IRC logs of #shogun for Monday, 2011-08-15

--- Log opened Mon Aug 15 00:00:08 2011
--- Day changed Mon Aug 15 2011
@sonney2kahh and enough coverage of examples for new languages like csharp, lua, java, ruby, ...00:00
@sonney2kif we don't manage all $LANG we will include the lang nevertheless but not mention it in release notes :D00:00
@sonney2kuh oh last release was in december last year00:02
@sonney2kit is really about time to have a new release00:02
@sonney2kone should actually release every 1-2 months00:03
@sonney2kwith not too big changes of course00:03
alesis-novikI'm making a few changes, I'll commit them a bit later00:07
blackburnwhoaa00:07
CIA-87shogun: Sergey Lisitsyn master * rcfe4efb / (13 files in 2 dirs): United Landmark/Classic MDS and Isomap stuff - http://bit.ly/qHb4FC00:07
CIA-87shogun: Sergey Lisitsyn master * r5e6a160 / (22 files in 5 dirs): Fixed Classic/Landmark modular examples - http://bit.ly/o53qvh00:07
blackburnshogun-buildbot: go! :D00:08
blackburnsonney2k: didn't catch the commit?00:09
@sonney2kblackburn, I think it is still busy00:10
blackburngot00:10
blackburnhey almost all tests are OK00:11
blackburnhmm00:12
blackburnserialization of svmlight00:12
blackburnand heiko's stuff00:12
blackburneverything else is ok00:12
@sonney2kmy poor machine rebooted again00:22
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@sonney2kf-x, why don't use use get_vector and return float32_t too?00:48
@sonney2kfor the online case00:48
f-xsonney2k: for which problem? the get_w() thing?00:49
CIA-87shogun: Sergey Lisitsyn master * r953fa3a / (2 files): Got graphical dimreduct examples to work again - http://bit.ly/n8J3Kp00:57
blackburnone more parallel algo00:57
CIA-87shogun: Sergey Lisitsyn master * r81cc6a2 / (2 files): Made LLE parallel - http://bit.ly/pamH0N00:57
blackburnsonney2k: can't get any speed burst :(01:00
blackburn4s for LLE on 1000 examples with k=200 and 3s for 2-threaded with same params01:03
blackburnmakes no sense :(01:03
blackburn32s vs 24s for k=50001:05
blackburnokay probably it can impact on ##@%@$% threaded system01:06
CIA-87shogun: Sergey Lisitsyn master * rc02be2d / (2 files): Added pthread_exit for Isomap and MDS - http://bit.ly/n3Mkil01:14
CIA-87shogun: Sergey Lisitsyn master * r4c5331c / (2 files): Removed unnecessary pthread_exit - http://bit.ly/nXtVJq01:56
CIA-87shogun: Sergey Lisitsyn master * rb219442 / (2 files): Made LTSA parallel - http://bit.ly/q65kYb01:56
CIA-87shogun: Sergey Lisitsyn master * r9f86e64 / (8 files): Added parameters addition to dimensionality reduction algos - http://bit.ly/pav0MP02:20
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CIA-87shogun: Alesis Novik master * r4560951 / (10 files in 4 dirs): Multiple fixes (SG*, log-likelihood instead of likelihood), improved documentation - http://bit.ly/ojI74s10:05
CIA-87shogun: Soeren Sonnenburg master * r0a08046 / (10 files in 4 dirs):10:05
CIA-87shogun: Merge pull request #296 from alesis/gmm10:05
CIA-87shogun: Multiple fixes (SG*, log-likelihood instead of likelihood), improved docu - http://bit.ly/p9XMcf10:05
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VojtechFrancHi alesis-novik11:21
blackburnVojtechFranc: have a minute for lame questions about kPCA?11:22
VojtechFrancof course, if I can answer it11:23
blackburnin your stprtoolbox I have found kpca.m for hmm fitting11:24
blackburnand what to use for transforming data?11:24
VojtechFrancfor hmm ??11:24
blackburnhehe sorry11:25
VojtechFrancthere is a function kernelproj(X, model) where model is obtained from kpca11:25
blackburnhmm is hmm not markov model11:25
blackburnkpcarec?11:25
VojtechFranchaha11:25
blackburnwhat is the purpose of kpcarec?11:25
VojtechFranckpcarec it does preimage computation11:25
VojtechFranci.e. given a point in the kernel space it finds the closes preimage in the input space11:26
blackburnah11:26
VojtechFrancit is useful e.g. in image denoising11:26
blackburnI see11:26
blackburnso for transforming data11:26
blackburnit is sufficient to fit kPCA11:26
blackburnand then do kernelproj on its model?11:27
VojtechFrancexactly, there is also example11:27
blackburnI'm asking because I have to implement it in shogun11:27
blackburnsoeren did init thing already11:27
blackburnbut not transform11:27
blackburnhmm kernelproj is even .c11:28
VojtechFrancit is easy11:28
VojtechFrancyes11:28
blackburnoh, getting grasp of it11:28
blackburnmany thanks11:29
VojtechFranccomputing the preimage is however a bit more difficult11:29
blackburnI don't really need it now11:29
VojtechFrancthen ok, but it is useful to generate nice figures ... :)11:29
VojtechFrancjust a joke11:30
blackburnwell of course but I simply can't put it into shogun preprocessor11:30
blackburnno inverse transform here :)11:30
VojtechFranchmm, apparantly there is a large room for improvements in shogun :)11:31
blackburnyeah it was yesterday's topic here11:32
alesis-novikHello VojtechFranc. I can't really chat right now, I was wondering if you would be available later today? I free up at 13:30 UTC, could we chat at say 14:00 UTC?11:41
VojtechFrancyes, no problem. 14:00 UTC is OK11:42
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@sonney2kblackburn, sure preimage would fit - it would be just a function preimage(features)12:45
@sonney2kbut VojtechFranc doesn't preimage only work for real valued data?12:45
blackburnhuh last algo to parallelize12:46
@sonney2kblackburn, btw you need huge data set to see any gains12:50
@sonney2kit doesn't matter if sth trains just a few seconds12:50
@sonney2kif you have sth that takes an hour then it is useful to parallelize12:51
blackburnyeah but I like to feel it is scalable (at least a little)12:51
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CIA-87shogun: Sergey Lisitsyn master * rcb38bbf / src/shogun/preprocessor/LocalTangentSpaceAlignment.cpp : Some clean for LTSA parallelization - http://bit.ly/pRyGR912:57
CIA-87shogun: Sergey Lisitsyn master * r62e6aee / (2 files): Made HLLE parallel - http://bit.ly/okRUGq12:57
blackburnsonney2k: all parallel!12:58
blackburnexcept Laplacian Eigenmaps and MultidimensionalScaling - makes no sense13:01
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VojtechFrancsonney2k, it is even worse. you need to solve the pre-image problem for each kernel separately. there are feasible solutions for Gaussian kernel and polynomial 2 kernel (also implemented in my toolbox)13:20
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blackburnHLLE for parkinsons dataset: http://dl.dropbox.com/u/10139213/shogun/parkinsons.pdf14:25
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serialhexshogun-buildbot status ruby_modular14:39
serialhexhmm.... it is not my slave :(14:39
serialhexshogun-buildbot status all14:40
serialhexnope, it dosnt listen to me... oh well :(14:41
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alesis-novikHello VojtechFranc16:04
VojtechFranchi alesis, give me 10 minutes please16:06
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VojtechFrancalesis-novik, ok I'm ready16:15
VojtechFrancwhat is the situation with the experiments and documentation?16:15
alesis-novikWell, I documented the code, not going into maths though16:15
alesis-novikI had some problems with the image benchmarks16:16
alesis-novikI think it's fixed now, but I need to rerun the tiger benchmark16:16
alesis-novikI also changed examples and clustering a bit16:16
alesis-novikso that it would return log-likelihood instead of likelihood16:16
VojtechFrancso now have completed the USPS and synthetic data benchmark?16:17
alesis-novikNo, I have completed USPS and 2 of the images16:17
VojtechFrancwhat about the synthetic?16:17
alesis-novikI haven't run them yet. Like I said, it takes a lot of time, which I can't always dedicate on my machine for benchmarking16:18
VojtechFrancok, have you included the benchmarking scripts to shogun?16:19
alesis-novikno, I'm not sure where I should put them either16:19
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VojtechFrancme neither, we can ask sonney2k.16:20
VojtechFrancsonney2k, alesis wrote some python scripts to benchmark the EM and SMEM algorithm. What is the proper place in shogun for these codes?16:21
VojtechFrancalesis-novik, I'd like to pass through all your codes onec again. Could you pls send me list of all files you modified/wrote?16:22
alesis-novikVojtechFranc, I'm also going to comment the examples and add them to examples/documented16:22
VojtechFrancit would be nice16:22
alesis-novikVojtechFranc, the ones to do with the project are distributions/Gaussian.*, clustering/GMM.* and a change in features/DotFeatures.*16:23
VojtechFrancand also the examples I guess16:24
alesis-novikcurrently undocumented/python_modular/clustering_gmm_modular.py16:25
alesis-novikundocumented/python_modular/graphical/em_1d_gmm.py16:26
alesis-novikundocumented/python_modular/graphical/em_2d_gmm.py16:26
alesis-novikundocumented/python_modular/graphical/smem_1d_gmm.py16:26
alesis-novikundocumented/python_modular/graphical/smem_2d_gmm.py16:26
VojtechFrancok16:26
VojtechFrancI'm just looking at the benchmark results you sent me: benchmark_usps_em/smem.txt16:27
VojtechFranccould you pls give me an exmplanation of the values16:27
VojtechFranc?16:27
VojtechFrancit seems tha for each run there are 3x the log-likelihoods and one value that might be std?16:28
alesis-novikI did in the letter, its average, std, max and min I believe16:28
VojtechFrancI see16:29
VojtechFrancI guess the log-likelihood values are not normalized to the number of examples?16:32
alesis-novikno, I didn't16:33
VojtechFrancit is interesting that both EM and SMEM achived the same maximal log-likelihood. this means that the SMEM is not very useful in this case...16:36
alesis-novikVojtechFranc, I believe it's because the initialization conditions are very good (k-means and 1-nn), so EM doesn't converge to local optima16:36
VojtechFrancprobably16:39
VojtechFrancalesis-novik, what remains to be done? to finish documenting the examples and the benchmarks?16:40
alesis-novikVojtechFranc, I guess. I think any further work should be left for post-release/GSoC16:40
alesis-novikVojtechFranc, do you think I should add mathematical detail to documentation. So far I've only added the PDF formula for Gaussian16:41
VojtechFrancyou mean the Oxygen documentation?16:42
alesis-novikyes16:42
VojtechFrancI don't think it is necessary. There might be a link to relevant papers.16:42
VojtechFrancI did git pull from your repository and try to compile. I got AL_KERNELCACHE -DUSE_HMMPARALLELSTRUCTURES -DUSE_HMMPARALLEL -DUSE_BIGSTATES -DUSE_HMMCACHE -DUSE_REFERENCE_COUNTING -DUSE_SVMLIGHT  -DSWIG_TYPE_TABLE=shogun -DSHOGUN -DLINUX -DHAVE_POWL -DHAVE_SQRTL -DHAVE_LOG2 -DHAVE_XML -DHAVE_ATLAS -DHAVE_LAPACK -DUSE_GZIP -DHAVE_LARGEFILE -DUSE_SHORTREAL_KERNELCACHE -DUSE_HMMPARALLELSTRUCTURES -DUSE_HMMPARALLEL -DUSE_BIGSTATES -16:43
VojtechFrancDUSE_HMMCACHE -DUSE_REFERENCE_COUNTING -DUSE_SVMLIGHT  -c -I. -I..  -I/usr/include/libxml2   -I../libshogun -I.. -o base/Version.cpp.o base/Version.cpp16:43
VojtechFrancbase/Version.cpp:24: error: ‘VERSION_PARAMETER’ was not declared in this scope16:43
VojtechFrancmake[1]: *** [base/Version.cpp.o] Error 116:43
VojtechFrancmake[1]: Leaving directory `/home/vojta/shogun/alesis_git_branch/shogun/src/shogun'16:43
VojtechFrancalesi-novik: don't you have an idea what might be wrong?16:44
alesis-novikwhich branch did you use?16:44
alesis-novikThe updated code is in the gmm branch, though you might as well use the shogun main branch, since I've pushed everything16:45
VojtechFrancI guess I'm using git://github.com/alesis/shogun16:47
alesis-novikyeah, it's a very old version there16:48
VojtechFrancmaybe I'm in a wrong dir I have several branches downloded...16:49
VojtechFrancthen I'll try the main shogun branch16:50
VojtechFrancok, I figured out that I was using the gmm branch at the end16:54
alesis-novikIs it working now?17:03
VojtechFrancyes it compiles. I tried the main shogun branch.17:09
VojtechFranchowever, it seems you didn't push the example scripts. did you?17:10
alesis-novikthe examples should be there17:14
VojtechFrancok, I need to go. I'll try it tomorrow ... cheers17:16
alesis-novikOk, tell me if anything goes wrong17:17
VojtechFrancok, cheers17:19
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blackburntoday is a soft pencils down?20:27
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blackburnserialhex: around?20:39
CIA-87shogun: Shashwat Lal Das master * r692f79f / (24 files in 5 dirs): Partial transition to float32_t for online framework. - http://bit.ly/r1T3ut20:44
CIA-87shogun: Shashwat Lal Das master * r2976834 / (25 files in 6 dirs): Working float64_t to float32_t transition for online framework. - http://bit.ly/pw2iHp20:44
CIA-87shogun: Shashwat Lal Das master * re034620 / examples/undocumented/libshogun/streaming_from_simple.cpp : Remove a doc typo. - http://bit.ly/qGVHyz20:44
CIA-87shogun: Soeren Sonnenburg master * r2f343fb / (13 files in 7 dirs):20:44
CIA-87shogun: Merge pull request #295 from frx/conv_to_3220:44
CIA-87shogun: Conversion of weight vector and related parameters to float in Online Framework - http://bit.ly/nAp8wr20:44
shogun-buildbotbuild #28 of libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org:5347/builders/libshogun/builds/28  blamelist: fraggerx@gmail.com20:46
@sonney2kgrmpf20:48
shogun-buildbotbuild #29 of libshogun is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org:5347/builders/libshogun/builds/2920:48
blackburngrmpf is something bad20:48
blackburn:D20:48
@sonney2kwhy does the buildbot sometimes checkout stone age old versions and then fail?20:49
@sonney2kand then directly afterwards use the correct version?20:49
blackburnno idea20:49
blackburnsonney2k: what do you think, should I add reconstruction error option for MDS/LLE/..?20:51
@sonney2kblackburn, this is nice to have but nothing essential - so yes but no high prio and of course up to you :)20:52
blackburnI think about integrating heiko's thing and my algos..20:52
@sonney2kblackburn, ok then please don't do that yet20:53
@sonney2kthis is post 1.0 stuff20:53
blackburnit is very inconvenient to get nice k value with only tries20:53
blackburnbut no automagic stuff for that20:53
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@sonney2kblackburn, I understand that but recall we have soft pencils down today20:54
@sonney2kand 1 more week of gsoc20:54
@sonney2kprio should be fixing bugs / documentation20:54
blackburnI'll finish doc stuff for my algos today20:54
@sonney2kblackburn, that other stuff is something for fall 2011 :)20:55
blackburnyeah sure20:56
@sonney2kblackburn, but it is certainly possible to connect CMethod  CPreprocessors20:56
@sonney2kand as soon as you do this you will have 'heiko' support :D20:57
blackburnCMethod?20:57
@sonney2kCMachine20:57
blackburnI should think about it20:58
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@sonney2kblackburn, btw the buildbot was right20:58
blackburnabout?20:58
@sonney2kabout the failure20:58
@sonney2kbuild failure20:58
@sonney2kit was trying to compile an older version from f-x20:58
blackburnnice20:59
@sonney2kand that one was really broken20:59
@sonney2know we only need stable build-slaves20:59
* blackburn have already spent 5 minutes to come up with sentence for doc20:59
blackburnit could be harder than I thought haha21:00
@sonney2kI think I will utilize the google money to get a more powerful server/hosting for shogun-toolbox.org21:00
blackburnso will you get it?21:00
@sonney2kblackburn, just write - it doesn't have to be perfect in the first iteration. recall that serialhex has your back21:00
@sonney2kblackburn, I don't know21:00
blackburnit is not fair TU get it21:00
@sonney2kin the worst case I pay these 120 EUR / year myself21:01
blackburnI could donate a part21:01
blackburnnot fair again21:02
blackburnsonney2k: I've read that instead of "class CDistance;" stuff here we could write "using class CDistance;"21:05
@sonney2kblackburn, I hope the project gets the money at some stage. I mean if we can afford a more powerful server to do all trac/git/ etc hosting21:05
@sonney2kthat would be perfectly fine21:06
blackburnoh no21:06
@sonney2kI hope we can convince some people to be build slaves21:06
blackburnwe can't21:06
blackburn:D21:06
blackburnI can but I have notebook - will not really help21:06
blackburnsonney2k: so what's up with our projects?21:09
@sonney2kblackburn, which porjects?21:09
blackburnI finished21:09
blackburnalesis?21:09
@sonney2kvojtech seemed happy21:09
blackburnf-x?21:09
@sonney2ksploving did all the $lang21:09
@sonney2kso also good21:09
blackburnso it is all ok?21:10
@sonney2kf-x did much more than I thought already before midterm21:10
@sonney2kthe framework was a lot of work21:10
@sonney2kso nice that he even started to port over vw21:10
@sonney2kand converted SGD etc21:10
@sonney2kheiko also did a great job21:11
@sonney2kto conclude - 100% success. however we still need some polishing to do a release21:11
blackburnyeah, f-x and heiko did a lot. I don't really think I did as much as they:)21:12
blackburnsonney2k: description is given in / description is given at?21:14
@sonney2kblackburn, ?21:15
blackburnneed english grammar advice hah21:15
@sonney2kfor examples?21:15
@sonney2kargh21:21
@sonney2knightly_all still doesn't compile21:21
@sonney2khttp://www.shogun-toolbox.org:5347/builders/nightly_all/builds/3/steps/compile/logs/stdio21:21
@sonney2kbut that very fast :D21:22
blackburn??21:22
blackburnwhy?21:22
@sonney2kblackburn, compiling was fast because it failed - I was just joking :)21:30
blackburnwhy it fails?21:30
@sonney2kCIA-87, tell us please21:31
@sonney2khmmhh why is CIA-87 quiet?21:31
@sonney2k9ca73170fb0f87974a3fcd3342136130d6b16544 fix build failure in ui trying to access protected member variable21:31
@sonney2k(just pushed)21:32
CIA-87shogun: Soeren Sonnenburg master * r9ca7317 / (src/shogun/mathematics/Math.h src/shogun/ui/SGInterface.cpp): fix build failure in ui trying to access protected member variable - http://bit.ly/pUtVdo21:33
@sonney2kblackburn, ^ there he is21:37
blackburnI see21:37
-!- sonney2k is now known as sonney2k|bughunt21:39
blackburnhaha21:39
-!- sonney2k|bughunt is now known as sonney2k21:39
blackburnwtf was it21:39
@sonney2kI am fixing one bug per day for this nightly_all21:39
@sonney2klets see if it will compile at some point or not21:40
@sonney2kblackburn, look we only have 853 warnings now ;D21:40
blackburnyeah I will spend some time today to fix some of them21:41
shogun-buildbotbuild #3 of nightly_none is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org:5347/builders/nightly_none/builds/321:42
-!- f-x [~user@117.192.199.77] has joined #shogun21:48
-!- in3xes [~in3xes@182.156.163.54] has quit [Ping timeout: 260 seconds]22:03
shogun-buildbotbuild #30 of libshogun is complete: Failure [failed compile]  Build details are at http://www.shogun-toolbox.org:5347/builders/libshogun/builds/30  blamelist: sonne@debian.org22:03
blackburnsonney2k: github down?22:04
blackburnI can't pull from it22:04
blackburnhm all ok22:06
blackburnfalse alarm22:06
-!- in3xes [~in3xes@49.201.194.3] has joined #shogun22:16
blackburnehh22:18
blackburnCIA-87: what's up with you?22:18
shogun-buildbotbuild #32 of libshogun is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org:5347/builders/libshogun/builds/3222:22
-!- in3xes [~in3xes@49.201.194.3] has quit [Quit: Leaving]22:28
CIA-87shogun: Sergey Lisitsyn master * r9d2dd54 / (8 files): Updated doc for dimensionality reduction algorithms - http://bit.ly/pNjvMO22:28
blackburnsonney2k: I like things a little more today :D22:33
shogun-buildbotbuild #26 of python_modular is complete: Failure [failed git]  Build details are at http://www.shogun-toolbox.org:5347/builders/python_modular/builds/26  blamelist: blackburn91@gmail.com22:39
CIA-87shogun: Sergey Lisitsyn master * r4826d03 / (9 files in 5 dirs): Moar doc - http://bit.ly/n4ZfJn22:41
@sonney2kblackburn, what is wrong with JL's covertree?23:38
blackburnsonney2k: nothing but later23:39
blackburnI will restore it when we have shogun 1.* milestone23:39
@sonney2kblackburn, yeah but then just create a new milestone and assign it there23:39
@sonney2kor mark it unassigned23:39
blackburnokay23:40
blackburnsonney2k: I sent an email to heiko about reported bug23:40
@sonney2kblackburn, do you think it would be worth to work on a pthread based parallelization framework?23:40
@sonney2kthanks23:40
@sonney2kI mean for shogun23:41
blackburncan you mind any framework for it?23:41
@sonney2kblackburn, yeah it is probably not so easy23:41
shogun-buildbotbuild #27 of python_modular is complete: Success [build successful]  Build details are at http://www.shogun-toolbox.org:5347/builders/python_modular/builds/2723:41
@sonney2kthere usually is very custom 'user' data23:41
blackburnwhoaa!23:42
* sonney2k checks the warnings count23:42
blackburn81923:42
@sonney2kyeah23:42
@sonney2kgoing down baby23:42
blackburnokay I'll make it <800 now for feeling more happy23:43
CIA-87shogun: Shashwat Lal Das master * rf2cce5f / (28 files in 7 dirs): Fixed most online framework warnings. - http://bit.ly/p4A7p623:57
CIA-87shogun: Shashwat Lal Das master * r693acf9 / doc/Doxyfile : Reverted Doxyfile. - http://bit.ly/qCJkoR23:57
CIA-87shogun: Soeren Sonnenburg master * rd05ad85 / (27 files in 6 dirs):23:57
CIA-87shogun: Merge pull request #297 from frx/streaming_vw23:57
CIA-87shogun: Missing/incorrect doc additions and corrections, plus load_regressor() for VW - http://bit.ly/oHbTn723:57
@sonney2kblackburn, maybe f-x just did23:57
@sonney2kwe will see :)23:58
blackburnI'm about to remove some more23:58
--- Log closed Tue Aug 16 00:00:38 2011

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