Open in new window / Try shogun cloud
--- Log opened Wed Feb 19 00:00:05 2014
@sonney2kwiking, maybe I just need to prefix it with \$ENV{DESTDIR}00:04
@sonney2kwiking, yes that fixes it00:06
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shogun-notifier-shogun: Soeren Sonnenburg :develop * 5f9be33 / src/interfaces/r_modular/CMakeLists.txt,src/interfaces/r_static/CMakeLists.txt:
shogun-notifier-shogun: fix install of r_static/modular interfaces when DESTDIR is set00:14
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shogun-notifier-shogun: Soeren Sonnenburg :develop * 3b51ef5 / src/interfaces/r_modular/CMakeLists.txt:
shogun-notifier-shogun: add another missing DESTDIR01:21
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travis-ci[travis-ci] it's Soeren Sonnenburg's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun:
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@HeikoSsonney2k: see example projects description in google doc, pls update and add what you think is needed02:59
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tom__I would like some advice on a multiclass unbalanced problem10:46
tom__I would like to use shogun for multiclass one-vs-rest classification10:47
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tom__Is ts possible to assign weights for pos/neg samples for each binary svm machine inside multiclassmachine shogun framework ?10:48
adrintom__: I'm not very familiar with shogun, but sometimes depending on the interface language you're using, available parameters change.11:03
adrintom__: I guess nowadays python is fairly complete in terms of feature support of the underlying C++ code, if I'm not totally wrong.11:04
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tom__I am using c++ interface11:45
sonne|worktom__: I don't think this is possible ATM11:46
tom__Is it possible to use CMulticlassSVM class and set K CMKLClassification svm machine as K binary classifier ?11:46
tom__I give a try and I got "train_machine is not yet implemented for SVM!"11:47
sonne|worktom__: but of course do-able. one could basically just set some C matrix which has a size of #examples * #classes11:47
sonne|worktom__: that splitting is done automatically11:49
sonne|worktom__: if you went that far you could just train your K machines yourself with whatever custom C settings11:50
sonne|worktom__: and then later put them into multiclass svm to use its apply() or do it yourself there too11:50
tom__thank you11:54
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sonne|workadrin: indeed there shouldn't be much difference between C++ and python_modular except that classes have no C prefix ;)11:59
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parijatsonne|work: online? good time to talk?12:04
sonne|workparijat: will be off for lunch soon12:05
sonne|workparijat: but maybe start typing!12:05
sonne|workparijat: and I reply when I am back or so12:05
parijatsonne|work:  sorry!12:07
sonne|workparijat: no reason to be sorry - I am happy that you ask here!12:08
parijatsonne|work: i wanted to ask about the pCA PR12:08
sonne|workI guess so12:08
parijatwhat did you mean by in-place?12:08
parijati mean i can get rid of the feature_matrix_centered. will that work?12:08
sonne|workparijat: previously the Feature matrix was directly modified12:08
sonne|workparijat: that is a bit hacky for sure but did make it work in low memory conditions12:09
parijatok. yes. but the feature matrix dimension is not correct12:09
sonne|workparijat: yes that would have to be corrected12:09
sonne|workbut that is it12:10
parijatso, in any case we would need a new matrix right?12:10
parijatmore so because the final portion of matrix needed is not continuous block in the old matrix12:11
parijatsonne|work: did I make sense?12:12
sonne|workparijat: yes but ...12:14
sonne|workparijat: I did 'hack' that by just moving the matrix columns to the very front and changing sizes12:15
sonne|workparijat: it certainly is a hack12:15
sonne|workbut it did help back then12:15
sonne|workparijat: sry afk12:17
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parijatok! but the final matrix to be returned should be of lesser dimension right? were you somehow able to return a submatrix12:19
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parijatsonne|work: whenever you are bach . :) My point was, I am directly modifying feature_matrix (m in our case) via Eigen3 interface matrix 'feature_matrix'. but the final result I am storing in a different matrix with proper target dimension which I return12:31
parijatHeikoS1: hello! :)12:32
HeikoS1parijat:  hi!12:33
parijatHeikoS1: i was just discussing about the in-place PCA thing with sonney2k :)12:33
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HeikoS1parijat: cool, any results on that?12:35
parijatHeikoS1: may be I am missing something trivial but you would need a new matrix anyways right? because the dimension of current matrix is not correct?12:36
HeikoS1parijat: maybe realloc helps? since the new matrix is smaller12:36
HeikoS1this should be in place12:36
HeikoS1parijat: tricky thing :) it only worked before since there was this size bug :)12:37
parijatHeikoS1: I mean the method returns SGMatrix of smaller size. I will have to form that maatrix anyways right?12:37
HeikoS1parijat: just to make sure I get everything, what are the matrices involved, how was it before, how is it now?12:38
parijatHeikoS1: earlier there was only this SGMatrix m obtained from features and it was returned12:40
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shogun-notifier-shogun: lambday :develop * 4fc837f / / (10 files):
shogun-notifier-shogun: ssk renamed to SubsequenceStringKernel for naming consistency12:40
shogun-notifier-shogun: Heiko Strathmann :develop * a2e27d9 / / (10 files):
shogun-notifier-shogun: Merge pull request #1879 from lambday/develop12:40
shogun-notifier-shogun: ssk renamed to SubsequenceStringKernel for naming consistency12:40
parijatHeikoS1: it had wrong dimensions12:40
HeikoS1parijat: my question is: is it possible to do this in place?12:40
HeikoS1via resizing something?12:41
HeikoS1or is that impossible12:41
HeikoS1am let me look at the code ....12:41
shogun-notifier-shogun-data: Parijat Mazumdar :master * a7c153f / testsuite/python2-tests/preprocessor_pca_modular0.txt:
shogun-notifier-shogun-data: PCA python-2 data changed12:41
shogun-notifier-shogun-data: Parijat Mazumdar :master * 865f0d2 / testsuite/python3-tests/preprocessor_pca_modular0.txt:
shogun-notifier-shogun-data: PCA python-3 data changed12:41
shogun-notifier-shogun-data: Heiko Strathmann :master * 70491d2 / testsuite/ (2 files):
shogun-notifier-shogun-data: Merge pull request #32 from mazumdarparijat/master12:41
shogun-notifier-shogun-data: PCA test data change12:41
parijatHeikoS1: I am not sure! let me check resizing of matrices12:42
parijatHeikoS1: unless we can resize an SGMatrix, I think no.12:44
HeikoS1parijat: its possible to resize, but dont we loose things then?12:44
parijatHeikoS1: no we want to lose some things12:44
HeikoS1parijat: looking at code currently12:45
HeikoS1afk for 5 mins, ill be back soon and then check12:45
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parijatHeikoS1: num_vectors remains same num_features changes12:45
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lambday_HeikoS1: hi!12:56
lambday_HeikoS1: I didn't get what you mean by update the data :(12:57
lambday_HeikoS1: the matrices are being returned as well as the kernel obj, right?12:57
HeikoS1lambday_:  hi!12:58
HeikoS1lambday_: if the kernel object is returned in the function, then the integration tests will fail after a class name change12:59
HeikoS1lambday_: so data needs to be updated12:59
HeikoS1with the new names12:59
lambday_HeikoS1: oh I didn't know that!13:00
lambday_HeikoS1: by data you mean shogun-data ?13:01
HeikoS1lambday_: yes13:01
parijatHeikoS1: the PCA data that you have already merged will cause travis failure for other PRs? because the PCA change in not merged yet13:07
lambday_HeikoS1: umm.. I am not getting - tests worked fine locally... you mean updating the submodule in buildbot?13:07
HeikoS1parijat: yes :)13:07
HeikoS1parijat: so better hurry up :D13:07
HeikoS1lambday_: mmh weird, this should have broken things, lets just wait and i fit stays green things are fine. Have an eye on the buildbot13:07
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lambday_HeikoS1: alrighty13:08
HeikoS1parijat: did you get my point with the realloc or doing vector wise projectsions?13:08
parijatHeikoS1: nope. could you explain again plz?13:08
HeikoS1parijat: ok, 1 sec ....13:09
HeikoS1finishing emali13:09
parijatHeikoS1: specifically how can I generate the final feature matrix with some of the cells of original feature matrix missing?13:11
parijatHeikoS1: I think I may have uunderstood your point! let me see if it works.13:16
HeikoS1parijat: you can use eigen3 views to access only subsets of the matrix13:17
HeikoS1but that depends on how its stored in memory13:17
HeikoS1and then you can do stuff, and aferwards cut off the remaining part with realloc13:17
parijatHeikoS1: yes. I got your point.13:19
HeikoS1parijat:  if all this doesnt work, you can do it like the existing implementation, i.e. vector wise13:19
HeikoS1thats same computational costs13:19
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HeikoS1(if done in serial)13:19
parijatyes actually I am trying to avoid looping! lets see13:20
HeikoS1parijat: would be best to do this in eigen3 since it might parallelise the operation internally13:22
HeikoS1so with the view, thats the best solution13:22
HeikoS1I am not sure about the cutting off13:22
HeikoS1parijat: the problem is that we reduce dimensions13:22
HeikoS1i.e. number of rows13:22
HeikoS1but we store matrices column by column13:23
parijatHeikoS1: yup! i am in absolutely 0 mood to let go of eigen313:23
HeikoS1so we cannot just cut off at the end13:23
HeikoS1we need to remove element from within the memory block13:23
HeikoS1ah thats messy13:23
HeikoS1maybe transpose before13:23
parijatHeikoS1: yes! I am thinking of taking transpose13:23
parijatyeah my point13:23
HeikoS1parijat: but transpose is slow13:23
HeikoS1no we dont want to do that13:23
HeikoS1I suggest to do this then:13:24
HeikoS1mmh tricky .....13:25
HeikoS1actually I dont see a way without transposing13:25
HeikoS1that doesnt allocate a new matrix13:25
HeikoS1ok then, transpose!13:25
HeikoS1its sensible since matrix multiplication is more expensive13:25
HeikoS1and allocating memory is also more expensive13:26
HeikoS1transposing back has the same problem when the matrix is not square anymore13:26
parijatHeikoS1: I can also loop element by element to fill up the first elements of feature matrix and then get rid of rest. and also change num_features and num_vectors in feature13:27
parijatwould that be less expensive?13:27
parijatgot my point?13:27
HeikoS1the "getting rid" is the problem13:27
HeikoS1cutting of in place is not possible in shoguns matrix format13:27
HeikoS1cutting off dimensions I mean13:28
HeikoS1so you could transpose and do it then13:28
HeikoS1and then transpose back13:28
HeikoS1the tranposing back should work in place in fact13:28
HeikoS1I was wrong earlier13:28
HeikoS1sorry for the mess ;)13:29
HeikoS1I think transpose is best, but make sure its in place and on the real matrix memory, not the eigen3 view13:29
parijatno if i line up the needed cells in the pointer to matrix and then use realloc??13:29
parijatlining up will be element by element operation13:29
HeikoS11.) transpose memory 2.)eigen3 view on subset 3.) projection view eigen3 multiplication 4.) realloc on the matrix memory to get rid of the last columns (aka dimensions since transposed) 4.) transpose back ..... all transposes should be in place13:30
HeikoS1parijat: no try to avoid loops over matrix elements, eigen3 calls are better13:30
HeikoS1parijat: since we can replace eigen3 with a multicore eigen3 or GPU eigen313:31
HeikoS1without having to change our code13:31
parijati think i am not able to convey my idea clearly! let me push my patch. In case you dont like it, I got the transpose thing. I will implement that13:32
parijatno i am not doing away with eigen3!13:32
HeikoS1parijat: hehe sorry13:42
HeikoS1could you explain me again? :)13:42
HeikoS1or just send, I will be able to have a look later today13:43
parijatHeikoS1: lets try with an example.13:43
HeikoS1parijat: interesting stuff this efficient linear algebra in c++, isnt it? :)13:43
parijatHeikoS1: yeah! :)13:43
HeikoS1cant do this stuff if matlab/python/R :)13:43
HeikoS1its always slower13:43
HeikoS1apart from the loops13:43
HeikoS1anyways, I gotta go, will be back later today, see you!13:43
parijatHeikoS1: yeah sure. I will push code for your perusal13:44
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wikingthis site is the awesomeness factor 2.0:
wikingshogun refactor should look like this imo14:44
sonne|workwiking: you mean no content?14:56
sonne|worktotally awesome!14:56
wikingi was refering to infinite canvas14:58
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lisitsynwiking: yeah the site is awesome though no info as sonne|work said :D15:16
wikinglisitsyn: was never talking about the content15:17
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lambday_HeikoS1: hey.. you were right.. changing name did break the integration test.. I had the something wrong at my side15:25
lambday_HeikoS1: tested locally again.. failing tests15:26
HeikoS1lambday_: thats good news then, all as expected :)15:26
lambday_HeikoS1: btw I started working on the multitask notebook.. reading malsar doc as well... thinking of including some real world example...15:27
HeikoS1lambday_: man thats great!15:27
lisitsynlambday_: hmm I have some draft of this notebook15:27
HeikoS1your other notebook was great, so looking forward to see it15:27
lisitsynif you could continue with it - would be fantastic :D15:28
HeikoS1lambday_, lisitsyn writing those notebooks is a great thing to practice writing about ML btw, it really helps for later15:28
HeikoS1lisitsyn: speaking of writing, we should write the GSoC veteran blog post15:28
HeikoS1lisitsyn: any suggestions?15:28
HeikoS1we should make something catchy, like a dialog between us or a fake interview or so15:28
lisitsynHeikoS1: what time works for you?15:28
HeikoS1lisitsyn:  what time?15:28
lisitsynHeikoS1: to take care of this :)15:29
HeikoS1lisitsyn: saturday afternoon?15:29
lisitsynshould be possible15:29
lambday_lisitsyn: could you please share with me what you already have? or.. you wanna finish this?15:29
lisitsynlambday_: I want but have time pressure15:30
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lambdaylisitsyn: umm... you'll do it best - its all your code...15:30
lisitsynlambday: sure15:30
HeikoS1lisitsyn: btw we desperately need a multiclass notebook15:31
HeikoS1lisitsyn: or extend the existing one15:31
HeikoS1with all the OvO and accuracy stuff15:31
HeikoS1like the guy in the mail asked15:31
HeikoS1lisitsyn: you should do that! you know best15:31
HeikoS1lisitsyn:  and then you should also document all classes :)15:31
lisitsynHeikoS1: I'll answer the mail tonight15:31
lambdayHeikoS1: umm should I go ahead with string kernel noteboook then? or focus on gsoc topics - lol I am all confused! :D15:31
lambdaysonney2k: I can create shogun tag on stack overflow I guess!15:32
HeikoS1lambday: what ever you want!15:33
HeikoS1lambday: you can start doing gsoc stuff when we are accepted :)15:33
lambdayHeikoS1: alright then - I'll start the string kernel one then - this one is gonna be huge!15:34
lisitsynHeikoS1: lambday: so I mean15:34
lisitsynwe should not duplicate the work on multitask notebook15:34
lambdaylisitsyn: yeah totally makes sense15:34
HeikoS1lisitsyn: just put the notebook into your git and then update there, then lambday can join forces if he wants15:34
lambdayyeah that sounds good :)15:35
* lambday goes back reading stuffs15:35
lisitsynHeikoS1: haha another duty ;)15:37
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lambdayHeikoS1: lisitsyn: can the notebook documentation page have titles for the notebooks and then one can put a toc sort of thing at the top so that its easier to browse?15:42
lambdaylike the ideas page15:43
HeikoS1lambday: great idea! could you hunt fernanod down on this? like pusing them to do it? :) I have not idea how the website works15:44
lambdayHeikoS1: neither do I or I would have done it! I can create an issue though and tag him :P15:45
HeikoS1lambday: thats good! but not enough to make it happen ;)15:46
lambdayHeikoS1: lol okay I will catch him at irc :)15:47
HeikoS1lambday: every day :)15:47
lambdaythe shogun-web repo is not the one that is used currently I guess :-/15:48
lambdaylast updated a month ago15:48
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sonne|worklambday: it is the one16:25
sonne|worklambday: could you please add the string kernel notebook?16:26
sonne|workI mean write one :D16:26
sonne|workor start at least16:26
lambdaysonne|work: hehe.. yeah I will asap..16:27
lambdaysonne|work: I found your thesis somewhere that had all the references to most of the string kernels that we have16:27
sonne|worklambday: I can give you the source code for string kernels if you do more than 1 kernel :D16:27
sonne|worklambday: the latex code I mean :D16:27
lambdaysonne|work: that would be really helpful :) I will also get to know about them :D16:28
lambdaysonne|work: oh btw do you agree that having a toc for the notebooks in the documentation page is a good idea?16:29
lambdayimo mini desc is helpful but toc would help largely in browsing16:29
lambdaybrb after dinner :)16:39
sonne|worklambday: sure!16:39
sonne|worklambday: just do it16:40
sonne|worklambday: and yes the code is up-to-date :D16:40
lambdaysonne|work: lol its django and I don't know anything - will try :D16:40
sonne|worklambday: hehe then better don't try it :)16:40
lambdaysonne|work: hehe! :D16:41
lambdaybrb :)16:41
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parijatHeikoS: I have pushed in the new code
parijatHeikoS: I believe this is better than taking transpose 2 times19:23
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parijatiglesiasg: hello!  hows life? :)19:47
@iglesiasghey parijat19:48
@iglesiasglife's good19:48
@iglesiasgparijat, what about you?19:48
parijatiglesiasg: good so far! :D19:48
@iglesiasgnice to hear19:48
parijatiglesiasg: i have been working on fixin the pca bug.19:48
@iglesiasgparijat, yeah, I have seen the commits and the comments from HeikoS and sonney2k19:49
parijatiglesiasg: running into troubles now n then! lets see how it turns out finally :)19:49
@iglesiasgit will be good ;)19:50
parijatiglesiasg: hoping so. ;)19:50
wikingiglesiasg: hey man20:09
wikingiglesiasg: so if i'm good then i should just copy-paste the html in your repo right?20:09
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wikingiglesiasg: i'll send you soon a PR with the other 2 projects and then i'll do the copy-paste...20:09
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@iglesiasgwiking, cool20:11
@iglesiasgwiking, sure do that, get the file and copy-paste20:12
parijatiglesiasg: I am getting this wierd exception in travis EXCEPTION 'module' object has no attribute '_Unpickler'20:17
parijatiglesiasg: any clue about it?20:17
@iglesiasgparijat, maybe it is an issue with serialization in Python?20:20
parijatsorry whats that?20:20
@iglesiasgparijat, serialization?20:21
parijatiglesiasg: yes20:22
@iglesiasgparijat, when the state of an object or a data structure in general is stored so that it can be used outside the program20:22
@iglesiasgparijat, maybe because you want to recover that state later, or maybe because you want to send over the network, etc20:23
@iglesiasgthe pickle module is used in Python for serialization, that's why I guessed so from Unpickler20:23
parijatiglesiasg: there might be a problem with the format in which output expected is stored?20:23
parijatiglesiasg: thats why I might be getting this exception?20:24
@iglesiasgparijat, I am not sure at all. Have you detected when was the first time the error happen?20:24
@iglesiasgsend me the link to the travis log you mean also please20:24
parijatiglesiasg: here
parijatiglesiasg: test 17320:25
@iglesiasgparijat, does it happen to you locally? Is it with python2 or python3?20:26
parijatiglesiasg: yes! with python 2. I thought it might be some random thing20:27
@iglesiasgparijat, I can restart the travis build and see if next time happens. Is it in your opened PR?20:28
parijatiglesiasg: thanks.20:29
@iglesiasgparijat, although I think it might be something else... mm20:30
@iglesiasgparijat, it is an integration test what is failing I think20:30
@iglesiasgintegration, indeed yeah20:30
parijatparijat: yup its integration test.20:31
wikingiglesiasg: pr sent20:31
@iglesiasgparijat, have you tried running that test locally?20:31
@iglesiasgwiking, done!20:31
wikingcool i'll now copy-paste20:32
@iglesiasgwiking, sure, thanks!20:32
wikinghope i dont delete some ideas :)20:32
@iglesiasghaha man that's been such a mistake from me, sorry really20:32
wikingiglesiasg: mmm do u know that not the full html is in the repo?20:33
@iglesiasgbut it didn't cross my mind at all20:33
@iglesiasgwiking, what? it is it is20:33
@iglesiasgthe one you have to copy for the ideas is20:33
wikingis missing20:33
wikingoh wait20:33
wikingthat part is missing20:33
wikingthe closing tags i've mentioned20:34
wikingno worries i'll add it like that20:34
wikingbut i have a backup of the prev one20:34
wikingif needed20:34
@iglesiasgsounds good20:34
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alamages /clear20:49
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--- Log closed Thu Feb 20 00:00:06 2014