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I didn't realise that regression problems were so closely related to classification. I think a little more needs to be done though.
encog-core-cs/Neural/Networks/Training/TrainingSetScore.cs is also tailored to regression training. Modifying this file will affect references and interfaces.
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The problem I see is that when using the EncogUtility's Train to error method the output error does not seem to correspond to the number of correct predictions my neural network makes.
For example I am trying to overtrain my network to get 100% correct answers (using my training set as an evaluation set also). Not for a real application. Just so that I can observe the error reduce.
I am seeing that whilst the error reduces the number of correct predictions increases for classification problems.