Hi All,
Im wanted to try Survival Analysis on Spark 1.6. I am successfully able to run
the AFT example provided. Now I tried to train the model with Ovarian data
which is standard data comes with Survival library in R.
Default Column Name : Futime,fustat,age,resid_ds,rx,ecog_ps
Here are the steps I have done :
* Loaded the data from csv to dataframe labeled as
val ovarian_data = sqlContext.read
.format("com.databricks.spark.csv")
.option("header", "true") // Use first line of all files as header
.option("inferSchema", "true") // Automatically infer data types
.load("Ovarian.csv").toDF("label", "censor", "age", "resid_ds", "rx",
"ecog_ps")
* Utilize the VectorAssembler() to create features from "age",
"resid_ds", "rx", "ecog_ps" like
val assembler = new VectorAssembler()
.setInputCols(Array("age", "resid_ds", "rx", "ecog_ps"))
.setOutputCol("features")
* Then I create a new dataframe with only 3 colums as :
val training = finalDf.select("label", "censor", "features")
* Finally Im passing it to AFT
val model = aft.fit(training)
Im getting the error as :
java.lang.AssertionError: assertion failed: AFTAggregator loss sum is infinity.
Error for unknown reason.
at scala.Predef$.assert(Predef.scala:179)
at
org.apache.spark.ml.regression.AFTAggregator.add(AFTSurvivalRegression.scala:480)
at
org.apache.spark.ml.regression.AFTCostFun$$anonfun$5.apply(AFTSurvivalRegression.scala:522)
at
org.apache.spark.ml.regression.AFTCostFun$$anonfun$5.apply(AFTSurvivalRegression.scala:521)
at
scala.collection.TraversableOnce$$anonfun$foldLeft$1.apply(TraversableOnce.scala:144)
at
scala.collection.TraversableOnce$$anonfun$foldLeft$1.apply(TraversableOnce.scala:144)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
I have tried to print the schema :
()root
|-- label: double (nullable = true)
|-- censor: double (nullable = true)
|-- features: vector (nullable = true)
Sample data training looks like
[59.0,1.0,[72.3315,2.0,1.0,1.0]]
[115.0,1.0,[74.4932,2.0,1.0,1.0]]
[156.0,1.0,[66.4658,2.0,1.0,2.0]]
[421.0,0.0,[53.3644,2.0,2.0,1.0]]
[431.0,1.0,[50.3397,2.0,1.0,1.0]]
Im not able to understand about the error, as if I use same data and create the
denseVector as given in Sample example of AFT, then code works completely fine.
But I would like to read the data from CSV file and then proceed.
Please suggest
Thanks &Regards
Stuti Awasthi
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