This is a really impressively put together piece of software and a great showcase for the MGL-PAX self-documentation framework. I'm getting a lot of inspiration from this stack lately.
Yeah I was going to comment that I was kind of astounded by the quality of the documentation. And though I haven't looked, that gives me high hopes for the code itself too. Usually well documented code tends to be well written code.
I find myself inspired as well. We should all aspire to document our code this thoroughly.
Please note that despite current lack of MGL-PAX (https://github.com/melisgl/mgl-pax) documentation, Boltzman Machines and Gaussian Processes are implemented and documented in the source, which is very well and cleanly written
> used by its author to win the Higgs Boson Machine Learning Challenge.