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From m...@apache.org
Subject spark git commit: [SPARK-9918] [MLLIB] remove runs from k-means and rename epsilon to tol
Date Thu, 13 Aug 2015 06:05:03 GMT
Repository: spark
Updated Branches:
  refs/heads/master d0b18919d -> 68f995714


[SPARK-9918] [MLLIB] remove runs from k-means and rename epsilon to tol

This requires some discussion. I'm not sure whether `runs` is a useful parameter. It certainly
complicates the implementation. We might want to optimize the k-means implementation with
block matrix operations. In this case, having `runs` may not be worth the trade-off. Also
it increases the communication cost in a single job, which might cause other issues.

This PR also renames `epsilon` to `tol` to have consistent naming among algorithms. The Python
constructor is updated to include all parameters.

jkbradley yu-iskw

Author: Xiangrui Meng <meng@databricks.com>

Closes #8148 from mengxr/SPARK-9918 and squashes the following commits:

149b9e5 [Xiangrui Meng] fix constructor in Python and rename epsilon to tol
3cc15b3 [Xiangrui Meng] fix test and change initStep to initSteps in python
a0a0274 [Xiangrui Meng] remove runs from k-means in the pipeline API


Project: http://git-wip-us.apache.org/repos/asf/spark/repo
Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/68f99571
Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/68f99571
Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/68f99571

Branch: refs/heads/master
Commit: 68f99571492f67596b3656e9f076deeb96616f4a
Parents: d0b1891
Author: Xiangrui Meng <meng@databricks.com>
Authored: Wed Aug 12 23:04:59 2015 -0700
Committer: Xiangrui Meng <meng@databricks.com>
Committed: Wed Aug 12 23:04:59 2015 -0700

----------------------------------------------------------------------
 .../org/apache/spark/ml/clustering/KMeans.scala | 51 ++++------------
 .../spark/ml/clustering/KMeansSuite.scala       | 12 +---
 python/pyspark/ml/clustering.py                 | 63 ++++----------------
 3 files changed, 26 insertions(+), 100 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/spark/blob/68f99571/mllib/src/main/scala/org/apache/spark/ml/clustering/KMeans.scala
----------------------------------------------------------------------
diff --git a/mllib/src/main/scala/org/apache/spark/ml/clustering/KMeans.scala b/mllib/src/main/scala/org/apache/spark/ml/clustering/KMeans.scala
index dc192ad..47a18cd 100644
--- a/mllib/src/main/scala/org/apache/spark/ml/clustering/KMeans.scala
+++ b/mllib/src/main/scala/org/apache/spark/ml/clustering/KMeans.scala
@@ -18,8 +18,8 @@
 package org.apache.spark.ml.clustering
 
 import org.apache.spark.annotation.Experimental
-import org.apache.spark.ml.param.{Param, Params, IntParam, DoubleParam, ParamMap}
-import org.apache.spark.ml.param.shared.{HasFeaturesCol, HasMaxIter, HasPredictionCol, HasSeed}
+import org.apache.spark.ml.param.{Param, Params, IntParam, ParamMap}
+import org.apache.spark.ml.param.shared._
 import org.apache.spark.ml.util.{Identifiable, SchemaUtils}
 import org.apache.spark.ml.{Estimator, Model}
 import org.apache.spark.mllib.clustering.{KMeans => MLlibKMeans, KMeansModel => MLlibKMeansModel}
@@ -27,14 +27,13 @@ import org.apache.spark.mllib.linalg.{Vector, VectorUDT}
 import org.apache.spark.sql.functions.{col, udf}
 import org.apache.spark.sql.types.{IntegerType, StructType}
 import org.apache.spark.sql.{DataFrame, Row}
-import org.apache.spark.util.Utils
 
 
 /**
  * Common params for KMeans and KMeansModel
  */
-private[clustering] trait KMeansParams
-    extends Params with HasMaxIter with HasFeaturesCol with HasSeed with HasPredictionCol
{
+private[clustering] trait KMeansParams extends Params with HasMaxIter with HasFeaturesCol
+  with HasSeed with HasPredictionCol with HasTol {
 
   /**
    * Set the number of clusters to create (k). Must be > 1. Default: 2.
@@ -46,31 +45,6 @@ private[clustering] trait KMeansParams
   def getK: Int = $(k)
 
   /**
-   * Param the number of runs of the algorithm to execute in parallel. We initialize the
algorithm
-   * this many times with random starting conditions (configured by the initialization mode),
then
-   * return the best clustering found over any run. Must be >= 1. Default: 1.
-   * @group param
-   */
-  final val runs = new IntParam(this, "runs",
-    "number of runs of the algorithm to execute in parallel", (value: Int) => value >=
1)
-
-  /** @group getParam */
-  def getRuns: Int = $(runs)
-
-  /**
-   * Param the distance threshold within which we've consider centers to have converged.
-   * If all centers move less than this Euclidean distance, we stop iterating one run.
-   * Must be >= 0.0. Default: 1e-4
-   * @group param
-   */
-  final val epsilon = new DoubleParam(this, "epsilon",
-    "distance threshold within which we've consider centers to have converge",
-    (value: Double) => value >= 0.0)
-
-  /** @group getParam */
-  def getEpsilon: Double = $(epsilon)
-
-  /**
    * Param for the initialization algorithm. This can be either "random" to choose random
points as
    * initial cluster centers, or "k-means||" to use a parallel variant of k-means++
    * (Bahmani et al., Scalable K-Means++, VLDB 2012). Default: k-means||.
@@ -136,9 +110,9 @@ class KMeansModel private[ml] (
 
 /**
  * :: Experimental ::
- * K-means clustering with support for multiple parallel runs and a k-means++ like initialization
- * mode (the k-means|| algorithm by Bahmani et al). When multiple concurrent runs are requested,
- * they are executed together with joint passes over the data for efficiency.
+ * K-means clustering with support for k-means|| initialization proposed by Bahmani et al.
+ *
+ * @see [[http://dx.doi.org/10.14778/2180912.2180915 Bahmani et al., Scalable k-means++.]]
  */
 @Experimental
 class KMeans(override val uid: String) extends Estimator[KMeansModel] with KMeansParams {
@@ -146,10 +120,9 @@ class KMeans(override val uid: String) extends Estimator[KMeansModel]
with KMean
   setDefault(
     k -> 2,
     maxIter -> 20,
-    runs -> 1,
     initMode -> MLlibKMeans.K_MEANS_PARALLEL,
     initSteps -> 5,
-    epsilon -> 1e-4)
+    tol -> 1e-4)
 
   override def copy(extra: ParamMap): KMeans = defaultCopy(extra)
 
@@ -174,10 +147,7 @@ class KMeans(override val uid: String) extends Estimator[KMeansModel]
with KMean
   def setMaxIter(value: Int): this.type = set(maxIter, value)
 
   /** @group setParam */
-  def setRuns(value: Int): this.type = set(runs, value)
-
-  /** @group setParam */
-  def setEpsilon(value: Double): this.type = set(epsilon, value)
+  def setTol(value: Double): this.type = set(tol, value)
 
   /** @group setParam */
   def setSeed(value: Long): this.type = set(seed, value)
@@ -191,8 +161,7 @@ class KMeans(override val uid: String) extends Estimator[KMeansModel]
with KMean
       .setInitializationSteps($(initSteps))
       .setMaxIterations($(maxIter))
       .setSeed($(seed))
-      .setEpsilon($(epsilon))
-      .setRuns($(runs))
+      .setEpsilon($(tol))
     val parentModel = algo.run(rdd)
     val model = new KMeansModel(uid, parentModel)
     copyValues(model)

http://git-wip-us.apache.org/repos/asf/spark/blob/68f99571/mllib/src/test/scala/org/apache/spark/ml/clustering/KMeansSuite.scala
----------------------------------------------------------------------
diff --git a/mllib/src/test/scala/org/apache/spark/ml/clustering/KMeansSuite.scala b/mllib/src/test/scala/org/apache/spark/ml/clustering/KMeansSuite.scala
index 1f15ac0..688b0e3 100644
--- a/mllib/src/test/scala/org/apache/spark/ml/clustering/KMeansSuite.scala
+++ b/mllib/src/test/scala/org/apache/spark/ml/clustering/KMeansSuite.scala
@@ -52,10 +52,9 @@ class KMeansSuite extends SparkFunSuite with MLlibTestSparkContext {
     assert(kmeans.getFeaturesCol === "features")
     assert(kmeans.getPredictionCol === "prediction")
     assert(kmeans.getMaxIter === 20)
-    assert(kmeans.getRuns === 1)
     assert(kmeans.getInitMode === MLlibKMeans.K_MEANS_PARALLEL)
     assert(kmeans.getInitSteps === 5)
-    assert(kmeans.getEpsilon === 1e-4)
+    assert(kmeans.getTol === 1e-4)
   }
 
   test("set parameters") {
@@ -64,21 +63,19 @@ class KMeansSuite extends SparkFunSuite with MLlibTestSparkContext {
       .setFeaturesCol("test_feature")
       .setPredictionCol("test_prediction")
       .setMaxIter(33)
-      .setRuns(7)
       .setInitMode(MLlibKMeans.RANDOM)
       .setInitSteps(3)
       .setSeed(123)
-      .setEpsilon(1e-3)
+      .setTol(1e-3)
 
     assert(kmeans.getK === 9)
     assert(kmeans.getFeaturesCol === "test_feature")
     assert(kmeans.getPredictionCol === "test_prediction")
     assert(kmeans.getMaxIter === 33)
-    assert(kmeans.getRuns === 7)
     assert(kmeans.getInitMode === MLlibKMeans.RANDOM)
     assert(kmeans.getInitSteps === 3)
     assert(kmeans.getSeed === 123)
-    assert(kmeans.getEpsilon === 1e-3)
+    assert(kmeans.getTol === 1e-3)
   }
 
   test("parameters validation") {
@@ -91,9 +88,6 @@ class KMeansSuite extends SparkFunSuite with MLlibTestSparkContext {
     intercept[IllegalArgumentException] {
       new KMeans().setInitSteps(0)
     }
-    intercept[IllegalArgumentException] {
-      new KMeans().setRuns(0)
-    }
   }
 
   test("fit & transform") {

http://git-wip-us.apache.org/repos/asf/spark/blob/68f99571/python/pyspark/ml/clustering.py
----------------------------------------------------------------------
diff --git a/python/pyspark/ml/clustering.py b/python/pyspark/ml/clustering.py
index 4833871..cb4c16e 100644
--- a/python/pyspark/ml/clustering.py
+++ b/python/pyspark/ml/clustering.py
@@ -19,7 +19,6 @@ from pyspark.ml.util import keyword_only
 from pyspark.ml.wrapper import JavaEstimator, JavaModel
 from pyspark.ml.param.shared import *
 from pyspark.mllib.common import inherit_doc
-from pyspark.mllib.linalg import _convert_to_vector
 
 __all__ = ['KMeans', 'KMeansModel']
 
@@ -35,7 +34,7 @@ class KMeansModel(JavaModel):
 
 
 @inherit_doc
-class KMeans(JavaEstimator, HasFeaturesCol, HasMaxIter, HasSeed):
+class KMeans(JavaEstimator, HasFeaturesCol, HasPredictionCol, HasMaxIter, HasTol, HasSeed):
     """
     K-means clustering with support for multiple parallel runs and a k-means++ like initialization
     mode (the k-means|| algorithm by Bahmani et al). When multiple concurrent runs are requested,
@@ -45,7 +44,7 @@ class KMeans(JavaEstimator, HasFeaturesCol, HasMaxIter, HasSeed):
     >>> data = [(Vectors.dense([0.0, 0.0]),), (Vectors.dense([1.0, 1.0]),),
     ...         (Vectors.dense([9.0, 8.0]),), (Vectors.dense([8.0, 9.0]),)]
     >>> df = sqlContext.createDataFrame(data, ["features"])
-    >>> kmeans = KMeans().setK(2).setSeed(1).setFeaturesCol("features")
+    >>> kmeans = KMeans(k=2, seed=1)
     >>> model = kmeans.fit(df)
     >>> centers = model.clusterCenters()
     >>> len(centers)
@@ -60,10 +59,6 @@ class KMeans(JavaEstimator, HasFeaturesCol, HasMaxIter, HasSeed):
 
     # a placeholder to make it appear in the generated doc
     k = Param(Params._dummy(), "k", "number of clusters to create")
-    epsilon = Param(Params._dummy(), "epsilon",
-                    "distance threshold within which " +
-                    "we've consider centers to have converged")
-    runs = Param(Params._dummy(), "runs", "number of runs of the algorithm to execute in
parallel")
     initMode = Param(Params._dummy(), "initMode",
                      "the initialization algorithm. This can be either \"random\" to " +
                      "choose random points as initial cluster centers, or \"k-means||\" "
+
@@ -71,21 +66,21 @@ class KMeans(JavaEstimator, HasFeaturesCol, HasMaxIter, HasSeed):
     initSteps = Param(Params._dummy(), "initSteps", "steps for k-means initialization mode")
 
     @keyword_only
-    def __init__(self, k=2, maxIter=20, runs=1, epsilon=1e-4, initMode="k-means||", initStep=5):
+    def __init__(self, featuresCol="features", predictionCol="prediction", k=2,
+                 initMode="k-means||", initSteps=5, tol=1e-4, maxIter=20, seed=None):
+        """
+        __init__(self, featuresCol="features", predictionCol="prediction", k=2, \
+                 initMode="k-means||", initSteps=5, tol=1e-4, maxIter=20, seed=None)
+        """
         super(KMeans, self).__init__()
         self._java_obj = self._new_java_obj("org.apache.spark.ml.clustering.KMeans", self.uid)
         self.k = Param(self, "k", "number of clusters to create")
-        self.epsilon = Param(self, "epsilon",
-                             "distance threshold within which " +
-                             "we've consider centers to have converged")
-        self.runs = Param(self, "runs", "number of runs of the algorithm to execute in parallel")
-        self.seed = Param(self, "seed", "random seed")
         self.initMode = Param(self, "initMode",
                               "the initialization algorithm. This can be either \"random\"
to " +
                               "choose random points as initial cluster centers, or \"k-means||\"
" +
                               "to use a parallel variant of k-means++")
         self.initSteps = Param(self, "initSteps", "steps for k-means initialization mode")
-        self._setDefault(k=2, maxIter=20, runs=1, epsilon=1e-4, initMode="k-means||", initSteps=5)
+        self._setDefault(k=2, initMode="k-means||", initSteps=5, tol=1e-4, maxIter=20)
         kwargs = self.__init__._input_kwargs
         self.setParams(**kwargs)
 
@@ -93,9 +88,11 @@ class KMeans(JavaEstimator, HasFeaturesCol, HasMaxIter, HasSeed):
         return KMeansModel(java_model)
 
     @keyword_only
-    def setParams(self, k=2, maxIter=20, runs=1, epsilon=1e-4, initMode="k-means||", initSteps=5):
+    def setParams(self, featuresCol="features", predictionCol="prediction", k=2,
+                  initMode="k-means||", initSteps=5, tol=1e-4, maxIter=20, seed=None):
         """
-        setParams(self, k=2, maxIter=20, runs=1, epsilon=1e-4, initMode="k-means||", initSteps=5):
+        setParams(self, featuresCol="features", predictionCol="prediction", k=2, \
+                  initMode="k-means||", initSteps=5, tol=1e-4, maxIter=20, seed=None)
 
         Sets params for KMeans.
         """
@@ -119,40 +116,6 @@ class KMeans(JavaEstimator, HasFeaturesCol, HasMaxIter, HasSeed):
         """
         return self.getOrDefault(self.k)
 
-    def setEpsilon(self, value):
-        """
-        Sets the value of :py:attr:`epsilon`.
-
-        >>> algo = KMeans().setEpsilon(1e-5)
-        >>> abs(algo.getEpsilon() - 1e-5) < 1e-5
-        True
-        """
-        self._paramMap[self.epsilon] = value
-        return self
-
-    def getEpsilon(self):
-        """
-        Gets the value of `epsilon`
-        """
-        return self.getOrDefault(self.epsilon)
-
-    def setRuns(self, value):
-        """
-        Sets the value of :py:attr:`runs`.
-
-        >>> algo = KMeans().setRuns(10)
-        >>> algo.getRuns()
-        10
-        """
-        self._paramMap[self.runs] = value
-        return self
-
-    def getRuns(self):
-        """
-        Gets the value of `runs`
-        """
-        return self.getOrDefault(self.runs)
-
     def setInitMode(self, value):
         """
         Sets the value of :py:attr:`initMode`.


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