[SPARK-15339][ML] ML 2.0 QA: Scala APIs and code audit for regression

## What changes were proposed in this pull request?
* ```GeneralizedLinearRegression``` API docs enhancement.
* The default value of ```GeneralizedLinearRegression``` ```linkPredictionCol``` is not set rather than empty. This will consistent with other similar params such as ```weightCol```
* Make some methods more private.
* Fix a minor bug of LinearRegression.
* Fix some other issues.

## How was this patch tested?
Existing tests.

Author: Yanbo Liang <ybliang8@gmail.com>

Closes #13129 from yanboliang/spark-15339.

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

@@ -89,8 +89,8 @@ private[regression] trait AFTSurvivalRegressionParams extends Params
   def getQuantilesCol: String = $(quantilesCol)
 
   /** Checks whether the input has quantiles column name. */
-  protected[regression] def hasQuantilesCol: Boolean = {
-    isDefined(quantilesCol) && $(quantilesCol) != ""
+  private[regression] def hasQuantilesCol: Boolean = {
+    isDefined(quantilesCol) && $(quantilesCol).nonEmpty
   }
 
   /**

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

@@ -43,6 +43,8 @@ private[regression] trait GeneralizedLinearRegressionBase extends PredictorParam
   with HasFitIntercept with HasMaxIter with HasTol with HasRegParam with HasWeightCol
   with HasSolver with Logging {
 
+  import GeneralizedLinearRegression._
+
   /**
    * Param for the name of family which is a description of the error distribution
    * to be used in the model.
@@ -54,8 +56,8 @@ private[regression] trait GeneralizedLinearRegressionBase extends PredictorParam
   @Since("2.0.0")
   final val family: Param[String] = new Param(this, "family",
     "The name of family which is a description of the error distribution to be used in the " +
-      "model. Supported options: gaussian(default), binomial, poisson and gamma.",
-    ParamValidators.inArray[String](GeneralizedLinearRegression.supportedFamilyNames.toArray))
+      s"model. Supported options: ${supportedFamilyNames.mkString(", ")}.",
+    ParamValidators.inArray[String](supportedFamilyNames.toArray))
 
   /** @group getParam */
   @Since("2.0.0")
@@ -71,9 +73,8 @@ private[regression] trait GeneralizedLinearRegressionBase extends PredictorParam
   @Since("2.0.0")
   final val link: Param[String] = new Param(this, "link", "The name of link function " +
     "which provides the relationship between the linear predictor and the mean of the " +
-    "distribution function. Supported options: identity, log, inverse, logit, probit, " +
-    "cloglog and sqrt.",
-    ParamValidators.inArray[String](GeneralizedLinearRegression.supportedLinkNames.toArray))
+    s"distribution function. Supported options: ${supportedLinkNames.mkString(", ")}",
+    ParamValidators.inArray[String](supportedLinkNames.toArray))
 
   /** @group getParam */
   @Since("2.0.0")
@@ -81,19 +82,23 @@ private[regression] trait GeneralizedLinearRegressionBase extends PredictorParam
 
   /**
    * Param for link prediction (linear predictor) column name.
-   * Default is empty, which means we do not output link prediction.
+   * Default is not set, which means we do not output link prediction.
    *
    * @group param
    */
   @Since("2.0.0")
   final val linkPredictionCol: Param[String] = new Param[String](this, "linkPredictionCol",
     "link prediction (linear predictor) column name")
-  setDefault(linkPredictionCol, "")
 
   /** @group getParam */
   @Since("2.0.0")
   def getLinkPredictionCol: String = $(linkPredictionCol)
 
+  /** Checks whether we should output link prediction. */
+  private[regression] def hasLinkPredictionCol: Boolean = {
+    isDefined(linkPredictionCol) && $(linkPredictionCol).nonEmpty
+  }
+
   import GeneralizedLinearRegression._
 
   @Since("2.0.0")
@@ -107,7 +112,7 @@ private[regression] trait GeneralizedLinearRegressionBase extends PredictorParam
         s"with ${$(family)} family does not support ${$(link)} link function.")
     }
     val newSchema = super.validateAndTransformSchema(schema, fitting, featuresDataType)
-    if ($(linkPredictionCol).nonEmpty) {
+    if (hasLinkPredictionCol) {
       SchemaUtils.appendColumn(newSchema, $(linkPredictionCol), DoubleType)
     } else {
       newSchema
@@ -205,7 +210,7 @@ class GeneralizedLinearRegression @Since("2.0.0") (@Since("2.0.0") override val
   /**
    * Sets the value of param [[weightCol]].
    * If this is not set or empty, we treat all instance weights as 1.0.
-   * Default is empty, so all instances have weight one.
+   * Default is not set, so all instances have weight one.
    *
    * @group setParam
    */
@@ -214,7 +219,7 @@ class GeneralizedLinearRegression @Since("2.0.0") (@Since("2.0.0") override val
 
   /**
    * Sets the solver algorithm used for optimization.
-   * Currently only support "irls" which is also the default solver.
+   * Currently only supports "irls" which is also the default solver.
    *
    * @group setParam
    */
@@ -239,10 +244,7 @@ class GeneralizedLinearRegression @Since("2.0.0") (@Since("2.0.0") override val
     }
     val familyAndLink = new FamilyAndLink(familyObj, linkObj)
 
-    val numFeatures = dataset.select(col($(featuresCol))).limit(1).rdd
-      .map { case Row(features: Vector) =>
-        features.size
-      }.first()
+    val numFeatures = dataset.select(col($(featuresCol))).first().getAs[Vector](0).size
     if (numFeatures > WeightedLeastSquares.MAX_NUM_FEATURES) {
       val msg = "Currently, GeneralizedLinearRegression only supports number of features" +
         s" <= ${WeightedLeastSquares.MAX_NUM_FEATURES}. Found $numFeatures in the input dataset."
@@ -294,7 +296,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
   override def load(path: String): GeneralizedLinearRegression = super.load(path)
 
   /** Set of family and link pairs that GeneralizedLinearRegression supports. */
-  private[ml] lazy val supportedFamilyAndLinkPairs = Set(
+  private[regression] lazy val supportedFamilyAndLinkPairs = Set(
     Gaussian -> Identity, Gaussian -> Log, Gaussian -> Inverse,
     Binomial -> Logit, Binomial -> Probit, Binomial -> CLogLog,
     Poisson -> Log, Poisson -> Identity, Poisson -> Sqrt,
@@ -302,17 +304,17 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
   )
 
   /** Set of family names that GeneralizedLinearRegression supports. */
-  private[ml] lazy val supportedFamilyNames = supportedFamilyAndLinkPairs.map(_._1.name)
+  private[regression] lazy val supportedFamilyNames = supportedFamilyAndLinkPairs.map(_._1.name)
 
   /** Set of link names that GeneralizedLinearRegression supports. */
-  private[ml] lazy val supportedLinkNames = supportedFamilyAndLinkPairs.map(_._2.name)
+  private[regression] lazy val supportedLinkNames = supportedFamilyAndLinkPairs.map(_._2.name)
 
-  private[ml] val epsilon: Double = 1E-16
+  private[regression] val epsilon: Double = 1E-16
 
   /**
    * Wrapper of family and link combination used in the model.
    */
-  private[ml] class FamilyAndLink(val family: Family, val link: Link) extends Serializable {
+  private[regression] class FamilyAndLink(val family: Family, val link: Link) extends Serializable {
 
     /** Linear predictor based on given mu. */
     def predict(mu: Double): Double = link.link(family.project(mu))
@@ -359,7 +361,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
    *
    * @param name the name of the family.
    */
-  private[ml] abstract class Family(val name: String) extends Serializable {
+  private[regression] abstract class Family(val name: String) extends Serializable {
 
     /** The default link instance of this family. */
     val defaultLink: Link
@@ -391,7 +393,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     def project(mu: Double): Double = mu
   }
 
-  private[ml] object Family {
+  private[regression] object Family {
 
     /**
      * Gets the [[Family]] object from its name.
@@ -412,7 +414,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
    * Gaussian exponential family distribution.
    * The default link for the Gaussian family is the identity link.
    */
-  private[ml] object Gaussian extends Family("gaussian") {
+  private[regression] object Gaussian extends Family("gaussian") {
 
     val defaultLink: Link = Identity
 
@@ -448,7 +450,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
    * Binomial exponential family distribution.
    * The default link for the Binomial family is the logit link.
    */
-  private[ml] object Binomial extends Family("binomial") {
+  private[regression] object Binomial extends Family("binomial") {
 
     val defaultLink: Link = Logit
 
@@ -492,7 +494,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
    * Poisson exponential family distribution.
    * The default link for the Poisson family is the log link.
    */
-  private[ml] object Poisson extends Family("poisson") {
+  private[regression] object Poisson extends Family("poisson") {
 
     val defaultLink: Link = Log
 
@@ -533,7 +535,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
    * Gamma exponential family distribution.
    * The default link for the Gamma family is the inverse link.
    */
-  private[ml] object Gamma extends Family("gamma") {
+  private[regression] object Gamma extends Family("gamma") {
 
     val defaultLink: Link = Inverse
 
@@ -578,7 +580,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
    *
    * @param name the name of link function.
    */
-  private[ml] abstract class Link(val name: String) extends Serializable {
+  private[regression] abstract class Link(val name: String) extends Serializable {
 
     /** The link function. */
     def link(mu: Double): Double
@@ -590,7 +592,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     def unlink(eta: Double): Double
   }
 
-  private[ml] object Link {
+  private[regression] object Link {
 
     /**
      * Gets the [[Link]] object from its name.
@@ -611,7 +613,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     }
   }
 
-  private[ml] object Identity extends Link("identity") {
+  private[regression] object Identity extends Link("identity") {
 
     override def link(mu: Double): Double = mu
 
@@ -620,7 +622,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     override def unlink(eta: Double): Double = eta
   }
 
-  private[ml] object Logit extends Link("logit") {
+  private[regression] object Logit extends Link("logit") {
 
     override def link(mu: Double): Double = math.log(mu / (1.0 - mu))
 
@@ -629,7 +631,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     override def unlink(eta: Double): Double = 1.0 / (1.0 + math.exp(-1.0 * eta))
   }
 
-  private[ml] object Log extends Link("log") {
+  private[regression] object Log extends Link("log") {
 
     override def link(mu: Double): Double = math.log(mu)
 
@@ -638,7 +640,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     override def unlink(eta: Double): Double = math.exp(eta)
   }
 
-  private[ml] object Inverse extends Link("inverse") {
+  private[regression] object Inverse extends Link("inverse") {
 
     override def link(mu: Double): Double = 1.0 / mu
 
@@ -647,7 +649,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     override def unlink(eta: Double): Double = 1.0 / eta
   }
 
-  private[ml] object Probit extends Link("probit") {
+  private[regression] object Probit extends Link("probit") {
 
     override def link(mu: Double): Double = dist.Gaussian(0.0, 1.0).icdf(mu)
 
@@ -658,7 +660,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     override def unlink(eta: Double): Double = dist.Gaussian(0.0, 1.0).cdf(eta)
   }
 
-  private[ml] object CLogLog extends Link("cloglog") {
+  private[regression] object CLogLog extends Link("cloglog") {
 
     override def link(mu: Double): Double = math.log(-1.0 * math.log(1 - mu))
 
@@ -667,7 +669,7 @@ object GeneralizedLinearRegression extends DefaultParamsReadable[GeneralizedLine
     override def unlink(eta: Double): Double = 1.0 - math.exp(-1.0 * math.exp(eta))
   }
 
-  private[ml] object Sqrt extends Link("sqrt") {
+  private[regression] object Sqrt extends Link("sqrt") {
 
     override def link(mu: Double): Double = math.sqrt(mu)
 
@@ -732,7 +734,7 @@ class GeneralizedLinearRegressionModel private[ml] (
     if ($(predictionCol).nonEmpty) {
       output = output.withColumn($(predictionCol), predictUDF(col($(featuresCol))))
     }
-    if ($(linkPredictionCol).nonEmpty) {
+    if (hasLinkPredictionCol) {
       output = output.withColumn($(linkPredictionCol), predictLinkUDF(col($(featuresCol))))
     }
     output.toDF()
@@ -860,7 +862,7 @@ class GeneralizedLinearRegressionSummary private[regression] (
    */
   @Since("2.0.0")
   val predictionCol: String = {
-    if (origModel.isDefined(origModel.predictionCol) && origModel.getPredictionCol != "") {
+    if (origModel.isDefined(origModel.predictionCol) && origModel.getPredictionCol.nonEmpty) {
       origModel.getPredictionCol
     } else {
       "prediction_" + java.util.UUID.randomUUID.toString

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

@@ -69,8 +69,8 @@ private[regression] trait IsotonicRegressionBase extends Params with HasFeatures
   setDefault(isotonic -> true, featureIndex -> 0)
 
   /** Checks whether the input has weight column. */
-  protected[ml] def hasWeightCol: Boolean = {
-    isDefined(weightCol) && $(weightCol) != ""
+  private[regression] def hasWeightCol: Boolean = {
+    isDefined(weightCol) && $(weightCol).nonEmpty
   }
 
   /**

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

@@ -161,9 +161,7 @@ class LinearRegression @Since("1.3.0") (@Since("1.3.0") override val uid: String
 
   override protected def train(dataset: Dataset[_]): LinearRegressionModel = {
     // Extract the number of features before deciding optimization solver.
-    val numFeatures = dataset.select(col($(featuresCol))).limit(1).rdd.map {
-      case Row(features: Vector) => features.size
-    }.first()
+    val numFeatures = dataset.select(col($(featuresCol))).first().getAs[Vector](0).size
     val w = if (!isDefined(weightCol) || $(weightCol).isEmpty) lit(1.0) else col($(weightCol))
 
     if (($(solver) == "auto" && $(elasticNetParam) == 0.0 &&
@@ -242,7 +240,7 @@ class LinearRegression @Since("1.3.0") (@Since("1.3.0") override val uid: String
         val coefficients = Vectors.sparse(numFeatures, Seq())
         val intercept = yMean
 
-        val model = new LinearRegressionModel(uid, coefficients, intercept)
+        val model = copyValues(new LinearRegressionModel(uid, coefficients, intercept))
         // Handle possible missing or invalid prediction columns
         val (summaryModel, predictionColName) = model.findSummaryModelAndPredictionCol()
 
@@ -254,7 +252,7 @@ class LinearRegression @Since("1.3.0") (@Since("1.3.0") override val uid: String
           model,
           Array(0D),
           Array(0D))
-        return copyValues(model.setSummary(trainingSummary))
+        return model.setSummary(trainingSummary)
       } else {
         require($(regParam) == 0.0, "The standard deviation of the label is zero. " +
           "Model cannot be regularized.")

mllib/src/test/scala/org/apache/spark/ml/regression/LinearRegressionSuite.scala

@@ -610,20 +610,31 @@ class LinearRegressionSuite
         val model1 = new LinearRegression()
           .setFitIntercept(fitIntercept)
           .setWeightCol("weight")
+          .setPredictionCol("myPrediction")
           .setSolver(solver)
           .fit(datasetWithWeightConstantLabel)
         val actual1 = Vectors.dense(model1.intercept, model1.coefficients(0),
             model1.coefficients(1))
         assert(actual1 ~== expected(idx) absTol 1e-4)
 
+        // Schema of summary.predictions should be a superset of the input dataset
+        assert((datasetWithWeightConstantLabel.schema.fieldNames.toSet + model1.getPredictionCol)
+          .subsetOf(model1.summary.predictions.schema.fieldNames.toSet))
+
         val model2 = new LinearRegression()
           .setFitIntercept(fitIntercept)
           .setWeightCol("weight")
+          .setPredictionCol("myPrediction")
           .setSolver(solver)
           .fit(datasetWithWeightZeroLabel)
         val actual2 = Vectors.dense(model2.intercept, model2.coefficients(0),
             model2.coefficients(1))
         assert(actual2 ~==  Vectors.dense(0.0, 0.0, 0.0) absTol 1e-4)
+
+        // Schema of summary.predictions should be a superset of the input dataset
+        assert((datasetWithWeightZeroLabel.schema.fieldNames.toSet + model2.getPredictionCol)
+          .subsetOf(model2.summary.predictions.schema.fieldNames.toSet))
+
         idx += 1
       }
     }
@@ -672,7 +683,7 @@ class LinearRegressionSuite
 
   test("linear regression model training summary") {
     Seq("auto", "l-bfgs", "normal").foreach { solver =>
-      val trainer = new LinearRegression().setSolver(solver)
+      val trainer = new LinearRegression().setSolver(solver).setPredictionCol("myPrediction")
       val model = trainer.fit(datasetWithDenseFeature)
       val trainerNoPredictionCol = trainer.setPredictionCol("")
       val modelNoPredictionCol = trainerNoPredictionCol.fit(datasetWithDenseFeature)
@@ -682,7 +693,7 @@ class LinearRegressionSuite
       assert(modelNoPredictionCol.hasSummary)
 
       // Schema should be a superset of the input dataset
-      assert((datasetWithDenseFeature.schema.fieldNames.toSet + "prediction").subsetOf(
+      assert((datasetWithDenseFeature.schema.fieldNames.toSet + model.getPredictionCol).subsetOf(
         model.summary.predictions.schema.fieldNames.toSet))
       // Validate that we re-insert a prediction column for evaluation
       val modelNoPredictionColFieldNames