[SPARK-11846] Add save/load for AFTSurvivalRegression and IsotonicRegression

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

@@ -21,20 +21,20 @@ import scala.collection.mutable
 
 import breeze.linalg.{DenseVector => BDV}
 import breeze.optimize.{CachedDiffFunction, DiffFunction, LBFGS => BreezeLBFGS}
+import org.apache.hadoop.fs.Path
 
-import org.apache.spark.{SparkException, Logging}
-import org.apache.spark.annotation.{Since, Experimental}
-import org.apache.spark.ml.{Model, Estimator}
+import org.apache.spark.annotation.{Experimental, Since}
 import org.apache.spark.ml.param._
 import org.apache.spark.ml.param.shared._
-import org.apache.spark.ml.util.{SchemaUtils, Identifiable}
-import org.apache.spark.mllib.linalg.{Vector, Vectors, VectorUDT}
-import org.apache.spark.mllib.linalg.BLAS
+import org.apache.spark.ml.util._
+import org.apache.spark.ml.{Estimator, Model}
+import org.apache.spark.mllib.linalg.{BLAS, Vector, VectorUDT, Vectors}
 import org.apache.spark.rdd.RDD
-import org.apache.spark.sql.{Row, DataFrame}
 import org.apache.spark.sql.functions._
 import org.apache.spark.sql.types.{DoubleType, StructType}
+import org.apache.spark.sql.{DataFrame, Row}
 import org.apache.spark.storage.StorageLevel
+import org.apache.spark.{Logging, SparkException}
 
 /**
  * Params for accelerated failure time (AFT) regression.
@@ -120,7 +120,8 @@ private[regression] trait AFTSurvivalRegressionParams extends Params
 @Experimental
 @Since("1.6.0")
 class AFTSurvivalRegression @Since("1.6.0") (@Since("1.6.0") override val uid: String)
-  extends Estimator[AFTSurvivalRegressionModel] with AFTSurvivalRegressionParams with Logging {
+  extends Estimator[AFTSurvivalRegressionModel] with AFTSurvivalRegressionParams
+  with DefaultParamsWritable with Logging {
 
   @Since("1.6.0")
   def this() = this(Identifiable.randomUID("aftSurvReg"))
@@ -243,6 +244,13 @@ class AFTSurvivalRegression @Since("1.6.0") (@Since("1.6.0") override val uid: S
   override def copy(extra: ParamMap): AFTSurvivalRegression = defaultCopy(extra)
 }
 
+@Since("1.6.0")
+object AFTSurvivalRegression extends DefaultParamsReadable[AFTSurvivalRegression] {
+
+  @Since("1.6.0")
+  override def load(path: String): AFTSurvivalRegression = super.load(path)
+}
+
 /**
  * :: Experimental ::
  * Model produced by [[AFTSurvivalRegression]].
@@ -254,7 +262,7 @@ class AFTSurvivalRegressionModel private[ml] (
     @Since("1.6.0") val coefficients: Vector,
     @Since("1.6.0") val intercept: Double,
     @Since("1.6.0") val scale: Double)
-  extends Model[AFTSurvivalRegressionModel] with AFTSurvivalRegressionParams {
+  extends Model[AFTSurvivalRegressionModel] with AFTSurvivalRegressionParams with MLWritable {
 
   /** @group setParam */
   @Since("1.6.0")
@@ -312,6 +320,58 @@ class AFTSurvivalRegressionModel private[ml] (
     copyValues(new AFTSurvivalRegressionModel(uid, coefficients, intercept, scale), extra)
       .setParent(parent)
   }
+
+  @Since("1.6.0")
+  override def write: MLWriter =
+    new AFTSurvivalRegressionModel.AFTSurvivalRegressionModelWriter(this)
+}
+
+@Since("1.6.0")
+object AFTSurvivalRegressionModel extends MLReadable[AFTSurvivalRegressionModel] {
+
+  @Since("1.6.0")
+  override def read: MLReader[AFTSurvivalRegressionModel] = new AFTSurvivalRegressionModelReader
+
+  @Since("1.6.0")
+  override def load(path: String): AFTSurvivalRegressionModel = super.load(path)
+
+  /** [[MLWriter]] instance for [[AFTSurvivalRegressionModel]] */
+  private[AFTSurvivalRegressionModel] class AFTSurvivalRegressionModelWriter (
+      instance: AFTSurvivalRegressionModel
+    ) extends MLWriter with Logging {
+
+    private case class Data(coefficients: Vector, intercept: Double, scale: Double)
+
+    override protected def saveImpl(path: String): Unit = {
+      // Save metadata and Params
+      DefaultParamsWriter.saveMetadata(instance, path, sc)
+      // Save model data: coefficients, intercept, scale
+      val data = Data(instance.coefficients, instance.intercept, instance.scale)
+      val dataPath = new Path(path, "data").toString
+      sqlContext.createDataFrame(Seq(data)).repartition(1).write.parquet(dataPath)
+    }
+  }
+
+  private class AFTSurvivalRegressionModelReader extends MLReader[AFTSurvivalRegressionModel] {
+
+    /** Checked against metadata when loading model */
+    private val className = classOf[AFTSurvivalRegressionModel].getName
+
+    override def load(path: String): AFTSurvivalRegressionModel = {
+      val metadata = DefaultParamsReader.loadMetadata(path, sc, className)
+
+      val dataPath = new Path(path, "data").toString
+      val data = sqlContext.read.parquet(dataPath)
+        .select("coefficients", "intercept", "scale").head()
+      val coefficients = data.getAs[Vector](0)
+      val intercept = data.getDouble(1)
+      val scale = data.getDouble(2)
+      val model = new AFTSurvivalRegressionModel(metadata.uid, coefficients, intercept, scale)
+
+      DefaultParamsReader.getAndSetParams(model, metadata)
+      model
+    }
+  }
 }
 
 /**

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

@@ -17,18 +17,22 @@
 
 package org.apache.spark.ml.regression
 
+import org.apache.hadoop.fs.Path
+
 import org.apache.spark.Logging
 import org.apache.spark.annotation.{Experimental, Since}
-import org.apache.spark.ml.{Estimator, Model}
 import org.apache.spark.ml.param._
-import org.apache.spark.ml.param.shared.{HasFeaturesCol, HasLabelCol, HasPredictionCol, HasWeightCol}
-import org.apache.spark.ml.util.{Identifiable, SchemaUtils}
+import org.apache.spark.ml.param.shared._
+import org.apache.spark.ml.regression.IsotonicRegressionModel.IsotonicRegressionModelWriter
+import org.apache.spark.ml.util._
+import org.apache.spark.ml.{Estimator, Model}
 import org.apache.spark.mllib.linalg.{Vector, VectorUDT, Vectors}
-import org.apache.spark.mllib.regression.{IsotonicRegression => MLlibIsotonicRegression, IsotonicRegressionModel => MLlibIsotonicRegressionModel}
+import org.apache.spark.mllib.regression.{IsotonicRegression => MLlibIsotonicRegression}
+import org.apache.spark.mllib.regression.{IsotonicRegressionModel => MLlibIsotonicRegressionModel}
 import org.apache.spark.rdd.RDD
-import org.apache.spark.sql.{DataFrame, Row}
 import org.apache.spark.sql.functions.{col, lit, udf}
 import org.apache.spark.sql.types.{DoubleType, StructType}
+import org.apache.spark.sql.{DataFrame, Row}
 import org.apache.spark.storage.StorageLevel
 
 /**
@@ -127,7 +131,8 @@ private[regression] trait IsotonicRegressionBase extends Params with HasFeatures
 @Since("1.5.0")
 @Experimental
 class IsotonicRegression @Since("1.5.0") (@Since("1.5.0") override val uid: String)
-  extends Estimator[IsotonicRegressionModel] with IsotonicRegressionBase {
+  extends Estimator[IsotonicRegressionModel]
+  with IsotonicRegressionBase with DefaultParamsWritable {
 
   @Since("1.5.0")
   def this() = this(Identifiable.randomUID("isoReg"))
@@ -179,6 +184,13 @@ class IsotonicRegression @Since("1.5.0") (@Since("1.5.0") override val uid: Stri
   }
 }
 
+@Since("1.6.0")
+object IsotonicRegression extends DefaultParamsReadable[IsotonicRegression] {
+
+  @Since("1.6.0")
+  override def load(path: String): IsotonicRegression = super.load(path)
+}
+
 /**
  * :: Experimental ::
  * Model fitted by IsotonicRegression.
@@ -194,7 +206,7 @@ class IsotonicRegression @Since("1.5.0") (@Since("1.5.0") override val uid: Stri
 class IsotonicRegressionModel private[ml] (
     override val uid: String,
     private val oldModel: MLlibIsotonicRegressionModel)
-  extends Model[IsotonicRegressionModel] with IsotonicRegressionBase {
+  extends Model[IsotonicRegressionModel] with IsotonicRegressionBase with MLWritable {
 
   /** @group setParam */
   @Since("1.5.0")
@@ -240,4 +252,61 @@ class IsotonicRegressionModel private[ml] (
   override def transformSchema(schema: StructType): StructType = {
     validateAndTransformSchema(schema, fitting = false)
   }
+
+  @Since("1.6.0")
+  override def write: MLWriter =
+    new IsotonicRegressionModelWriter(this)
+}
+
+@Since("1.6.0")
+object IsotonicRegressionModel extends MLReadable[IsotonicRegressionModel] {
+
+  @Since("1.6.0")
+  override def read: MLReader[IsotonicRegressionModel] = new IsotonicRegressionModelReader
+
+  @Since("1.6.0")
+  override def load(path: String): IsotonicRegressionModel = super.load(path)
+
+  /** [[MLWriter]] instance for [[IsotonicRegressionModel]] */
+  private[IsotonicRegressionModel] class IsotonicRegressionModelWriter (
+      instance: IsotonicRegressionModel
+    ) extends MLWriter with Logging {
+
+    private case class Data(
+        boundaries: Array[Double],
+        predictions: Array[Double],
+        isotonic: Boolean)
+
+    override protected def saveImpl(path: String): Unit = {
+      // Save metadata and Params
+      DefaultParamsWriter.saveMetadata(instance, path, sc)
+      // Save model data: boundaries, predictions, isotonic
+      val data = Data(
+        instance.oldModel.boundaries, instance.oldModel.predictions, instance.oldModel.isotonic)
+      val dataPath = new Path(path, "data").toString
+      sqlContext.createDataFrame(Seq(data)).repartition(1).write.parquet(dataPath)
+    }
+  }
+
+  private class IsotonicRegressionModelReader extends MLReader[IsotonicRegressionModel] {
+
+    /** Checked against metadata when loading model */
+    private val className = classOf[IsotonicRegressionModel].getName
+
+    override def load(path: String): IsotonicRegressionModel = {
+      val metadata = DefaultParamsReader.loadMetadata(path, sc, className)
+
+      val dataPath = new Path(path, "data").toString
+      val data = sqlContext.read.parquet(dataPath)
+        .select("boundaries", "predictions", "isotonic").head()
+      val boundaries = data.getAs[Seq[Double]](0).toArray
+      val predictions = data.getAs[Seq[Double]](1).toArray
+      val isotonic = data.getBoolean(2)
+      val model = new IsotonicRegressionModel(
+        metadata.uid, new MLlibIsotonicRegressionModel(boundaries, predictions, isotonic))
+
+      DefaultParamsReader.getAndSetParams(model, metadata)
+      model
+    }
+  }
 }

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

@@ -21,14 +21,15 @@ import scala.util.Random
 
 import org.apache.spark.SparkFunSuite
 import org.apache.spark.ml.param.ParamsSuite
-import org.apache.spark.ml.util.MLTestingUtils
+import org.apache.spark.ml.util.{DefaultReadWriteTest, MLTestingUtils}
 import org.apache.spark.mllib.linalg.{Vector, Vectors}
 import org.apache.spark.mllib.random.{ExponentialGenerator, WeibullGenerator}
-import org.apache.spark.mllib.util.TestingUtils._
 import org.apache.spark.mllib.util.MLlibTestSparkContext
-import org.apache.spark.sql.{Row, DataFrame}
+import org.apache.spark.mllib.util.TestingUtils._
+import org.apache.spark.sql.{DataFrame, Row}
 
-class AFTSurvivalRegressionSuite extends SparkFunSuite with MLlibTestSparkContext {
+class AFTSurvivalRegressionSuite
+  extends SparkFunSuite with MLlibTestSparkContext with DefaultReadWriteTest {
 
   @transient var datasetUnivariate: DataFrame = _
   @transient var datasetMultivariate: DataFrame = _
@@ -332,4 +333,32 @@ class AFTSurvivalRegressionSuite extends SparkFunSuite with MLlibTestSparkContex
           assert(prediction ~== model.predict(features) relTol 1E-5)
     }
   }
+
+  test("read/write") {
+    def checkModelData(
+        model: AFTSurvivalRegressionModel,
+        model2: AFTSurvivalRegressionModel): Unit = {
+      assert(model.intercept === model2.intercept)
+      assert(model.coefficients === model2.coefficients)
+      assert(model.scale === model2.scale)
+    }
+    val aft = new AFTSurvivalRegression()
+    testEstimatorAndModelReadWrite(aft, datasetMultivariate,
+      AFTSurvivalRegressionSuite.allParamSettings, checkModelData)
+  }
+}
+
+object AFTSurvivalRegressionSuite {
+
+  /**
+   * Mapping from all Params to valid settings which differ from the defaults.
+   * This is useful for tests which need to exercise all Params, such as save/load.
+   * This excludes input columns to simplify some tests.
+   */
+  val allParamSettings: Map[String, Any] = Map(
+    "predictionCol" -> "myPrediction",
+    "fitIntercept" -> true,
+    "maxIter" -> 2,
+    "tol" -> 0.01
+  )
 }

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

@@ -19,12 +19,14 @@ package org.apache.spark.ml.regression
 
 import org.apache.spark.SparkFunSuite
 import org.apache.spark.ml.param.ParamsSuite
-import org.apache.spark.ml.util.MLTestingUtils
+import org.apache.spark.ml.util.{DefaultReadWriteTest, MLTestingUtils}
 import org.apache.spark.mllib.linalg.Vectors
 import org.apache.spark.mllib.util.MLlibTestSparkContext
 import org.apache.spark.sql.{DataFrame, Row}
 
-class IsotonicRegressionSuite extends SparkFunSuite with MLlibTestSparkContext {
+class IsotonicRegressionSuite
+  extends SparkFunSuite with MLlibTestSparkContext with DefaultReadWriteTest {
+
   private def generateIsotonicInput(labels: Seq[Double]): DataFrame = {
     sqlContext.createDataFrame(
       labels.zipWithIndex.map { case (label, i) => (label, i.toDouble, 1.0) }
@@ -164,4 +166,32 @@ class IsotonicRegressionSuite extends SparkFunSuite with MLlibTestSparkContext {
 
     assert(predictions === Array(3.5, 5.0, 5.0, 5.0))
   }
+
+  test("read/write") {
+    val dataset = generateIsotonicInput(Seq(1, 2, 3, 1, 6, 17, 16, 17, 18))
+
+    def checkModelData(model: IsotonicRegressionModel, model2: IsotonicRegressionModel): Unit = {
+      assert(model.boundaries === model2.boundaries)
+      assert(model.predictions === model2.predictions)
+      assert(model.isotonic === model2.isotonic)
+    }
+
+    val ir = new IsotonicRegression()
+    testEstimatorAndModelReadWrite(ir, dataset, IsotonicRegressionSuite.allParamSettings,
+      checkModelData)
+  }
+}
+
+object IsotonicRegressionSuite {
+
+  /**
+   * Mapping from all Params to valid settings which differ from the defaults.
+   * This is useful for tests which need to exercise all Params, such as save/load.
+   * This excludes input columns to simplify some tests.
+   */
+  val allParamSettings: Map[String, Any] = Map(
+    "predictionCol" -> "myPrediction",
+    "isotonic" -> true,
+    "featureIndex" -> 0
+  )
 }