First my disclaimer, I am one of the main developers of the Encog project. This means that I am more familiar with Enkog, that Neurof and, perhaps, was biased towards him. In my opinion, the relative strength of each of them is as follows. Encog supports many interchangeable machine learning methods and training methods. Neuroph is VERY focused on neural networks and you can express the connection between anything. Therefore, if you are going to create very non-standard (research) neural networks of different typologies than typical Elman / Jordan, NEAT, HyperNEAT, Feedforward networks, then Neuroph will be well suited to the calculation.
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