There is a very common structure to this. Despite neural nets having their own baggage, they're worth understanding.
The structure you're wanting is definitely in there. Edit: Yes a bit of self promotion here. Just making a point with patterns I've found as I've built this out.
See:
https://github.com/agibsonccc/java-deeplearning/blob/master/...
https://github.com/agibsonccc/java-deeplearning/blob/master/...
Half the battle is understanding the linear algebra going on here. Beyond that you can pretty much do everything with one set of algorithms and terminology.
For those who go WTF java are you insane? The core idea I'm linking to here is the fact that deep nets are composed of singular neural networks with slight variations having a very common structure for both the singular layer as well as the deep nets themselves.