On Thu, 26 Apr 2018, Richard Dinga wrote: > Hi, > I am trying to get a probability prediction for each sample from > cross-validation. I used .ca.stats.sets to get those, however, for GNB > these all look like this:
> print cvte.ca.stats.sets[0][2] > [[-1009.22758728 -1079.77409491] > [ -795.59690176 -1038.32481958] > [ -875.73917377 -1189.377741 ] > ..., > [-1483.49338276 -856.61441132] > [-1308.29372328 -815.90664933] > [-1169.79999768 -737.54291075]] > I thought these are log probabilities, but after exponentiation, they are > all 0, although based on accuracy and AUC the classifier works fine. > Any idea how to fix this or is this as good as it can get? My ultimate goal > is to get GNB probabilities from GNB searchlight. Trying the same thing > using SMLR seems to produce valid probabilities (in a sane range and rows > sums to 1). > Best regards, > Richard Try using setting normalize=True for your GNB. Here is from GNB? in ipython, check other parameters which might be relevant: normalize : bool, optional Normalize (log)prob by P(data). Requires probabilities thus for `logprob` case would require exponentiation of 'logprob's, thus disabled by default since does not impact classification output. Constraints: value must be convertible to type bool. [Default: False] -- Yaroslav O. Halchenko Center for Open Neuroscience http://centerforopenneuroscience.org Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419 WWW: http://www.linkedin.com/in/yarik _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list Pkg-ExpPsy-PyMVPA@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa