Currently the framework only supports undirected graphs, so directed graphical models wouldn't be supported as input. I can't really judge how useful it would be to take a Bayesian net as input, sounds a bit hacky to me. But in principle you could train a neural net on any kind of graph, someone recently suggested to take the connection graph of another neural net as input and try to learn some function on that. But again, it's really hard to judge in advance how useful such approaches would be ;)
