run multiclass classification using spark ml pipeline - scala

I just started using spark ML pipeline to implement a multiclass classifier using LogisticRegressionWithLBFGS (which accepts as a parameters number of classes)
I followed this example:
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.rdd.RDD
import org.apache.spark.ml.Pipeline
import org.apache.spark.ml.classification.LogisticRegression
import org.apache.spark.ml.feature.{HashingTF, Tokenizer}
import org.apache.spark.mllib.linalg.Vector
import org.apache.spark.sql.{Row, SQLContext}
case class LabeledDocument(id: Long, text: String, label: Double)
case class Document(id: Long, text: String)
val conf = new SparkConf().setAppName("SimpleTextClassificationPipeline")
val sc = new SparkContext(conf)
val sqlContext = new SQLContext(sc)
import sqlContext.implicits._
// Prepare training documents, which are labeled.
val training = sc.parallelize(Seq(
LabeledDocument(0L, "a b c d e spark", 1.0),
LabeledDocument(1L, "b d", 0.0),
LabeledDocument(2L, "spark f g h", 1.0),
LabeledDocument(3L, "hadoop mapreduce", 0.0)))
// Configure an ML pipeline, which consists of three stages: tokenizer, hashingTF, and lr.
val tokenizer = new Tokenizer()
.setInputCol("text")
.setOutputCol("words")
val hashingTF = new HashingTF()
.setNumFeatures(1000)
.setInputCol(tokenizer.getOutputCol)
.setOutputCol("features")
val lr = new LogisticRegression()
.setMaxIter(10)
.setRegParam(0.01)
val pipeline = new Pipeline()
.setStages(Array(tokenizer, hashingTF, lr))
// Fit the pipeline to training documents.
val model = pipeline.fit(training.toDF)
// Prepare test documents, which are unlabeled.
val test = sc.parallelize(Seq(
Document(4L, "spark i j k"),
Document(5L, "l m n"),
Document(6L, "mapreduce spark"),
Document(7L, "apache hadoop")))
// Make predictions on test documents.
model.transform(test.toDF)
.select("id", "text", "probability", "prediction")
.collect()
.foreach { case Row(id: Long, text: String, prob: Vector, prediction: Double) =>
println("($id, $text) --> prob=$prob, prediction=$prediction")
}
sc.stop()
The problem is that the LogisticRegression class used by ML use by default 2 classes (line 176) : override val numClasses: Int = 2
Any idea how to solve this problem?
Thanks

As Odomontois already mentioned, if you'd like to use basic NLP pipelines using Spark ML Pipelines you have only 2 options:
One vs. Rest and pass existing LogisticRegression, i.e. new OneVsRest().setClassifier(logisticRegression)
Use bag of words (CountVectorizer in terms of Spark) and NaiveBayes classifier that supports multiclass classification

But your test samples only have 2 classes.. Why would it do otherwise in "auto" mode? You can force to have a multinomial classifer though:
https://spark.apache.org/docs/2.2.0/api/scala/index.html#org.apache.spark.ml.classification.LogisticRegression
val family: Param[String]
Param for the name of family which is a description of the label distribution to be used in the model. Supported options:
"auto": Automatically select the family based on the number of classes: If numClasses == 1 || numClasses == 2, set to "binomial". Else, set to "multinomial"
"binomial": Binary logistic regression with pivoting.
"multinomial": Multinomial logistic (softmax) regression without pivoting. Default is "auto".

Related

Use saved Spark mllib decision tree binary classification model to predict on new data

I am using Spark version 2.2.0 and scala version 2.11.8.
I created and saved a decision tree binary classification model using following code:
package...
import org.apache.spark.{SparkConf, SparkContext}
import org.apache.spark.mllib.tree.DecisionTree
import org.apache.spark.mllib.tree.model.DecisionTreeModel
import org.apache.spark.mllib.util.MLUtils
import org.apache.spark.sql.SparkSession
object DecisionTreeClassification {
def main(args: Array[String]): Unit = {
val sparkSession = SparkSession.builder
.master("local[*]")
.appName("Decision Tree")
.getOrCreate()
// Load and parse the data file.
val data = MLUtils.loadLibSVMFile(sparkSession.sparkContext, "path/to/file/xyz.txt")
// Split the data into training and test sets (20% held out for testing)
val splits = data.randomSplit(Array(0.8, 0.2))
val (trainingData, testData) = (splits(0), splits(1))
// Train a DecisionTree model.
// Empty categoricalFeaturesInfo indicates all features are continuous.
val numClasses = 2
val categoricalFeaturesInfo = Map[Int, Int]()
val impurity = "gini"
val maxDepth = 5
val maxBins = 32
val model = DecisionTree.trainClassifier(trainingData, numClasses, categoricalFeaturesInfo,
impurity, maxDepth, maxBins)
// Evaluate model on test instances and compute test error
val labelAndPreds = testData.map { point =>
val prediction = model.predict(point.features)
(point.label, prediction)
}
val testErr = labelAndPreds.filter(r => r._1 != r._2).count().toDouble / testData.count()
println(s"Test Error = $testErr")
println(s"Learned classification tree model:\n ${model.toDebugString}")
// Save and load model
model.save(sparkSession.sparkContext, "target/tmp/myDecisionTreeClassificationModel")
val sameModel = DecisionTreeModel.load(sparkSession.sparkContext, "target/tmp/myDecisionTreeClassificationModel")
// $example off$
sparkSession.sparkContext.stop()
}
}
Now, I want to predict a label (0 or 1) for a new data using this saved model. I am new to Spark, can anybody please let me know how to do that?
I found answer to this question so I thought I should share it if someone is looking for the answer to similar question
To make prediction for new data simply add few lines before stopping the spark session:
val newData = MLUtils.loadLibSVMFile(sparkSession.sparkContext, "path/to/file/abc.txt")
val newDataPredictions = newData.map
{ point =>
val newPrediction = model.predict(point.features)
(point.label, newPrediction)
}
newDataPredictions.foreach(f => println("Predicted label", f._2))

How to cast a variable of type MLlib vector type to ML vector type? [duplicate]

I am trying to create a LDA model on a JSON file.
Creating a spark context with the JSON file :
import org.apache.spark.sql.SparkSession
val sparkSession = SparkSession.builder
.master("local")
.appName("my-spark-app")
.config("spark.some.config.option", "config-value")
.getOrCreate()
val df = spark.read.json("dbfs:/mnt/JSON6/JSON/sampleDoc.txt")
Displaying the df should show the DataFrame
display(df)
Tokenize the text
import org.apache.spark.ml.feature.RegexTokenizer
// Set params for RegexTokenizer
val tokenizer = new RegexTokenizer()
.setPattern("[\\W_]+")
.setMinTokenLength(4) // Filter away tokens with length < 4
.setInputCol("text")
.setOutputCol("tokens")
// Tokenize document
val tokenized_df = tokenizer.transform(df)
This should be displaying the tokenized_df
display(tokenized_df)
Get the stopwords
%sh wget http://ir.dcs.gla.ac.uk/resources/linguistic_utils/stop_words > -O /tmp/stopwords
Optional: copying the stopwords to the tmp folder
%fs cp file:/tmp/stopwords dbfs:/tmp/stopwords
Collecting all the stopwords
val stopwords = sc.textFile("/tmp/stopwords").collect()
Filtering out the stopwords
import org.apache.spark.ml.feature.StopWordsRemover
// Set params for StopWordsRemover
val remover = new StopWordsRemover()
.setStopWords(stopwords) // This parameter is optional
.setInputCol("tokens")
.setOutputCol("filtered")
// Create new DF with Stopwords removed
val filtered_df = remover.transform(tokenized_df)
Displaying the filtered df should verify the stopwords got removed
display(filtered_df)
Vectorizing the frequency of occurrence of words
import org.apache.spark.mllib.linalg.Vectors
import org.apache.spark.sql.Row
import org.apache.spark.ml.feature.CountVectorizer
// Set params for CountVectorizer
val vectorizer = new CountVectorizer()
.setInputCol("filtered")
.setOutputCol("features")
.fit(filtered_df)
Verify the vectorizer
vectorizer.transform(filtered_df)
.select("id", "text","features","filtered").show()
After this I am seeing an issue in fitting this vectorizer in LDA. The issue which I believe is CountVectorizer is giving sparse vector but LDA requires dense vector. Still trying to figure out the issue.
Here is the exception where map is not able to convert.
import org.apache.spark.mllib.linalg.Vector
val ldaDF = countVectors.map {
case Row(id: String, countVector: Vector) => (id, countVector)
}
display(ldaDF)
Exception :
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 4083.0 failed 4 times, most recent failure: Lost task 0.3 in stage 4083.0 (TID 15331, 10.209.240.17): scala.MatchError: [0,(1252,[13,17,18,20,30,37,45,50,51,53,63,64,96,101,108,125,174,189,214,221,224,227,238,268,291,309,328,357,362,437,441,455,492,493,511,528,561,613,619,674,764,823,839,980,1098,1143],[1.0,1.0,2.0,1.0,1.0,1.0,2.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,3.0,1.0,2.0,1.0,5.0,1.0,2.0,2.0,1.0,4.0,1.0,2.0,3.0,1.0,1.0,1.0,1.0,1.0,2.0,1.0,1.0,1.0,1.0,1.0,2.0,1.0,2.0,1.0,1.0,1.0])] (of class org.apache.spark.sql.catalyst.expressions.GenericRowWithSchema)
There is a working sample for LDA which is not throwing any issue
import org.apache.spark.mllib.linalg.Vectors
import org.apache.spark.sql.Row
import org.apache.spark.mllib.linalg.Vector
import org.apache.spark.mllib.clustering.{DistributedLDAModel, LDA}
val a = Vectors.dense(Array(1.0,2.0,3.0))
val b = Vectors.dense(Array(3.0,4.0,5.0))
val df = Seq((1L,a),(2L,b),(2L,a)).toDF
val ldaDF = df.map { case Row(id: Long, countVector: Vector) => (id, countVector) }
val model = new LDA().setK(3).run(ldaDF.javaRDD)
display(df)
The only difference is in the second snippet we are having a dense matrix.
This has nothing to do with sparsity. Since Spark 2.0.0 ML Transformers no longer generate o.a.s.mllib.linalg.VectorUDT but o.a.s.ml.linalg.VectorUDT and are mapped locally to subclasses of o.a.s.ml.linalg.Vector. These are not compatible with old MLLib API which is moving towards deprecation in Spark 2.0.0.
You can convert between to "old" using Vectors.fromML:
import org.apache.spark.mllib.linalg.{Vectors => OldVectors}
import org.apache.spark.ml.linalg.{Vectors => NewVectors}
OldVectors.fromML(NewVectors.dense(1.0, 2.0, 3.0))
OldVectors.fromML(NewVectors.sparse(5, Seq(0 -> 1.0, 2 -> 2.0, 4 -> 3.0)))
but it make more sense to use ML implementation of LDA if you already use ML transformers.
For convenience you can use implicit conversions:
import scala.languageFeature.implicitConversions
object VectorConversions {
import org.apache.spark.mllib.{linalg => mllib}
import org.apache.spark.ml.{linalg => ml}
implicit def toNewVector(v: mllib.Vector) = v.asML
implicit def toOldVector(v: ml.Vector) = mllib.Vectors.fromML(v)
}
I changed:
val ldaDF = countVectors.map {
case Row(id: String, countVector: Vector) => (id, countVector)
}
to:
val ldaDF = countVectors.map { case Row(docId: String, features: MLVector) =>
(docId.toLong, Vectors.fromML(features)) }
And it worked like a charm! It is aligned with what #zero323 has written.
List of imports:
import org.apache.spark.ml.feature.{CountVectorizer, RegexTokenizer, StopWordsRemover}
import org.apache.spark.ml.linalg.{Vector => MLVector}
import org.apache.spark.mllib.clustering.{LDA, OnlineLDAOptimizer}
import org.apache.spark.mllib.linalg.Vectors
import org.apache.spark.sql.{Row, SparkSession}
Solution is very simple guys.. find below
//import org.apache.spark.mllib.linalg.Vector
import org.apache.spark.ml.linalg.Vector

How to predict kmeans cluster with Spark org.apache.spark.ml.clustering.{KMeans, KMeansModel}

i have a problem with the two different MLLIB Implementations (org.apache.spark.ml. and org.apache.spark.mllib) and KMeans. I am using the new implementation of org.apache.spark.ml which is using Dataframes but I'm struggeling with the documentation and how to predict a cluster index.
import org.apache.spark.ml.clustering.{KMeans, KMeansModel}
import org.apache.spark.ml.feature.LabeledPoint
import org.apache.spark.ml.linalg.Vectors
import org.apache.spark.sql.{Row, SparkSession}
/**
* An example showcasing the use of kMeans
*/
object ExploreKMeans {
// Spark configuration.
// Retrieve sparkContext with spark.sparkContext.
private val spark = SparkSession.builder()
.appName("com.example.ml.exploration.kMeans")
.master("local[*]")
.getOrCreate()
// This import, after the definition of a valid SQLContext defines implicits for converting RDDs to Dataframes over .toDF().
import spark.implicits._
def main(args: Array[String]): Unit = {
val data = spark.sparkContext.parallelize(Array((5.0, 2.0,1.5), (2.0, 2.5,2.3), (1.0, 2.1,4.2), (2.0, 5.5, 8.5)))
val df = data.toDF().map { row =>
val label = row(0).asInstanceOf[Double]
val value1 = row(1).asInstanceOf[Double]
val value2 = row(2).asInstanceOf[Double]
LabeledPoint(label, Vectors.dense(value1,value2))
}
val kmeans = new KMeans().setK(3).setSeed(1L)
val model: KMeansModel = kmeans.fit(df)
// Evaluate clustering by computing Within Set Sum of Squared Errors.
val WSSSE = model.computeCost(df)
println(s"Within Set Sum of Squared Errors = $WSSSE")
// Shows the result.
println("Cluster Centers: ")
model.clusterCenters.foreach(println)
//TODO How to predict cluster index?
//model.predict(???
}
}
How do I use the model to predict the cluster index of new values? The model.predict function is not visible. This API is really confusing...
well, a easier way to do this is:
model.summary.predictions.show
Ok, I got it. Predictions are now done with the transform method:
println("Transform ")
val transformed = model.transform(df)
transformed.collect().foreach(println)
Cluster Centers:
[2.25,1.9]
[5.5,8.5]
[2.1,4.2]
Transform:
[5.0,[2.0,1.5],0]
[2.0,[2.5,2.3],0]
[1.0,[2.1,4.2],2]
[2.0,[5.5,8.5],1]

Cannot pass arrays from MongoDB into Spark Machine Learning functions that require Vectors

My use case:
Read data from a MongoDB collection of the form:
{
"_id" : ObjectId("582cab1b21650fc72055246d"),
"label" : 167.517838916715,
"features" : [
10.0964787450654,
218.621137772497,
18.8833848806122,
11.8010251302327,
1.67037687829152,
22.0766170950477,
11.7122322171201,
12.8014773524475,
8.30441804118235,
29.4821268054137
]
}
And pass it to the org.apache.spark.ml.regression.LinearRegression class to create a model for predictions.
My problem:
The Spark connector reads in "features" as Array[Double].
LinearRegression.fit(...) expects a DataSet with a Label column and a Features column.
The Features column must be of type VectorUDT (so DenseVector or SparseVector will work).
I cannot .map features from Array[Double] to DenseVector because there is no relevant Encoder:
Error:(23, 11) Unable to find encoder for type stored in a Dataset. Primitive types (Int, String, etc) and Product types (case classes) are supported by importing spark.implicits._ Support for serializing other types will be added in future releases.
.map{case Row(label: Double, features: Array[Double]) => Row(label, Vectors.dense(features))}
Custom Encoders cannot be defined.
My question:
Is there a way I can set the configuration of the Spark connector to
read in the "features" array as a Dense/SparseVector?
Is there any
other way I can achieve this (without, for example, using an
intermediary .csv file and loading that using libsvm)?
My code:
import com.mongodb.spark.MongoSpark
import org.apache.spark.ml.linalg.Vectors
import org.apache.spark.ml.regression.LinearRegression
import org.apache.spark.sql.{Row, SparkSession}
case class DataPoint(label: Double, features: Array[Double])
object LinearRegressionWithMongo {
def main(args: Array[String]) {
val spark = SparkSession
.builder()
.appName("LinearRegressionWithMongo")
.master("local[4]")
.config("spark.mongodb.input.uri", "mongodb://127.0.0.1/LinearRegressionTest.DataPoints")
.getOrCreate()
import spark.implicits._
val dataPoints = MongoSpark.load(spark)
.map{case Row(label: Double, features: Array[Double]) => Row(label, Vectors.dense(features))}
val splitData = dataPoints.randomSplit(Array(0.7, 0.3), 42)
val training = splitData(0)
val test = splitData(1)
val linearRegression = new LinearRegression()
.setLabelCol("label")
.setFeaturesCol("features")
.setRegParam(0.0)
.setElasticNetParam(0.0)
.setMaxIter(100)
.setTol(1e-6)
// Train the model
val startTime = System.nanoTime()
val linearRegressionModel = linearRegression.fit(training)
val elapsedTime = (System.nanoTime() - startTime) / 1e9
println(s"Training time: $elapsedTime seconds")
// Print the weights and intercept for linear regression.
println(s"Weights: ${linearRegressionModel.coefficients} Intercept: ${linearRegressionModel.intercept}")
val modelEvaluator = new ModelEvaluator()
println("Training data results:")
modelEvaluator.evaluateRegressionModel(linearRegressionModel, training, "label")
println("Test data results:")
modelEvaluator.evaluateRegressionModel(linearRegressionModel, test, "label")
spark.stop()
}
}
Any help would be ridiculously appreciated!
There is quick fix for this. If data has been loaded into a DataFrame called df which has:
id - SQL double.
features - SQL array<double>.
like this one
val df = Seq((1.0, Array(2.3, 3.4, 4.5))).toDF("id", "features")
you select columns you need for downstream processing:
val idAndFeatures = df.select("id", "features")
convert to statically typed Dataset:
val tuples = idAndFeatures.as[(Double, Seq[Double])]
map and convert back to Dataset[Row]:
val spark: SparkSession = ???
import spark.implicits._
import org.apache.spark.ml.linalg.Vectors
tuples.map { case (id, features) =>
(id, Vectors.dense(features.toArray))
}.toDF("id", "features")
You can find a detailed explanation what is the difference compared to you current approach here.

How to extract variable weight from spark pipeline logistic model?

I am currently trying to learn Spark Pipeline (Spark 1.6.0). I imported datasets (train and test) as oas.sql.DataFrame objects. After executing the following codes, the produced model is a oas.ml.tuning.CrossValidatorModel.
You can use model.transform (test) to predict based on the test data in Spark. However, I would like to compare the weights that model used to predict with that from R. How to extract the weights of the predictors and intercept (if any) of model? The Scala codes are:
import sqlContext.implicits._
import org.apache.spark.mllib.linalg.{Vectors, Vector}
import org.apache.spark.SparkContext
import org.apache.spark.mllib.regression.LabeledPoint
import org.apache.spark.ml.Pipeline
import org.apache.spark.ml.classification.{LogisticRegression, LogisticRegressionModel}
import org.apache.spark.ml.evaluation.BinaryClassificationEvaluator
import org.apache.spark.ml.tuning.{ParamGridBuilder, CrossValidator}
val conTrain = sc.textFile("AbsolutePath2Train.txt")
val conTest = sc.textFile("AbsolutePath2Test.txt")
// parse text and convert to sql.DataFrame
val train = conTrain.map { line =>
val parts = line.split(",")
LabeledPoint(parts(0).toDouble, Vectors.dense(parts(1).split(" +").map(_.toDouble)))
}.toDF()
val test =conTest.map{ line =>
val parts = line.split(",")
LabeledPoint(parts(0).toDouble, Vectors.dense(parts(1).split(" +").map(_.toDouble)))
}.toDF()
// set parameter space and evaluation method
val lr = new LogisticRegression().setMaxIter(400)
val pipeline = new Pipeline().setStages(Array(lr))
val paramGrid = new ParamGridBuilder().addGrid(lr.regParam, Array(0.1, 0.01)).addGrid(lr.fitIntercept).addGrid(lr.elasticNetParam, Array(0.0, 0.5, 1.0)).build()
val cv = new CrossValidator().setEstimator(pipeline).setEvaluator(new BinaryClassificationEvaluator).setEstimatorParamMaps(paramGrid).setNumFolds(2)
// fit logistic model
val model = cv.fit(train)
// If you want to predict with test
val pred = model.transform(test)
My spark environment is not accessible. Thus, these codes are retyped and rechecked. I hope they are correct. So far, I have tried searching on webs, asking others. About my coding, welcome suggestions, and criticisms.
// set parameter space and evaluation method
val lr = new LogisticRegression().setMaxIter(400)
val pipeline = new Pipeline().setStages(Array(lr))
val paramGrid = new ParamGridBuilder().addGrid(lr.regParam, Array(0.1, 0.01)).addGrid(lr.fitIntercept).addGrid(lr.elasticNetParam, Array(0.0, 0.5, 1.0)).build()
val cv = new CrossValidator().setEstimator(pipeline).setEvaluator(new BinaryClassificationEvaluator).setEstimatorParamMaps(paramGrid).setNumFolds(2)
// you can print lr model coefficients as below
val model = cv.bestModel.asInstanceOf[PipelineModel]
val lrModel = model.stages(0).asInstanceOf[LogisticRegressionModel]
println(s"LR Model coefficients:\n${lrModel.coefficients.toArray.mkString("\n")}")
Two steps:
Get the best pipeline from cross validation result.
Get the LR Model from the best pipeline. It's the first stage in your code example.
I was looking for exactly the same thing. You might already have the answer, but anyway, here it is.
import org.apache.spark.ml.classification.LogisticRegressionModel
val lrmodel = model.bestModel.asInstanceOf[LogisticRegressionModel]
print(model.weight, model.intercept)
I am still not sure about how to extract weights from "model" above. But by restructuring the process towards the official tutorial, the following works on spark-1.6.0:
import org.apache.spark.ml.evaluation.BinaryClassificationEvaluator
import org.apache.spark.ml.tuning.{ParamGridBuilder, TrainValidationSplit}
val lr = new LogisticRegression().setMaxIter(400)
val paramGrid = new ParamGridBuilder().addGrid(lr.regParam, Array(0.1, 0.01)).addGrid(lr.fitIntercept).addGrid(lr.elasticNetParam, Array(0.0, 0.5, 1.0)).build()
val trainValidationSplit = new TrainValidationSplit().setEstimator(lr).setEvaluator(new BinaryClassificationEvaluator).setEstimatorParamMaps(paramGrid).setTrainRatio(0.8)
val restructuredModel = trainValidationSplit.fit(train)
val lrmodel = restructuredModel.bestModel.asInstanceOf[LogisticRegressionModel]
lrmodel.weigths
lrmodel.intercept
I noticed the difference between "lrmodel" here and "model" generated above:
model.bestModel --> gives oas.ml.Model[_] = pipeline_****
restructuredModel.bestModel --> gives oas.ml.Model[_] = logreg_****
That's why we can cast resturcturedModel.bestModel as LogisticRegressionModel but not that of model.bestModel. I'll add more when I understand the reason of the differences.