I'm working on a recursive auto-encoder. The neural network takes two 2D images each shaped (28,28,1) and combined to create an input of (28,28,2). They are encoded into a (28,28,1) shape, and decoded back into the original shape (28,28,2). Thus, the encoded form of data can be fed into the auto-encoder for recursive operation.
We can assume that channel 1 is a new image, and channel 2 is previously encoded data. How do I create a loss function that penalises more heavily for mistakes reconstructing channel 2 (as this will carry previously encoded data)?
I am working in Keras, with a Tensorflow back-end.
Alternatively, is there a way to train the network as a complete tree, as opposed to doing it only for single two input - two output blocks at a time?