IRC logs of #shogun for Saturday, 2011-04-09

--- Log opened Sat Apr 09 00:00:36 2011
blackburn1that's the reason why I have a different picture in doc00:00
@sonney2kgive me a sec00:03
blackburn1okay, no problem :)00:03
* sonney2k is removing libshogun/classifier/boosting00:03
-!- blackburn1 is now known as blackburn00:05
blackburnsonney2k: I removed it locally, it is working now00:05
CIA-31shogun: Soeren Sonnenburg master * r9bb3b2e / (229 files in 13 dirs):00:14
CIA-31shogun: remove boosting directory00:14
CIA-31shogun: If we merge again we have to merge with newer00:14
CIA-31shogun: multiboost algorithms anyway. The current ones show many warnings and00:14
CIA-31shogun: cause errors when generating the documentation. - http://bit.ly/hgDnvL00:14
CIA-31shogun: Soeren Sonnenburg master * rd7503c3 / src/modular/Classifier.i : remove also includes of boosting algos for now. - http://bit.ly/eoBd4C00:14
@sonney2kblackburn, OK I've removed it for now00:16
@sonney2kwe have a branch for that merge anyways so does not matter yet00:16
@sonney2kand should fix our problems00:16
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blackburnsonney2k: I have another problem :)00:22
@bettybooho00:22
@sonney2k?00:22
blackburnsonney2k: these pictures of equations are enumerated00:22
@sonney2krm -rf html00:22
@sonney2kand do again00:23
@sonney2kmake doc00:23
blackburnshould I send doc/html entirely00:23
blackburn?00:23
@sonney2kno ignore doc completely00:23
blackburnexcept doc for wave kernel?00:23
blackburnI not pretty sure that understand you right00:24
blackburnwhen sending a patch introducing that kernel, should I add to that commit .html and .png?00:25
@sonney2kblackburn, no00:25
@sonney2kwe generate the docuemntation from the source code00:25
blackburnI understand that00:26
@sonney2kso doc/html is generated from the headers00:26
blackburnnot understand why I messed with documentation :)00:26
@sonney2kso don't send anything in doc00:26
blackburnI'm a bit stupid today :D00:26
blackburnsonney2k: is it better to send a patch to ML? I could send it straightly to you00:29
@sonney2kblackburn, it is always better to do things in public - other people can comment and also they see that you are active00:30
@sonney2kdon't be afraid / ashamed00:30
blackburnah, I see00:30
@sonney2kyou are doing a good job so there is no need for such feelings00:31
blackburnpatch is ready, going to test it last time00:32
blackburnsonney2k: all the ML is filled by 'I have successfully installed shogun' :D00:33
@sonney2kat least :)00:34
@bettybooyeah00:34
@sonney2kso no excuses to not get it to work00:34
blackburnsonney2k: I could translate installation guide or etc to russian, should I?00:35
@sonney2kblackburn, but that is a lot of work - would be cool though00:36
* sonney2k wonders what hidden messages blackburn might include.00:36
blackburnwhat kind of?00:37
blackburnhttp://www.shogun-toolbox.org/doc/ but there is no much information00:38
blackburnI mean translating 'Installation Screenshots Tutorial Examples Implemented Methods Interfaces Frequently Asked Questions Authors License'00:38
blackburnand home for doc00:38
blackburnsonney2k: I could add a comment to my proposal with that offer :)00:40
@bettyboolol ;>00:40
@sonney2khttp://www.shogun-toolbox.org/doc_cn/python_examples.html00:42
@sonney2kit looks so ... just great00:42
@sonney2kblackburn, it would definitely be cool!00:42
@sonney2kI cannot proof-read it though :)00:43
blackburnsonney2k: If I'll go to GSoC I hope to stay within team, so I have no need to write some trash :)00:44
blackburnlike I sent today :D00:44
@sonney2kheh00:44
@sonney2kdon't worry...00:44
blackburnbtw, new patch is here00:45
blackburnsonney2k: is it okay to make some addition to my proposal?00:47
blackburnin comments I mean00:47
@sonney2kyes sure00:48
CIA-31shogun: Sergey Lisitsyn master * r9d96f57 / (4 files in 2 dirs): Introduced new kernel: WaveKernel - http://bit.ly/dThciv00:50
blackburnsonney2k: what's with another one? :)00:53
CIA-31shogun: Sergey Lisitsyn master * r33d7b29 / (2 files): Made HistogramIntersectionKernel generalized with introducing parameter beta - http://bit.ly/fsmaI300:56
@sonney2kblackburn, thanks for the patches :)00:56
blackburnah, sorry :)00:56
@bettyboorahaha ;>00:57
blackburnsonney2k: there is a small typo in wave kernel description00:57
blackburnK(x,x') = \frac{\theta}{\| x-y \|} \sin \frac{\| x-y \|}{\theta}00:57
blackburnmy fault00:57
blackburnbut sending commit with it could be a smallest commit ever seen :)00:57
@sonney2kblackburn, I suggest you start using github... fork shogun there and fix it then send a pull request ...00:58
@sonney2kor send a patch again00:58
blackburnsonney2k: I will send you last patch in a 5 minute, okay? and tomorrow will fork shogun, etc00:59
@sonney2kno rush00:59
@sonney2kthanks for your contributions!00:59
blackburnit is a cauchy kernel, very similar to wave00:59
blackburna bit copypaste01:00
blackburnsonney2k: I don't worth thanks :)01:01
@bettyboohihi ;D01:01
serialhexsonney2k: are you still awake??  (it's like 1am there)01:07
@sonney2kserialhex, I have to do a review...01:08
serialhexsonney2k: ahh... ok.  i was just wondering if you have the exponential or log kernels hiding somewhere not on the methods page.  otherwise i'm going to implement them (and possibly more)01:09
@sonney2kserialhex, the exponential / gaussian kernel - in fact kernel 3-5 are too similar to justify different names01:11
@sonney2kso yes they are there01:11
serialhexahh, ok01:11
@sonney2kserialhex, actually not 100% true01:11
@sonney2kthe exponential kernel would make sense ...01:12
serialhexok, can do... i'll do that and the bayesian  one too probably01:12
* serialhex gets to werk01:12
@sonney2kone could potentially modify the gaussian kernel to be 'exponential'01:13
blackburnsonney2k: I'll send a last patch using mail list in a two minutes, okay?01:14
serialhexok, i'll take a look at that01:14
@sonney2kblackburn, thanks - but no rush. I really have to do that review now.01:14
blackburnsonney2k: ah, sorry01:14
blackburnjust trying get things done and go sleep :)01:15
serialhexyeah, the exp looks REALLY easy, i'll get that one & probably a few more sonney2k01:15
@sonney2kblackburn, ok01:16
blackburnand at least have to fed my bear, drink vodka and go to KGB :D01:17
@sonney2klike all Russians do presumably ;-)01:18
@bettyboo;D01:18
@sonney2kwell done betty!01:18
@bettyboosonney2k: well I have done for matlab interface only01:18
serialhexshe's good!01:18
@sonney2kI hope knrrrd will tell me about her super secret algorithms01:18
brocollistarted sifting through apps yet sonney2k? ;)01:25
@sonney2kbrocolli, no doing a review01:25
brocollinice, journal?01:25
brocollior AAAI01:26
blackburnoh, it's working right. have to drink vodka now01:31
blackburnsonney2k: I answered you in ML with another one patch. it's the last :) won't disturb you no more01:31
@bettyboo;>01:31
blackburnsorry for being annoying01:32
@sonney2kbrocolli, ICML still01:33
brocolliNoice!01:33
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@sonney2kblackburn, next time please split the patch into two commits01:35
@sonney2kone fixing the typo and one introducing the new kernel01:35
blackburnsonney2k: sorry, it was so small :) I may do it now01:35
@bettybooyep01:35
@sonney2kblackburn, yes sure but this is just wrong with git (ask yoh about this  - he will lecture you :)01:36
blackburnsonney2k: okay :) will do it next time01:37
@bettyboofunny ;D01:37
CIA-31shogun: Sergey Lisitsyn master * r4fed492 / (5 files in 2 dirs): Introduced new kernel: CauchyKernel, corrected misprint at WaveKernel description - http://bit.ly/eUUGN701:37
blackburnsonney2k: thank you01:38
@sonney2kblackburn, there is one more thing - serialization support for your kernels - have a look at gaussian kernel: there is a m_paramters->add line ... you also need this for your new kernels to save parameters01:38
@sonney2kblackburn, this way you can pickle the kernel from python01:38
blackburnsonney2k: okay, I will do01:38
@sonney2kdon't do it now but at some point OK01:38
blackburni have 3.39 AM here, so will not do now :)01:39
@sonney2kwell thanks and have a good sleep then!01:40
blackburnI think not going sleep: have to wake up at 7-40 :))01:40
blackburnsonney2k: later I'll modify CKNN and will do that serialization support01:40
blackburnhope there will not take place a 'commit race' :)01:41
@bettybooHA ;>01:41
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* sonney2k has finished his review01:45
@sonney2kand hurray off to bed01:45
@bettyboonite01:45
blackburngood night, Sören01:46
blackburngood night, everyone :)01:46
@bettyboofunny :>01:46
blackburnbettyboo: you too01:47
@bettybooblackburn: Then there's Learning Kernel Classifiers by the great Ralf Herbrich, but it's too rigorous for some.01:47
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serialhexbrocolli: you awake?02:48
serialhexguess not...02:50
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serialhexbettyboo: hey, how are you?08:14
@bettybooserialhex: so it is hello, how are you?08:14
serialhexbettyboo: i am good... kind of tired though, yourself?08:14
@bettybooserialhex: that is, a basis vector is only associated with ONE example of the training data08:14
serialhexbettyboo: that is very true, but why?08:15
@bettybooserialhex: it is generated automatically ... build first08:16
@bettyboonothing08:16
serialhexnothing? really bettyboo08:16
@bettybooserialhex: Vapnik is pretty old-school research, the fundamentals of SVMs can be found even in his 1970's books08:16
serialhexi know that bettyboo, tell me something i dont know08:17
@bettybooserialhex: I don't know what that bot is telling all the time.. :)08:17
@bettybooserialhex, never mind ;>08:17
serialhexnow THAT i agree with :P08:17
@bettyboo;D serialhex08:17
serialhex:D bettyboo08:17
@bettybooserialhex: speedups for the special case where kernel is linear or a string kernel08:17
serialhexbettyboo: nice08:18
@bettybooserialhex: Don't forget nice people like Chris M. Bishop08:18
serialhexyeah, he's alright even though he works at microsoft08:19
serialhexdo you like microsoft bettyboo08:19
@bettybooserialhex: I don't worth thanks :)08:19
serialhexi dont work either bettyboo08:21
@bettybooserialhex: it works well in my machine now08:22
serialhexwhat do you do for money?? bettyboo??08:22
@bettybooserialhex: i think features can not handle this case.08:22
serialhexno, maybe not bettyboo08:22
@bettybooserialhex: i would imagine so... if you have 100 dimensions & not all of them are needed, then you'll have to sift through a bunch of 100 dimensional arrays all over the place... way slow!!08:22
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siddharthsonney2k, can GPL copyright header be embedded automatically?14:29
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@sonney2ksiddharth, hmmhh I always copy & paste it15:01
siddharthsonney2k, ok..Also I forked shogun today...so after some code changes I should commit and then pull request right?15:03
siddharthinstead of sending patch15:04
@sonney2ksiddharth, yes15:05
CIA-31shogun: asia master * r385ae97 / (2 files): Introduced new kernel: Multiquadric Kernel (+8 more commits...) - http://bit.ly/gwqxOK15:25
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blackburnhello there15:59
@bettybooblackburn, ho15:59
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ZiyuanHow to assign EKernelType,16:34
ZiyuanIf we implement new kernels independently.16:34
josipHello, I have a "structured" data set. In the sense that, I have several subjects and each subject has multiple patterns (actually mamography images). I want to do cross-validation, but teh split has to be done on patients, not on the data points. Is this possible in Shogun? I have this done with some scripts, but I'd love to get rid off thhem16:35
@bettyboocu16:35
josipnot images, but features extracted from candidate regions of the mamography images16:35
serialhexsonney2k: hey, i'm working on getting that patch fixed up... it's being a PITA though :P16:47
siddharthZiyuan, change in the Kernel.h file16:54
ZiyuanI know16:55
ZiyuanBut I mean, how to avoid collision16:55
Ziyuanor to organize reasonably16:56
siddharthZiyuan, do git show...this will allow you to see current patches applied...then accordingly make the changes17:01
ZiyuanOKOK...17:20
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ZiyuanHmm...I installed libatlas-dev and libatlas-base-dev but fail to get Atlas support.20:43
ZiyuanAnd atlas3-headers/atlas3-base-dev cannot be found.20:43
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yayo3hi20:48
ZiyuanI am a newbie of developing under linux so please don't mind my asking unwise questions...20:48
Ziyuanhi20:48
siddharthsonney2k, how to correct whitespace errors while applying patch?20:58
siddharthshould we ignore them?20:58
siddharthgit config core.whitespace=nowarn20:58
@sonney2ksiddharth, I prefer fixing them21:04
@sonney2kI use vim for editing so I search for ' $' and erase the spaces21:04
@sonney2kI guess there are scripts doing that though21:05
@sonney2kZiyuan, please force enable lapack in shogun configure (--enable-lapack IIRC)21:05
@sonney2kthen you should get some more meaningful error msg21:05
blackburn1sonney2k: if you have much time please take a look at pull requests, it seems to be ready21:06
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ZiyuanOK, thank you sonney21:10
ZiyuanMore: When I make the stuff in examples/documented/libshogun, I've got many "undefined reference" errors.21:11
@sonney2kZiyuan, that shouldn't happen21:18
@sonney2kis the include path / link path perhaps wrong21:18
CIA-31shogun: Justin Patera master * redb5c2c / src/libshogun/kernel/ExponentialKernel.cpp : Fixing serializattion stuff in ExponentialKernel (and learning git the hard way :P ) (+7 more commits...) - http://bit.ly/i1d3QK21:21
serialhexYAY!!!  i've been commited!! :P21:23
@bettyboo;> serialhex21:23
serialhexwe should celebrate bettyboo!!  what do you want??  vodka?  yager? beer??21:24
@bettybooserialhex: make doc21:24
serialhexi dont know how to make a doc bettyboo, tell me how to make one21:24
@bettybooserialhex: to show changes we have to do make install right?21:24
serialhexthere you go again... always talking about your ML stuff... i dont think you ever really listen to me bettyboo!21:25
@bettybooserialhex: is enjoying the Berlin sun - dont you think that is fair?21:25
serialhex:P  i'm enjoying the sun, just not in berlin21:26
ZiyuanI am checking21:26
blackburn(11:24:34 PM) bettyboo: serialhex: make doc21:27
@bettybooblackburn: I don't know what implies this way21:27
blackburnoh, it made my day :D21:27
blackburnvodka? beer? make doc!21:27
serialhex:P21:27
serialhexyeah... she's cool!21:27
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@sonney2kblackburn, I sent you a comment to your patch via github21:32
blackburnsonney2k: I see, will do a fix in a minute21:32
@sonney2kblackburn, I haven't used this so far - did you get an email reply21:33
blackburn"shogun-toolbox кому: мне", yeap21:33
blackburnI received an email from github21:34
@sonney2kvery good21:36
blackburnsonney2k: should getters and setters will be 'set_q_param' just like 'q_param'?21:36
@sonney2kblackburn, I would just name the member varialbe m_q21:36
@sonney2kand that's it21:36
blackburnokay21:36
blackburnset_q will stay set_q, right?21:36
@sonney2kso we know that this is from the class21:36
@sonney2kyes21:36
@sonney2kand you can still use q21:36
blackburnmay be do the same with k?21:37
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@sonney2kyes then21:37
blackburnsonney2k: done21:42
@sonney2kblackburn, one last one line patch21:46
blackburnokay21:46
@sonney2kk_ -> k :)21:46
@sonney2kthen I cannot find anything further :)21:46
@bettyboosonney2k, ;D21:46
blackburnthe greatest one21:46
blackburnwill be a milestone for shogun toolbox21:46
@sonney2kblackburn, thanks for all your work21:47
blackburnsonney2k: no problem, thank you :)21:48
@bettyboo;D21:48
blackburnsonney2k: and another fix in a minute. m_q(1.0) should be before train_labels21:52
@sonney2kok21:52
blackburn./classifier/KNN.h:191: warning: ‘shogun::CKNN::train_labels’ will be initialized after21:52
blackburn./classifier/KNN.h:179: warning:   ‘float64_t shogun::CKNN::m_q’21:52
blackburnclassifier/KNN.cpp:20: warning:   when initialized here21:52
blackburnif I understand it right21:52
dvevrehey all. i've a basic question.. is there any reason for not adding 'width' through m_parameters->add in DistanceKernel?21:54
@bettyboomoin dvevre21:54
blackburndvevre: I think it should be there21:55
blackburndvevre: I did it in WaveKernel and CauchyKernel which are very similar to DistanceKernel21:55
dvevreblackburn: yeah.21:55
dvevrei checked, but it hasn't been added that way21:55
dvevreso i was wondering if there was some particular reason why21:55
blackburnsonney2k: now no warnings, seems that it is ready21:56
dvevrebettyboo: hello! i had to wiki what 'moin' meant :)21:58
@bettyboodvevre: it would really make sense to do the octave / and older matlab binary formats too... for that look also at the source of octave (it's linked to at the gsoc page)21:58
dvevrebettyboo: right. i'll take a look right away21:59
@bettyboodvevre: if you have much time please take a look at pull requests, it seems to be ready21:59
@bettyboo*oink* ;>21:59
blackburnoh, my sentence!21:59
CIA-31shogun: Sergey Lisitsyn master * rde4b2cc / (2 files): Fixed some naming - http://bit.ly/fDO8lM22:01
CIA-31shogun: Sergey Lisitsyn master * r02dab1c / src/libshogun/classifier/KNN.cpp : Changed initialization order to avoid warnings. - http://bit.ly/fX553y22:01
CIA-31shogun: Sergey Lisitsyn master * ra9264fb / src/libshogun/classifier/KNN.cpp : Removed _ from k_. (Commit the Great) - http://bit.ly/hd87eK22:01
CIA-31shogun: Soeren Sonnenburg master * r6c3339d / (6 files in 2 dirs): Merge branch 'master' of https://github.com/SergeyLisitsyn/shogun into SergeyLisitsyn-master - http://bit.ly/gq7tbR22:01
blackburnoh no22:01
blackburn*thought that all 10 will be here*22:01
blackburnI really like Commit the Great22:02
@sonney2kblackburn, thanks again - yes CIA-31 is cool22:02
blackburnsonney2k: thank you for watching mistakes :)22:03
@sonney2kdvevre, it is a bug22:03
dvevresonney2k: should i modify it?22:04
@sonney2kdvevre, serialization is rather new so please send a patch22:04
@sonney2kvery welcome22:04
dvevresonney2k: sure :)22:04
@bettyboohe22:04
@sonney2kblackburn, I am overlooking many small mistakes - oh well thanks for being patient wit me22:04
blackburnsonney2k: it's better for both of us :)22:05
@bettyboo;>22:05
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* sonney2k loses track of all the patches22:32
@sonney2kI guess doing it all via github would drastically simplify things for me22:32
blackburnsonney2k: you could say it in ml :)22:33
@bettyboo;>22:33
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@sonney2kblackburn, how do you do a pull request?22:33
blackburnhm.. how detailly should I describe it?22:33
blackburnah! http://help.github.com/fork-a-repo/22:34
blackburnhere it is22:34
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blackburnsonney2k: it is sufficient to fork repo and configure remote for upstream22:36
@sonney2kblackburn, and then how do you do a pull request such that I can see it?22:36
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blackburnsonney2k: it is on personal fork's page, there is a 'pull request' button22:37
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blackburnas I understand, there is no way to do it via git, so only via github.com22:37
blackburnsonney2k: you can find about it here: http://help.github.com/pull-requests/22:38
@sonney2kblackburn, ahh great - I will write sth. to the ml22:39
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blackburnsonney2k: mention there about 'git fetch upstream' and 'git merge upstream'22:41
blackburnsonney2k: with it there won't be a problem with ~20 patches in pull request :)22:42
@bettyboo;>22:42
blackburnlike it was22:42
blackburnsonney2k: seems that to demarcate different pulls we should use branches22:48
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blackburni.e. one pull request for some kernel and another for some classifier22:49
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@sonney2kblackburn, yes - but most people just do one change - so it is ok22:56
blackburnsonney2k: I'll answer you in ML about 'git remote add upstream'23:03
blackburnsonney2k: answered in ML with some addition23:11
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@sonney2kthanks23:25
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CIA-31shogun: Soeren Sonnenburg master * r15b28f1 / (42 files in 7 dirs):23:43
CIA-31shogun: get_name needs to return the class name (withough C prefix)23:43
CIA-31shogun: This patch goes through all *.h files changing get_name to return the23:43
CIA-31shogun: class name of the of the class withouth the C prefix. Since Array*.h23:43
CIA-31shogun: contained functions to set the array name, the array set_name and23:43
CIA-31shogun: get_name functions have been renamed to set_array_name / get_array_name23:43
CIA-31shogun: to fix the naming clash. - http://bit.ly/ikr2zl23:43
CIA-31shogun: Marcin Copik master * ra1b95d5 / src/libshogun/lib/File.cpp : Added implementation of functions for I/O of bool matrices and string lists - http://bit.ly/gRWLxu23:43
CIA-31shogun: Soeren Sonnenburg master * r461e05d / (2 files): Merge branch 'master' of https://github.com/frx/shogun - http://bit.ly/dUD1es23:45
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yayo3so sonney2k, you want us to resend the already sent patches through github?23:54
@sonney2kyayo3, errm not the ones that are already applied of course - only future patches / the ones that have not yet been applied23:55
yayo3ok23:56
--- Log closed Sun Apr 10 00:00:36 2011

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