[pymvpa] adding GPR: some questions

Emanuele Olivetti emanuele at relativita.com
Mon May 19 21:57:58 UTC 2008

Yaroslav Halchenko wrote:
> CONGRATULATIONS!!!! We have 2 experienced kid cares in the team (Michael
> and yours truly) and the 3rd active member is in the similar situation
> to yours -- just give him few more month ;-) So if anything -- we might
> serve as a good source of information on babies side as well ;-)

So I'm expecting soon a [pymvpa-daycare] list ;)

> Let me first give you a slight update -- recently we have done quite a
> bit of refactoring and introducing new features (mostly internal, ie not
> altering user visible API) which are not yet in the master branch. Don't
> worry about them -- we will take care about tuning up your code so it
> takes advantage from those changes ;-) Just lets stay tuned (I am sorry
> if this update is vague on words)

If you are referring to "[Pkg-exppsy-pymvpa] Restructuring mvpa module
by Michael Hanke then I understand there are many changes there. I'll
stay tuned.

> Let me now go through the questions:
>> - where should I put the variance of each prediction? GPR compute mean and
>> variance of each prediction. Mean is returned by _predict. What about
>> variance?
> Since none of the other classifier/regressors has variance computed (at
> least so it is visible outside) I think the best would be just to add
> another StateVariable into your GPR class and store the values there.
> Does it sound like a good fit? ;-)

I'm very happy there is a proper place for this information. I still
don't understand clearly how to add another StateVariable but
I guess is something achievable if you suggest me this. Let mi dig
a bit.

>> - would you like to have a look to my commits/patches and send me feedback?
> I would be thrilled to do so, or we can simply add you into exppsy
> project on alioth, so you could simply push your changes (ie your whole
> branch). That would be the most effective way I guess. If you don't mind
> to proceed that way -- just register yourself on
> http://alioth.debian.org/
> and provide us with login name (or request to join the exppsy team, I
> think there must be a 'link' to do that)
> Then we will grant you access to git repository

Many thanks to your detailed information (via skype). I was able to
get an account on alioth and push my branch. I still need help but
this major step is done. Thanks again.

>> - Yaroslav mentioned to send patches by email. I'm still learning git
>> and fighting with git-format-patch. Any hint?
> imho it works fine, what obstacles did you hit (git gives us hick up in
> various aspects from time to time, so it would be of no surprise that
> you hit some other stone on the way). Usually I just did
> git-format-patch and was sending that battery of patches from my regular
> mail client. Or you could try do smth like
> git-format-patch --stdout master | git-send-email --to yoh at onerussian.com

Even this works now (I shall definitely study more git!).

>> - is it OK to name "kernel.py" and "gpr.py" my two new files? I can't
>> find rules on this but looks like other files.
> you mean under mvpa/clfs right? then sure! though we kept thinking about
> crafting our kernel.py but so far there were no direct urge thus we
> didn't do that, but having your kernel.py we might see better if we
> might need to elaborate it more for other uses.

Exactly. My Kernel class is super simple now. My idea is to let it
handle most of the hyperparameter search code, like first derivatives
of the kernel etc. I guess I'll need some hand-made kernel with
unusual constraints on hyperparameters in near future.

> ...
>> ======================================================================
>> It seems that GPR is not able to learn a simple dataset (as well as
>> RidgeReg, as the source says). Is this a big problem?
> the problem only that someone needs to sit down and tune unittest up so
> finally it works for all the classifiers ;-) so don't worry about it for
> now, and just add another or into
> if isinstance(clf, RidgeReg):
> ;-)

Excellent. Looking forward to push other code soon.


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