IRC logs of #shogun for Saturday, 2011-04-16

--- Log opened Sat Apr 16 00:00:36 2011
alesis-novik4 pints later, I return02:33
serialhexniiice, how are things alesis-novik?02:38
* serialhex thinks of pippin from LotR every time he hears 'pint'02:39
alesis-novikGood so far, going to fix some other things in the pull request02:39
serialhexcool cool02:39
* serialhex has been lazy these past few days02:40
alesis-novikThere... Now I can think about starting working on 1 dimensional EM02:43
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alesis-novikRight, new plan: go to sleep relatively early today and get up relatively early tomorrow to do work04:07
serialhex:D that'll work alesis-novik!04:08
@bettyboo;>04:08
serialhex'nite!04:09
alesis-novikgoodnight :)04:12
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siddharthanyone here?07:32
@sonney2kdammed, took the whole night07:57
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@mlsecsonney2k: No sleep?09:48
@mlsecHmm09:49
@mlsecbettyboo: did you talk to sonney2k?09:49
@bettyboomlsec: when you told me to integrate shogun with the parser yesterday, what things about shogun did you have in mind?09:49
blackburnbettyboo: make doc09:49
@bettybooblackburn: qdrgsm@blackburn-R519:~/Documents/GSoC-SHOGUN/shogun_myfork/shogun/examples/undocumented/python_modular$ python kernel_exponential_modular.py09:50
blackburn:D09:50
@mlsecThat's your code. Nice catch09:50
blackburnI see :)09:51
blackburnbettyboo: make doc09:51
@bettybooblackburn: (only the .h file needs to be documented)09:51
@mlsecSurprisingly good.09:52
@mlsecBreakfast time!!09:53
blackburnhm, that's a good idea09:55
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@sonney2kblackburn, ok...11:27
blackburnsonney2k: ok abouuut?11:27
@sonney2kabout perf measures :)11:30
CIA-110shogun: Alesis Novik master * rc702400 / src/libshogun/distributions/Gaussian.cpp : Fixed - http://bit.ly/eWZZjO11:32
CIA-110shogun: Soeren Sonnenburg master * r6e6999c / (5 files in 3 dirs): Merge branch 'master' of https://github.com/alesis/shogun - http://bit.ly/gMtBn011:32
@sonney2kalesis-novik, I applied you patches - next time please use more meaningful commit msg12:05
@sonney2kI mean 'fixed' doesn't really tell anyone (besides me *today*) what you did :)12:05
blackburnCommit: 31434 files, description "Fixed some performance issues"   :D12:08
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blackburnrghhh12:19
Tanmoy@sonney2k do we have an implementation of Bessel function ?12:25
siddharthnope12:33
Tanmoymaybe need to implement it from GSL ?12:35
Tanmoyeven LAPACK does not have it12:35
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yayo3hey13:23
yayo3how does disabling of features that require LAPACK when there's none work?13:33
yayo3I can't seem to find it13:36
yayo3but it needs to be done for the Gaussian distribution, because current master won't compile on Mac OS at all (there's no lapack and stuff)13:38
yayo3but there's aparently BLAS and LAPACK integrated in Mac OS, so I'm diving into configure once more :)13:47
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@sonney2kyayo3, where does it fail - in Gaussian.cpp ?14:43
@sonney2kif so ... git pull14:44
CIA-110shogun: Soeren Sonnenburg master * rebf4cf6 / (2 files): Add HAVE_LAPACK checks to Gaussian distribution - http://bit.ly/ii0qrA14:44
yayo3yep. thanks.14:46
* sonney2k takes a nap14:48
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dvevresonney2k: i've made a StreamingFeatures class implementing the get_next_feature_vector method.. haven't modified the I/O back-end much,15:21
dvevrecan i mail it to you for opinions on the implementation?15:22
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dvevresonney2k: mail sent15:32
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yayo3sonney2k: there's still a problem with tha guassian stuff. it uses function that's only in ATLAS16:00
yayo3clapack_dpotri to be exact. there's clapack_dpotrf reimplemented in shogun but not this one16:01
yayo3so it won't compile on computers without ATLAS. While Mac OS have LAPACK integrated and I'm working on using it, there's no ATLAS here16:03
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alesis-novikMorning people and bots16:08
yayo3hi16:08
alesis-novikyayo3, I'll look into that16:08
yayo3alesis that guassian stuff is your, right?16:08
yayo3oh, you saw. good :)16:08
yayo3anyway good morning :)16:08
siddharthhi all16:21
siddharthIs there any way to access the elements of an 'i'th index feature vector?16:22
alesis-novikwhat class for features are you using siddharth ?16:23
siddharthCdotfeatures16:23
siddharthi was trying get_feature_vector()...but getting segmentation fault :|16:24
alesis-novikthen you might be trying to get a feature that isn't there16:24
siddharthnope features are there16:25
siddharthw8 let me see once again if I am making some mistake16:27
siddharthalesis-novik, I am doing this16:34
siddharthw_dim=features->get_dim_feature_space();16:34
siddharth                int32_t num_vec=features->get_num_vectors();16:34
siddharth                for (int32_t i=0; i<num_vec; i++)16:34
siddharth                {16:34
siddharth                        features->get_feature_vector(dst,alen,i);16:34
siddharthoutput of num_vec == 316:35
siddharthso the features exist16:35
alesis-novikwhat are dst and alen?16:35
siddharthfloat64_t** dst; to store the feature vector16:36
siddharthcopy16:36
siddharthalen==length of the feature vector16:37
alesis-novikalen is int32_t* ?16:37
siddharthyes16:37
siddharthhttp://www.shogun-toolbox.org/doc/classshogun_1_1CDotFeatures.html#a6c74837680cf15810c9b989a6908de0916:38
alesis-novikand were does it break?16:38
alesis-novikdoes the code actually break at get_feature_vector or somewhere further?16:38
siddharthfurther I am doing some more calculations16:39
siddharthbut i can break it16:39
alesis-novikcan you post the code in pastebin or somewhere?16:39
siddharthok w816:39
siddharthalesis-novik, maybe u can try urself...just add 'features->get_feature_vector()' in SVMSGD.cpp in classifier/svm in the train function16:46
siddharthif u have time16:47
alesis-novikwait, did you post the code anywhere?16:49
siddharthits a lengthy code...I am trying myself in this code SVMSGD.cpp16:49
alesis-novikbecause I'm using get_feature_vector() in my code, but it doesn't break, so just randomly adding it in other places won't really achieve anything16:50
siddharthyes but you will get segmentation fault while running this classifier after adding these lines16:51
siddharthyou can run the code from here... examples/documented/libshogun/classifier_minimal_svm.cpp .In this just change the classifier name from LibSVM to SVMSGD16:53
siddharthor you can run from python interface16:58
alesis-noviksiddharth, can you show me what you do with dst and alen after you get them?17:00
siddharthalesis-novik, I am not using them as of now...17:00
alesis-novikso just adding get_feature_vector produces seg-faults?17:01
siddharthyeah17:01
siddharthalesis-novik,you can run the code from static/modular interface17:04
siddharthalesis-novik, I will be back in 10 min...have to go17:05
* siddharth brb17:05
yayo3alesis-novik: what does clapack_dpotri() do?17:07
alesis-novikcomputes the inverse of a matrix using stuff from dpotrf17:08
alesis-novikif done a small patch that might help17:09
siddharthalesis-novik, any findings?17:27
alesis-noviksiddharth, as far as I can tell without actually testing it, it shouldn't cause any problems...17:27
siddharthnot able to find the error17:28
siddharthalesis-novik, I have posted the code..u can have a look at that17:47
siddharthhttp://codepad.org/BkqLEVvk17:47
siddharthi have also marked where I have done the changes17:47
siddharth/CHANGES------------------------17:47
alesis-novikWill take a look now siddharth17:52
alesis-novikah18:08
alesis-novikright18:08
alesis-novikYou should probably change18:08
alesis-novikfloat64_t** dst;18:08
alesis-novikint32_t* alen;18:08
alesis-novikfeatures->get_feature_vector(dst,alen,i);18:08
alesis-novikto18:09
alesis-novik float64_t* dst;18:09
alesis-novikint32_t alen;18:09
alesis-novikfeatures->get_feature_vector(&dst,&alen,i);18:09
siddharthalesis-novik, hmm let me try18:09
alesis-novikbecause get_feature_vector does *len = dim, which if no memory is allocated, gets you your faults18:10
siddharthohh did not see the function18:11
siddharthya solved18:11
siddharththanks :)18:11
alesis-noviksonney2k, I've made a new pull request. I think I might have done some stuff you already added, not too sure.18:15
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alesis-novikThere, fixed some of the merging issues, should be fine now. Main points of interest are changes in lapack.h/.cpp and PCACut.cpp18:28
yayo3aaaaaaaaaaaaand we have BLAS and LAPACK Mac OS support :)18:30
* yayo3 's gotta run18:31
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blackburnsonney2k: here?20:50
CIA-110shogun: Jakub Jirku master * r0911622 / (src/configure src/libshogun/lib/lapack.h): Mac OS BLAS and LAPACK support - http://bit.ly/eH6SsL20:50
CIA-110shogun: Jakub Jirku master * rc8026b1 / src/configure : Configure fix - http://bit.ly/egj0f120:51
@sonney2kblackburn, yes20:52
blackburnsonney2k: have time for discuss some issues with 'evaluation'?20:52
@sonney2klets try20:59
blackburnso, we could have some 'Evaluation.h' with virtual evaluate(), right?21:00
CIA-110shogun: Soeren Sonnenburg master * r9988d90 / (2 files): rename member variables to start with m_ to fix warnings - http://bit.ly/eFEH5p21:00
blackburnCEvaluation, sorry21:00
blackburnand there could be things like in mldata-utils: CRegressionEvaluate, CClassificationEvaluate, inherited from CEvaluate21:01
blackburnevaluate() there would be something like init: it computes some things and then one can compute ROC or mean absolute error21:02
blackburnsonney2k: am I going in right direction?21:04
@sonney2ksonney2k, or just CAccuracy derived from CEvaluation21:05
@sonney2kblackburn, there a two ways: Either we have one class CEvaluation which gets two label objects as input21:06
@sonney2kand then all the different evaluation functions21:06
blackburnsonney2k: why CAccuracy? both for regression and classification?21:06
@sonney2kor various evaluation classes21:06
@sonney2kblackburn, accuracy is only defined for Classification.21:07
@sonney2kMSE would be for regression...21:07
blackburnsonney2k: ah, I mean it, sorry for misunderstanding terms :)21:07
blackburnsonney2k: so, classes for evaluating these types will be specified21:10
blackburnsonney2k: and I could implement for clustering too21:10
serialhexbettyboos next project: http://xkcd.com/329/21:16
@bettybooserialhex: I guess you need to assume that the number of features is known and that you have to read that many bytes or so to get the next vector21:16
@sonney2kyes21:16
@sonney2kblackburn, I don't know what do you prefer a evaluation class and derived classes or jsut one class21:17
blackburnsonney2k: derived classes seems to be better21:17
blackburnsonney2k: what way do you prefer?21:18
@sonney2kblackburn, then one has to assume that each method returns a label object as outputs21:18
@sonney2kand then one could compare the true label object with the predicted one21:18
@sonney2ksounds good to me21:18
blackburnsonney2k: each method of ..?21:19
@sonney2kin case labels become to complex we have to have more than the current label object - but an interface21:19
@sonney2kmethod == SVM etc21:19
blackburneh, but thought evaluation works only with labels21:20
blackburnfor example, when classifying, we just do some e.evalute(labels,right_labels) and after that can do e.ROC() or etc21:21
@sonney2kserialhex, heh :)21:21
@sonney2kblackburn, yes21:22
@sonney2kbut the predicted labels come from a method right21:22
blackburnlabels = SVM.classify() and then e.evaluate(labels, right_labels)?21:23
@sonney2kexactly21:23
blackburnwhat you mean saying labels become to complex?21:23
@sonney2kblackburn, e.g. a graph, or some other thing21:25
blackburndon't sure I understand what is complex labels..21:25
blackburnah21:25
blackburnsonney2k: how could it be?21:25
@sonney2kblackburn, structured output prediction... predict a graph21:25
blackburnso in that case there will not any 'evaluate()' in CEvaluation21:25
blackburnall things will be overloaded21:26
blackburnin derived classes21:26
@sonney2kblackburn, well then we simply need a StructuredLabel object derived from CLables21:26
blackburnsonney2k: well, but what should we do for clustering?21:27
@sonney2kehh no idea yet21:28
blackburnwe should use objects as labels21:28
blackburnand may be we will even need CDistance21:29
@sonney2kactually a clustering is just some integer class assignment21:29
@sonney2kso some integer vector is sufficient21:29
@sonney2kno need to do anything then21:29
blackburnhm. okay, I'm just about some internal cluster distances and etc21:30
@sonney2kblackburn, but doesn't matter right? I mean that is in the perfmeasure then21:30
blackburnah, okay, will implement it in this way ;)21:31
blackburnsonney2k: I will make a pull request with draft design (CEvaluation - CClassifyEvaluation, CRegressionEvaluation, ...) - for discuss methods to be implemented, okay?21:32
@sonney2kblackburn, I would only do CEvaluation and derive directly from there21:33
@sonney2ke.g. CEvalution, CAccuracy, CBalancedError, CMeanSquaredError etc...21:33
blackburnis CEvaluation base class?21:34
@sonney2kyes - the interface21:34
blackburnwhat is BalancedError?21:34
@sonney2kBAL21:35
blackburnanyway now I will just port things available in mldata-utils21:36
blackburnsorry, but I don't know what it is :(21:36
@sonney2kblackburn, ahh then look in mldata-utils - I documented all functions in there21:36
@sonney2kand BAL is there too21:36
blackburnsonney2k: ok, thank you21:36
@sonney2kok ... time for dinner21:37
blackburnenjoy your meal21:37
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Tanmoyok when i am trying to push it says Oops! The shogun-toolbox:master branch is already up-to-date with Tankiit:master — maybe you want to try something else?21:52
blackburndid your set up your git properly?21:55
blackburnbtw what are you doing exactly, pushing your commits to your fork?21:57
Tanmoyi think  so the setup is fine21:57
Tanmoyyup21:57
alesis-novikEvening folks21:57
Tanmoyevening21:57
blackburnbut for some reason it says sth about 'shogun-toolbox', looks like you try to commit in main repo..21:58
blackburnalesis-novik: evening21:58
alesis-noviksonney2k, around?22:01
blackburnalesis-novik: (11:37:12 PM) sonney2k: ok ... time for dinner22:01
alesis-novikok then22:02
Tanmoyhmm well i forked it made changes22:02
Tanmoycommitted22:02
Tanmoyand then tried pushing22:02
Tanmoyi think i did what is reqd22:02
blackburndid you clone your fork?22:02
Tanmoyyup22:03
blackburnthen don't know :)22:03
Tanmoythis is what push is doing22:03
Tanmoyssh: connect to host hithub.com port 22: Connection timed out22:03
blackburnhithub?22:03
Tanmoyyeah22:04
Tanmoy:22:04
Tanmoyok got it now22:04
blackburnwhat is hithub :D22:04
Tanmoytypo22:05
Tanmoyok done22:07
Tanmoythanks blackburn22:07
blackburnnp, Tanmoy22:07
Tanmoy@blackburn hows the graph library coming up22:10
blackburnTanmoy: now working on CEvaluation class and it's derivates22:10
blackburnwill you need it soon?22:10
Tanmoynope had some ideas22:11
Tanmoyr u working on it22:11
Tanmoyor u planing to merge some library22:11
blackburnnope, think will implement some 'compact' graph class22:11
blackburnanyway we don't need serious graph library22:12
Tanmoyhmm modules of finding_neigbors,BFS, DFS shld do22:13
blackburnit seems to be a minimal graph 'library'22:13
Tanmoyok gr822:15
blackburnthink I will work on it during next week22:16
alesis-novikRight, while I'm waiting for comments on my pull request, I might as well start working on the next thing22:18
blackburnalesis-novik: just not commit next thing before pull will be closed :)22:18
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blackburnseems many candidates are flunked by themselves :)22:20
@bettyboo;D22:20
blackburnonly 5-6-7 ones are active now22:21
alesis-novikThat's why I decided to only apply to 1 project, so I can focus on it instead of spreading out and really not doing anything at all22:22
serialhexwell if there's only 5 the i guess they 'win' by default :D22:22
blackburnalesis-novik: me too22:23
blackburnserialhex: that will be fine :)22:23
serialhexi agree blackburn!!22:24
serialhexi take it tanmoy got his github troubles figured out?22:24
serialhexFFS!!! i hate stinging bugs!!!22:24
blackburnserialhex: yeap, he fixed his 'hithub'22:24
serialhex:P cool, i was having a bunch of troubles with it before, but now i've got the hang of it... i'm glad it's fixed22:25
serialhex~43,608,608.5494047km until spring classes end :D22:26
blackburnwas ist das?22:27
serialhex~5,460,804.968458357km until shogun candidates are announced :D22:28
serialhexhow far we have to travel before these events happen :P22:28
blackburnwith 'c' speed? :)22:28
alesis-novikI wonder how many applicants have submitted anything so far...22:28
serialhexthough i dont know if in russia you use a "," or "." for thousands, millions & such...22:28
blackburnalesis-novik: submitted what?22:29
alesis-novika patch or any code22:29
blackburnalesis-novik: not so many, only 1/3 of all candidates22:29
serialhexwe can count: https://github.com/shogun-toolbox/shogun/commits/master22:29
blackburnserialhex: we don't use for sth like 1,000 but use ',' for 10,022:30
blackburnhttps://github.com/shogun-toolbox/shogun/contributors22:30
serialhexi think less... sonney2k said there were 60 applicants and i'm not sure there were 20 ppl22:30
serialhexahh, even better :D22:30
blackburnI really laugh always when see 'invalid-email-address (You didn't set your git config correctly)'22:30
blackburnthe most funny contributor22:31
serialhexwho is that??? :P22:31
blackburnsome spanish guy, who fucked up his git22:31
serialhexniiice22:32
alesis-novik:)22:32
@bettyboo;D22:32
alesis-novikEven if there were 60 applicants, I assume they won't really consider people who haven't submitted anything...22:32
serialhexanyway blackburn, i made a calculator that figure out how far you travel in a given amount of time.22:32
serialhexprobably not al22:32
serialhexit's here: https://github.com/serialhex/fun-stuff/blob/master/spaceship_earth.rb22:33
blackburnalesis-novik: at least some applicant contributors don't do anything now22:33
blackburnalesis-novik: more than half of them implement some kernel at first :D22:34
blackburnimplemented*22:34
serialhexit takes the time in the future and optionally your latitue and the time you want "now" to be based of of, and calculates how far you travel (through space)22:34
serialhexyeah, and theres only like 4 of us who communicate on the channel...22:35
alesis-novikserialhex, I really like google calculator, it can compute complex things like (number of horns on a unicorn/the answer to life, the universe and everything)22:35
serialhexlol i know, it rocks!22:35
blackburnserialhex: may be a little more, 5-622:35
blackburnlet's count :D22:35
serialhexsomething around there :P22:35
@bettyboohihi?22:35
serialhexhihi bettyboo!!22:36
@bettybooserialhex: >>> x=Labels()22:36
blackburnserialhex, alesis-novik, I, heiko, yayo3, siddharth, dvevre22:36
blackburnseems to be 722:36
@sonney2kalesis-novik, I still don't get your follow up pull requests btw22:42
@sonney2kalesis-novik, did you rebase your commit against master?22:42
serialhexyeah, alesis-novik probably made the same mistake i did...22:44
@sonney2kalesis-novik, would you mind putting the gaussian pdf formula in gaussian.h?22:45
alesis-noviksonney2k, I did, under compute PDF function22:45
serialhexi was using the fork queue on github to keep my fork up to date, which added all those other commits.22:45
@sonney2kalesis-novik, I would prefer if you put it in the class description22:46
alesis-noviksonney2k, should I remove it from computePDF or keep it in both places?22:47
@sonney2kremove from computepdf (it is enough to state that it computes the gaussian pdf as described in class descr)22:47
serialhexalesis-novik: if that is what you did you can rebase your fork on your computer & when it asks you to change stuff simply --skip a bunch of times (assuming that it's up-to-date on your computer) and that should fix the problem22:47
@sonney2kalesis-novik, don't have time to look at your other patch in detail now - looks good but I have to have a closer look.22:48
@sonney2kthanks!22:48
blackburnsonney2k: get_accuracy() or accuracy()?22:49
@sonney2kblackburn, err multiple classes or one?22:49
blackburnsonney2k: binary classification22:49
@sonney2kc++ classes that is22:50
blackburna.22:50
blackburnCAccuracy :)22:50
blackburnah!22:50
blackburnyou mean the way I implement it?22:51
blackburnCEvaluation and derivates: CAccuracy, ...22:51
alesis-noviksonney2k, I added the formula to the Class description as well22:51
blackburnsonney2k: so how better, get_accuracy() or accuracy(), get_BAL() or BAL()?22:52
CIA-110shogun: Soeren Sonnenburg master * r1ee5185 / (4 files in 2 dirs): Merge branch 'master' of https://github.com/kisa12012/shogun - http://bit.ly/eHg5Qw22:52
@sonney2kblackburn, I thought you are doing several classes. And then only modify the evaluate function?22:54
blackburnsonney2k: we don't decided how 'several' it could be..22:54
blackburnsonney2k: should it be a class for BAL, a class for error, etc?22:55
blackburnsonney2k: just say how often do you use multiple evaluations same time22:56
blackburni.e. if multiple of them often get used same time - it is better to do one 'big' class for classify22:57
blackburnoh, I see now how I raveled: I tried to implement BAL in CAccuracy :D22:58
@sonney2kblackburn, I think one only ever uses one.22:58
@sonney2kheh22:59
@sonney2kI am too tired now22:59
@sonney2ksorry22:59
@sonney2kcu tomorrow22:59
blackburnsonney2k: thank you, you helped me ;)22:59
blackburnsee you22:59
alesis-noviksee you22:59
--- Log closed Sun Apr 17 00:00:36 2011

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