The method that is normally used for this in the biological literature (including the Kashtan & Alon paper mentioned above), and in papers by e.g. CHAI dealing with identifying modularity in deep modern networks, is taken from graph theory. It involves the measure Q, which is defined as follows:
FWIW I do not use this measure in my papers, but instead use a different graph-theoretic measure. (I also get the sense that Q is more of a network theory thing than a graph theory thing)
FWIW I do not use this measure in my papers, but instead use a different graph-theoretic measure. (I also get the sense that Q is more of a network theory thing than a graph theory thing)