[Mne_analysis] GSoC Idea, Improving decode module

Denis-Alexander Engemann denis.engemann at gmail.com
Thu Mar 17 03:24:24 EDT 2016
Search archives:

Hi Ashish
can you check your spam folder? We used the email that appears here on the
mailinglist when you are writing.

Denis

On Thu, Mar 17, 2016 at 7:25 AM Asish Panda <asishrocks95 at gmail.com> wrote:

> Thank you for responding. I am afraid I didn't get any invitation. Could
> you kindly re-send it or perhaps share a link here?
>
>
> Asish Panda
>
> On Thu, Mar 17, 2016 at 2:48 AM, Denis-Alexander Engemann <
> denis.engemann at gmail.com> wrote:
>
>> Hi Ashish,
>>
>> we totally agree with you. With Jean-Rémi we just set up a main project
>> and API proposal. See dropbox paper invitation. Let's start a private
>> discussion over the next days based on that draft.
>>
>> Denis
>>
>>
>>
>> On Wed, Mar 16, 2016 at 8:31 PM Asish Panda <asishrocks95 at gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I have been thinking about the priorities of tasks, and I feel that the
>>> visualization can done after gsoc. As the main aim is to first make
>>> decoding more compatible with scikit-learn, we could also probably shift
>>> i/o task for later.
>>> Let me know what you guys think. We can discuss this here, gitter, or
>>> over hangouts, whichever is more suitable for you guys.
>>>
>>> Thank you
>>>
>>> Asish Panda
>>>
>>> On Tue, Mar 15, 2016 at 11:20 AM, Asish Panda <asishrocks95 at gmail.com>
>>> wrote:
>>>
>>>>
>>>>
>>>> On Mon, Mar 14, 2016 at 7:21 PM, Denis-Alexander Engemann <
>>>> denis.engemann at gmail.com> wrote:
>>>>
>>>>> Looks also good to me.
>>>>>
>>>>> At the same time it's ambitions, which is great! We should, however,
>>>>> see what are the most important goals such that the rest can be seen as
>>>>> nice to have additions but won't determine your overall GSOC success.
>>>>> One tiny remark: we should not go use pickling for persistence for
>>>>> several reasons. Short: it's not made for long-lived persistence and will
>>>>> break. We will rather look into something like saving the estimator
>>>>> attributes and their constructor parameters into hd5 files and
>>>>> re-instantiate the objects based on this information.
>>>>> We might need a hangoug or skype together to decide about the
>>>>> priorities of all the elements you listed.
>>>>>
>>>> I agree. We should have priorities sorted out. When would be a good
>>>> idea to have a hangout? I am usually free after 10pm, +5:30GMT.
>>>>
>>>>>
>>>>> --Denis
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Mon, Mar 14, 2016 at 2:40 PM JR KING <jeanremi.king at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Thanks Asish.
>>>>>>
>>>>>> It's good overall. I added some corrections.
>>>>>>
>>>>> Thank you for your help! :)
>>>>
>>>>>
>>>>>> Hope that helps,
>>>>>>
>>>>>> JR
>>>>>>
>>>>>> On 14 March 2016 at 03:38, Asish Panda <asishrocks95 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hello everyone
>>>>>>>
>>>>>>> Thank you for explaining me the details. Based on that and the
>>>>>>> original idea I have drafted an initial proposal. Please give me your
>>>>>>> reviews and let me know if I am understanding your points correctly. You
>>>>>>> can check out the
>>>>>>> project details section in the wiki page
>>>>>>> <https://github.com/kaichogami/mne-python/wiki/GSoC-Proposal#project-detail>
>>>>>>> .
>>>>>>>
>>>>>>> Thank you
>>>>>>> Asish Panda
>>>>>>>
>>>>>>> On Fri, Mar 11, 2016 at 6:06 AM, Phillip Alday <
>>>>>>> Phillip.Alday at unisa.edu.au> wrote:
>>>>>>>
>>>>>>>> Hi guys,
>>>>>>>>
>>>>>>>> PyMVPA might be a good place to look for inspiration and maybe
>>>>>>>> integration: http://www.pymvpa.org/
>>>>>>>>
>>>>>>>> They have a really nice workflow and API.
>>>>>>>>
>>>>>>>> Best,
>>>>>>>> Phillip
>>>>>>>>
>>>>>>>>
>>>>>>>> > On 11 Mar 2016, at 08:57, JR KING <jeanremi.king at gmail.com>
>>>>>>>> wrote:
>>>>>>>> >
>>>>>>>> > Hi Asish,
>>>>>>>> >
>>>>>>>> > As Denis said, the decoding module is one possible target. Just
>>>>>>>> FYI, there are other possibilities too: e.g. across-subjects stats and viz
>>>>>>>> isn't really well developed/documented.
>>>>>>>> >
>>>>>>>> > Currently the decoding classes have been developed separately, by
>>>>>>>> different authors and with different architectures. IMO, one great goal
>>>>>>>> would thus be to
>>>>>>>> >
>>>>>>>> > 1. (hard) homogenize the existing functions so that they all
>>>>>>>> become strictly compatible with sklearn (i.e, based on BaseEstimator_,
>>>>>>>> using fit, transform, predict and score methods).
>>>>>>>> >
>>>>>>>> > 2. (medium-hard): develop transformer objects that would
>>>>>>>> ultimately allow the users to pipe multiple processing steps: e.g. we
>>>>>>>> typically aim at getting:
>>>>>>>> > make_pipeline(TimeFreq(), InverseTransform(), DataVectorizer(),
>>>>>>>> LogisticRegression())
>>>>>>>> > or
>>>>>>>> > make_pipeline(Filter(10, 30), Covariances(method='shrunk'),
>>>>>>>> Xdawn(n_components=4), TangentSpace(), SVM(kernel='linear'))
>>>>>>>> >
>>>>>>>> > for which all the steps could be typically initialized with
>>>>>>>> inst.info and would take an X and a y to be
>>>>>>>> fitted/predicted/scored.
>>>>>>>> >
>>>>>>>> > 3. (easy) Setup a systematic i/o to store the estimators, the
>>>>>>>> predictions and the scores.
>>>>>>>> >
>>>>>>>> > As a concrete example, to optimize memory and CPU, the GAT
>>>>>>>> currently stores the predictions (y_pred_) in the object, and the scoring
>>>>>>>> approach is performed outside the CV. This storing and scoring isn't
>>>>>>>> following sklearn API. Consequently, one cannot use cross_val_score(GAT).
>>>>>>>> Typically refactoring this kind of feature requires some deep thinking
>>>>>>>> because, unlike sklearn, several decoding module are applied in a "mass
>>>>>>>> multivariate" way: i.e. many multivariate models are fitted on
>>>>>>>> independent/partially common/or even identical data. Optimizing memory and
>>>>>>>> CPU is thus probably the main challenge here.
>>>>>>>> >
>>>>>>>> > I would consequently start by tackling the easy/medium problem
>>>>>>>> first (e.g. i/o in all decoding classes, vizualizing the fitted
>>>>>>>> weights/patterns for each decoding method), and see how we can develop some
>>>>>>>> transformers, such as EpochVectorizer, that would be common across decoding
>>>>>>>> modules to format.
>>>>>>>> >
>>>>>>>> > Hope this helps,
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > JR
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > In summary, this project will involve a series of usability
>>>>>>>> improvements for the decoding module and extend its functionality.
>>>>>>>> > I feel the above statement is quite vague for writing a detailed
>>>>>>>> plan in the proposal. Or perhaps the "improvements" can only be known while
>>>>>>>> the objectives(listed above) are being fulfilled?
>>>>>>>> > Lastly, going a little out of topic, could you now please
>>>>>>>> elaborate on how to set up the cleaner framework of the decoding module,
>>>>>>>> that you mentioned in the last message?
>>>>>>>> >
>>>>>>>> > Thank you
>>>>>>>> > Asish Panda
>>>>>>>> >
>>>>>>>> > On Fri, Feb 26, 2016 at 9:50 PM, Asish Panda <
>>>>>>>> asishrocks95 at gmail.com> wrote:
>>>>>>>> > Hello Jean
>>>>>>>> >
>>>>>>>> > Thank you very much for your response and the issues. I will get
>>>>>>>> my hand dirty right away! :)
>>>>>>>> >
>>>>>>>> > Thank you
>>>>>>>> > Asish Panda
>>>>>>>> >
>>>>>>>> > On Fri, Feb 26, 2016 at 8:37 PM, JR KING <jeanremi.king at gmail.com>
>>>>>>>> wrote:
>>>>>>>> > Hi Asish,
>>>>>>>> >
>>>>>>>> > Thanks for your interest!.
>>>>>>>> >
>>>>>>>> > You can start with one of these easy PR:
>>>>>>>> > https://github.com/mne-tools/mne-python/issues/2874
>>>>>>>> > https://github.com/mne-tools/mne-python/issues/2176
>>>>>>>> > https://github.com/mne-tools/mne-python/issues/2189 (probably
>>>>>>>> needs a bit of discussion)
>>>>>>>> >
>>>>>>>> > Once you're there I can suggest you some more fun things that you
>>>>>>>> could do to set up a cleaner framework for the decoding module.
>>>>>>>> >
>>>>>>>> > All the best,
>>>>>>>> >
>>>>>>>> > Jean-Rémi
>>>>>>>> >
>>>>>>>> > On 26 February 2016 at 09:57, Asish Panda <asishrocks95 at gmail.com>
>>>>>>>> wrote:
>>>>>>>> > Hello everyone,
>>>>>>>> >
>>>>>>>> > I am looking forward to participate in GSoC and I am interested
>>>>>>>> in the idea of improving the decode module. I have installed and set up the
>>>>>>>> development environment and have been trying to get familiar with various
>>>>>>>> modules. However being quite new to MEG, EEG I'm looking for some pointers
>>>>>>>> to start as well as prerequisites to work on decode module.
>>>>>>>> > Lastly I apologize if I have been rude in any manner.
>>>>>>>> >
>>>>>>>> > Thank you
>>>>>>>> > Asish Panda
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > Mne_analysis mailing list
>>>>>>>> > Mne_analysis at nmr.mgh.harvard.edu
>>>>>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > The information in this e-mail is intended only for the person to
>>>>>>>> whom it is
>>>>>>>> > addressed. If you believe this e-mail was sent to you in error
>>>>>>>> and the e-mail
>>>>>>>> > contains patient information, please contact the Partners
>>>>>>>> Compliance HelpLine at
>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent
>>>>>>>> to you in error
>>>>>>>> > but does not contain patient information, please contact the
>>>>>>>> sender and properly
>>>>>>>> > dispose of the e-mail.
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > Mne_analysis mailing list
>>>>>>>> > Mne_analysis at nmr.mgh.harvard.edu
>>>>>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > The information in this e-mail is intended only for the person to
>>>>>>>> whom it is
>>>>>>>> > addressed. If you believe this e-mail was sent to you in error
>>>>>>>> and the e-mail
>>>>>>>> > contains patient information, please contact the Partners
>>>>>>>> Compliance HelpLine at
>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent
>>>>>>>> to you in error
>>>>>>>> > but does not contain patient information, please contact the
>>>>>>>> sender and properly
>>>>>>>> > dispose of the e-mail.
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > Mne_analysis mailing list
>>>>>>>> > Mne_analysis at nmr.mgh.harvard.edu
>>>>>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > The information in this e-mail is intended only for the person to
>>>>>>>> whom it is
>>>>>>>> > addressed. If you believe this e-mail was sent to you in error
>>>>>>>> and the e-mail
>>>>>>>> > contains patient information, please contact the Partners
>>>>>>>> Compliance HelpLine at
>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent
>>>>>>>> to you in error
>>>>>>>> > but does not contain patient information, please contact the
>>>>>>>> sender and properly
>>>>>>>> > dispose of the e-mail.
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > _______________________________________________
>>>>>>>> > Mne_analysis mailing list
>>>>>>>> > Mne_analysis at nmr.mgh.harvard.edu
>>>>>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > The information in this e-mail is intended only for the person to
>>>>>>>> whom it is
>>>>>>>> > addressed. If you believe this e-mail was sent to you in error
>>>>>>>> and the e-mail
>>>>>>>> > contains patient information, please contact the Partners
>>>>>>>> Compliance HelpLine at
>>>>>>>> > http://www.partners.org/complianceline . If the e-mail was sent
>>>>>>>> to you in error
>>>>>>>> > but does not contain patient information, please contact the
>>>>>>>> sender and properly
>>>>>>>> > dispose of the e-mail.
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Mne_analysis mailing list
>>>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>>
>>>>>>>>
>>>>>>>> The information in this e-mail is intended only for the person to
>>>>>>>> whom it is
>>>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>>>> the e-mail
>>>>>>>> contains patient information, please contact the Partners
>>>>>>>> Compliance HelpLine at
>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>>> you in error
>>>>>>>> but does not contain patient information, please contact the sender
>>>>>>>> and properly
>>>>>>>> dispose of the e-mail.
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Mne_analysis mailing list
>>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>>
>>>>>>>
>>>>>>> The information in this e-mail is intended only for the person to
>>>>>>> whom it is
>>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>>> the e-mail
>>>>>>> contains patient information, please contact the Partners Compliance
>>>>>>> HelpLine at
>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>>> you in error
>>>>>>> but does not contain patient information, please contact the sender
>>>>>>> and properly
>>>>>>> dispose of the e-mail.
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Mne_analysis mailing list
>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>>
>>>>>>
>>>>>> The information in this e-mail is intended only for the person to
>>>>>> whom it is
>>>>>> addressed. If you believe this e-mail was sent to you in error and
>>>>>> the e-mail
>>>>>> contains patient information, please contact the Partners Compliance
>>>>>> HelpLine at
>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>>> you in error
>>>>>> but does not contain patient information, please contact the sender
>>>>>> and properly
>>>>>> dispose of the e-mail.
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Mne_analysis mailing list
>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>
>>>>>
>>>>> The information in this e-mail is intended only for the person to whom
>>>>> it is
>>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>>> e-mail
>>>>> contains patient information, please contact the Partners Compliance
>>>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>> you in error
>>>>> but does not contain patient information, please contact the sender
>>>>> and properly
>>>>> dispose of the e-mail.
>>>>>
>>>>>
>>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160317/59a3eace/attachment-0001.html 


More information about the Mne_analysis mailing list