[BioC] initializing DirichletMultinomial::dmn

Charles Berry ccberry at ucsd.edu
Thu Jul 10 23:45:03 CEST 2014


I'd like to be able to specify the starting 'centers' for dmn().

Details:

IIUC DirichletMultinomial::dmn(count, k) will initialize the EM algorithm 
using a kmeans heuristic for selecting the starting point. Replicate runs on
the same data can yield stark differences in the result. 

I have a dataset in which it seems that naively chosen random starting
centers rarely minimize a goodness-of-fit criterion.

The release version of dmn() does not currently allow for specification of
starting values. I wonder if there are plans to extend it in this manner?

Best,

Chuck



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