<div dir="ltr">Hi Ashish,<div><br></div><div>we totally agree with you. W<span style="line-height:1.5">ith 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.</span></div><div><span style="line-height:1.5"><br></span></div><div><span style="line-height:1.5">Denis</span></div><div><br></div><div> </div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Mar 16, 2016 at 8:31 PM Asish Panda <<a href="mailto:asishrocks95@gmail.com">asishrocks95@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<br><br>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.<br>Let me know what you guys think. We can discuss this here, gitter, or over hangouts, whichever is more suitable for you guys.<br><br>Thank you</div><div dir="ltr"><br>Asish Panda</div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 15, 2016 at 11:20 AM, Asish Panda <span dir="ltr"><<a href="mailto:asishrocks95@gmail.com" target="_blank">asishrocks95@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote"><span>On Mon, Mar 14, 2016 at 7:21 PM, Denis-Alexander Engemann <span dir="ltr"><<a href="mailto:denis.engemann@gmail.com" target="_blank">denis.engemann@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Looks also good to me.<div><br><div>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.</div><div>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.</div><div>We might need a hangoug or skype together to decide about the priorities of all the elements you listed.</div></div></div></blockquote></span><div>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.</div><span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><span><font color="#888888"><div><br></div><div>--Denis</div><div><br></div><div><br></div><div><br></div></font></span></div></div><div><div><br><div class="gmail_quote"><div dir="ltr">On Mon, Mar 14, 2016 at 2:40 PM JR KING <<a href="mailto:jeanremi.king@gmail.com" target="_blank">jeanremi.king@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Thanks Asish.<br><br>It's good overall. I added some corrections. <br></div></div></div></blockquote></div></div></div></blockquote></span><div>Thank you for your help! :) </div><div><div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><br></div>Hope that helps,<br><br></div>JR<br></div><div class="gmail_extra"><br><div class="gmail_quote">On 14 March 2016 at 03:38, Asish Panda <span dir="ltr"><<a href="mailto:asishrocks95@gmail.com" target="_blank">asishrocks95@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello everyone<br><br>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<div>project details section in the <a href="https://github.com/kaichogami/mne-python/wiki/GSoC-Proposal#project-detail" target="_blank">wiki page</a>.</div><div><br></div><div>Thank you<span><font color="#888888"><br>Asish Panda</font></span></div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Mar 11, 2016 at 6:06 AM, Phillip Alday <span dir="ltr"><<a href="mailto:Phillip.Alday@unisa.edu.au" target="_blank">Phillip.Alday@unisa.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi guys,<br>
<br>
PyMVPA might be a good place to look for inspiration and maybe integration: <a href="http://www.pymvpa.org/" rel="noreferrer" target="_blank">http://www.pymvpa.org/</a><br>
<br>
They have a really nice workflow and API.<br>
<br>
Best,<br>
Phillip<br>
<div><div><br>
<br>
> On 11 Mar 2016, at 08:57, JR KING <<a href="mailto:jeanremi.king@gmail.com" target="_blank">jeanremi.king@gmail.com</a>> wrote:<br>
><br>
> Hi Asish,<br>
><br>
> 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.<br>
><br>
> Currently the decoding classes have been developed separately, by different authors and with different architectures. IMO, one great goal would thus be to<br>
><br>
> 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).<br>
><br>
> 2. (medium-hard): develop transformer objects that would ultimately allow the users to pipe multiple processing steps: e.g. we typically aim at getting:<br>
> make_pipeline(TimeFreq(), InverseTransform(), DataVectorizer(), LogisticRegression())<br>
> or<br>
> make_pipeline(Filter(10, 30), Covariances(method='shrunk'), Xdawn(n_components=4), TangentSpace(), SVM(kernel='linear'))<br>
><br>
> for which all the steps could be typically initialized with <a href="http://inst.info" rel="noreferrer" target="_blank">inst.info</a> and would take an X and a y to be fitted/predicted/scored.<br>
><br>
> 3. (easy) Setup a systematic i/o to store the estimators, the predictions and the scores.<br>
><br>
> 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.<br>
><br>
> 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.<br>
><br>
> Hope this helps,<br>
><br>
><br>
> JR<br>
><br>
><br>
> In summary, this project will involve a series of usability improvements for the decoding module and extend its functionality.<br>
> 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?<br>
> 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?<br>
><br>
> Thank you<br>
> Asish Panda<br>
><br>
> On Fri, Feb 26, 2016 at 9:50 PM, Asish Panda <<a href="mailto:asishrocks95@gmail.com" target="_blank">asishrocks95@gmail.com</a>> wrote:<br>
> Hello Jean<br>
><br>
> Thank you very much for your response and the issues. I will get my hand dirty right away! :)<br>
><br>
> Thank you<br>
> Asish Panda<br>
><br>
> On Fri, Feb 26, 2016 at 8:37 PM, JR KING <<a href="mailto:jeanremi.king@gmail.com" target="_blank">jeanremi.king@gmail.com</a>> wrote:<br>
> Hi Asish,<br>
><br>
> Thanks for your interest!.<br>
><br>
> You can start with one of these easy PR:<br>
> <a href="https://github.com/mne-tools/mne-python/issues/2874" rel="noreferrer" target="_blank">https://github.com/mne-tools/mne-python/issues/2874</a><br>
> <a href="https://github.com/mne-tools/mne-python/issues/2176" rel="noreferrer" target="_blank">https://github.com/mne-tools/mne-python/issues/2176</a><br>
> <a href="https://github.com/mne-tools/mne-python/issues/2189" rel="noreferrer" target="_blank">https://github.com/mne-tools/mne-python/issues/2189</a> (probably needs a bit of discussion)<br>
><br>
> 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.<br>
><br>
> All the best,<br>
><br>
> Jean-Rémi<br>
><br>
> On 26 February 2016 at 09:57, Asish Panda <<a href="mailto:asishrocks95@gmail.com" target="_blank">asishrocks95@gmail.com</a>> wrote:<br>
> Hello everyone,<br>
><br>
> 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.<br>
> Lastly I apologize if I have been rude in any manner.<br>
><br>
> Thank you<br>
> Asish Panda<br>
><br>
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