc
+from pyspark.streaming import DStream
 
-__all__ = ['KMeansModel', 'KMeans', 'GaussianMixtureModel', 'GaussianMixture']
+__all__ = ['KMeansModel', 'KMeans', 'GaussianMixtureModel', 'GaussianMixture',
+           'StreamingKMeans', 'StreamingKMeansModel']
 
 
 @inherit_doc
@@ -98,6 +102,9 @@ def predict(self, x):
         """Find the cluster to which x belongs in this model."""
         best = 0
         best_distance = float("inf")
+        if isinstance(x, RDD):
+            return x.map(self.predict)
+
         x = _convert_to_vector(x)
         for i in xrange(len(self.centers)):
             distance = x.squared_distance(self.centers[i])
@@ -264,6 +271,198 @@ def train(cls, rdd, k, convergenceTol=1e-3, maxIterations=100, seed=None, initia
         return GaussianMixtureModel(weight, mvg_obj)
 
 
+class StreamingKMeansModel(KMeansModel):
+    """
+    .. note:: Experimental
+
+    Clustering model which can perform an online update of the centroids.
+
+    The update formula for each centroid is given by
+
+    * c_t+1 = ((c_t * n_t * a) + (x_t * m_t)) / (n_t + m_t)
+    * n_t+1 = n_t * a + m_t
+
+    where
+
+    * c_t: Centroid at the n_th iteration.
+    * n_t: Number of samples (or) weights associated with the centroid
+           at the n_th iteration.
+    * x_t: Centroid of the new data closest to c_t.
+    * m_t: Number of samples (or) weights of the new data closest to c_t
+    * c_t+1: New centroid.
+    * n_t+1: New number of weights.
+    * a: Decay Factor, which gives the forgetfulness.
+
+    Note that if a is set to 1, it is the weighted mean of the previous
+    and new data. If it set to zero, the old centroids are completely
+    forgotten.
+
+    :param clusterCenters: Initial cluster centers.
+    :param clusterWeights: List of weights assigned to each cluster.
+
+    >>> initCenters = [[0.0, 0.0], [1.0, 1.0]]
+    >>> initWeights = [1.0, 1.0]
+    >>> stkm = StreamingKMeansModel(initCenters, initWeights)
+    >>> data = sc.parallelize([[-0.1, -0.1], [0.1, 0.1],
+    ...                        [0.9, 0.9], [1.1, 1.1]])
+    >>> stkm = stkm.update(data, 1.0, u"batches")
+    >>> stkm.centers
+    array([[ 0.,  0.],
+           [ 1.,  1.]])
+    >>> stkm.predict([-0.1, -0.1])
+    0
+    >>> stkm.predict([0.9, 0.9])
+    1
+    >>> stkm.clusterWeights
+    [3.0, 3.0]
+    >>> decayFactor = 0.0
+    >>> data = sc.parallelize([DenseVector([1.5, 1.5]), DenseVector([0.2, 0.2])])
+    >>> stkm = stkm.update(data, 0.0, u"batches")
+    >>> stkm.centers
+    array([[ 0.2,  0.2],
+           [ 1.5,  1.5]])
+    >>> stkm.clusterWeights
+    [1.0, 1.0]
+    >>> stkm.predict([0.2, 0.2])
+    0
+    >>> stkm.predict([1.5, 1.5])
+    1
+    """
+    def __init__(self, clusterCenters, clusterWeights):
+        super(StreamingKMeansModel, self).__init__(centers=clusterCenters)
+        self._clusterWeights = list(clusterWeights)
+
+    @property
+    def clusterWeights(self):
+        """Return the cluster weights."""
+        return self._clusterWeights
+
+    @ignore_unicode_prefix
+    def update(self, data, decayFactor, timeUnit):
+        """Update the centroids, according to data
+
+        :param data: Should be a RDD that represents the new data.
+        :param decayFactor: forgetfulness of the previous centroids.
+        :param timeUnit: Can be "batches" or "points". If points, then the
+                         decay factor is raised to the power of number of new
+                         points and if batches, it is used as it is.
+        """
+        if not isinstance(data, RDD):
+            raise TypeError("Data should be of an RDD, got %s." % type(data))
+        data = data.map(_convert_to_vector)
+        decayFactor = float(decayFactor)
+        if timeUnit not in ["batches", "points"]:
+            raise ValueError(
+                "timeUnit should be 'batches' or 'points', got %s." % timeUnit)
+        vectorCenters = [_convert_to_vector(center) for center in self.centers]
+        updatedModel = callMLlibFunc(
+            "updateStreamingKMeansModel", vectorCenters, self._clusterWeights,
+            data, decayFactor, timeUnit)
+        self.centers = array(updatedModel[0])
+        self._clusterWeights = list(updatedModel[1])
+        return self
+
+
+class StreamingKMeans(object):
+    """
+    .. note:: Experimental
+
+    Provides methods to set k, decayFactor, timeUnit to configure the
+    KMeans algorithm for fitting and predicting on incoming dstreams.
+    More details on how the centroids are updated are provided under the
+    docs of StreamingKMeansModel.
+
+    :param k: int, number of clusters
+    :param decayFactor: float, forgetfulness of the previous centroids.
+    :param timeUnit: can be "batches" or "points". If points, then the
+                     decayfactor is raised to the power of no. of new points.
+    """
+    def __init__(self, k=2, decayFactor=1.0, timeUnit="batches"):
+        self._k = k
+        self._decayFactor = decayFactor
+        if timeUnit not in ["batches", "points"]:
+            raise ValueError(
+                "timeUnit should be 'batches' or 'points', got %s." % timeUnit)
+        self._timeUnit = timeUnit
+        self._model = None
+
+    def latestModel(self):
+        """Return the latest model"""
+        return self._model
+
+    def _validate(self, dstream):
+        if self._model is None:
+            raise ValueError(
+                "Initial centers should be set either by setInitialCenters "
+                "or setRandomCenters.")
+        if not isinstance(dstream, DStream):
+            raise TypeError(
+                "Expected dstream to be of type DStream, "
+                "got type %s" % type(dstream))
+
+    def setK(self, k):
+        """Set number of clusters."""
+        self._k = k
+        return self
+
+    def setDecayFactor(self, decayFactor):
+        """Set decay factor."""
+        self._decayFactor = decayFactor
+        return self
+
+    def setHalfLife(self, halfLife, timeUnit):
+        """
+        Set number of batches after which the centroids of that
+        particular batch has half the weightage.
+        """
+        self._timeUnit = timeUnit
+        self._decayFactor = exp(log(0.5) / halfLife)
+        return self
+
+    def setInitialCenters(self, centers, weights):
+        """
+        Set initial centers. Should be set before calling trainOn.
+        """
+        self._model = StreamingKMeansModel(centers, weights)
+        return self
+
+    def setRandomCenters(self, dim, weight, seed):
+        """
+        Set the initial centres to be random samples from
+        a gaussian population with constant weights.
+        """
+        rng = random.RandomState(seed)
+        clusterCenters = rng.randn(self._k, dim)
+        clusterWeights = tile(weight, self._k)
+        self._model = StreamingKMeansModel(clusterCenters, clusterWeights)
+        return self
+
+    def trainOn(self, dstream):
+        """Train the model on the incoming dstream."""
+        self._validate(dstream)
+
+        def update(rdd):
+            self._model.update(rdd, self._decayFactor, self._timeUnit)
+
+        dstream.foreachRDD(update)
+
+    def predictOn(self, dstream):
+        """
+        Make predictions on a dstream.
+        Returns a transformed dstream object
+        """
+        self._validate(dstream)
+        return dstream.map(lambda x: self._model.predict(x))
+
+    def predictOnValues(self, dstream):
+        """
+        Make predictions on a keyed dstream.
+        Returns a transformed dstream object.
+        """
+        self._validate(dstream)
+        return dstream.mapValues(lambda x: self._model.predict(x))
+
+
 def _test():
     import doctest
     globs = globals().copy()