Hello again, 

Sorry I accidentally got it posted, while I was still continuing to write. 
Runing the partial derivative block seems to raise the error 

theano.gof.fg.MissingInputError: ("An input of the graph, used to compute 
Elemwise{Cast{float64}}(mask_1), was not provided and not given a value.Use 
the Theano flag exception_verbosity='high',for more information on this 
error.", mask_1)

Starngely, It works when the network a single layer. Upon increasing the 
number of layers, the error shows up.
I am using Theano (0.8.2).

Any help would be greatly appreciated. 
best regards,
Satyan

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