If you are talking about evolution, then it's likely you need something like a recursive neural network (RNN), which [neuralnet] can't create (at least not yet). Unless this evolution you mention can be encapsulated in one snapshot. If it's spectral snapshots with a 256 bin resolution, and you need four of these snapshots to classify your data, then a network with 1024 inputs could worh with [neuralnet].
The MNIST dataset example (example 4) is a classification example. You should follow that to build your network structure (concerning activation functions, loss function, etc.).
With the current versino of the object you can also build autoencoders, which can be sort of good for compressing data. That being said, you could perhaps use an autoencoder and map the values in the latent space. The next version will hopefully include variational autoencoders (working on this), so that could also be an option.
As I don't know the structure of your data though, I don't think I can be of more help right now.