We went around this may-pole a while ago. It is the same if the matrix is binary. It isn't otherwise. Whether this code might someday be used in a context with non-binary inputs is an open question. Likewise, whether it is worth saving some time by omitting a thresholding operation to binarize the matrix is similarly not clear.
My feeling is that assuming a binary matrix is fine. On Wed, Aug 6, 2014 at 5:54 PM, Dmitriy Lyubimov <dlie...@gmail.com> wrote: > is this > > val bcastNumInteractions = > drmBroadcast(drmI.numNonZeroElementsPerColumn) > > any different from just saying `drmI.colSums`? > > > On Wed, Aug 6, 2014 at 4:49 PM, Dmitriy Lyubimov <dlie...@gmail.com> > wrote: > > > > > > > > > On Wed, Aug 6, 2014 at 4:21 PM, Dmitriy Lyubimov <dlie...@gmail.com> > > wrote: > > > > I suppose in that context LLR is considered a distance (higher scores > mean > >> more `distant` items, co-occurring by chance only)? > >> > > > > Self-correction on this one -- having given a quick look at llr paper > > again, it looks like it is actually a similarity (higher scores meaning > > more stable co-occurrences, i.e. it moves in the opposite direction of > > p-value if it had been a classic test > > > > > >> [1] http://ssc.io/wp-content/uploads/2012/06/rec11-schelter.pdf > >> > >> -d > >> > > > > >
