How can I train a classifier with instances within a partition while its classification algorithm depends on the partition index? For example, suppose the following code snippet:
val data = MLUtils.loadLibSVMFile(sc, "path to SVM file")
val r = data.mapPartitionsWithIndex((index,localdata)=>{
if (index % 2 == 0)
{
// train a NaiveBayes with localdata
NaiveBayes.train(localdata) // Error => found:iterator[LabeledPoint] , required: RDD[labeledPoint]
}
else
{
// train a DecisionTree classifier with localdata
DecisionTree.train(localdata) // Error => found:iterator[LabeledPoint] , required: RDD[labeledPoint]
}
})
It sounds to me that the error is right, because the tasks are executed within their separated JVM and could not be distributed from a map task. That is why I can not access the SparkContext in my tasks. However, does anyone have an alternate suggestion for doing my purpose?
based on the discussion in above comments section -
you can give a try to this-
val rdd = MLUtils.loadLibSVMFile(sc, "path to SVM file")
// approach -1
val nb = rdd.sample(withReplacement = false, fraction = 0.5) // sample 50% of the record
val dt = rdd.sample(withReplacement = false, fraction = 0.5) // sample 50% of the record
//or approach-2
val (nb, dt) = rdd.randomSplit(Array(0.5, 0.5))
// apply algo
NaiveBayes.train(nb)
DecisionTree.train(dt, strategy= ..)
Related
I have successfully trained an XGBoost model where trainDF is a dataframe hacing two columns: features and label where we have 11k 1s and 57M 0's (unbalanced dataset). Everything works fine.
val udnersample = 0.1
// Undersampling of 0's -- choosing 10%
val training1 = output1.filter($"datestr" < end_period1 &&
$"label" === 1)
val training0 = output1.filter($"datestr" < end_period1 &&
$"label" === 0).sample(
false, undersample)
val training = training0.unionAll(training1)
val traindDF = training.select("label",
"features").toDF("label", "features")}
val paramMap = List("eta" -> 0.05,
"max_depth" -> 6,
"objective" -> "binary:logistic").toMap
val num_trees = 400
val num_cores = 200
val XGBModel = XGBoost.trainWithDataFrame(trainDF,
paramMap,
num_trees,
num_cores,
useExternalMemory = true)
Then, I want to change the y label with some windowing, so that in each group, I can predict y label earlier.
val sum_label = "sum_label"
val label_window_length = 19
val sliding_window_label = Window.partitionBy("id").orderBy(
asc("timestamp")).rowsBetween(0, label_window_length)
val training_source = output1.filter($"datestr" <
end_period1).withColumn(
sum_label, sum($"label").over(sliding_window_label)).drop(
"label").withColumnRenamed(sum_label, "label")
val training1 = training_source.filter(col("label") === 1)
val training0 = training_source.filter(col("label") === 0).sample(false, 0.099685)
val training = training0.unionAll(training1)
val traindDF = training.select("label",
"features").toDF("label", "features")}
The result has 57M 0's and 214k 1's (soughly the same number of rows though). No NAs in "label" column of trainDF and the type is still double (nullable=true). Then xgboost fails:
Name: ml.dmlc.xgboost4j.java.XGBoostError
Message: XGBoostModel training failed
StackTrace: at ml.dmlc.xgboost4j.scala.spark.XGBoost$.postTrackerReturnProcessing(XGBoost.scala:316)
at ml.dmlc.xgboost4j.scala.spark.XGBoost$.trainWithRDD(XGBoost.scala:293)
at ml.dmlc.xgboost4j.scala.spark.XGBoostEstimator.train(XGBoostEstimator.scala:138)
at ml.dmlc.xgboost4j.scala.spark.XGBoostEstimator.train(XGBoostEstimator.scala:35)
at org.apache.spark.ml.Predictor.fit(Predictor.scala:118)
at ml.dmlc.xgboost4j.scala.spark.XGBoost$.trainWithDataFrame(XGBoost.scala:169)
I can include the logs as needed. My confusion is that using the windowing function and literally not changing any other setting, causes XGB to fail. I would appreciate any thoughts on this.
It turns out that saving the table traindDF in hive and reloading it into Spark solves the problem:
traindDF.write.mode("overwrite").saveAsTable("database.tablename")
Then, you can easily load the table:
val traindDF = spark.sql("""select * from database.tablename""")
This trick solved the problem. It seems like spark windowing function is a bit unstable and saving the result into a hive table makes it work.
A better way to do this is using windowing functions in hive instead of Spark.
I'm new in Scala and Spark in general. I'm using this code for Regression (based on this link Spark official site):
import org.apache.spark.mllib.regression.LabeledPoint
import org.apache.spark.mllib.regression.LinearRegressionModel
import org.apache.spark.mllib.regression.LinearRegressionWithSGD
import org.apache.spark.mllib.linalg.Vectors
// Load and parse the data
val data = sc.textFile("Year100")
val parsedData = data.map { line =>
val parts = line.split(',')
LabeledPoint(parts(0).toDouble, Vectors.dense(parts(1).split(' ').map(_.toDouble)))
}.cache()
// Building the model
val numIterations = 100
val stepSize = 0.00000001
val model = LinearRegressionWithSGD.train(parsedData, numIterations,stepSize )
// Evaluate model on training examples and compute training error
val valuesAndPreds = parsedData.map { point =>
val prediction = model.predict(point.features)
(point.label, prediction)
}
val MSE = valuesAndPreds.map{case(v, p) => math.pow((v - p), 2)}.mean()
println("training Mean Squared Error = " + MSE)
The dataset that I'm using can be seen here: Pastebin link.
So my question is: why MSE equals as 889717.74 (which is a huge number)?
Edit: As the commentators suggested, I tried these:
1) I changed the step to default and the MSE now returns as NaN
2) If I try this constructor:
LinearRegressionWithSGD.train(parsedData, numIterations,stepSize,intercept=True) the spark-shell returns an error (error: not found:value True)
You've passed a tiny step size and capped the number of iterations at 100. The maximum value by which your parameters can change is 0.00000001 * 100 = 0.000001. Try using the default step size, I imagine that will fix it.
I'm running a Bernoulli Naive Bayes using code:
val splits = MyData.randomSplit(Array(0.75, 0.25), seed = 2L)
val training = splits(0).cache()
val test = splits(1)
val model = NaiveBayes.train(training, lambda = 3.0, modelType = "bernoulli")
My question is how can I get the probability of membership to class 0 (or 1) and count AUC. I want to get similar result to LogisticRegressionWithSGD or SVMWithSGD where I was using this code:
val numIterations = 100
val model = SVMWithSGD.train(training, numIterations)
model.clearThreshold()
// Compute raw scores on the test set.
val labelAndPreds = test.map { point =>
val prediction = model.predict(point.features)
(prediction, point.label)
}
// Get evaluation metrics.
val metrics = new BinaryClassificationMetrics(labelAndPreds)
val auROC = metrics.areaUnderROC()
Unfortunately this code isn't working for NaiveBayes.
Concerning the probabilities for Bernouilli Naive Bayes, here is an example :
// Building dummy data
val data = sc.parallelize(List("0,1 0 0", "1,0 1 0", "1,0 0 1", "0,1 0 1","1,1 1 0"))
// Transforming dummy data into LabeledPoint
val parsedData = data.map { line =>
val parts = line.split(',')
LabeledPoint(parts(0).toDouble, Vectors.dense(parts(1).split(' ').map(_.toDouble)))
}
// Prepare data for training
val splits = parsedData.randomSplit(Array(0.75, 0.25), seed = 2L)
val training = splits(0).cache()
val test = splits(1)
val model = NaiveBayes.train(training, lambda = 3.0, modelType = "bernoulli")
// labels
val labels = model.labels
// Probabilities for all feature vectors
val features = parsedData.map(lp => lp.features)
model.predictProbabilities(features).take(10) foreach println
// For one specific vector, I'm taking the first vector in the parsedData
val testVector = parsedData.first.features
println(s"For vector ${testVector} => probability : ${model.predictProbabilities(testVector)}")
As for the AUC :
// Compute raw scores on the test set.
val labelAndPreds = test.map { point =>
val prediction = model.predict(point.features)
(prediction, point.label)
}
// Get evaluation metrics.
val metrics = new BinaryClassificationMetrics(labelAndPreds)
val auROC = metrics.areaUnderROC()
Concerning the inquiry from the chat :
val results = parsedData.map { lp =>
val probs: Vector = model.predictProbabilities(lp.features)
(for (i <- 0 to (probs.size - 1)) yield ((lp.label, labels(i), probs(i))))
}.flatMap(identity)
results.take(10).foreach(println)
// (0.0,0.0,0.59728640251696)
// (0.0,1.0,0.40271359748304003)
// (1.0,0.0,0.2546873180388961)
// (1.0,1.0,0.745312681961104)
// (1.0,0.0,0.47086939671877026)
// (1.0,1.0,0.5291306032812298)
// (0.0,0.0,0.6496075621805428)
// (0.0,1.0,0.3503924378194571)
// (1.0,0.0,0.4158585282373076)
// (1.0,1.0,0.5841414717626924)
and if you are only interested in the argmax classes :
val results = training.map { lp => val probs: Vector = model.predictProbabilities(lp.features)
val bestClass = probs.argmax
(labels(bestClass), probs(bestClass))
}
results.take(10) foreach println
// (0.0,0.59728640251696)
// (1.0,0.745312681961104)
// (1.0,0.5291306032812298)
// (0.0,0.6496075621805428)
// (1.0,0.5841414717626924)
Note: Works with Spark 1.5+
EDIT: (for Pyspark users)
It seems like some are having troubles getting probabilities using pyspark and mllib. Well that's normal, spark-mllib doesn't present that function for pyspark.
Thus you'll need to use the spark-ml DataFrame-based API :
from pyspark.sql import Row
from pyspark.ml.linalg import Vectors
from pyspark.ml.classification import NaiveBayes
df = spark.createDataFrame([
Row(label=0.0, features=Vectors.dense([0.0, 0.0])),
Row(label=0.0, features=Vectors.dense([0.0, 1.0])),
Row(label=1.0, features=Vectors.dense([1.0, 0.0]))])
nb = NaiveBayes(smoothing=1.0, modelType="bernoulli")
model = nb.fit(df)
model.transform(df).show(truncate=False)
# +---------+-----+-----------------------------------------+----------------------------------------+----------+
# |features |label|rawPrediction |probability |prediction|
# +---------+-----+-----------------------------------------+----------------------------------------+----------+
# |[0.0,0.0]|0.0 |[-1.4916548767777167,-2.420368128650429] |[0.7168141592920354,0.28318584070796465]|0.0 |
# |[0.0,1.0]|0.0 |[-1.4916548767777167,-3.1135153092103742]|[0.8350515463917526,0.16494845360824742]|0.0 |
# |[1.0,0.0]|1.0 |[-2.5902671654458262,-1.7272209480904837]|[0.29670329670329676,0.7032967032967034]|1.0 |
# +---------+-----+-----------------------------------------+----------------------------------------+----------+
You'll just need to select your prediction column and compute your AUC.
For more information about Naive Bayes in spark-ml, please refer to the official documentation here.
I want to run logistic regression 100 times with random splitting into test and training. I want to then save the performance metrics for individual runs and then later use them for gaining insight into the performance.
for (index <- 1 to 100) {
val splits = training_data.randomSplit(Array(0.90, 0.10), seed = index)
val training = splits(0).cache()
val test = splits(1)
logrmodel = train_LogisticRegression_model(training)
performLogisticRegressionRuns(logrmodel, test, index)
}
spark.stop()
}
def performLogisticRegressionRuns(model: LogisticRegressionModel, test: RDD[LabeledPoint], iterationcount: Int) {
private val sb = StringBuilder.newBuilder
// Compute raw scores on the test set. Once I cle
model.clearThreshold()
val predictionAndLabels = test.map { case LabeledPoint(label, features) =>
val prediction = model.predict(features)
(prediction, label)
}
val bcmetrics = new BinaryClassificationMetrics(predictionAndLabels)
// I am showing two sample metrics, but I am collecting more including recall, area under roc, f1 score etc....
val precision = bcmetrics.precisionByThreshold()
precision.foreach { case (t, p) =>
// If threshold is 0.5 as what we want, then get the precision and append it to the string. Idea is if score is <0.5 class 0, else class 1.
if (t == 0.5) {
println(s"Threshold is: $t, Precision is: $p")
sb ++= p.toString() + "\t"
}
}
val auROC = bcmetrics.areaUnderROC
sb ++= iteration + auPRC.toString() + "\t"
I want to save the performance results of each iteration in separate file. I tried this, but it does not work, any help with this will be great
val data = spark.parallelize(sb)
val filename = "logreg-metrics" + iterationcount.toString() + ".txt"
data.saveAsTextFile(filename)
}
I was able to resolve this, I did the following. I converted the String to a list.
val data = spark.parallelize(List(sb))
val filename = "logreg-metrics" + iterationcount.toString() + ".txt"
data.saveAsTextFile(filename)
I'm using Naive Bayes with Apache Spark MLlib for Text classification follow tutorial: http://avulanov.blogspot.com/2014/08/text-classification-with-apache-spark.html
/* instantiate Spark context (not needed for running inside Spark shell */
val sc = new SparkContext("local", "test")
/* word to vector space converter, limit to 10000 words */
val htf = new HashingTF(10000)
/* load positive and negative sentences from the dataset */
/* let 1 - positive class, 0 - negative class */
/* tokenize sentences and transform them into vector space model */
val positiveData = sc.textFile("/data/rt-polaritydata/rt-polarity.pos")
.map { text => new LabeledPoint(1, htf.transform(text.split(" ")))}
val negativeData = sc.textFile("/data/rt-polaritydata/rt-polarity.neg")
.map { text => new LabeledPoint(0, htf.transform(text.split(" ")))}
/* split the data 60% for training, 40% for testing */
val posSplits = positiveData.randomSplit(Array(0.6, 0.4), seed = 11L)
val negSplits = negativeData.randomSplit(Array(0.6, 0.4), seed = 11L)
/* union train data with positive and negative sentences */
val training = posSplits(0).union(negSplits(0))
/* union test data with positive and negative sentences */
val test = posSplits(1).union(negSplits(1))
/* Multinomial Naive Bayesian classifier */
val model = NaiveBayes.train(training)
/* predict */
val predictionAndLabels = test.map { point =>
val score = model.predict(point.features)
(score, point.label)
}
/* metrics */
val metrics = new MulticlassMetrics(predictionAndLabels)
/* output F1-measure for all labels (0 and 1, negative and positive) */
metrics.labels.foreach( l => println(metrics.fMeasure(l)))
But, after training data. What should I do if I want to know sentence "Have a nice day" is positive or negative?
Thank you.
Generally speaking you need two things to make prediction on a raw data:
Apply the same transformations you've used for training data. If some transformer require fitting (like IDF, normalization, encoding) you have to use one fitted on a trained data. Since your approach is extremely simplistic all you need here is something like this:
val testData = htf.transform("Have a nice day".split(" "))
Use predict method of the trained model:
model.predict(testData)