IRC logs of #shogun for Monday, 2013-06-03

--- Log opened Mon Jun 03 00:00:29 2013
van51sonney2k: I made a PR about the CCombinedDotFeatures00:01
van51sonney2k: review it when you have time and let me know if we should run an example again00:02
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sonne|workhey foulwall!09:10
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gsomixgood morning!09:23
gsomixsonne|work: "Our Work Is Never Over"? :)09:27
sonne|workgsomix: what do you mean?09:27
gsomixsonne|work: it's just question "are you working?" in sophisticated form. text from Daft Punk composition. nevermind.09:31
sonne|workgsomix: yes indeed I am at work and even working ;)09:40
sonne|workgsomix: btw your PR is not there yet right?09:40
sonne|workgsomix: I was thinking that maybe we can speed up things a bit more even but lets get the initial version done first09:41
gsomixsonne|work: there is. I have updated it at night. https://github.com/shogun-toolbox/shogun/pull/113009:42
sonne|workgsomix: ohh please write a test for that09:44
sonne|workbtw I didn't realize that you submitted the PR...09:44
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gsomixsonne|work: ok. this is unreadable again? :(09:45
gsomix*is this09:48
sonne|workgsomix: no no but we need a test09:49
sonne|workgsomix: for both the circular buffer and the line reader09:49
gsomixsonne|work: ok. which data set I shoudl use for testing? Human.dat is just bzipped.09:52
sonne|workgsomix: just read the source code of the test with a very small buffer09:52
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@wikingvgorbati: ping10:52
@wikingvgorbati: the problem with the rng does still exists i guess10:53
@wikingright?10:53
sonne|workwiking: what?10:55
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vgorbatiwiking: I thought so10:55
@wikingsonne|work: there was some error with rng generation for one module10:55
@wikingvgorbati: told me so10:55
@wikingi mean across different OSes10:56
vgorbatiwiking: yes I did. but sonney|work convinced me, that it is not rng problem, since unit tests for rng on my machine were ok10:56
vgorbatiwiking: the output for one integration test was definitely different on different OSes, so I thought it was because of a rng. But it looks like the problem is in some other stuff10:58
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@wikingvgorbati: hehehe that could be for a lot of other reasons... but then again it's a good guess to start with PRNG10:58
@wikingthe problem is that PRNG is implemented within shogun now10:59
@wikingso it really should not10:59
@wikingdiffer amongs different os/archs10:59
@wikinggsomix: daft punk \o/11:00
vgorbatiwiking: yes, that was the obvious reason to start with. The test is for dimension reduction method in tapkee, that involves random number generation, but it also involves other stuff, so some investigation is needed11:00
@wikingvgorbati: lisityn will take care of it i hope :)11:01
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sonne|workwiking: speaking of which there he is11:25
sonne|worklisitsyn: any news on the test bugfix (vgorbatis code)11:26
sonne|workvgorbati: btw just do neural networks then - but make sure you check out torch{>=5} and lush and theano to see how others do it11:27
sonne|workvgorbati: maybe you can even borrow some code :)11:27
vgorbatisonne|work: yes, sure.11:29
@lisitsynsonne|work: argh no news sorry11:32
sonne|worklisitsyn: btw how are your teeth?11:32
@lisitsynsonne|work: hmm quite ok why?11:33
@lisitsynsonne|work: ahh you mean these month-long dentist visits?11:33
sonne|workyes your chill out sessions11:33
@lisitsynI should continue actually11:34
@lisitsyn:D11:34
@lisitsynsonne|work: I accidentally got to pass some exams11:34
@lisitsynthat's why I am losing this test thing11:34
sonne|worklisitsyn: ohh nice I hope it was worth being lazy >:->11:35
@lisitsynsonne|work: ohh I should kick you too then! :)11:36
@lisitsynsonne|work: what's with welcome mail for workshop?11:36
@lisitsynyou told me you will fix it11:36
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sonne|workohh kick ass time11:37
gsomixsonne|work: will be nice photo/video from workshop?11:39
@lisitsyngerman video you know11:40
gsomixlisitsyn: ;)11:40
gsomixthis will be enough11:41
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@lisitsynsonne|work: I am thinking of some cloud showcase for the workshop11:42
@lisitsynwe should discuss contents of our talks end of this month I think11:43
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@lisitsyniglesiasg: how is it going?11:43
@iglesiasglisitsyn: hi! all fine, what about you?11:44
@lisitsyniglesiasg: fine too - is your stuff ready?11:47
sonne|workstuff == thesis?11:48
@lisitsynyes sonne|work11:49
@iglesiasglisitsyn: yeah! waiting for my supervisor to give feedback11:49
@iglesiasglisitsyn: want to give a glance to it?11:50
@lisitsyniglesiasg: yes would be happy to!11:50
@iglesiasgok, give me a second11:50
@lisitsyniglesiasg: btw did you prepare something on your berlin trip?11:50
@lisitsyn1.5 months left!11:51
@iglesiasglisitsyn: I am on it11:51
@iglesiasglisitsyn: https://dl.dropboxusercontent.com/u/11020840/pfc.pdf11:51
@iglesiasgnormally these projects are rather long in here...11:52
@iglesiasgfor me that's way too many pages but it is actually short compared to some people present around here11:52
@lisitsyniglesiasg: your acknowledgements is empty! supervisor would be unhappy ;)11:52
@lisitsynel aprendizaje estructurado!11:53
@iglesiasghaha11:53
@lisitsyniglesiasg: I like the layout pretty much11:53
@iglesiasglisitsyn: thanks!11:53
@iglesiasgI cpied it from Patrick's thesis :P11:53
@lisitsyniglesiasg: is it standard or yours?11:53
@lisitsynahh11:53
@lisitsyniglesiasg: are you free to play around with your layout?11:54
@iglesiasghe had a git repo with a chapter from his thesis11:54
@iglesiasgto some extent11:54
@iglesiasgbasically cover is fixed11:54
@lisitsynI would be punished for such layout here11:55
@lisitsyn:D11:55
@iglesiasgwhy?11:55
@lisitsynwell they won't let me in11:55
@iglesiasgI think it looks nice11:55
@lisitsynyes11:55
@lisitsynbut they don't want nice looking11:55
@lisitsynthey want GOST :)11:55
@lisitsynstandard that is11:55
@iglesiasglisitsyn: have you checked some figures?11:55
@iglesiasgtikz all the way!11:55
@lisitsyntikz? really?11:55
@iglesiasgand some others with shogun11:56
@lisitsyntikz is such a pain11:56
@iglesiasgsee page 2011:56
@iglesiasgsimple stuff but it looks nice I think11:56
@lisitsynyeah11:57
@lisitsynit just takes too much time for me11:57
@iglesiasgand page 45 with Viterbi decoding11:57
@lisitsynto produce something reasonable11:57
@iglesiasgPatrick has some really fancy stuff with tikz in his thesis11:58
@lisitsyniglesiasg: you may also put our paper here11:59
@lisitsynat least we can put it to arxiv11:59
@iglesiasglisitsyn: can I put a reference to sth not published yet??11:59
@iglesiasgok12:00
@lisitsynyeah with some note12:00
@iglesiasgit sounds nice :)12:00
@lisitsynI can submit it to arxiv right away12:00
@lisitsynsonne|work: am I right it is ok to submit a paper considered by jmlr to arxiv?12:00
sonne|worklisitsyn: not sure but I think so12:01
@lisitsyn"Authors may post their submitted manuscripts to open e-print archives, such as arXiv."12:03
@iglesiasglisitsyn: I can take care of it if you wish12:06
lambdaywhile checking switch over all ptypes, is it okay to keep those null (like SGObject) for features and stuffs?12:13
lambdaysince we'll only need complex64_t for matrix and vector12:13
lambdayand a few math functions...12:13
@lisitsyniglesiasg: how much time do you have to change it a bit?12:13
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@lisitsyniglesiasg: no I mean it could take a bit of time12:14
@lisitsynto publish it at arxiv12:14
@iglesiasglisitsyn: aham I see12:14
@lisitsynbut yeah you are free to submit it too12:14
@iglesiasglisitsyn: I rather take care of cleaning all my branch first and fix a couple of things so I can merge my PR first12:15
@lisitsynI hereby grant you such permission ;)12:15
@iglesiasghaha ok12:15
@lisitsynI think any of us is granted with such permission actually12:15
@lisitsynso if you want submit it right away12:15
@iglesiasglisitsyn: but do we have to change some stuff like layout or so?12:15
@lisitsyniglesiasg: yes I think so12:29
@lisitsynsome arxiv speciifc stuff12:29
@iglesiasgI see12:34
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lambdayHeikoS: hi13:30
@HeikoSlambday: hi!13:30
@HeikoShow is it going?13:30
lambdayHeikoS: how are you?13:30
@HeikoSI am tired from the weekend ;)13:30
@HeikoShow are you?13:30
lambdayI'm good... :)13:31
@HeikoShow are the complex things going?13:31
lambdayfor switch over all ptypes, I've kept it NULL just like SGObject in the class_list.cpp.py... because we don't need it for the features and stuff13:32
lambdaymatrix, vector, sparse matrix, sparse vector - done13:32
lambdaymath - done13:32
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@HeikoSlambday:  nice!13:32
lambdayparameter - added13:32
lambdayserialization - done13:33
lambdaymodular typemap - left :(13:33
@HeikoSgot a meeting now, be back in a bit13:33
lambdayHeikoS: okay.. see you :)13:33
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vgorbatiHeikoS: hello, a few weeks ago you gave a link to the book about bayesian approach and machine learning to one guy. I have lost the link accidentally, could you please paste it one more time?14:04
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sonne|worklambday: sounds very good!14:05
lambdaysonne|work: I added few useless stuffs too... will remove it14:09
lambdaysonne|work: will just be back after having some food.. didn't have breakfast, didn't have lunch today :(14:09
sonne|workerrm well get some!14:09
lambdaybrb14:10
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foulwallping sonney2k, sonne|work15:08
@HeikoSlambday, vgorbati back15:19
@HeikoSvgorbati: did you mean the GP for machine learning book?15:19
@HeikoSor the david  barber one?15:20
vgorbatiHeikoS: no, I remember it was bayesian (at least at the beginning of the book)15:20
@HeikoSBayesian Reasoning and Machine Learning?15:20
vgorbatiHeikoS: could you please give a link, I'll check then)15:20
@HeikoSgoogle for this title and append "David Barber"15:20
vgorbatiHeikoS: ok, thanks15:20
@HeikoSis it the one?15:20
vgorbatiHeikoS: yes, thanks a lot, it is really a good one15:21
@HeikoSyep its quite nice15:21
@HeikoSthough sometimes a bit complicated15:22
@lisitsynHeikoS: complicated for you? I should not get to that book ever15:28
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@HeikoSlisitsyn: I prefer simple things!15:48
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lambdayHeikoS: sorry I was away15:54
@HeikoSvotjakovr: nice with your blog!15:54
votjakovrHeikoS: Hi, thanks :)15:56
@HeikoSvotjakovr: did you manage to do all the tax-form stuff?16:00
@lisitsynwhat tax-form :D16:00
@HeikoSlisitsyn: gsoc money16:01
votjakovrHeikoS: yep, i sent it16:01
@HeikoSvotjakovr: nice, how is the state on the re-structuring?16:01
@lisitsynahhh that thing16:01
@lisitsynnot really a tax thing16:01
@lisitsynHeikoS: btw did you have to pay some taxes from your gsoc $?16:02
@HeikoSlisitsyn: nope16:02
@HeikoSno income in Germany16:02
@lisitsynHeikoS: good16:02
@HeikoSbut did it from Germany16:02
@lisitsynehm?16:02
@lisitsynso did you?16:03
@HeikoSlisitsyn: ehm sorry typo16:03
@HeikoSno of course not16:03
@HeikoSI was here16:03
@HeikoSfirst time in Germany16:03
@HeikoSnever paid anything16:03
@lisitsyngot it16:03
@lisitsynHeikoS: I am just curious how is it done in first world countries :D16:04
@HeikoSvery complicated everything16:04
votjakovrHeikoS: I'm working on it... I added enum for inference type casting, moved latent features to FITC, removed m_data_means and m_label_vector from InferenceMethod class16:04
lambdayits just one page saying that I didn't do anything while residing in the US, right?16:04
@HeikoSvotjakovr: that sounds good!16:04
@HeikoSlambday: yes16:05
lambdayhmmm16:05
lambdayHeikoS: by the way, I am not sure about the modular typemaps16:05
lambdaydo I have to do something with the swig files or something?16:05
@HeikoSvotjakovr: what about this pulling a general GP class out from the regression framework? You wanted to do this a bit later right?16:06
@HeikoSlambday: thats easy16:06
votjakovrHeikoS: yep16:06
@HeikoSlambday: have a look at the files for python16:07
@HeikoSevery class has to be added - done16:07
lambdayHeikoS: okay I'm checking16:07
@HeikoSto add a new type, talk to lisitsyn or sonney2k, sonne|work I have never done this, but it should be straight foward16:07
@lisitsynwhat type16:07
@lisitsyn?16:07
@HeikoSvotjakovr: I suggest this to be next after the current changes16:07
lambdaycomplex64_t16:07
@HeikoSlisitsyn: compley numbers16:07
@lisitsynfor features?16:08
lambdaypython has complex double or something?16:08
@HeikoSlisitsyn: no16:08
lambdaynah for matrices and vectors16:08
@HeikoSlambday: To be honest, I dont know ;) chceking16:08
lambdayHeikoS: neither do I :(16:08
@HeikoSlambday:16:08
@lisitsynpython can haz16:08
@lisitsyncomplex16:08
@HeikoSstart ipython16:08
@HeikoS--pylab16:08
@HeikoSand do complex<tab>16:08
votjakovrHeikoS: I agree :)16:09
@HeikoSyoull see numpy has all these types16:09
@HeikoSIn [3]: complex64(1)16:09
@HeikoSOut[3]: (1+0j)16:09
@lisitsynHeikoS: IIRC built-in16:09
@lisitsynjust 'j'16:09
@HeikoSlisitsyn:  yes its numpy16:09
@lisitsynno, not numpy I think16:09
@lisitsynbuilt-in16:09
@HeikoSvotjakovr: cool, this should be it for framework specific changes then, afterwards, we could start drawing diagrams of the new classification parts16:09
@HeikoSlisitsyn: yes, but numpy adds different sizes16:10
@HeikoSIn [5]: complex6416:10
@HeikoSOut[5]: numpy.complex6416:10
@HeikoSIn [6]: complex12816:10
@HeikoSOut[6]: numpy.complex12816:10
lambdayHeikoS: NameError: name 'complex64' is not defined16:10
lambday:(16:10
@HeikoSlambday: did you start with --pylab?16:10
lambdayyeah16:10
@HeikoSfrom numpy import complex6416:11
votjakovrHeikoS: yep, I think it's better to draw diagram for whole framework including regression part.16:11
@HeikoSwhat does that give?16:11
lambdayoh yeah16:11
lambdaythat works :)16:11
lambdayyay16:11
@HeikoSvotjakovr: yes, good idea, but try to keep it simple, since this is only about getting a big picture overview (no getters/setters, too many variables etc)16:11
@HeikoSvotjakovr: only things like features, etc should be in there16:12
lambdayokay I'm checking python_modular swig_typemaps.i then16:12
@HeikoSlambday: yes, cool16:13
@HeikoSlambday: note that the typemaps are not priority for now16:13
votjakovrHeikoS: Ok16:13
@HeikoSas long as you did not add your classes to swig, everything will work fine16:13
@HeikoS(though not be available for swig for now=16:13
@HeikoSwe can do these things later16:13
lambdayHeikoS: okay... that sounds better16:13
@HeikoSwhen all modular stuff is added16:14
@HeikoSthen you can do it all at once16:14
lambdayHeikoS: that's better16:14
@HeikoSso I would suggest, if the c++ parts work, lets press on16:14
lambdayHeikoS: okay.. so I'm cleaning up, and submitting a PR16:14
@HeikoSlambday: nice!16:14
lambday(this time its really gonna look ugly :(, its so big and so many things changed, even I lost track.. thanks to git it remembers everything :D )16:15
@HeikoSlambday: yes, but its hard to do this in little steps16:15
@HeikoSmake sure that it will be sent as one commit16:15
lambdayHeikoS: alright16:15
@HeikoSso that the buildbot doesn not fail on al lthe sub-commits16:15
@HeikoSand make sure unit-tests of new code are included,16:15
@HeikoSthis makes it easier16:15
lambdayokay16:15
lambdayI added few useless stuffs in CMath, wasn't sure about those.. some useless SG_ERROR msgs... I think we don't really need that..16:16
@HeikoSsuch as?16:16
lambdaywhat you said, that it gives error in compile time. should be enough for the user16:16
lambdayright?16:16
@HeikoSI see, so the error messages are in fact never produced since one cannot compile the code?16:17
lambdayno no16:17
lambdayit compiles... but when you use that method it shows the error message16:17
@HeikoSthats very useful!16:17
lambdaybut it that really needed? since its not a template class16:17
@HeikoSlambday: I dont get it16:18
lambdayHeikoS: CMath has few static template methods... I wrote many error msgs for complex64_t for many of them...16:19
@HeikoSok16:19
@HeikoSthats all good16:19
lambdayokay I'll send the PR... then you can have a look16:19
lambdaynot removing anything then16:19
lambdayby the way, if I configure shogun with --disable-eigen3, make unit-tests gives compilation errors :-/16:20
@HeikoSlambday: which ones?16:21
lambdaySGObject16:22
@HeikoSehm?16:23
@HeikoSreally16:23
lambdaywait16:23
lambdayhttps://gist.github.com/lambday/569851416:24
lambdayreally weird16:25
@HeikoSwell, probably some problems with #defines and stuff, GaussianKernel not declard etc16:26
@HeikoSwill have a look later16:27
lambdayHeikoS: okay..16:27
lambdayI have added one unit test for math complex stuffs, another for sgvector complex stuffs16:28
lambdayrest, haven't written yet16:28
@HeikoSlambday: ok, we can already merge, but please do the tests next then16:28
@HeikoSI know its a little annoying but these are very fundamental things which made sure to work16:29
lambdayHeikoS: yes.. I was thinking to add those now in fact, instead of doing it later...16:29
@HeikoSsubmit the patch first and then do them16:30
@HeikoSotherwise it will get too messy16:30
lambdayHeikoS: alright.. okay :)16:30
lambdaychecking and cleaning up then...16:30
@iglesiasgsomeone has compiled with directors enabled? I think it is broken16:37
@iglesiasgit is an easy fix, just wanted to check if someone found it as well16:37
@HeikoSiglesiasg: I dont have compiled this sorry16:38
@HeikoSiglesiasg: have you used the directors stuff yet?16:39
@iglesiasgHeikoS: yeah, all the time for my thesis :)16:39
@iglesiasgI implemented a structured model in python16:39
@HeikoSiglesiasg: cool!, maybe you can tell me a bit about it? what do you use it for?16:39
@HeikoSI see16:39
@iglesiasgHeikoS: I can put you the example where I use it16:39
@iglesiasgso I have my StructuredOutputMachine16:40
@HeikoSso I want to do something, but I am not too sure whether its possible16:40
@HeikoSbut yeah, explain first :)16:40
@iglesiasgthat it basically solves an optimization problem for structured SVMs16:40
@iglesiasgthis problem has some application dependent parts16:40
@iglesiasgthere are a couple of functions that change if you are dealing with e.g. sequences, or graphs, or other kind of structured objects16:41
@iglesiasgthese application dependent functions are encapsulated in a structured model16:41
@iglesiasgso using director classes16:41
@iglesiasgI can implement a structured model in a target language16:41
@iglesiasgand the code in the StructuredOutputMachine is "calling" this code in the target language16:42
@HeikoSso one can have an abstract method, that is being called from a c++ implementation16:42
@HeikoSbut this method is actually implemented in say python16:42
@iglesiasgyes16:42
@HeikoSand then I can call the c++ implementation from octave16:42
@HeikoSwhich then calls the python code16:43
@HeikoS?16:43
@iglesiasgI haven't tried the case of calling from octave, but yes it should work16:43
@HeikoSI meant just any other language16:43
@iglesiasgyeah16:43
@HeikoSthis is awesome16:43
@HeikoSso what I want to do is16:43
@iglesiasgpretty cool yeah16:43
@iglesiasgwe should eternally thank gsomix :)16:43
@HeikoSto write a general MCMC framework ( to generate samples from distributions)16:44
@HeikoSfor this, there will be a lot of code16:44
@HeikoSbut obviously, we cannot code up every distribution one wants to sample16:44
gsomixiglesiasg: wut?16:44
gsomixah, ok16:44
@HeikoSand the c++ code would need to call a method called say log_pdf()16:44
@HeikoSbut this has to be a user provided unfction16:45
@HeikoSfunction16:45
@HeikoSbut I dont want to make people code this up in c++16:45
@HeikoSso they can do it in pytho16:45
@HeikoSbut things would still work16:45
@HeikoShow hard is it to do that?16:45
@HeikoSso if I have a base class CMCMCTarget16:45
@HeikoSwhich has some abstract methods16:45
@HeikoSwhat do I need to do in order to implement them in python16:46
@iglesiasgso I know the C++ part16:46
@iglesiasgyou need to do a Director class, which is pretty straightforward16:46
@iglesiasgand then your python class extends this director class16:46
@iglesiasgsee for example DirectorDotFeatures16:46
@HeikoSdoes the user has to write it?16:47
@iglesiasgno16:47
@HeikoSnice16:47
@iglesiasgin your case you will need to do a16:47
@iglesiasgDirectorMCMCTarget16:47
@iglesiasgHeikoS: the thing is that this probably requires some SWIG code, I am not sure though16:48
@iglesiasggsomix: for directors, you need the director class in C++ and SWIG code as well or just the director?16:48
@HeikoSok, but I can prepare everything and the user just has to extend an existing python class with the method?16:49
@iglesiasgHeikoS: yes, that is the workflow16:49
gsomixiglesiasg: just director class in C++.16:49
@iglesiasggsomix: good16:49
@HeikoSgsomix, iglesiasg, awesome! :)16:49
@HeikoSthis is exactly what I needed16:50
@iglesiasgHeikoS: just a remark16:50
@HeikoSfrom which languages does this work?16:50
@HeikoSand how expensive is it?16:50
@iglesiasgHeikoS: you don't actually extend an existing python class, you extend an existing C++ class from python16:50
@HeikoSI see,16:50
@iglesiasgHeikoS: that's interesting, I wanted to see how slow was it from say pure C++ but never tried it at the end16:51
@iglesiasgif you meant that with expensive16:51
@HeikoSiglesiasg: this probably depends on the method16:52
@HeikoSin general I mean16:52
@HeikoSbut I was interested in the amount of overhead16:52
@iglesiasgdefinitely16:52
@iglesiasgno idea16:52
@iglesiasglisitsyn mentioned once that it could be slow16:52
gsomixvery slow16:54
gsomixcu later16:54
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@HeikoSiglesiasg: ok, very slow :)16:54
@iglesiasghehe16:54
votjakovrHeikoS: i have a question: i'd like to scale SGMatrix (simple multiply by a real number), what is the best way for doing this?16:57
@HeikoSvotjakovr: either there is already a method to do this. If not, you could create one, use eigen's Map, or just write the loop16:58
@HeikoShaving a method scale(T scalar) would be probably good anyway16:59
sonne|workvotjakovr: just make sure you have the implementation only in the .cpp file and no dependency to eigen in the .h17:00
@HeikoSvotjakovr, sonne|work if you add this to SGMatrix, then better not use eigen anyway17:00
votjakovrHeikoS:  Ok, I'll add it17:00
@HeikoSsonne|work: btw I really dont like our matrix representation17:00
sonne|workgtg17:01
@lisitsynHeikoS: what do you don't like?17:02
@HeikoSlisitsyn: its not oop17:02
@HeikoSboth matrix and vector should be scalable17:02
@HeikoSfor example17:02
@lisitsynscalable?17:02
@HeikoSso only one method17:02
@HeikoSmultiply by scalar17:02
@HeikoSbut this is not reflecte17:02
@HeikoSd17:02
@lisitsynahh17:02
@lisitsynI would not do anything like that in sgmatrix17:03
@lisitsynI don't like we put such methods here17:03
@lisitsynas I consider it as just a wrapper for swig deals and storages17:03
@HeikoSlisitsyn: agreed!17:03
@HeikoSvotjakovr: then please dont add this method17:03
@lisitsynI'd rather add a method17:03
@lisitsynthat returns eigen map17:03
@lisitsynfor that matrix17:03
@HeikoSvotjakovr: ^17:04
@HeikoSgood idea17:04
@HeikoSwe can in fact then also start to remove all these matrix functions from there (mean/covariance etc)17:04
@lisitsynand then we do matrix.map().whatever we ever wanted()17:04
@HeikoSlisitsyn: thats much better17:04
@HeikoSthen I will like the current classes again :D17:04
@lisitsynhah alright17:04
@HeikoSyou are right, they are rather wrappers17:05
@HeikoSgotta go now, see you later17:05
@lisitsynme too17:05
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votjakovrHeikoS: so you think, that it is better to use eigen3 for that purposes?17:07
@HeikoSvotjakovr: yes I strongly agree with sergey17:07
@HeikoSthe SGMatrix class should have a method to return an eigen3 matrix17:07
@HeikoSand then you can use the usual operations on that17:07
@HeikoSthen code is very clean and we are not re-inventing the wheel all the time17:08
@HeikoSvotjakovr: https://github.com/shogun-toolbox/shogun/issues/113917:12
votjakovrHeikoS: oh yep, i agree, it will be great17:12
@HeikoSvotjakovr: nice! :)17:12
@HeikoSgotta go now,see you!17:12
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votjakovrHeikoS: cu17:12
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shogun-notifier-shogun: iglesias :develop * 8496e3f / src/shogun/ (13 files): https://github.com/shogun-toolbox/shogun/commit/8496e3f75c3a73073815f6ede5c64360f93de4a317:21
shogun-notifier-shogun: Add support for continuous features or observations to the HMSVM17:21
shogun-notifier-shogun: - Major changes in HMSVMModel17:21
shogun-notifier-shogun: - Add convenience init_training method in StructuredModel17:21
shogun-notifier-shogun: - TwoStateModel::simulate_two_state_data -> simulate_data with arguments17:21
shogun-notifier-shogun: - Fix bug with default value of m_use_director_risk in StructuredModel cto.17:21
shogun-notifier-shogun: iglesias :develop * f4f4e2c / examples/undocumented/python_modular/ (6 files): https://github.com/shogun-toolbox/shogun/commit/f4f4e2c2f53b42460348efcf29d784c9cfc1b5a917:21
shogun-notifier-shogun: Rename old HMSVM python examples to discrete and add new ones for PLiFs17:21
shogun-notifier-shogun: iglesias :develop * 64e789a / / (22 files): https://github.com/shogun-toolbox/shogun/commit/64e789a970759437e078e5cbdeedb685148e4ef217:21
shogun-notifier-shogun: Several minor improvements in the SO framework and the HMSVM17:21
shogun-notifier-shogun: Fernando Iglesias :develop * 923f9b3 / / (33 files): https://github.com/shogun-toolbox/shogun/commit/923f9b343f4ea81b7663e14eaa40bf0bba17f75e17:21
shogun-notifier-shogun: Merge pull request #1089 from iglesias/feature/hmsvm_plifs17:21
shogun-notifier-shogun:17:21
shogun-notifier-shogun: Support for continuous features with the HM-SVM using PLiFs17:21
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gsomixgood evening17:34
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yoohiall17:37
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lisitsynhttp://izbicki.me/blog/hlearn-cross-validates-400x-faster-than-weka17:59
@iglesiasghehe18:03
@iglesiasgthat seems pretty exaggerated18:03
@iglesiasgaah it is another algorithm18:04
@iglesiasgand they are using there >100 folds18:04
@iglesiasglisitsyn: is it normal to use so many? I have normally gone with 5 hehe18:05
lisitsyniglesiasg: noooo idea!18:05
lisitsynwell 1000 folds is ehm18:05
lisitsynpretty much yes18:06
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van51sonney2k: are you here19:34
van51?19:34
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@sonney2kvan51, hey!19:47
van51sonney2k: hello!19:47
van51sonney2k: first of all, I edited the PR19:48
van51in regards to your comments19:48
@sonney2klambday, you are a superhero!19:48
van51secondly, we managed to meet today :D19:48
van51and we said we continue our interactions mainly through emails at least with Olivier and Benoit19:49
van51and they wanted to know whether we would have to continue CC'ing you19:49
van51not that they mind or anything19:49
lambdaysonney2k: watching the travis build like I watch a status bar while downloading.. :(19:49
van51lambday: I do that too!19:50
lambdayvan51: :)19:50
@sonney2klambday, I had a look over your code. It is good to merge from my side!19:50
@sonney2klambday, so as soon as the bb turns green I will merge19:50
lambdaysonney2k: thanks19:51
lambdaysonney2k: if this works, I'm gonna give myself a huge treat... some fancy restaurants for sure :-/19:51
lambdaysonney2k: the macro idea was a life-saver19:53
@sonney2kvan51, regarding the PR we still need a unit test (again) and yes you are right I have to find some example19:53
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@sonney2kvan51, regarding the PR we still need a unit test (again) and yes you are right I have to find some example20:00
lambdaysonney2k: something failed :(20:05
lambdaysonney2k: oh its just cause of high precision20:05
lambdaysonney2k: should I change it now? in the unit-test I mean?20:07
@sonney2klambday, yes precision of double is just 1e-1620:07
@sonney2kso don't go above that20:07
lambdaysonney2k: okay20:07
@sonney2k1e-15 is reasonable20:07
lambdaysonney2k: okay.. I'll change it20:07
lisitsynsonney2k: do you agree with our thoughts on sgmatrix?20:08
lambdayah, finally! :D20:18
lambdaysonney2k: should I change it in this PR or in the next PR? I'll be editing CJacobiEllipticFunctions in the next PR with this complex64_t..20:19
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@sonney2klambday, just change it in this PR and force push. I am currently checking why it is deviating at all though20:22
lambdaysonney2k: alright20:22
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shogun-notifier-shogun-demo: foulwall :master * b16be7b / / (10 files): https://github.com/shogun-toolbox/shogun-demo/commit/b16be7bfa4389e8e14214215dfdaf5b34c19e74020:25
shogun-notifier-shogun-demo: Simplify the argument panel. when creating new demos, developer only20:25
shogun-notifier-shogun-demo: need to fillin a python dict with types and names of each argument.20:25
shogun-notifier-shogun-demo: Soeren Sonnenburg :master * 05615f2 / / (10 files): https://github.com/shogun-toolbox/shogun-demo/commit/05615f2c7b988ca9b137f9ffc2c123a4399903b720:25
shogun-notifier-shogun-demo: Merge pull request #5 from foulwall/refractor20:25
shogun-notifier-shogun-demo:20:25
shogun-notifier-shogun-demo: Simplify the argument panel.20:25
lambdaysonney2k: changed20:31
lambdayargh!20:39
@sonney2klambday, ok it seems this NEAR stuff is for double only20:44
@sonney2kso don't try to be overly accurate20:44
lambdaysonney2k: okay..20:45
lambdaybut in many cases I've kept it as 1e-19, whenever it passed20:45
shogun-notifier-shogun: lambday :develop * 97f4e8f / / (22 files): https://github.com/shogun-toolbox/shogun/commit/97f4e8f6a1ed7d1037a29b974885116619f3587520:45
shogun-notifier-shogun: ptype complex64_t added20:45
shogun-notifier-shogun: Soeren Sonnenburg :develop * bc4689c / / (22 files): https://github.com/shogun-toolbox/shogun/commit/bc4689c0c06768661d35cf137f883b14348aa5ff20:45
shogun-notifier-shogun: Merge pull request #1140 from lambday/develop20:45
shogun-notifier-shogun:20:45
shogun-notifier-shogun: ptype complex64_t added20:45
@sonney2klambday, alright then20:45
lambdaysonney2k: thank you :) :)20:46
lambdayphew!20:47
shogun-notifier-shogun: Soeren Sonnenburg :develop * 2e6b11f / examples/undocumented/ (3 files): https://github.com/shogun-toolbox/shogun/commit/2e6b11fc1804435c3db7dd1c5fc078301369d31e20:47
shogun-notifier-shogun: drop useless unused includes20:47
@sonney2kvan51, there is actually no committed example using that :/20:47
@sonney2kvan51, I only had some research code written like about 4 years ago so all we can rely on is your tests for now20:48
@sonney2kvan51, however whenever you make some progress with hashing we can resurrect the old code and make it a real example20:49
@sonney2kvan51, ahh and yes please keep me in the CC if possible thanks!20:49
van51sonney2k: ok sounds like a plan :)20:49
van51we will!20:49
van51although with quoc it will probably be gtalk conversations20:50
@sonney2kvan51, ok then please ping me when you have updated the PR20:50
@sonney2kvan51, yeah do as you can but keep me updated then20:50
van51yeah ofc20:52
shogun-buildbotbuild #894 of cyg1 - libshogun is complete: Failure [failed configure]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/894  blamelist: lambday <heavensdevil6909@gmail.com>20:58
lambdayfailed??20:58
shogun-buildbotbuild #1062 of bsd1 - libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1062  blamelist: lambday <heavensdevil6909@gmail.com>20:58
@sonney2klambday, ahh cyg ...21:00
@sonney2khmmhh bsd?!21:00
* sonney2k checks21:00
lambdayyeah bsd :(21:00
@sonney2kwiking, http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1062/steps/compile/logs/stdio21:01
@sonney2klambday, is complex standard stuff?21:01
lambdaysonney2k: yes!21:01
lisitsynwhy real(c_real)?21:02
shogun-buildbotbuild #1063 of bsd1 - libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1063  blamelist: Soeren Sonnenburg <sonne@debian.org>21:02
lambdaylisitsyn: to set the real and imag21:03
lambdayit worked here21:03
lisitsynlambday: why not real() = c_real?21:04
lisitsynlambday: i have such methods in my std lib too21:04
lisitsynnot sure about bsd21:04
lambdaylisitsyn: bad :(21:05
@sonney2klambday, real(val) and imag(val) are C++11 extensions21:05
lambdayI'm gonna have to change those then... :(21:05
@sonney2klambday, as are proj(), asin(), acos(), a*21:05
lambdaysonney2k: so we shouldn't be using them?21:06
@sonney2klambday, well we could have a configure check testing for it21:06
@sonney2kbut I am afraid it won't save us21:06
lambdaysonney2k: asin, acos thing we need for the project :(21:06
lisitsynsonney2k: can't see where is it stated21:06
@sonney2klisitsyn, http://books.google.de/books?id=9DEJKhasp7gC&pg=PT1310&lpg=PT1310&dq=c%2B%2B+complex+standard&source=bl&ots=_917L8IrRD&sig=EqmCPSeGuAsrFivfrVgA4lqLICU&hl=en&sa=X&ei=pOisUZHxKouqPJfEgKAE&redir_esc=y21:07
lisitsynsonney2k: well real() returns reference21:08
lisitsynwe still can real() = 3 I think?21:08
@sonney2kwell we have 3 options: 1) we require c++11 compilers21:09
@sonney2k2) we don't use st'21:10
@sonney2kstl's complex type but one from some other lib21:10
lisitsynsonney2k: what is wrong with older std?21:10
@sonney2k3) we work around it21:10
@sonney2kasin, acos etc missing which lambday needs21:10
lisitsynah okay21:11
lambdaymake it c++11 compilers :(21:11
lambdayconfigure won't help?21:11
@sonney2khmmhh, all difficult. shogun currently works with zero dependencies21:12
gsomixsonney2k, tnx for review. working...21:12
@sonney2kjust the parts that are unavailable (like blas/lapack/eigen/nlopt/ etc etc) won't work21:13
shogun-buildbotbuild #895 of cyg1 - libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/895  blamelist: Soeren Sonnenburg <sonne@debian.org>21:13
@sonney2kI mean parts depending on the libs that are unavailable won't work21:13
@sonney2kbut that is ok21:13
lambdaysonney2k: I'm sorry... we don't need asin, acos..21:13
lambdaysorry for the confusion21:13
@sonney2kwhat researchers I met most complained about shogun back then was21:14
@sonney2kthat they couldn't get it compiled(!)21:14
@sonney2ktoo complex. too difficult to get to work21:14
@sonney2kso I am not too fond of creating hard dependencies21:14
lambdaysonney2k: okay... but I just checked and we don't need asin, acos, atan etc...21:14
@sonney2klambday, ok perfect :D21:15
lambdayso, if the serialization thing can be taken care of21:15
@sonney2k?21:15
lambdayI'll check the real() = some_val thing that lisitsyn was sayng21:15
lambdayif that works, then we're good I guess?21:15
lambdaysonney2k: its easy to change I guess21:20
@sonney2klambday, yes it works21:21
@sonney2klambday, so just change it to x.real() = foo21:21
lambdaysonney2k: okay21:21
lambdaychanging..21:21
@sonney2kgsomix, I still don't understand your code...21:22
@sonney2kgsomix, could you please explain how circular buffer works21:22
@sonney2kI mean what is write_to_buffer doing?21:23
lambdaysonney2k: changed.. sending PR21:28
gsomixsonney2k, method just locates free memory in buffer and copies data to it. logically just append array of bytes to end of buffer. but free memory can be situated as at end and at begin of physical memory, because buffer is ring (just imagine the tape with glued ends).21:32
gsomixsonney2k, I hope this helped21:32
lambdaymy hostel has this weird policy since last 4-5 days that exactly 1:30 at night (20 UTC) my internet gets disconnected.. comes back 3:30 hrs later21:34
@sonney2kgsomix, hmmhh so you do harddisk reads in smaller blocks then right?21:36
gsomixsonney2k, yep. size of blocks is configurable21:37
@sonney2kI still don't have the full picture21:37
@sonney2kso lets start an example21:38
@sonney2kI read in say 1MB of data from the file21:38
@sonney2kinto my circular buffer (I hope)21:38
@sonney2kthen go through the buffer until I find no more '\n'21:39
@sonney2ksay 10KB before the end of the buffer21:39
@sonney2kgsomix, then I do what?21:39
@sonney2kand my circular buffer is fixed size 1 MB here right?!21:40
gsomixsonney2k, just read another 1MB of data. then 10KB copies into end of physical memory of buffer, and 990KB at begin.21:40
gsomixsonney2k, yep21:40
gsomixerrr21:40
gsomix990 copies at begin21:40
gsomixso... you should reat 990K from file21:41
gsomix*read21:41
gsomixand write to buffer21:41
gsomixbecause available only 990KB of free space in buffer. logical begin of buffer then at (end of physical block - 10KB) position.21:43
@sonney2kgsomix, so you read as much as you need to fill in the 1MB21:43
gsomixsonney2k, no more than chunk_size (maximal size of block to read)21:45
@sonney2kgsomix, ok I see. lets say now you have still a 1MB buffer but the string is 500k long and you don't find another string in there21:48
@sonney2kso you read again 500k right?21:48
gsomixyep21:48
@sonney2kand if you don't find anything in there we say ERROR21:48
@sonney2k?21:49
gsomixyes. method get_next_line just returns -1.21:49
@sonney2kgsomix, btw for the last line one does not need to find a delimiter at the end21:51
lambdaysonney2k: please have a look at the PR when you're free.. just used it in two places.. rest should be fine I think.. I'll probably get disconnected in 8 mins :(21:52
@sonney2kgsomix, I don't get the difference between buffersize and chunksize...21:55
gsomixsonney2k, buffer_size is max size of line, chunk_size if max size of block to read.21:56
shogun-notifier-shogun: lambday :develop * badadc2 / src/shogun/io/ (2 files): https://github.com/shogun-toolbox/shogun/commit/badadc2a210f87935c703d1d1e8796b77fa84fb421:56
shogun-notifier-shogun: real/imag(val) replaced by real()/imag()=val21:56
shogun-notifier-shogun: Soeren Sonnenburg :develop * b290b09 / src/shogun/io/ (2 files): https://github.com/shogun-toolbox/shogun/commit/b290b0905a67657f4e422ecdd1623a1b1ce75feb21:56
shogun-notifier-shogun: Merge pull request #1141 from lambday/develop21:56
shogun-notifier-shogun:21:56
shogun-notifier-shogun: real/imag(val) replaced by real()/imag()=val to make it work on non C++11 compliant compilers21:56
@sonney2kgsomix, then please write this in the doxygen docu21:57
gsomixsonney2k, ok21:57
@sonney2kgsomix, or even better name the parameter like that21:57
@sonney2kgsomix, max_line_length21:57
* gsomix afk21:58
-!- votjakovr [~votjakovr@host-46-241-3-209.bbcustomer.zsttk.net] has quit [Quit: Leaving]21:59
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@sonney2kso there we have lambday's reliably predicted disconnect22:01
shogun-buildbotbuild #1064 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1064  blamelist: lambday <heavensdevil6909@gmail.com>22:18
shogun-buildbotbuild #1188 of deb3 - modular_interfaces is complete: Failure [failed test ruby_modular]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/1188  blamelist: Soeren Sonnenburg <sonne@debian.org>22:19
shogun-buildbotbuild #896 of cyg1 - libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/896  blamelist: lambday <heavensdevil6909@gmail.com>22:23
shogun-buildbotbuild #897 of cyg1 - libshogun is complete: Failure [failed configure]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/cyg1%20-%20libshogun/builds/897  blamelist: Soeren Sonnenburg <sonne@debian.org>22:23
shogun-buildbotbuild #1065 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/bsd1%20-%20libshogun/builds/1065  blamelist: Soeren Sonnenburg <sonne@debian.org>22:30
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shogun-buildbotbuild #1189 of deb3 - modular_interfaces is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/118923:11
gsomixmay the forc^Wvalgrind be with you23:20
gsomixsonney2k, so, I have fixed memory leaks. example for LineReader is ready. example for buffer and many_delimiters_read will be tomorrow.23:27
gsomixsonney2k, now I need to prepare for pass-fail exam. dsp, dsp...23:29
@iglesiasggood luck with it gsomix23:57
gsomixiglesiasg, thanks. this is small exam. most interesting will be at the end of June, huh.23:59
--- Log closed Tue Jun 04 00:00:03 2013

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