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Made a terrible mistake - trained the model on the entire dataset not just the training data.
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nn.rb

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@@ -21,7 +21,7 @@
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training_y_data = y_data[test_set_size .. y_data.size]
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# Setup training data model
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train = RubyFann::TrainData.new( :inputs=> x_data, :desired_outputs=>y_data );
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train = RubyFann::TrainData.new( :inputs=> training_x_data, :desired_outputs=>training_y_data );
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# Setup model and train using training data
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model = RubyFann::Standard.new(

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