[nicwilson]

I imagine that if you have one discrete layer from input to hidden that you could then treat the hidden layer(s) dynamics as continuous from there on until the next change of dimension. You should still be able to back propagate through a continuous-discrete or discrete-continuous boundary. There should be a lot of literature on this in control systems simulation.

The other thing you can do is to "pad" the input up to be the size of the hidden layers.