Fpr chi square2

mllib/src/main/scala/org/apache/spark/ml/feature/ChiSqSelector.scala

@@ -54,6 +54,29 @@ private[feature] trait ChiSqSelectorParams extends Params
 
   /** @group getParam */
   def getNumTopFeatures: Int = $(numTopFeatures)
+
+  final val percentile = new DoubleParam(this, "percentile",
+    "Percentile of features that selector will select, ordered by statistics value descending.",
+    ParamValidators.gtEq(0))
+  setDefault(percentile -> 10)
+
+  /** @group getParam */
+  def getPercentile: Double = $(percentile)
+
+  final val alpha = new DoubleParam(this, "alpha",
+    "The highest p-value for features to be kept.",
+    ParamValidators.gtEq(0))
+  setDefault(alpha -> 0.05)
+
+  /** @group getParam */
+  def getAlpha: Double = $(alpha)
+
+  final val selectorType = new Param[String](this, "selectorType",
+    "ChiSqSelector Type: KBest, Percentile, Fpr")
+  setDefault(selectorType -> "KBest")
+
+  /** @group getParam */
+  def getChiSqSelectorType: String = $(selectorType)
 }
 
 /**
@@ -67,9 +90,27 @@ final class ChiSqSelector @Since("1.6.0") (@Since("1.6.0") override val uid: Str
   @Since("1.6.0")
   def this() = this(Identifiable.randomUID("chiSqSelector"))
 
+  @Since("2.1.0")
+  var chiSqSelector: feature.ChiSqSelector = null
+
   /** @group setParam */
-  @Since("1.6.0")
-  def setNumTopFeatures(value: Int): this.type = set(numTopFeatures, value)
+  @Since("2.1.0")
+  def setNumTopFeatures(value: Int): this.type = {
+    set(selectorType, "KBest")
+    set(numTopFeatures, value)
+  }
+
+  @Since("2.1.0")
+  def setPercentile(value: Double): this.type = {
+    set(selectorType, "Percentile")
+    set(percentile, value)
+  }
+
+  @Since("2.1.0")
+  def setAlpha(value: Double): this.type = {
+    set(selectorType, "Fpr")
+    set(alpha, value)
+  }
 
   /** @group setParam */
   @Since("1.6.0")
@@ -91,8 +132,38 @@ final class ChiSqSelector @Since("1.6.0") (@Since("1.6.0") override val uid: Str
         case Row(label: Double, features: Vector) =>
           OldLabeledPoint(label, OldVectors.fromML(features))
       }
-    val chiSqSelector = new feature.ChiSqSelector($(numTopFeatures)).fit(input)
-    copyValues(new ChiSqSelectorModel(uid, chiSqSelector).setParent(this))
+    $(selectorType) match {
+      case "KBest" =>
+        chiSqSelector = new feature.ChiSqSelector().setNumTopFeatures($(numTopFeatures))
+      case "Percentile" =>
+        chiSqSelector = new feature.ChiSqSelector().setPercentile($(percentile))
+      case "Fpr" =>
+        chiSqSelector = new feature.ChiSqSelector().setAlpha($(alpha))
+      case _ => throw new Exception("Unknown ChiSqSelector Type.")
+    }
+    val model = chiSqSelector.fit(input)
+    copyValues(new ChiSqSelectorModel(uid, model).setParent(this))
+  }
+
+  @Since("2.1.0")
+  def selectKBest(value: Int): ChiSqSelectorModel = {
+    require(chiSqSelector != null, "ChiSqSelector has not been created.")
+    val model = chiSqSelector.selectKBest(value)
+    copyValues(new ChiSqSelectorModel(uid, model).setParent(this))
+  }
+
+  @Since("2.1.0")
+  def selectPercentile(value: Double): ChiSqSelectorModel = {
+    require(chiSqSelector != null, "ChiSqSelector has not been created.")
+    val model = chiSqSelector.selectPercentile(value)
+    copyValues(new ChiSqSelectorModel(uid, model).setParent(this))
+  }
+
+  @Since("2.1.0")
+  def selectFpr(value: Double): ChiSqSelectorModel = {
+    require(chiSqSelector != null, "ChiSqSelector has not been created.")
+    val model = chiSqSelector.selectFpr(value)
+    copyValues(new ChiSqSelectorModel(uid, model).setParent(this))
   }
 
   @Since("1.6.0")

mllib/src/main/scala/org/apache/spark/mllib/feature/ChiSqSelector.scala

@@ -27,22 +27,27 @@ import org.apache.spark.annotation.Since
 import org.apache.spark.mllib.linalg.{DenseVector, SparseVector, Vector, Vectors}
 import org.apache.spark.mllib.regression.LabeledPoint
 import org.apache.spark.mllib.stat.Statistics
+import org.apache.spark.mllib.stat.test.ChiSqTestResult
 import org.apache.spark.mllib.util.{Loader, Saveable}
 import org.apache.spark.rdd.RDD
 import org.apache.spark.SparkContext
 import org.apache.spark.sql.{Row, SparkSession}
 
+@Since("2.1.0")
+object ChiSqSelectorType extends Enumeration {
+  type SelectorType = Value
+  val KBest, Percentile, Fpr = Value
+}
+
 /**
  * Chi Squared selector model.
  *
- * @param selectedFeatures list of indices to select (filter). Must be ordered asc
+ * @param selectedFeatures list of indices to select (filter).
  */
 @Since("1.3.0")
 class ChiSqSelectorModel @Since("1.3.0") (
   @Since("1.3.0") val selectedFeatures: Array[Int]) extends VectorTransformer with Saveable {
 
-  require(isSorted(selectedFeatures), "Array has to be sorted asc")
-
   protected def isSorted(array: Array[Int]): Boolean = {
     var i = 1
     val len = array.length
@@ -69,21 +74,22 @@ class ChiSqSelectorModel @Since("1.3.0") (
    * Preserves the order of filtered features the same as their indices are stored.
    * Might be moved to Vector as .slice
    * @param features vector
-   * @param filterIndices indices of features to filter, must be ordered asc
+   * @param filterIndices indices of features to filter
    */
   private def compress(features: Vector, filterIndices: Array[Int]): Vector = {
+    val orderedIndices = filterIndices.sorted
     features match {
       case SparseVector(size, indices, values) =>
-        val newSize = filterIndices.length
+        val newSize = orderedIndices.length
         val newValues = new ArrayBuilder.ofDouble
         val newIndices = new ArrayBuilder.ofInt
         var i = 0
         var j = 0
         var indicesIdx = 0
         var filterIndicesIdx = 0
-        while (i < indices.length && j < filterIndices.length) {
+        while (i < indices.length && j < orderedIndices.length) {
           indicesIdx = indices(i)
-          filterIndicesIdx = filterIndices(j)
+          filterIndicesIdx = orderedIndices(j)
           if (indicesIdx == filterIndicesIdx) {
             newIndices += j
             newValues += values(i)
@@ -101,7 +107,7 @@ class ChiSqSelectorModel @Since("1.3.0") (
         Vectors.sparse(newSize, newIndices.result(), newValues.result())
       case DenseVector(values) =>
         val values = features.toArray
-        Vectors.dense(filterIndices.map(i => values(i)))
+        Vectors.dense(orderedIndices.map(i => values(i)))
       case other =>
         throw new UnsupportedOperationException(
           s"Only sparse and dense vectors are supported but got ${other.getClass}.")
@@ -171,14 +177,47 @@ object ChiSqSelectorModel extends Loader[ChiSqSelectorModel] {
 
 /**
  * Creates a ChiSquared feature selector.
- * @param numTopFeatures number of features that selector will select
- *                       (ordered by statistic value descending)
- *                       Note that if the number of features is less than numTopFeatures,
- *                       then this will select all features.
  */
-@Since("1.3.0")
-class ChiSqSelector @Since("1.3.0") (
-  @Since("1.3.0") val numTopFeatures: Int) extends Serializable {
+@Since("2.1.0")
+class ChiSqSelector @Since("2.1.0") () extends Serializable {
+  private var numTopFeatures: Int = 50
+  private var percentile: Double = 10.0
+  private var alpha: Double = 0.05
+  private var selectorType = ChiSqSelectorType.KBest
+  private var chiSqTestResult: Array[ChiSqTestResult] = _
+
+  @Since("1.3.0")
+  def this(numTopFeatures: Int) {
+    this()
+    this.numTopFeatures = numTopFeatures
+  }
+
+  @Since("2.1.0")
+  def setNumTopFeatures(value: Int): this.type = {
+    numTopFeatures = value
+    selectorType = ChiSqSelectorType.KBest
+    this
+  }
+
+  @Since("2.1.0")
+  def setPercentile(value: Double): this.type = {
+    percentile = value
+    selectorType = ChiSqSelectorType.Percentile
+    this
+  }
+
+  @Since("2.1.0")
+  def setAlpha(value: Double): this.type = {
+    alpha = value
+    selectorType = ChiSqSelectorType.Fpr
+    this
+  }
+
+  @Since("2.1.0")
+  def setChiSqSelectorType(value: ChiSqSelectorType.Value): this.type = {
+    selectorType = value
+    this
+  }
 
   /**
    * Returns a ChiSquared feature selector.
@@ -189,11 +228,35 @@ class ChiSqSelector @Since("1.3.0") (
    */
   @Since("1.3.0")
   def fit(data: RDD[LabeledPoint]): ChiSqSelectorModel = {
-    val indices = Statistics.chiSqTest(data)
-      .zipWithIndex.sortBy { case (res, _) => -res.statistic }
-      .take(numTopFeatures)
-      .map { case (_, indices) => indices }
-      .sorted
+    chiSqTestResult = Statistics.chiSqTest(data)
+    selectorType match {
+      case ChiSqSelectorType.KBest => selectKBest(numTopFeatures)
+      case ChiSqSelectorType.Percentile => selectPercentile(percentile)
+      case ChiSqSelectorType.Fpr => selectFpr(alpha)
+      case _ => throw new Exception("Unknown ChiSqSelector Type")
+    }
+  }
+
+  @Since("2.1.0")
+  def selectKBest(value: Int): ChiSqSelectorModel = {
+    val indices = chiSqTestResult.zipWithIndex.sortBy { case (res, _) => -res.statistic }
+    .take(numTopFeatures)
+    .map { case (_, indices) => indices }
+    new ChiSqSelectorModel(indices)
+  }
+
+  @Since("2.1.0")
+  def selectPercentile(value: Double): ChiSqSelectorModel = {
+    val indices = chiSqTestResult.zipWithIndex.sortBy { case (res, _) => -res.statistic }
+    .take((chiSqTestResult.length * percentile / 100).toInt)
+    .map { case (_, indices) => indices }
+    new ChiSqSelectorModel(indices)
+  }
+
+  @Since("2.1.0")
+  def selectFpr(value: Double): ChiSqSelectorModel = {
+    val indices = chiSqTestResult.zipWithIndex.filter{ case (res, _) => res.pValue < alpha }
+    .map { case (_, indices) => indices }
     new ChiSqSelectorModel(indices)
   }
 }

mllib/src/test/scala/org/apache/spark/ml/feature/ChiSqSelectorSuite.scala

@@ -49,16 +49,23 @@ class ChiSqSelectorSuite extends SparkFunSuite with MLlibTestSparkContext
       .map(x => (x._1.label, x._1.features, x._2))
       .toDF("label", "data", "preFilteredData")
 
-    val model = new ChiSqSelector()
+    val selector = new ChiSqSelector()
       .setNumTopFeatures(1)
       .setFeaturesCol("data")
       .setLabelCol("label")
       .setOutputCol("filtered")
 
-    model.fit(df).transform(df).select("filtered", "preFilteredData").collect().foreach {
+    selector.fit(df).transform(df).select("filtered", "preFilteredData").collect().foreach {
       case Row(vec1: Vector, vec2: Vector) =>
         assert(vec1 ~== vec2 absTol 1e-1)
     }
+
+    selector.selectPercentile(34).transform(df)
+    .select("filtered", "preFilteredData").collect().foreach {
+      case Row(vec1: Vector, vec2: Vector) =>
+        assert(vec1 ~== vec2 absTol 1e-1)
+    }
+
   }
 
   test("ChiSqSelector read/write") {

mllib/src/test/scala/org/apache/spark/mllib/feature/ChiSqSelectorSuite.scala

@@ -65,6 +65,24 @@ class ChiSqSelectorSuite extends SparkFunSuite with MLlibTestSparkContext {
     assert(filteredData == preFilteredData)
   }
 
+  test("ChiSqSelector by FPR transform test (sparse & dense vector)") {
+    val labeledDiscreteData = sc.parallelize(
+      Seq(LabeledPoint(0.0, Vectors.sparse(4, Array((0, 8.0), (1, 7.0)))),
+        LabeledPoint(1.0, Vectors.sparse(4, Array((1, 9.0), (2, 6.0), (3, 4.0)))),
+        LabeledPoint(1.0, Vectors.dense(Array(0.0, 9.0, 8.0, 4.0))),
+        LabeledPoint(2.0, Vectors.dense(Array(8.0, 9.0, 5.0, 9.0)))), 2)
+    val preFilteredData =
+      Set(LabeledPoint(0.0, Vectors.dense(Array(0.0))),
+        LabeledPoint(1.0, Vectors.dense(Array(4.0))),
+        LabeledPoint(1.0, Vectors.dense(Array(4.0))),
+        LabeledPoint(2.0, Vectors.dense(Array(9.0))))
+    val model = new ChiSqSelector().setAlpha(0.1).fit(labeledDiscreteData)
+    val filteredData = labeledDiscreteData.map { lp =>
+      LabeledPoint(lp.label, model.transform(lp.features))
+    }.collect().toSet
+    assert(filteredData == preFilteredData)
+  }
+
   test("model load / save") {
     val model = ChiSqSelectorSuite.createModel()
     val tempDir = Utils.createTempDir()