[SPARK-20449][ML] Upgrade breeze version to 0.13.1

## What changes were proposed in this pull request?
Upgrade breeze version to 0.13.1, which fixed some critical bugs of L-BFGS-B.

## How was this patch tested?
Existing unit tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes apache#17746 from yanboliang/spark-20449.

LICENSE

@@ -297,3 +297,4 @@ The text of each license is also included at licenses/LICENSE-[project].txt.
      (MIT License) RowsGroup (http://datatables.net/license/mit)
      (MIT License) jsonFormatter (http://www.jqueryscript.net/other/jQuery-Plugin-For-Pretty-JSON-Formatting-jsonFormatter.html)
      (MIT License) modernizr (https://github.com/Modernizr/Modernizr/blob/master/LICENSE)
+     (MIT License) machinist (https://github.com/typelevel/machinist)

R/pkg/inst/tests/testthat/test_mllib_classification.R

@@ -288,18 +288,18 @@ test_that("spark.mlp", {
     c(0, 0, 0, 0, 0, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9))
   mlpPredictions <- collect(select(predict(model, mlpTestDF), "prediction"))
   expect_equal(head(mlpPredictions$prediction, 10),
-               c("1.0", "1.0", "1.0", "1.0", "2.0", "1.0", "2.0", "2.0", "1.0", "0.0"))
+               c("1.0", "1.0", "2.0", "1.0", "2.0", "1.0", "2.0", "2.0", "1.0", "0.0"))
 
   model <- spark.mlp(df, label ~ features, layers = c(4, 3), maxIter = 2, initialWeights =
     c(0.0, 0.0, 0.0, 0.0, 0.0, 5.0, 5.0, 5.0, 5.0, 5.0, 9.0, 9.0, 9.0, 9.0, 9.0))
   mlpPredictions <- collect(select(predict(model, mlpTestDF), "prediction"))
   expect_equal(head(mlpPredictions$prediction, 10),
-               c("1.0", "1.0", "1.0", "1.0", "2.0", "1.0", "2.0", "2.0", "1.0", "0.0"))
+               c("1.0", "1.0", "2.0", "1.0", "2.0", "1.0", "2.0", "2.0", "1.0", "0.0"))
 
   model <- spark.mlp(df, label ~ features, layers = c(4, 3), maxIter = 2)
   mlpPredictions <- collect(select(predict(model, mlpTestDF), "prediction"))
   expect_equal(head(mlpPredictions$prediction, 10),
-               c("1.0", "1.0", "1.0", "1.0", "0.0", "1.0", "0.0", "2.0", "1.0", "0.0"))
+               c("1.0", "1.0", "1.0", "1.0", "0.0", "1.0", "0.0", "0.0", "1.0", "0.0"))
 
   # Test formula works well
   df <- suppressWarnings(createDataFrame(iris))
@@ -310,8 +310,8 @@ test_that("spark.mlp", {
   expect_equal(summary$numOfOutputs, 3)
   expect_equal(summary$layers, c(4, 3))
   expect_equal(length(summary$weights), 15)
-  expect_equal(head(summary$weights, 5), list(-1.1957257, -5.2693685, 7.4489734, -6.3751413,
-               -10.2376130), tolerance = 1e-6)
+  expect_equal(head(summary$weights, 5), list(-0.5793153, -4.652961, 6.216155, -6.649478,
+               -10.51147), tolerance = 1e-3)
 })
 
 test_that("spark.naiveBayes", {

dev/deps/spark-deps-hadoop-2.6

@@ -19,8 +19,8 @@ avro-mapred-1.7.7-hadoop2.jar
 base64-2.3.8.jar
 bcprov-jdk15on-1.51.jar
 bonecp-0.8.0.RELEASE.jar
-breeze-macros_2.11-0.12.jar
-breeze_2.11-0.12.jar
+breeze-macros_2.11-0.13.1.jar
+breeze_2.11-0.13.1.jar
 calcite-avatica-1.2.0-incubating.jar
 calcite-core-1.2.0-incubating.jar
 calcite-linq4j-1.2.0-incubating.jar
@@ -129,6 +129,8 @@ libfb303-0.9.3.jar
 libthrift-0.9.3.jar
 log4j-1.2.17.jar
 lz4-1.3.0.jar
+machinist_2.11-0.6.1.jar
+macro-compat_2.11-1.1.1.jar
 mail-1.4.7.jar
 mesos-1.0.0-shaded-protobuf.jar
 metrics-core-3.1.2.jar
@@ -162,13 +164,13 @@ scala-parser-combinators_2.11-1.0.4.jar
 scala-reflect-2.11.8.jar
 scala-xml_2.11-1.0.2.jar
 scalap-2.11.8.jar
-shapeless_2.11-2.0.0.jar
+shapeless_2.11-2.3.2.jar
 slf4j-api-1.7.16.jar
 slf4j-log4j12-1.7.16.jar
 snappy-0.2.jar
 snappy-java-1.1.2.6.jar
-spire-macros_2.11-0.7.4.jar
-spire_2.11-0.7.4.jar
+spire-macros_2.11-0.13.0.jar
+spire_2.11-0.13.0.jar
 stax-api-1.0-2.jar
 stax-api-1.0.1.jar
 stream-2.7.0.jar

dev/deps/spark-deps-hadoop-2.7

@@ -19,8 +19,8 @@ avro-mapred-1.7.7-hadoop2.jar
 base64-2.3.8.jar
 bcprov-jdk15on-1.51.jar
 bonecp-0.8.0.RELEASE.jar
-breeze-macros_2.11-0.12.jar
-breeze_2.11-0.12.jar
+breeze-macros_2.11-0.13.1.jar
+breeze_2.11-0.13.1.jar
 calcite-avatica-1.2.0-incubating.jar
 calcite-core-1.2.0-incubating.jar
 calcite-linq4j-1.2.0-incubating.jar
@@ -130,6 +130,8 @@ libfb303-0.9.3.jar
 libthrift-0.9.3.jar
 log4j-1.2.17.jar
 lz4-1.3.0.jar
+machinist_2.11-0.6.1.jar
+macro-compat_2.11-1.1.1.jar
 mail-1.4.7.jar
 mesos-1.0.0-shaded-protobuf.jar
 metrics-core-3.1.2.jar
@@ -163,13 +165,13 @@ scala-parser-combinators_2.11-1.0.4.jar
 scala-reflect-2.11.8.jar
 scala-xml_2.11-1.0.2.jar
 scalap-2.11.8.jar
-shapeless_2.11-2.0.0.jar
+shapeless_2.11-2.3.2.jar
 slf4j-api-1.7.16.jar
 slf4j-log4j12-1.7.16.jar
 snappy-0.2.jar
 snappy-java-1.1.2.6.jar
-spire-macros_2.11-0.7.4.jar
-spire_2.11-0.7.4.jar
+spire-macros_2.11-0.13.0.jar
+spire_2.11-0.13.0.jar
 stax-api-1.0-2.jar
 stax-api-1.0.1.jar
 stream-2.7.0.jar

mllib/src/main/scala/org/apache/spark/ml/regression/GeneralizedLinearRegression.scala

@@ -894,10 +894,10 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
 
   private[regression] object Probit extends Link("probit") {
 
-    override def link(mu: Double): Double = dist.Gaussian(0.0, 1.0).icdf(mu)
+    override def link(mu: Double): Double = dist.Gaussian(0.0, 1.0).inverseCdf(mu)
 
     override def deriv(mu: Double): Double = {
-      1.0 / dist.Gaussian(0.0, 1.0).pdf(dist.Gaussian(0.0, 1.0).icdf(mu))
+      1.0 / dist.Gaussian(0.0, 1.0).pdf(dist.Gaussian(0.0, 1.0).inverseCdf(mu))
     }
 
     override def unlink(eta: Double): Double = dist.Gaussian(0.0, 1.0).cdf(eta)

mllib/src/main/scala/org/apache/spark/mllib/clustering/LDAModel.scala

@@ -788,20 +788,14 @@ class DistributedLDAModel private[clustering] (
   @Since("1.5.0")
   def topTopicsPerDocument(k: Int): RDD[(Long, Array[Int], Array[Double])] = {
     graph.vertices.filter(LDA.isDocumentVertex).map { case (docID, topicCounts) =>
-      // TODO: Remove work-around for the breeze bug.
-      // https://github.com/scalanlp/breeze/issues/561
-      val topIndices = if (k == topicCounts.length) {
-        Seq.range(0, k)
-      } else {
-        argtopk(topicCounts, k)
-      }
+      val topIndices = argtopk(topicCounts, k)
       val sumCounts = sum(topicCounts)
       val weights = if (sumCounts != 0) {
-        topicCounts(topIndices) / sumCounts
+        topicCounts(topIndices).toArray.map(_ / sumCounts)
       } else {
-        topicCounts(topIndices)
+        topicCounts(topIndices).toArray
       }
-      (docID.toLong, topIndices.toArray, weights.toArray)
+      (docID.toLong, topIndices.toArray, weights)
     }
   }
 

mllib/src/test/scala/org/apache/spark/mllib/optimization/LBFGSSuite.scala

@@ -191,8 +191,8 @@ class LBFGSSuite extends SparkFunSuite with MLlibTestSparkContext with Matchers
     // With smaller convergenceTol, it takes more steps.
     assert(lossLBFGS3.length > lossLBFGS2.length)
 
-    // Based on observation, lossLBFGS2 runs 5 iterations, no theoretically guaranteed.
-    assert(lossLBFGS3.length == 6)
+    // Based on observation, lossLBFGS3 runs 7 iterations, no theoretically guaranteed.
+    assert(lossLBFGS3.length == 7)
     assert((lossLBFGS3(4) - lossLBFGS3(5)) / lossLBFGS3(4) < convergenceTol)
   }
 

pom.xml

@@ -658,7 +658,7 @@
       <dependency>
         <groupId>org.scalanlp</groupId>
         <artifactId>breeze_${scala.binary.version}</artifactId>
-        <version>0.12</version>
+        <version>0.13.1</version>
         <exclusions>
           <!-- This is included as a compile-scoped dependency by jtransforms, which is
                a dependency of breeze. -->

python/pyspark/ml/classification.py

@@ -190,30 +190,28 @@ class LogisticRegression(JavaEstimator, HasFeaturesCol, HasLabelCol, HasPredicti
     >>> blor = LogisticRegression(maxIter=5, regParam=0.01, weightCol="weight")
     >>> blorModel = blor.fit(bdf)
     >>> blorModel.coefficients
-    DenseVector([5.5...])
+    DenseVector([5.4...])
     >>> blorModel.intercept
-    -2.68...
+    -2.63...
     >>> mdf = sc.parallelize([
     ...     Row(label=1.0, weight=2.0, features=Vectors.dense(1.0)),
     ...     Row(label=0.0, weight=2.0, features=Vectors.sparse(1, [], [])),
     ...     Row(label=2.0, weight=2.0, features=Vectors.dense(3.0))]).toDF()
     >>> mlor = LogisticRegression(maxIter=5, regParam=0.01, weightCol="weight",
     ...     family="multinomial")
     >>> mlorModel = mlor.fit(mdf)
-    >>> print(mlorModel.coefficientMatrix)
-    DenseMatrix([[-2.3...],
-                 [ 0.2...],
-                 [ 2.1... ]])
+    >>> mlorModel.coefficientMatrix
+    DenseMatrix(3, 1, [-2.3..., 0.2..., 2.1...], 1)
     >>> mlorModel.interceptVector
-    DenseVector([2.0..., 0.8..., -2.8...])
+    DenseVector([2.1..., 0.6..., -2.8...])
     >>> test0 = sc.parallelize([Row(features=Vectors.dense(-1.0))]).toDF()
     >>> result = blorModel.transform(test0).head()
     >>> result.prediction
     0.0
     >>> result.probability
     DenseVector([0.99..., 0.00...])
     >>> result.rawPrediction
-    DenseVector([8.22..., -8.22...])
+    DenseVector([8.12..., -8.12...])
     >>> test1 = sc.parallelize([Row(features=Vectors.sparse(1, [0], [1.0]))]).toDF()
     >>> blorModel.transform(test1).head().prediction
     1.0
@@ -1490,9 +1488,9 @@ class OneVsRest(Estimator, OneVsRestParams, MLReadable, MLWritable):
     >>> ovr = OneVsRest(classifier=lr)
     >>> model = ovr.fit(df)
     >>> [x.coefficients for x in model.models]
-    [DenseVector([3.3925, 1.8785]), DenseVector([-4.3016, -6.3163]), DenseVector([-4.5855, 6.1785])]
+    [DenseVector([4.9791, 2.426]), DenseVector([-4.1198, -5.9326]), DenseVector([-3.314, 5.2423])]
     >>> [x.intercept for x in model.models]
-    [-3.64747..., 2.55078..., -1.10165...]
+    [-5.06544..., 2.30341..., -1.29133...]
     >>> test0 = sc.parallelize([Row(features=Vectors.dense(-1.0, 0.0))]).toDF()
     >>> model.transform(test0).head().prediction
     1.0