Scale a column of SparseVectors without UDF - scala

I have a dataframe with a feature column of SparseVector. I need to scale each row by a scalar. I have a working implementation below that employs a UDF. The following depicts the original and scaled feature columns:
+-------------------+-------+-------------------+
| features|weights| scaledFeatures|
+-------------------+-------+-------------------+
|(6,[0,1],[0.5,1.0])| 1.0|(6,[0,1],[0.5,1.0])|
|(6,[2,3],[1.5,2.0])| 2.0|(6,[2,3],[3.0,4.0])|
|(6,[4,5],[0.5,1.0])| 3.0|(6,[4,5],[1.5,3.0])|
+-------------------+-------+-------------------+
Is there a way to do this using Spark's native, and optimized, methods instead of a UDF?
Similarly, is there a Spark-native way to scale a SparseVector by a scalar? See the line below the "Scale the SparseVector" comment in the UDF defined below.
import org.apache.spark.ml.linalg.SparseVector
import org.apache.spark.sql.SparkSession
import org.apache.spark.sql.functions.{col, udf}
// Scaling a SparseVector column
val data = Array(
(new SparseVector(6, Array(0,1), Array(0.5, 1.0)), 1.0),
(new SparseVector(6, Array(2,3), Array(1.5, 2.0)), 2.0),
(new SparseVector(6, Array(4,5), Array(0.5, 1.0)), 3.0)
)
val df = spark.createDataFrame(data).toDF("features", "weights")
val scaleUDF = udf((sv: SparseVector, w: Double) => {
// Scale the SparseVector
val unzipped = sv.indices.zip(sv.values).map(iv => (iv._1, iv._2*w)).unzip
new SparseVector(sv.size, unzipped._1, unzipped._2)
})
val scaledDF = df.withColumn("scaledFeatures", scaleUDF(col("features"), col("weights")))
scaledDF.show()
+-------------------+-------+-------------------+
| features|weights| scaledFeatures|
+-------------------+-------+-------------------+
|(6,[0,1],[0.5,1.0])| 1.0|(6,[0,1],[0.5,1.0])|
|(6,[2,3],[1.5,2.0])| 2.0|(6,[2,3],[3.0,4.0])|
|(6,[4,5],[0.5,1.0])| 3.0|(6,[4,5],[1.5,3.0])|
+-------------------+-------+-------------------+

Related

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.

Can't run LDA on Dataset[(scala.Long, org.apache.spark.mllib.linalg.Vector)] in Spark 2.0

I am following this tutorial video on LDA example and I'm getting the following issue :
<console>:37: error: overloaded method value run with alternatives:
(documents: org.apache.spark.api.java.JavaPairRDD[java.lang.Long,org.apache.spark.mllib.linalg.Vector])org.apache.spark.mllib.clustering.LDAModel <and>
(documents: org.apache.spark.rdd.RDD[(scala.Long, org.apache.spark.mllib.linalg.Vector)])org.apache.spark.mllib.clustering.LDAModel
cannot be applied to (org.apache.spark.sql.Dataset[(scala.Long, org.apache.spark.mllib.linalg.Vector)])
val model = run(lda_countVector)
^
So I want to convert this DF to RDD but it is always assigned as DataSet for me. Can anyone please look into this issue?
// Convert DF to RDD
import org.apache.spark.mllib.linalg.Vector
val lda_countVector = countVectors.map { case Row(id: Long, countVector: Vector) => (id, countVector) }
// import org.apache.spark.mllib.linalg.Vector
// lda_countVector: org.apache.spark.sql.Dataset[(Long, org.apache.spark.mllib.linalg.Vector)] = [_1: bigint, _2: vector]
Spark API changed between 1.x and 2.x branch. In particular DataFrame.map returns Dataset not an RDD so the result is not compatible with old MLlib RDD-based API. You should convert data to RDD first as followed :
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.rdd.map {
case Row(id: Long, countVector: Vector) => (id, countVector)
}
val model = new LDA().setK(3).run(ldaDF)
or you can convert to typed dataset and then to RDD:
val model = new LDA().setK(3).run(df.as[(Long, Vector)].rdd)

RandomForestClassifier was given input with invalid label column error in Apache Spark

I am trying to find Accuracy using 5-fold cross validation using Random Forest Classifier Model in SCALA. But i am getting the following error while running:
java.lang.IllegalArgumentException: RandomForestClassifier was given input with invalid label column label, without the number of classes specified. See StringIndexer.
Getting the above error at line---> val cvModel = cv.fit(trainingData)
The code which i used for cross validation of data set using random forest is as follows:
import org.apache.spark.ml.Pipeline
import org.apache.spark.ml.tuning.{ParamGridBuilder, CrossValidator}
import org.apache.spark.ml.classification.RandomForestClassifier
import org.apache.spark.ml.evaluation.MulticlassClassificationEvaluator
import org.apache.spark.mllib.linalg.Vectors
import org.apache.spark.mllib.regression.LabeledPoint
val data = sc.textFile("exprogram/dataset.txt")
val parsedData = data.map { line =>
val parts = line.split(',')
LabeledPoint(parts(41).toDouble,
Vectors.dense(parts(0).split(',').map(_.toDouble)))
}
val splits = parsedData.randomSplit(Array(0.6, 0.4), seed = 11L)
val training = splits(0)
val test = splits(1)
val trainingData = training.toDF()
val testData = test.toDF()
val nFolds: Int = 5
val NumTrees: Int = 5
val rf = new
RandomForestClassifier()
.setLabelCol("label")
.setFeaturesCol("features")
.setNumTrees(NumTrees)
val pipeline = new Pipeline()
.setStages(Array(rf))
val paramGrid = new ParamGridBuilder()
.build()
val evaluator = new MulticlassClassificationEvaluator()
.setLabelCol("label")
.setPredictionCol("prediction")
.setMetricName("precision")
val cv = new CrossValidator()
.setEstimator(pipeline)
.setEvaluator(evaluator)
.setEstimatorParamMaps(paramGrid)
.setNumFolds(nFolds)
val cvModel = cv.fit(trainingData)
val results = cvModel.transform(testData)
.select("label","prediction").collect
val numCorrectPredictions = results.map(row =>
if (row.getDouble(0) == row.getDouble(1)) 1 else 0).foldLeft(0)(_ + _)
val accuracy = 1.0D * numCorrectPredictions / results.size
println("Test set accuracy: %.3f".format(accuracy))
Can any one please explain what is the mistake in the above code.
RandomForestClassifier, same as many other ML algorithms, require specific metadata to be set on the label column and labels values to be integral values from [0, 1, 2 ..., #classes) represented as doubles. Typically this is handled by an upstream Transformers like StringIndexer. Since you convert labels manually metadata fields are not set and classifier cannot confirm that these requirements are satisfied.
val df = Seq(
(0.0, Vectors.dense(1, 0, 0, 0)),
(1.0, Vectors.dense(0, 1, 0, 0)),
(2.0, Vectors.dense(0, 0, 1, 0)),
(2.0, Vectors.dense(0, 0, 0, 1))
).toDF("label", "features")
val rf = new RandomForestClassifier()
.setFeaturesCol("features")
.setNumTrees(5)
rf.setLabelCol("label").fit(df)
// java.lang.IllegalArgumentException: RandomForestClassifier was given input ...
You can either re-encode label column using StringIndexer:
import org.apache.spark.ml.feature.StringIndexer
val indexer = new StringIndexer()
.setInputCol("label")
.setOutputCol("label_idx")
.fit(df)
rf.setLabelCol("label_idx").fit(indexer.transform(df))
or set required metadata manually:
val meta = NominalAttribute
.defaultAttr
.withName("label")
.withValues("0.0", "1.0", "2.0")
.toMetadata
rf.setLabelCol("label_meta").fit(
df.withColumn("label_meta", $"label".as("", meta))
)
Note:
Labels created using StringIndexer depend on the frequency not value:
indexer.labels
// Array[String] = Array(2.0, 0.0, 1.0)
PySpark:
In Python metadata fields can be set directly on the schema:
from pyspark.sql.types import StructField, DoubleType
StructField(
"label", DoubleType(), False,
{"ml_attr": {
"name": "label",
"type": "nominal",
"vals": ["0.0", "1.0", "2.0"]
}}
)

Spark: How to transform LabeledPoint features values from int to 0/1?

I want to run Naive Bayes in Spark, but to do this I have to transform features values from my LabeledPoint to 0/1. My LabeledPoint looks like this:
scala> transformedData.collect()
res29: Array[org.apache.spark.mllib.regression.LabeledPoint] = Array((0.0,(400036,[7744],[2.0])), (0.0,(400036,[7744,8608],[3.0,3.0])), (0.0,(400036,[7744],[2.0])), (0.0,(400036,[133,218,2162,7460,7744,9567],[1.0,1.0,2.0,1.0,42.0,21.0])), (0.0,(400036,[133,218,1589,2162,2784,2922,3274,6914,7008,7131,7460,8608,9437,9567,199999,200021,200035,200048,200051,200056,200058,200064,200070,200072,200075,200087,400008,400011],[4.0,1.0,6.0,53.0,6.0,1.0,1.0,2.0,11.0,17.0,48.0,3.0,4.0,113.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,28.0,1.0,1.0,1.0,1.0,1.0,4.0])), (0.0,(400036,[1589,3585,4830,6935,6936,7744,400008,400011],[2.0,6.0,3.0,52.0,4.0,3.0,1.0,2.0])), (0.0,(400036,[1589,2162,2784,2922,4123,7008,7131,7792,8608],[23.0,70.0,1.0,2.0,2.0,1.0,1.0,2.0,2.0])), (0.0,(400036,[4830,6935,6936,400008,400011],[1.0,36.0...
How can I transform those features values into 1 (it's sparse representation so there will be no 0) ?
I guess you're looking for something like this:
import org.apache.spark.mllib.linalg.Vectors
import org.apache.spark.mllib.regression.LabeledPoint
import org.apache.spark.rdd.RDD
val transformedData = sc.parallelize(Seq(
LabeledPoint(1.0, Vectors.sparse(5, Array(1, 3), Array(9.0, 3.2))),
LabeledPoint(5.0, Vectors.sparse(5, Array(0, 2, 4), Array(1.0, 2.0, 3.0)))
))
def binarizeFeatures(rdd: RDD[LabeledPoint]) = rdd.map{
case LabeledPoint(label, features) => {
val v = features.toSparse
LabeledPoint(lab,
Vectors.sparse(v.size, v.indices, Array.fill(v.numNonzeros)(1.0)))}}
binarizeFeatures(transformedData).collect
// Array[org.apache.spark.mllib.regression.LabeledPoint] = Array(
// (1.0,(5,[1,3],[1.0,1.0])),
// (1.0,(5,[0,2,4],[1.0,1.0,1.0])))