[pymvpa] comparing accuracies of a 3-way classifier and a 2-way classifier

Nick Oosterhof n.n.oosterhof at googlemail.com
Sat Sep 22 10:20:38 BST 2018

Hi Michael,

On Fri, 21 Sep 2018 at 18:28, Michael Bannert <mbannert at tuebingen.mpg.de>

> i have predictions from a 3-way classification and a 2-way
> classification that i would like to compare with one another. how could
> i do this?
> 1) i could subtract the chance level from each accuracy score, i.e.,
> subtract 1/3 from the 3-way classification accuracy and 1/2 from 2-way
> classification. not ideal because percentage changes above chance are
> not directly comparable anymore. but the approach is pretty intuitive
> and permutation inference against chance levels would still be valid.

You may want to take into account differences in number of predictions for
the 2-way versus 3-way, if any, because expected variance in accuracy
depends on the number of samples (and number of classes). This in turn
would affect the relative impact of the 2-way versus 3-way classification.
Maybe convert the accuracies to z-scores based on a binomial distribution,
and look at the difference between 2-way and 3-way classification z-scores
at the participant-level? Note that the z-scores at the participant level
may not be completely valid due to non-independence of predictions, but I
don't expect this to be a concern at the group-analysis level.
In any case using permutation testing sounds like a good idea.

> 2) use a different performance metric like (adjusted) mutual information
> maybe? methodologically more appropriate probably but maybe confusing
> for the readers.
> 3) but perhaps there are even better ways to do this. for example
> examine the 3-by-3 and 2-by-2 confusion matrices and compare
> main-diagonal with off-diagonal entries?

This might work but I cannot provide good advice on this. I would suggest
to keep it simple enough that results can be explained and interpreted

(on a personal note: it's been a while since Princeton times!)

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