I can imagine two methods, but I don't know if there is a better one. The two methods that I imagine are:
- In the same session, after training the autoencoder, just build a new graph using the encoding subgraph of the autoencoder as the input
- After training the autoencoder, save the trained weights. This way, you don't have to train the autoencoder and the new other network in the same session. (kind of a variant of method 1)