[pymvpa] adding GPR: some questions

[Emanuele Olivetti]

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
layout"
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.


Emanuele