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The newer version of spark,adam,sparklingwater for "Genomic Analysis Using ADAM, Spark and Deep Learning" to the people who want to reproduce the test #2

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The newer version of spark,adam,sparklingwater for "Genomic Analysis Using ADAM, Spark and Deep Learning" to the people who want to reproduce the test #2

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4 changes: 2 additions & 2 deletions src/main/scala/com/neilferguson/PopStrat.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ object PopStrat {
val sc = new SparkContext(conf)

// Create a set of the populations that we want to predict
val populations = Set("GBR", "ASW", "CHB")
val populations = Set("ACB", "ASW", "BEB", "CDX", "CEU", "CHB", "CHS", "CLM", "ESN", "FIN", "GBR", "GIH")

// Create a map of sample ID -> population so that we can filter out the samples we're not interested in
val panel: Map[String,String] = extract(panelFile, (sampleID: String, pop: String) => populations.contains(pop))
Expand Down Expand Up @@ -116,7 +116,7 @@ object PopStrat {
deepLearningParameters._train = training
deepLearningParameters._valid = test
deepLearningParameters._response_column = "Region"
deepLearningParameters._epochs = 10
deepLearningParameters._epochs = 50
deepLearningParameters._activation = Activation.RectifierWithDropout
deepLearningParameters._hidden = Array[Int](100,100)

Expand Down