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/*
* Licensed to the Apache Software Foundation (ASF) under one or more
* contributor license agreements. See the NOTICE file distributed with
* this work for additional information regarding copyright ownership.
* The ASF licenses this file to You under the Apache License, Version 2.0
* (the "License"); you may not use this file except in compliance with
* the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.apache.spark.ml.classification
import org.apache.hadoop.fs.Path
import org.apache.spark.annotation.Since
import org.apache.spark.ml.PredictorParams
import org.apache.spark.ml.linalg._
import org.apache.spark.ml.param.{DoubleParam, Param, ParamMap, ParamValidators}
import org.apache.spark.ml.param.shared.HasWeightCol
import org.apache.spark.ml.util._
import org.apache.spark.mllib.util.MLUtils
import org.apache.spark.sql.{Dataset, Row}
import org.apache.spark.sql.functions.{col, lit}
import org.apache.spark.sql.types.DoubleType
/**
* Params for Naive Bayes Classifiers.
*/
private[ml] trait NaiveBayesParams extends PredictorParams with HasWeightCol {
/**
* The smoothing parameter.
* (default = 1.0).
* @group param
*/
final val smoothing: DoubleParam = new DoubleParam(this, "smoothing", "The smoothing parameter.",
ParamValidators.gtEq(0))
/** @group getParam */
final def getSmoothing: Double = $(smoothing)
/**
* The model type which is a string (case-sensitive).
* Supported options: "multinomial" and "bernoulli".
* (default = multinomial)
* @group param
*/
final val modelType: Param[String] = new Param[String](this, "modelType", "The model type " +
"which is a string (case-sensitive). Supported options: multinomial (default) and bernoulli.",
ParamValidators.inArray[String](NaiveBayes.supportedModelTypes.toArray))
/** @group getParam */
final def getModelType: String = $(modelType)
}
/**
* Naive Bayes Classifiers.
* It supports Multinomial NB
* ([[http://nlp.stanford.edu/IR-book/html/htmledition/naive-bayes-text-classification-1.html]])
* which can handle finitely supported discrete data. For example, by converting documents into
* TF-IDF vectors, it can be used for document classification. By making every vector a
* binary (0/1) data, it can also be used as Bernoulli NB
* ([[http://nlp.stanford.edu/IR-book/html/htmledition/the-bernoulli-model-1.html]]).
* The input feature values must be nonnegative.
*/
@Since("1.5.0")
class NaiveBayes @Since("1.5.0") (
@Since("1.5.0") override val uid: String)
extends ProbabilisticClassifier[Vector, NaiveBayes, NaiveBayesModel]
with NaiveBayesParams with DefaultParamsWritable {
import NaiveBayes._
@Since("1.5.0")
def this() = this(Identifiable.randomUID("nb"))
/**
* Set the smoothing parameter.
* Default is 1.0.
* @group setParam
*/
@Since("1.5.0")
def setSmoothing(value: Double): this.type = set(smoothing, value)
setDefault(smoothing -> 1.0)
/**
* Set the model type using a string (case-sensitive).
* Supported options: "multinomial" and "bernoulli".
* Default is "multinomial"
* @group setParam
*/
@Since("1.5.0")
def setModelType(value: String): this.type = set(modelType, value)
setDefault(modelType -> NaiveBayes.Multinomial)
/**
* Sets the value of param [[weightCol]].
* If this is not set or empty, we treat all instance weights as 1.0.
* Default is not set, so all instances have weight one.
*
* @group setParam
*/
@Since("2.1.0")
def setWeightCol(value: String): this.type = set(weightCol, value)
override protected def train(dataset: Dataset[_]): NaiveBayesModel = {
trainWithLabelCheck(dataset, positiveLabel = true)
}
/**
* ml assumes input labels in range [0, numClasses). But this implementation
* is also called by mllib NaiveBayes which allows other kinds of input labels
* such as {-1, +1}. `positiveLabel` is used to determine whether the label
* should be checked and it should be removed when we remove mllib NaiveBayes.
*/
private[spark] def trainWithLabelCheck(
dataset: Dataset[_],
positiveLabel: Boolean): NaiveBayesModel = {
if (positiveLabel) {
val numClasses = getNumClasses(dataset)
if (isDefined(thresholds)) {
require($(thresholds).length == numClasses, this.getClass.getSimpleName +
".train() called with non-matching numClasses and thresholds.length." +
s" numClasses=$numClasses, but thresholds has length ${$(thresholds).length}")
}
}
val modelTypeValue = $(modelType)
val requireValues: Vector => Unit = {
modelTypeValue match {
case Multinomial =>
requireNonnegativeValues
case Bernoulli =>
requireZeroOneBernoulliValues
case _ =>
// This should never happen.
throw new UnknownError(s"Invalid modelType: ${$(modelType)}.")
}
}
val numFeatures = dataset.select(col($(featuresCol))).head().getAs[Vector](0).size
val w = if (!isDefined(weightCol) || $(weightCol).isEmpty) lit(1.0) else col($(weightCol))
// Aggregates term frequencies per label.
// TODO: Calling aggregateByKey and collect creates two stages, we can implement something
// TODO: similar to reduceByKeyLocally to save one stage.
val aggregated = dataset.select(col($(labelCol)), w, col($(featuresCol))).rdd
.map { row => (row.getDouble(0), (row.getDouble(1), row.getAs[Vector](2)))
}.aggregateByKey[(Double, DenseVector)]((0.0, Vectors.zeros(numFeatures).toDense))(
seqOp = {
case ((weightSum: Double, featureSum: DenseVector), (weight, features)) =>
requireValues(features)
BLAS.axpy(weight, features, featureSum)
(weightSum + weight, featureSum)
},
combOp = {
case ((weightSum1, featureSum1), (weightSum2, featureSum2)) =>
BLAS.axpy(1.0, featureSum2, featureSum1)
(weightSum1 + weightSum2, featureSum1)
}).collect().sortBy(_._1)
val numLabels = aggregated.length
val numDocuments = aggregated.map(_._2._1).sum
val labelArray = new Array[Double](numLabels)
val piArray = new Array[Double](numLabels)
val thetaArray = new Array[Double](numLabels * numFeatures)
val lambda = $(smoothing)
val piLogDenom = math.log(numDocuments + numLabels * lambda)
var i = 0
aggregated.foreach { case (label, (n, sumTermFreqs)) =>
labelArray(i) = label
piArray(i) = math.log(n + lambda) - piLogDenom
val thetaLogDenom = $(modelType) match {
case Multinomial => math.log(sumTermFreqs.values.sum + numFeatures * lambda)
case Bernoulli => math.log(n + 2.0 * lambda)
case _ =>
// This should never happen.
throw new UnknownError(s"Invalid modelType: ${$(modelType)}.")
}
var j = 0
while (j < numFeatures) {
thetaArray(i * numFeatures + j) = math.log(sumTermFreqs(j) + lambda) - thetaLogDenom
j += 1
}
i += 1
}
val pi = Vectors.dense(piArray)
val theta = new DenseMatrix(numLabels, numFeatures, thetaArray, true)
new NaiveBayesModel(uid, pi, theta).setOldLabels(labelArray)
}
@Since("1.5.0")
override def copy(extra: ParamMap): NaiveBayes = defaultCopy(extra)
}
@Since("1.6.0")
object NaiveBayes extends DefaultParamsReadable[NaiveBayes] {
/** String name for multinomial model type. */
private[classification] val Multinomial: String = "multinomial"
/** String name for Bernoulli model type. */
private[classification] val Bernoulli: String = "bernoulli"
/* Set of modelTypes that NaiveBayes supports */
private[classification] val supportedModelTypes = Set(Multinomial, Bernoulli)
private[NaiveBayes] def requireNonnegativeValues(v: Vector): Unit = {
val values = v match {
case sv: SparseVector => sv.values
case dv: DenseVector => dv.values
}
require(values.forall(_ >= 0.0),
s"Naive Bayes requires nonnegative feature values but found $v.")
}
private[NaiveBayes] def requireZeroOneBernoulliValues(v: Vector): Unit = {
val values = v match {
case sv: SparseVector => sv.values
case dv: DenseVector => dv.values
}
require(values.forall(v => v == 0.0 || v == 1.0),
s"Bernoulli naive Bayes requires 0 or 1 feature values but found $v.")
}
@Since("1.6.0")
override def load(path: String): NaiveBayes = super.load(path)
}
/**
* Model produced by [[NaiveBayes]]
* @param pi log of class priors, whose dimension is C (number of classes)
* @param theta log of class conditional probabilities, whose dimension is C (number of classes)
* by D (number of features)
*/
@Since("1.5.0")
class NaiveBayesModel private[ml] (
@Since("1.5.0") override val uid: String,
@Since("2.0.0") val pi: Vector,
@Since("2.0.0") val theta: Matrix)
extends ProbabilisticClassificationModel[Vector, NaiveBayesModel]
with NaiveBayesParams with MLWritable {
import NaiveBayes.{Bernoulli, Multinomial}
/**
* mllib NaiveBayes is a wrapper of ml implementation currently.
* Input labels of mllib could be {-1, +1} and mllib NaiveBayesModel exposes labels,
* both of which are different from ml, so we should store the labels sequentially
* to be called by mllib. This should be removed when we remove mllib NaiveBayes.
*/
private[spark] var oldLabels: Array[Double] = null
private[spark] def setOldLabels(labels: Array[Double]): this.type = {
this.oldLabels = labels
this
}
/**
* Bernoulli scoring requires log(condprob) if 1, log(1-condprob) if 0.
* This precomputes log(1.0 - exp(theta)) and its sum which are used for the linear algebra
* application of this condition (in predict function).
*/
private lazy val (thetaMinusNegTheta, negThetaSum) = $(modelType) match {
case Multinomial => (None, None)
case Bernoulli =>
val negTheta = theta.map(value => math.log(1.0 - math.exp(value)))
val ones = new DenseVector(Array.fill(theta.numCols) {1.0})
val thetaMinusNegTheta = theta.map { value =>
value - math.log(1.0 - math.exp(value))
}
(Option(thetaMinusNegTheta), Option(negTheta.multiply(ones)))
case _ =>
// This should never happen.
throw new UnknownError(s"Invalid modelType: ${$(modelType)}.")
}
@Since("1.6.0")
override val numFeatures: Int = theta.numCols
@Since("1.5.0")
override val numClasses: Int = pi.size
private def multinomialCalculation(features: Vector) = {
val prob = theta.multiply(features)
BLAS.axpy(1.0, pi, prob)
prob
}
private def bernoulliCalculation(features: Vector) = {
features.foreachActive((_, value) =>
require(value == 0.0 || value == 1.0,
s"Bernoulli naive Bayes requires 0 or 1 feature values but found $features.")
)
val prob = thetaMinusNegTheta.get.multiply(features)
BLAS.axpy(1.0, pi, prob)
BLAS.axpy(1.0, negThetaSum.get, prob)
prob
}
override protected def predictRaw(features: Vector): Vector = {
$(modelType) match {
case Multinomial =>
multinomialCalculation(features)
case Bernoulli =>
bernoulliCalculation(features)
case _ =>
// This should never happen.
throw new UnknownError(s"Invalid modelType: ${$(modelType)}.")
}
}
override protected def raw2probabilityInPlace(rawPrediction: Vector): Vector = {
rawPrediction match {
case dv: DenseVector =>
var i = 0
val size = dv.size
val maxLog = dv.values.max
while (i < size) {
dv.values(i) = math.exp(dv.values(i) - maxLog)
i += 1
}
val probSum = dv.values.sum
i = 0
while (i < size) {
dv.values(i) = dv.values(i) / probSum
i += 1
}
dv
case sv: SparseVector =>
throw new RuntimeException("Unexpected error in NaiveBayesModel:" +
" raw2probabilityInPlace encountered SparseVector")
}
}
@Since("1.5.0")
override def copy(extra: ParamMap): NaiveBayesModel = {
copyValues(new NaiveBayesModel(uid, pi, theta).setParent(this.parent), extra)
}
@Since("1.5.0")
override def toString: String = {
s"NaiveBayesModel (uid=$uid) with ${pi.size} classes"
}
@Since("1.6.0")
override def write: MLWriter = new NaiveBayesModel.NaiveBayesModelWriter(this)
}
@Since("1.6.0")
object NaiveBayesModel extends MLReadable[NaiveBayesModel] {
@Since("1.6.0")
override def read: MLReader[NaiveBayesModel] = new NaiveBayesModelReader
@Since("1.6.0")
override def load(path: String): NaiveBayesModel = super.load(path)
/** [[MLWriter]] instance for [[NaiveBayesModel]] */
private[NaiveBayesModel] class NaiveBayesModelWriter(instance: NaiveBayesModel) extends MLWriter {
private case class Data(pi: Vector, theta: Matrix)
override protected def saveImpl(path: String): Unit = {
// Save metadata and Params
DefaultParamsWriter.saveMetadata(instance, path, sc)
// Save model data: pi, theta
val data = Data(instance.pi, instance.theta)
val dataPath = new Path(path, "data").toString
sparkSession.createDataFrame(Seq(data)).repartition(1).write.parquet(dataPath)
}
}
private class NaiveBayesModelReader extends MLReader[NaiveBayesModel] {
/** Checked against metadata when loading model */
private val className = classOf[NaiveBayesModel].getName
override def load(path: String): NaiveBayesModel = {
val metadata = DefaultParamsReader.loadMetadata(path, sc, className)
val dataPath = new Path(path, "data").toString
val data = sparkSession.read.parquet(dataPath)
val vecConverted = MLUtils.convertVectorColumnsToML(data, "pi")
val Row(pi: Vector, theta: Matrix) = MLUtils.convertMatrixColumnsToML(vecConverted, "theta")
.select("pi", "theta")
.head()
val model = new NaiveBayesModel(metadata.uid, pi, theta)
DefaultParamsReader.getAndSetParams(model, metadata)
model
}
}
}
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