This toolbox is outdated and no longer maintained.
There are much better tools available for deep learning than this toolbox, e.g. Theano, torch or tensorflow
I would suggest you use one of the tools mentioned above rather than use this toolbox.
A Matlab toolbox for Deep Learning.
Deep Learning is a new subfield of machine learning that focuses on learning deep hierarchical models of data. It is inspired by the human brain's apparent deep (layered, hierarchical) architecture. A good overview of the theory of Deep Learning theory is Learning Deep Architectures for AI
For a more informal introduction, see the following videos by Geoffrey Hinton and Andrew Ng.
The Next Generation of Neural Networks (Hinton, 2007)
Recent Developments in Deep Learning (Hinton, 2010)
Unsupervised Feature Learning and Deep Learning (Ng, 2011)
If you use this toolbox in your research please cite:
Prediction as a candidate for learning deep hierarchical models of data (Palm, 2012)
Directories included in the toolbox
NN/ - A library for Feedforward Backpropagation Neural Networks
CNN/ - A library for Convolutional Neural Networks
DBN/ - A library for Deep Belief Networks
SAE/ - A library for Stacked Auto-Encoders
CAE/ - A library for Convolutional Auto-Encoders
util/ - Utility functions used by the libraries
data/ - Data used by the examples
tests/ - unit tests to verify toolbox is working
For references on each library check REFS.md