Jul 29, 2013 — Modularity Optimization Algorithm of Newman — When we create a network, we are concerned about how the components are broken into groups, and how those groups are connected.  This is relevant to graph theory, where the basic idea is to have entities in some system represented... Read more

Jul 25, 2013 — Flatten 3D Data to Vector, and back to 3D in R — There is surprisingly little help online about how to flatten some 3D data, and then “unflatten” it back to its original size. Why would you want this functionality? Many machine learning algorithms that work with images treat pixel values as... Read more

Jul 24, 2013 — Archetypal Analysis — Archetypal Analysis is an unsupervised learning algorithm that postulates that each of our set of observations is some combination of some number, K, “pure subtypes,” or archetypes.  I’ll also refer to these as prototypes.  In the simple case of adult human... Read more

Jul 24, 2013 — Non-Negative Matrix Factorization — Non-negative matrix factorization (nnmf) is an unsupervised machine learning method for (you predicted it, strictly positive) data!  The goal of nnmf, of course, is dimensionality reduction.  We start with a dataset, X (size N x p), and want to decompose... Read more