cross_entropy_cost.py shamelessly copied from https://triangleinequality.wordpress.com/2014/08/12/theano-autoencoders-and-mnist/
Others are a little bit of effort from my side and Abhinav Agarwal's side during our project work or so called internship in winters.
If you ever do clone, for sure edit the path from where your program has to load the MNIST data.