Open in new window / Try shogun cloud
--- Log opened Mon Sep 23 00:00:11 2013
-!- gsomix [~gsomix@83.234.54.128] has joined #shogun00:14
gsomixsonimperator, van_solo hey, star wars party?00:15
van_sologsomix: yeah and we are looking for a chewbacca00:15
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gLandovan_solo, not today00:28
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van_solohaha nice choice gLando00:32
van_soloI don't think we are going to find one00:32
van_solowe should just rename the buildbot :p00:32
gLandovan_solo, yep. buildbot only does that growls and roars00:34
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lisitsynHeikowankenobi: oh man you too00:48
@Heikowankenobihaha :)00:48
lisitsynHeikoWanHeikobi Heikowankenobi00:50
van_sologLando: will you export LineReader to the modular interfaces?01:01
gLandovan_solo, not sure.01:01
van_sologLando: It had freed my hands with reading \0 delimited files :)01:02
gLandovan_solo, ok.01:02
gLandovan_solo, how urgent is this needed?01:03
van_sologLando: I've found some python specific stuff I'll try those for now01:03
van_sologLando: not really urgent. it was more of a question01:03
van_sologLando: I can do it locally if it comes to that, so no worries :)01:04
gLandovan_solo, ok.01:04
gLandovan_solo, you know, I'm guilty of... sealing you in carbonite. so I'll do it for you.01:08
van_sologLando: haha do that and maybe I'll forgive you01:09
gLando/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../x86_64-linux-gnu/crt1.o: In function `_start':01:51
gLando(.text+0x20): undefined reference to `main'01:51
gLandocollect2: error: ld returned 1 exit status01:51
gLandovery nice error01:51
gLandowhile linking converter_jade_bss01:52
-!- lambday [67157f4c@gateway/web/freenode/ip.103.21.127.76] has joined #shogun02:18
lambdayHeikowankenobi: hi02:18
lambday:D02:18
@Heikowankenobilambday: hey! :)02:18
lambdayhahaha02:18
lambdaynice name :D02:18
@Heikowankenobiyeah people are freaking out here! :)02:19
lambdayHeikowankenobi: I started it as luke :D02:19
@Heikowankenobilambday: haha really? :D02:19
lambdayyep :D02:19
gLandosonimperator, https://github.com/shogun-toolbox/shogun/pull/1651 updated02:19
lambdayHeikowankenobi: is it okay if I add the histogram later?02:20
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shogun-notifier-shogun: Heiko Strathmann :gp_notebook * 7d24649 / tests/integration/python_modular/tester.py: https://github.com/shogun-toolbox/shogun/commit/7d24649783b153e3648fef55bcd6f592efbff42902:20
shogun-notifier-shogun: suggestion for output in case of failing integration test02:20
shogun-notifier-shogun: Heiko Strathmann :gp_notebook * ded9eb2 / doc/ipython-notebooks/gaussian_process/gaussian_process_classification.ipynb: https://github.com/shogun-toolbox/shogun/commit/ded9eb2ebe3d0558d27db09e45396e5614e07b9a02:20
shogun-notifier-shogun: initial draft for gp notebook02:20
@Heikowankenobilambday: got other plans for tomorrow? :)02:21
lambdayHeikowankenobi: yeah... really gotta get into insti stuffs now02:21
lambdayHeikowankenobi: I'll remove the outputs02:21
@Heikowankenobilambday: I would like to see the thing finished before tomorrow night, but dont worry if you are in trouble02:22
@Heikowankenobilambday: the histogram should be easy to fix though02:22
@Heikowankenobijust hist of the samples you already have in there02:22
@Heikowankenobitwo lines02:22
@Heikowankenobilambday: but yeah not really ultra important02:22
lambdayHeikowankenobi: yeah once I figure out how to plot it properly its not much work02:22
lambdayhistograms are always confusing to me :-/02:23
shogun-notifier-shogun: Heiko Strathmann :develop * 7d24649 / tests/integration/python_modular/tester.py: https://github.com/shogun-toolbox/shogun/commit/7d24649783b153e3648fef55bcd6f592efbff42902:23
shogun-notifier-shogun: suggestion for output in case of failing integration test02:23
shogun-notifier-shogun: Heiko Strathmann :develop * 85eeb68 / tests/integration/python_modular/tester.py: https://github.com/shogun-toolbox/shogun/commit/85eeb689b0fac2c33da68faec10fdb1d35bcbc2902:23
shogun-notifier-shogun: Merge pull request #1658 from karlnapf/develop02:23
shogun-notifier-shogun:02:23
shogun-notifier-shogun: suggestion for output in case of failing integration test02:23
lambdayHeikowankenobi: but checking ImportErrors... confused..02:23
lambdayHeikowankenobi: should I just guard the whole thing in try catch?02:23
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@Heikowankenobilambday: didnt I give you code?02:27
@Heikowankenobilambday: ah yes, that is what I had in mind, but that is in fact stupid02:27
@Heikowankenobilambday: so lets just install everything on the notebook machine02:27
@Heikowankenobilambday: dont worry about this then, sorry for the confusion02:27
@Heikowankenobihistogram plotting is very easy02:28
@Heikowankenobitry this:02:28
lambdayHeikowankenobi: yeah it should be, otherwise just blank outputs in the notebooks won't be useful :(02:28
@Heikowankenobihist(randn(1000)*0.2)02:28
@Heikowankenobiand then hist(randn(1000))02:28
@Heikowankenobiautomagically puts them in one plot with different colours02:28
lambdayHeikowankenobi: alright trying02:28
@Heikowankenobilambday: exactly, blanking is not useful02:28
@Heikowankenobilambday: and then legend(["a", "b"])02:31
@Heikowankenobiand then maybe02:31
@Heikowankenobiplot([true_logdet, true_logdet], [0,some-value], linewidth=3) for the true value line02:31
shogun-buildbotbuild #1795 of bsd1 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/1795  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>02:31
lambdayHeikowankenobi: wow this works02:32
lambdayHeikowankenobi: and plotting straight line?02:32
@Heikowankenobilambday: see above02:32
lambdayoh02:32
lambdaysorry I missed that02:32
gLandonite02:33
@Heikowankenobino worries02:33
lambdaychecking02:33
@HeikowankenobigLando: nite! :)02:33
lambdaygLando: fernando?02:34
gLandolambday, nice try, but no. :)02:35
lambdaygLando: wiking02:35
lambday:D02:35
lambdaygLando: good night02:36
shogun-notifier-shogun: Roman Votyakov :develop * d255abb / / (76 files): https://github.com/shogun-toolbox/shogun/commit/d255abb1d4c562a2ea8bc280b3994a0569ed8ec602:44
shogun-notifier-shogun: refactor gradient model selection framework02:44
shogun-notifier-shogun: Heiko Strathmann :develop * 6ddd47d / / (76 files): https://github.com/shogun-toolbox/shogun/commit/6ddd47d286ebf3ad045dd921eeda2e4ef14ee62d02:44
shogun-notifier-shogun: Merge pull request #1640 from votjakovr/feature/gp_refactoring02:44
shogun-notifier-shogun:02:44
shogun-notifier-shogun: Refactor gradient model selection02:44
gLandoHeikowankenobi, btw I sent small patch. https://github.com/shogun-toolbox/shogun/pull/1662 And it's green for clang now.02:44
@HeikowankenobigLando: checking02:44
shogun-notifier-shogun: Evgeniy Andreev :develop * 27deaee / examples/undocumented/libshogun/converter_jade_bss.cpp: https://github.com/shogun-toolbox/shogun/commit/27deaeeb8291daead04abd4b3df306bc4feca74e02:46
shogun-notifier-shogun: fix converter_jade_bss example02:46
shogun-notifier-shogun: Heiko Strathmann :develop * 5d1a561 / examples/undocumented/libshogun/converter_jade_bss.cpp: https://github.com/shogun-toolbox/shogun/commit/5d1a5612aaab2c74835ea2373be1aad46302d99702:46
shogun-notifier-shogun: Merge pull request #1662 from gsomix/feature/jade_bss02:46
shogun-notifier-shogun:02:46
shogun-notifier-shogun: Fix converter_jade_bss example02:46
gLandoHeikowankenobi, cool! for now I can sleep with no worries...02:46
@HeikowankenobigLando: hehe :) Shogun worries you in your dreams? :D02:47
@Heikowankenobisame here, haha ;)02:47
gLandoHeikowankenobi, sometimes. no more often than girls02:49
gLandook02:49
@HeikowankenobigLando: phew! thats good02:49
@HeikowankenobigLando: speaking of, I am joining mine now :) see you later02:49
shogun-buildbotbuild #1526 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1526  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>02:55
lambdayHeikowankenobi: updated the notebook02:57
@Heikowankenobilambday: wow that was fast! :)02:57
@Heikowankenobilambday: mmmh parsing the diff is like impossible, I will just trust you! :)02:59
shogun-notifier-shogun: lambday :develop * 2e242a3 / doc/ipython-notebooks/logdet/logdet.ipynb: https://github.com/shogun-toolbox/shogun/commit/2e242a354911479cf11df2ce76124662dcdbd16002:59
shogun-notifier-shogun: ipython notebook added (log-det)02:59
shogun-notifier-shogun: Heiko Strathmann :develop * 301733a / doc/ipython-notebooks/logdet/logdet.ipynb: https://github.com/shogun-toolbox/shogun/commit/301733ade16aa11a9f0a3a9c85c01f875f9afaec02:59
shogun-notifier-shogun: Merge pull request #1659 from lambday/feature/log_determinant02:59
shogun-notifier-shogun:02:59
shogun-notifier-shogun: ipython notebook added (log-det)02:59
@Heikowankenobilambday: could you quickly update the old gist you sent around? I sent that to some people03:00
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shogun-buildbotbuild #1876 of deb3 - modular_interfaces is complete: Failure [failed test python modular test ruby modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1876  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>03:20
shogun-buildbotbuild #1527 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1527  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>03:22
shogun-notifier-shogun: Heiko Strathmann :gp_notebook * d8fe94e / doc/ipython-notebooks/gaussian_process/gaussian_process_classification.ipynb: https://github.com/shogun-toolbox/shogun/commit/d8fe94edd497ae069634d47798eed7c310e0888303:22
shogun-notifier-shogun: initial draft for gp notebook03:22
shogun-buildbotbuild #1877 of deb3 - modular_interfaces is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/187703:29
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travis-ci[travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167038103:36
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shogun-buildbotbuild #1796 of bsd1 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/1796  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Roman Votyakov <votjakovr@gmail.com>03:45
shogun-buildbotbuild #1248 of rpm1 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/rpm1%20-%20libshogun/builds/1248  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Roman Votyakov <votjakovr@gmail.com>03:48
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shogun-buildbotbuild #134 of precise - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/precise%20-%20libshogun/builds/134  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Roman Votyakov <votjakovr@gmail.com>03:57
shogun-buildbotbuild #169 of FC19 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/FC19%20-%20libshogun/builds/169  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Roman Votyakov <votjakovr@gmail.com>03:58
shogun-buildbotbuild #168 of FCRH - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/FCRH%20-%20libshogun/builds/168  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Roman Votyakov <votjakovr@gmail.com>03:58
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shogun-buildbotbuild #464 of nightly_all is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/nightly_all/builds/46404:05
shogun-buildbotbuild #1528 of cyg1 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1528  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Roman Votyakov <votjakovr@gmail.com>04:15
shogun-buildbotbuild #33 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/33  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>04:21
shogun-buildbotbuild #19 of clang34 - undefined behaviour analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20undefined%20behaviour%20analysis/builds/19  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>04:31
shogun-buildbotbuild #23 of clang34 - thread analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20thread%20analysis/builds/23  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>04:48
shogun-buildbotbuild #27 of debian wheezy - memcheck is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/2704:52
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travis-ci[travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167041304:54
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travis-ci[travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167073305:41
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ChengI've got a newbie question: I can't seem to use cmake properly, using the instructions in README.cmake05:53
ChengI get the error:05:53
ChengCMake Error: Attempt to add a custom rule to output "/Users/cheng.ong/External/shogun/src/interfaces/python_modular/abstract_types_extension.i.rule" which already has a custom rule.05:53
ChengAnd so on...05:54
ChengI'm on the develop branch of git.05:54
Chengcmake version 2.8.11.2 on OSX06:00
wikingCheng: remove the symlinks in /Users/cheng.ong/External/shogun/src/interfaces/python_modular/06:21
wikingbut only thr symlinks06:22
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travis-ci[travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167077006:27
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Chengwiking: Thanks for the suggestion, but I don't see any symlinks06:52
shogun-buildbotbuild #34 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/34  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>06:56
gLandogood morning07:05
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shogun-buildbotbuild #35 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/35  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>07:37
wikingCheng: /Users/cheng.ong/External/shogun/src/interfaces/python_modular/abstract_types_extension.i.rule is a symlink to /Users/cheng.ong/External/shogun/src/interfaces/modular/abstract_types_extension.i.rule07:48
shogun-buildbotbuild #20 of clang34 - undefined behaviour analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20undefined%20behaviour%20analysis/builds/20  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Roman Votyakov07:49
shogun-buildbot<votjakovr@gmail.com>07:49
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travis-ci[travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167107007:51
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Cheng400L-97169:python_modular cheng.ong$ pwd /Users/cheng.ong/External/shogun/src/interfaces/python_modular 400L-97169:python_modular cheng.ong$ ls *.rule ls: *.rule: No such file or directory07:55
ChengSorry, missing newlines. Basically I don't have any files with .rule extensions07:56
shogun-buildbotbuild #24 of clang34 - thread analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20thread%20analysis/builds/24  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Heiko Strathmann <heiko.strathmann@gmail.com>, lambday <heavensdevil6909@gmail.com>, Roman Votyakov <votjakovr@gmail.com>08:04
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travis-ci[travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167142308:42
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shogun-notifier-shogun: Viktor Gal :develop * c2f889d / src/shogun/base/class_list.cpp.py: https://github.com/shogun-toolbox/shogun/commit/c2f889d79ac0f6ec2de1f79b3e9dc6d818fa93d409:02
shogun-notifier-shogun: Add HAVE_NLOPT to class_list generator script for blacklisting09:02
shogun-buildbotbuild #1797 of bsd1 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/1797  blamelist: Viktor Gal <viktor.gal@maeth.com>09:08
shogun-buildbotbuild #170 of FC19 - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/FC19%20-%20libshogun/builds/17009:20
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shogun-buildbotbuild #1249 of rpm1 - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/rpm1%20-%20libshogun/builds/124909:25
sonne|workfoulwall: OK?09:25
besser82G'Morning, Folks :D09:26
sonne|workbesser82: moin!09:26
besser82soone|work: Did you get my msg, from yesterday?09:26
besser82soone|work: About TJ's concern making LightSVM GPL'ed or sth....09:26
sonne|workbesser82: yes09:27
besser82soone|work: Did hegive you any explanation, why?09:27
besser82sonne|work: Did hegive you any explanation, why?09:27
sonne|workbesser82: yeah09:27
sonne|worknot everyone likes that work can be used by others even commerically09:28
sonne|workbut besser82 write him an email maybe he changed his mind09:28
besser82sonne|work: I'll do,  maybe AGPLv3+ might change his mind :)09:29
shogun-buildbotbuild #135 of precise - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/precise%20-%20libshogun/builds/13509:29
sonne|workbesser82: no09:29
besser82sonne|work: hmm...09:29
besser82sonne|work: I'll write him; let's wait for the comeback....09:30
shogun-buildbotbuild #169 of FCRH - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/FCRH%20-%20libshogun/builds/16909:33
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hushelliglesiasg: hey09:48
@iglesiasghushell, hi!09:49
hushelliglesiasg: how is going?09:49
@iglesiasghushell, just fine, for you?09:49
hushelliglesiasg: could you help me merge the last PR?09:49
@iglesiasghushell, did you update the file loading after you submited the new data file in shogun-data?09:49
hushelliglesiasg: just finished a workshop paper, I am working on my gsoc now :)09:49
hushelliglesiasg: yep, you merged the .mat file for me09:50
shogun-buildbotbuild #1529 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1529  blamelist: Viktor Gal <viktor.gal@maeth.com>09:50
@iglesiasghushell, I mean in the notebook09:50
@iglesiasghushell, since the file changed, I guess the notebook needed to be updated as well09:50
hushelliglesiasg: let me double check, but I remember it should be there09:50
hushelliglesiasg: yeah, I used the correct file name09:51
@iglesiasghushell, oook then we should be ready to go09:52
hushelliglesiasg: thanks!09:52
shogun-notifier-shogun: hushell :develop * 9f3af69 / / (10 files): https://github.com/shogun-toolbox/shogun/commit/9f3af69b3624e10412d0efaa04bd40d13ea8ec1909:52
shogun-notifier-shogun: ipython notebook of factor graph model09:52
shogun-notifier-shogun: Fernando Iglesias :develop * e3f0d4f / / (10 files): https://github.com/shogun-toolbox/shogun/commit/e3f0d4ff9cc81f6b89bbb4e4a33dad454b7bbe0e09:52
shogun-notifier-shogun: Merge pull request #1607 from hushell/develop09:52
shogun-notifier-shogun:09:52
shogun-notifier-shogun: ipython notebook of factor graph model09:52
hushelliglesiasg: I'll commit the SGD stuff before the deadline, still working on it :)09:53
@iglesiasghushell, all right, good luck!09:53
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hushelliglesiasg: thanks, I got an idea to rearrange a bit our SOSVM code, but let's talk about this later this week09:55
@iglesiasgok09:55
shogun-notifier-shogun: van51 :develop * 069cb0e / doc/ipython-notebooks/classification/HashedDocDotFeatures.ipynb: https://github.com/shogun-toolbox/shogun/commit/069cb0ef89cc9101c542c5e6daced0c8ea492a5010:00
shogun-notifier-shogun: Added notebook for HashedDocDotFeaturs10:00
shogun-notifier-shogun: Soeren Sonnenburg :develop * fff5bd5 / doc/ipython-notebooks/classification/HashedDocDotFeatures.ipynb: https://github.com/shogun-toolbox/shogun/commit/fff5bd5be23aa2368d72edc9f934f9ee2e63cb4a10:00
shogun-notifier-shogun: Merge pull request #1660 from van51/feature/notebook10:00
shogun-notifier-shogun:10:00
shogun-notifier-shogun: Added notebook for HashedDocDotFeaturs10:00
sonne|workgsomix: any news on protobuf?10:10
sonne|workfoulwall: ping?10:10
gsomixsonne|work, yep. added set/get_matrix methods and types into Chunks.proto10:11
sonne|workgsomix: ok so I guess vector / matrix are done then right?10:11
gsomixsonne|work, writing macro and unit-tests10:13
gsomixsonne|work, btw why we need uint64_t for lenght of vector?10:13
gsomix*length10:13
sonne|workgsomix: if so please send a PR for that and then we still have to do SGStringLists (which is easy - just the same as vector but multiple of them) and sparse10:13
sonne|workgsomix: it might become bigger than uint32 at some point and protbuf will not waste bytes anyway so whenever you write uint32 there you could as well just use uint6410:14
gsomixsonne|work, ah, ok.10:14
sonne|workgsomix: the only question remains if we want to represent sparse/strings as efficient as possible or as convenient as possible10:15
gsomixsonne|work, so it means that sizes of messages should be uint64_t too, right?10:15
sonne|workgsomix: I mean one could write out huge arrays with the values and then with the indices separately10:15
shogun-buildbotbuild #1798 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/1798  blamelist: hushell <dom343@gmail.com>10:15
sonne|workgsomix: yeah why not10:15
sonne|work(but 1MB * 2**32 is hard to reach I guess...)10:16
sonne|workbut doesn't hurt10:16
gsomixok10:16
sonne|workgsomix: so any thoughts about sparse?10:17
sonne|workgsomix: what do you prefer? writing out all nnz values in one go?10:17
sonne|workso basically column compressed storage like?10:17
sonne|workI guess that would be most efficient (space wise etc) for the file10:18
gsomixsonne|work, << convenient as possible | <ShogunVersion> <SparseMatrix header> <SparseVector 1 header> <data messages> ... and so on10:18
gsomixbut I'm not sure10:18
sonne|workand I also guess speed wise since you can write big chunks of 1 MB all the time10:19
sonne|workone could do the same for strings10:19
sonne|workI mean write out the huge block of strings (all strings concatenated)10:19
sonne|workand the string lengths10:19
sonne|workI guess we should do it this way since one might have say 100 million strings of small length10:20
gsomixsonne|work, yep, I think so.10:20
sonne|workand then the overhead would be drastic if not done otherwise10:20
sonne|worksame with sparse10:20
sonne|workgsomix: so do strings first right after your next PR10:21
sonne|workand hurry up man!10:21
gsomixsonne|work, ok10:21
shogun-buildbotbuild #1799 of bsd1 - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/179910:22
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travis-ci[travis-ci] it's Viktor Gal's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167779310:22
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gsomixwiking, yo10:24
gsomixsonne|work, btw what's better solution for message objects? keep it in stack and copy while returning from read_header()? or work with it on the heap+pointers?10:40
shogun-buildbotbuild #1530 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1530  blamelist: hushell <dom343@gmail.com>, Fernando Iglesias <fernando.iglesiasg@gmail.com>10:40
sonne|workgsomix: I have no idea if they keep data on the stack - if they do then pointers!10:41
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van51hello10:45
sonne|workhey van51!10:45
sonne|workI only had very minor comments - I guess you've seen.10:45
van51sonne|work: yeah I've seen them. Will make the changes now :)10:45
shogun-notifier-shogun: Soeren Sonnenburg :develop * 690e9de / README.cmake: https://github.com/shogun-toolbox/shogun/commit/690e9de1bd60b228f019c5db62ce5a8cfcff7e6e10:53
shogun-notifier-shogun: mention how to bundle eigen310:53
shogun-buildbotbuild #1531 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1531  blamelist: Soeren Sonnenburg <sonne@debian.org>, van51 <vangelis_51@hotmail.com>11:13
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travis-ci[travis-ci] it's Fernando Iglesias's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167889711:17
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shogun-buildbotbuild #1880 of deb3 - modular_interfaces is complete: Failure [failed test libshogun]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1880  blamelist: Soeren Sonnenburg <sonne@debian.org>, hushell <dom343@gmail.com>, Fernando Iglesias <fernando.iglesiasg@gmail.com>, van51 <vangelis_51@hotmail.com>11:27
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sonne|workvan51: done?11:41
van51sonne|work: yeah, pushed. For the setters I had to propagate them up to the converter that's why it touched more files11:42
shogun-buildbotbuild #1532 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1532  blamelist: Soeren Sonnenburg <sonne@debian.org>11:46
sonne|work(van51 - I don't get notified at work so just tell me here)11:47
sonne|workgsomix: you too ^11:47
shogun-notifier-shogun: van51 :develop * 58458df / / (6 files): https://github.com/shogun-toolbox/shogun/commit/58458df0de1c407dbf57d4dafa091defa9572d2811:48
shogun-notifier-shogun: Added full functionality of HashedDocDotFeatures to the streaming version and fixed a unit test file that failed at times11:48
shogun-notifier-shogun: Soeren Sonnenburg :develop * a9b8552 / / (6 files): https://github.com/shogun-toolbox/shogun/commit/a9b8552b98213a16f67f8bca42c913fb4a5bb2fd11:48
shogun-notifier-shogun: Merge pull request #1650 from van51/feature/fix_test11:48
shogun-notifier-shogun:11:48
shogun-notifier-shogun: StreamingHashedDocDotFeatures11:48
shogun-notifier-shogun: van51 :develop * 08f892c / / (5 files): https://github.com/shogun-toolbox/shogun/commit/08f892c52085639128d901ff6dc9525f31ab349211:49
shogun-notifier-shogun: Random kitchen sinks11:49
shogun-notifier-shogun: Soeren Sonnenburg :develop * ec60496 / / (5 files): https://github.com/shogun-toolbox/shogun/commit/ec60496d26aebc2cd79e90949895ac4c891d243911:49
shogun-notifier-shogun: Merge pull request #1606 from van51/feature/rks11:49
shogun-notifier-shogun:11:49
shogun-notifier-shogun: Random kitchen sink framework11:49
sonne|workgsomix: any news?11:49
sonne|workand foulwall ping again?!11:49
shogun-buildbotbuild #36 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/36  blamelist: Viktor Gal <viktor.gal@maeth.com>11:50
shogun-buildbotbuild #21 of clang34 - undefined behaviour analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20undefined%20behaviour%20analysis/builds/21  blamelist: Viktor Gal <viktor.gal@maeth.com>12:01
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travis-ci[travis-ci] it's Soeren Sonnenburg's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1167909512:07
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shogun-buildbotbuild #25 of clang34 - thread analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20thread%20analysis/builds/25  blamelist: Viktor Gal <viktor.gal@maeth.com>12:17
shogun-buildbotbuild #30 of debian wheezy - memcheck is complete: Failure [failed memory check]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/30  blamelist: Viktor Gal <viktor.gal@maeth.com>12:19
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shogun-notifier-shogun: Roman Votyakov :develop * 24632fb / / (2 files): https://github.com/shogun-toolbox/shogun/commit/24632fbfc34fa88d3da1dd29d9cf96b51b9d8e6212:30
shogun-notifier-shogun: increase accuracy of gradient search and check parameters in unit test12:30
shogun-notifier-shogun: Heiko Strathmann :develop * c30dbe2 / / (2 files): https://github.com/shogun-toolbox/shogun/commit/c30dbe2847c7d78b49a338be5a089eef5a1cdf2d12:30
shogun-notifier-shogun: Merge pull request #1663 from votjakovr/feature/gp_refactoring12:30
shogun-notifier-shogun:12:30
shogun-notifier-shogun: Increase default accuracy of gradient search and check parameters in unit test12:30
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shogun-buildbotbuild #1533 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1533  blamelist: Soeren Sonnenburg <sonne@debian.org>, van51 <vangelis_51@hotmail.com>12:53
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shogun-buildbotbuild #1881 of deb3 - modular_interfaces is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1881  blamelist: Soeren Sonnenburg <sonne@debian.org>13:25
shogun-buildbotbuild #1882 of deb3 - modular_interfaces is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/188213:35
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gsomixsonne|work, I was debugging. https://github.com/shogun-toolbox/shogun/pull/165113:54
sonne|workgsomix: ok just one minor comment and then it is good13:56
sonne|workwiking: how can we run protoc before compiling shogun?13:57
gsomixsonne|work, wiking said that he need to write some hack for cmake.13:58
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gsomixsonne|work, but there is another problem. for now we cannot compile .cc files, but protoc produces code only in this way.13:58
sonne|workgsomix: well we generate lib/versionstring.h already so it should be doable13:58
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besser82sonne|work: I can implement a way on refactoring CMake-buildsys :)13:59
shogun-buildbotbuild #1534 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1534  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>13:59
besser82sonne|work: will be finished within next ~2-3 days14:00
sonne|workbesser82: not sure what you are saying but any help welcome :)14:00
besser82sonne|work: I currently refactoring the CMake-buildsys in agreement with wiking, to get out all glitches and/or quick'n'dirty workarounds ;)14:01
sonne|workahh nice14:01
gsomixsonne|work, ok. I need cup of tea and then will do string lists14:02
besser82sonne|work: so everything will be run out of src tree and lots of other stuff to come ;)14:02
besser82sonne|work: even with testsuite being able to be run from build-tree ;)14:02
sonne|workgsomix: please fix the PR and then comment the PROTOBUF detection and let me merge it14:03
sonne|workthen continue14:03
sonne|workbesser82: ahh nice highly needed14:03
sonne|workbesser82: even more important currently is that one cannot build shogun when it is already installed in /usr/local due to include clashes14:04
besser82sonne|work: np. will be fixed, too ;)14:04
sonne|workso include path order needs to be changed14:04
sonne|workbesser82: ahh ok then just do whatever you do :)14:04
besser82sonne|work, wiking: do you agree with me to restructure source-tree as well? Like placing headers in seperate dir and suchss14:05
besser82s/ss/?/g14:05
sonne|workbesser82: errm you mean shogun/src ?14:06
besser82sonne|work, wiking: yes14:06
sonne|workwhat is wrong / what would you do?14:06
besser82sonne|work: nothing really wrong, but would be abit "?bersichtlicher" ;)14:07
sonne|workwell make an example14:07
besser82sonne|work: now it is src/shogun/*/*.{h,c,cpp,py,...}14:08
sonne|workyes14:08
sonne|workand cxx once swig is done14:09
sonne|workand .cc for protobuf later too14:09
besser82sonne|work: I think having it like src/include, src/shogun and so on14:09
besser82sonne|work: swig and protobuf will get generated out of tree ;)14:09
besser82sonne|work: like build/$cloned_dir_structure/...14:10
sonne|worksounds very reasonable14:10
sonne|workbut I cannot speak for all14:10
besser82sonne|work: who else to ask?14:11
sonne|workiglesiasg, lisitsyn, wiking, van51 - any thoughts on besser82's suggestion?14:11
@iglesiasglet me read14:11
sonne|workbesser82: well HeikoS and the ones above :)14:11
@iglesiasgbesser82, so headers in a separate soource tree?14:11
@iglesiasgI think I have to look up "?bersichtlicher" :D14:12
besser82iglesiasg: yes, and probably *.py as well14:12
besser82iglesiasg: ?bersichtlicher == clear, more semantic  ;)14:13
@iglesiasgbesser82, hehe yeah just saw14:13
@iglesiasgbesser82, so it is basically a matter of taste, right?14:13
@iglesiasgno technical advantages/disadvantages?14:13
besser82iglesiasg: a matter of taste, common-sense and good pratice ;)14:13
besser82iglesiasg: mashing up all in one dir or so was from "old" autocrap" times ;)14:14
@iglesiasgbesser82, hehe14:14
@iglesiasgfor me it is fine, sure14:14
besser82iglesiasg: kk, just the rest's agreement required, then ;)14:15
@iglesiasgI think I have seen this headers/implementation files separation in PCL before14:15
@iglesiasgthe first second I was like wtf!?! hehe14:15
besser82iglesiasg: and some other projects as well ;)  might be a bit confusing on the first look :D14:16
@iglesiasg:)14:16
besser82iglesiasg: main goal is to have clear seperation between sources and build-tree, headers and impl, different stuff from impl14:17
sonne|workbesser82: what needs attention here is that we want at some point follow the d pointer approach14:17
sonne|workbesser82: i.e. only have interfaces .h files exposed to the outside14:17
sonne|workand encapsulate the rest in Impl classes14:18
sonne|workso one would just have to copy headers over14:18
@iglesiasgsonne|work, let's check how they do it in QT then14:18
sonne|workcurrently headers are both interface and whatever14:18
besser82sonne|work: so you want to have distiction between interf-haeders and impl-headers, right?14:19
sonne|workyes14:19
sonne|workI mean if you restructure then lets not do that again in a few months14:19
besser82sonne|work: would be really easy with that split dir approach ;)14:20
@iglesiasgso QT people have in the same dirs cpp, and h files14:20
sonne|workwell how?14:20
besser82sonne|work: let's split-up the include-dir to interface and impl ;)14:20
@iglesiasgbut maybe I guess it should not be a limitation to separate them in order to use d pointer14:20
besser82iglesiasg, sonne|work: let's split-up the include-dir to interface and impl ;)14:21
lisitsyn1yes I like splitting14:21
lisitsyn1besser82: sonne|work: ^14:21
besser82iglesiasg, sonne|work: like include/implementation  include/public14:21
sonne|worklisitsyn1 prolly A.vim won't work any longer14:21
* besser82 lisitsyn1 +1 :D14:21
lisitsyn1sonne|work: yeah true14:22
besser82sonne|work, lisitsyn1: you don't use eclipse ???  XD14:23
sonne|workiglesiasg, besser82 actually the d ptr stuff shouldn't need includes at all or?14:23
shogun-buildbotbuild #37 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/37  blamelist: van51 <vangelis_51@hotmail.com>14:23
sonne|workbesser82: nope vim14:23
sonne|workI mean non public includes14:23
besser82sonne|work: afaik, no14:23
lisitsyn1besser82: I don't14:24
sonne|workbesser82: I am failing to do this properly with C++14:26
besser82sonne|work: what dpointer, seperated includes or eclipse???14:26
@iglesiasgbesser82, http://qt-project.org/wiki/Dpointer14:27
@iglesiasgbesser82,  and this one http://en.wikipedia.org/wiki/Opaque_pointer14:27
besser82sonne|work: So dpointers should be pretty straight forward with c++14:29
gsomixsonne|work, done. https://github.com/shogun-toolbox/shogun/pull/165114:29
sonne|workgsomix: github down?14:30
gsomixsonne|work, nope14:30
sonne|workunreachable here14:30
besser82sonne|work: let me finish-off that cmake and then let's get those dpointers done :D14:30
sonne|workbesser82: just do :)14:31
shogun-buildbotbuild #31 of debian wheezy - memcheck is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/debian%20wheezy%20-%20memcheck/builds/3114:31
besser82but if there's anybody out here with big affinity or interest in RHEL/CentOS, I might need some help on backporting lots of stuff to them14:33
besser82like python2.6, eigen3, even more ;)14:34
sonne|workbesser82: there probably is but not here I am afraid14:36
besser82sonne|work: I'm afraid, too  :(   But I just wanted to ask here, since it's perfectly about BRs of SHOGUN ;)14:37
lisitsyn1yeah d-pointers are easy14:37
sonne|workBRs ?14:38
lisitsyn1struct Impl;14:38
lisitsyn1Impl* impl;14:38
lisitsyn1that's it :D14:38
besser82sonne|work: BuildRequires14:38
besser82sonne|work: like build-deps in Debian ;)14:38
sonne|worklisitsyn1: yeah but the difficulty is to do the proper interface - so not at all easy!14:38
lisitsyn1sonne|work: what inteface?14:38
besser82lisitsyn1: to the hidden impl ;)14:39
sonne|workyeah which functions do you expose and which not14:39
lisitsyn1it is up to you, what is proper here?14:39
sonne|workthis decision!14:39
lisitsyn1you don't expose anything14:39
sonne|workyeah difficult to decide14:39
besser82lisitsyn1: you expose public interfaces14:39
besser82lisitsyn1: which should be kept binary compatible14:40
lisitsyn1class PublicObject14:40
lisitsyn1{14:40
lisitsyn1public: void doStuff();14:40
lisitsyn1private: struct Impl; Impl* impl;14:40
lisitsyn1}14:40
besser82lisitsyn1: that's what dpointer are about ;)14:40
lisitsyn1what to expose here?14:40
sonne|workvan51: btw nice ipython notebook!14:41
lisitsyn1besser82: are you talking about setting that Impl with some public interface to stone?14:43
lisitsyn1I don't care about binary compatibility to be honest hehe14:44
lisitsyn1I don't see we slow down API changes14:45
van51sonne|work: thanks! let me know if you have any suggestions about it14:46
sonne|workvan51: Well only thing that is sub-optimal is that you didnt' re-run the tests for spectrum etc in that comparison14:47
sonne|workapart from that all good14:47
van51sonne|work: hmm I can run them then and update it accordingly14:48
@iglesiasgvan51, I am reading it atm :)14:48
sonne|workvan51: maybe this is sth for your kitchen sinks http://www.robots.ox.ac.uk/~vedaldi/assets/pubs/vedaldi11efficient.pdf14:49
sonne|workwe have that as homegenous kernel map currently in shogun14:49
sonne|workbut not as dot features14:49
van51iglesiasg: cool :) if you also have any suggestions feel free to tell me!14:50
@iglesiasgvan51, one question!14:50
van51sonne|work: I will take a look14:50
van51iglesiasg: shoot14:50
@iglesiasgvan51, "First of all, the dimensionality of the feature space (or else, the number of distinct tokens in the collection) is usually not known beforehand and requires a pass over the entire dataset to be calculated. This can make the creation of the document-term matrix trickier."14:50
@iglesiasgvan51, why does it get trickier if you have to do a first pass to count the number of distinct tokens?14:51
sonne|workiglesiasg: online learning?14:51
sonne|workiglesiasg: you don't know the number of dims beforehand14:51
@iglesiasgtrue, it is an issue in online learning14:51
sonne|workso what do you do then14:51
@iglesiasgI didn't consider it14:52
@iglesiasgvan51, so a shy suggestion from my part is to say that ^ becomes an issue in online learning :)14:53
van51iglesiasg: yes I could elaborate a bit more there14:55
sonne|workiglesiasg: even in the standard case you would have to compute all e.g. n-grams to determine the biggest index14:56
@iglesiasgsonne|work, but that is something you would need to do afterwards anyway, right?14:57
sonne|workiglesiasg: well you do it while training only...14:58
@iglesiasgsonne|work, sure. I am talking about training14:58
sonne|workso you don't have these all available explictly14:58
@iglesiasgvan51, cool notebook indeed! It's nice to know more about your project15:02
van51iglesiasg: I'm glad that you like it15:02
van51all the other notebooks I 've seen looked very detailed and well-worked that I was worried that mine was kind of sloppy15:03
shogun-buildbotbuild #38 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/38  blamelist: Soeren Sonnenburg <sonne@debian.org>, van51 <vangelis_51@hotmail.com>15:03
@iglesiasgall right, lunch time. See you!15:06
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shogun-buildbotbuild #22 of clang34 - undefined behaviour analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20undefined%20behaviour%20analysis/builds/22  blamelist: Soeren Sonnenburg <sonne@debian.org>, van51 <vangelis_51@hotmail.com>15:13
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travis-ci[travis-ci] it's Soeren Sonnenburg's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1168051115:17
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shogun-buildbotbuild #26 of clang34 - thread analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20thread%20analysis/builds/26  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Soeren Sonnenburg <sonne@debian.org>, van51 <vangelis_51@hotmail.com>, Roman Votyakov <votjakovr@gmail.com>15:28
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@HeikoSvotjakovr: hey!15:41
@HeikoSvotjakovr: thanks for the latest patch, any thoughts about the surface plot of the ML?15:42
@HeikoSvotjakovr: also, I wanted to hear about the notebook15:43
@HeikoSdid you see the draft?15:43
sonne|workbesser82: there is HeikoS!15:43
@HeikoSsonne|work: ah, what did I do wrong? :)15:43
besser82HeikoS: nothing ;)15:43
@HeikoSbesser82: hi then :)15:43
besser82HeikoS: You'rethe last one to vote ;)15:43
@HeikoSvote?15:43
@HeikoSGPU based eigen3 backends :D15:44
@HeikoS??15:44
besser82HeikoS: Let's make that german ;)15:44
@HeikoSdistributed matrix matrix multiplication :D ? :)15:44
votjakovrHeikoS: hi! I haven't think about surface plot yet :) Now i'm working on hiv example15:46
@HeikoSvotjakovr: okay, dont worry aobut the surface plot for now, maybe later15:48
votjakovrHeikoS: how is it better to solve the problem? classify R5X4 vs all?15:48
@HeikoSvotjakovr: okay cool, do things work?15:48
@HeikoSvotjakovr: did you have a look into the paper?15:48
votjakovrHeikoS: very briefly15:48
@HeikoSvotjakovr: I forgot what I exactly did back then, but got very good performance15:49
@HeikoSvotjakovr: yeah I think thats a sensible idea to do15:51
votjakovrHeikoS: just for sure: we get protein sequences and usage of coreceptor15:52
@HeikoSvotjakovr: yeah you just get two sets of sequences for the alphabet of aminoacids (20 letters)15:52
@HeikoSvotjakovr: there might be some letters in there that correspond do "dont know" or so, and shogun might complain about that, but its not very important for distant-segments string kernel, only for the specturm kernel we have in shogun15:53
besser82sonne|work: Heiko says +1, too :D15:54
votjakovrHeikoS: hmm i've downloaded the data and protein's string length are different15:56
votjakovrHeikoS: ~ 33-37 characters15:56
@HeikoSvotjakovr: yes, thats the point of string kernels15:56
@HeikoSthey can handle different lengths15:56
@HeikoSvotjakovr: magic, isnt it ? :)15:57
votjakovrHeikoS: ok cool :)15:57
votjakovrHeikoS: so we decided to classify R5X4 vs R5 and X4, right?15:58
@HeikoSvotjakovr: the kernel has two parameters15:58
@HeikoSvotjakovr: which you cannot choose via gradient descent15:58
@HeikoSthey are discrete15:58
votjakovrHeikoS: yep i see15:58
@HeikoSvotjakovr: so I just realised we at some point need something to do a grid-search using the marginal likelihood ;)15:58
votjakovrHeikoS: ah :)15:59
@HeikoSvotjakovr: but that also later15:59
@HeikoSthe string example is just to demonstrate how cool we are ;)15:59
votjakovrHeikoS: huh15:59
votjakovrHeikoS: BTW thank you, for the cool notebook draft :)16:04
@HeikoSvotjakovr: no worries, its just a very basic skeleton yet. I will do some parts for toy GP classification now if you dont mind?16:04
votjakovrHeikoS: ok, thanks16:05
shogun-buildbotbuild #39 of clang34 - static analysis is complete: Failure [failed analyse]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20static%20analysis/builds/39  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>16:10
shogun-buildbotbuild #23 of clang34 - undefined behaviour analysis is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/clang34%20-%20undefined%20behaviour%20analysis/builds/23  blamelist: Heiko Strathmann <heiko.strathmann@gmail.com>, Roman Votyakov <votjakovr@gmail.com>16:19
besser82lisitsyn1: https://koji.fedoraproject.org/koji/packageinfo?packageID=17051  :D16:24
besser82lisitsyn1: in repos for tomorrow  :D16:25
votjakovrHeikoS: hmm... unfortunately we have his: http://github.com/shogun-toolbox/shogun/blob/develop/src/shogun/machine/gp/InferenceMethod.cpp#L30416:37
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@HeikoSvotjakovr: ah shit16:38
@HeikoSvotjakovr: what do you think, how much effort is it to make things work for other types of features?16:38
votjakovrHeikoS: hmm... how could we this say for string features?16:42
@HeikoSvotjakovr: what is m_feat used for?16:42
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votjakovrHeikoS: this is X - matrix, which contains features16:43
@HeikoSbut it is the dot product wiht itself right?16:44
votjakovrHeikoS: ah, ok16:45
votjakovrHeikoS: it is used for mean16:46
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votjakovrHeikoS: to compute values of mean function16:46
votjakovrHeikoS: and derivatives16:47
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shogun-notifier-shogun: Heiko Strathmann :gp_notebook * 8051c74 / doc/ipython-notebooks/gaussian_process/gaussian_process_classification.ipynb: https://github.com/shogun-toolbox/shogun/commit/8051c74824634677b29b182e0ff7f2a56003347a16:47
shogun-notifier-shogun: some updates on binary classification16:47
@HeikoSvotjakovr: the mean function in shogun is limited to R^n right?16:48
@HeikoSvotjakovr: ah thats annoying, I totally missed that16:48
votjakovrHeikoS: currently yes16:48
@HeikoSvotjakovr:  in fact the mean function should be defined as m(x) : Y^n -> R16:48
@HeikoSshit16:49
@HeikoSits like the kernel/covariance, defined on features16:49
@HeikoSvotjakovr: ok, we cannot change that now16:49
@HeikoShave to postpone16:49
@HeikoSvotjakovr: sorry for having missed that :(16:49
@HeikoSvotjakovr: I mean it is possible, but we will have to change a few internals for that16:49
votjakovrHeikoS: ah, me too16:49
@HeikoSvotjakovr: ok then, we will have to skip the string GP16:49
@HeikoSand rather go for some other std datasets16:49
@HeikoSvotjakovr: I suggest you do the UCI glass dataset16:50
@HeikoSwindow-glass vs non-window glass16:50
@HeikoSin fact, I should have code for that somewhere, let me search16:50
@HeikoSvotjakovr: https://github.com/karlnapf/kameleon-mcmc/blob/master/main/gp/GPData.py16:51
@HeikoSthere I load the glass data, its the file from16:51
@HeikoSvotjakovr: http://archive.ics.uci.edu/ml/datasets/Glass+Identification16:51
@HeikoSvotjakovr: and https://github.com/karlnapf/kameleon-mcmc/blob/master/main/gp/scripts/glass_gaussian_ard.py loads the data and preprocesses it16:52
@HeikoSvotjakovr: maybe start with that first16:53
@HeikoSvotjakovr: btw I just updated the notebook, so make sure to rebase from time to time to avoid clashes16:53
votjakovrHeikoS: oh, thanks16:53
@HeikoSvotjakovr: I have to go now, will be back later tonight, might be after the deadline16:53
@HeikoSvotjakovr: but dont worry, will still merge things then :)16:54
votjakovrHeikoS: ok :)16:54
@HeikoSvotjakovr: but try to finish this glass dataset at least, and if you find time, go for some regression data16:54
@HeikoSvotjakovr: if things are not completely polished by tonight, we can still improve things before the release. Though it would be good if you added stuff today.16:55
@HeikoSvotjakovr: ok, see you later!16:55
votjakovrHeikoS: see you16:55
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lisitsyn1besser82: cool thanks!17:13
besser82lisitsyn1: np.  :D17:14
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shogun-notifier-shogun: Evgeniy Andreev :develop * 478fe75 / / (8 files): https://github.com/shogun-toolbox/shogun/commit/478fe75987dc676dd9733d3e52f582cdf70dc7d217:25
shogun-notifier-shogun: add ProtobufFile17:25
shogun-notifier-shogun: Soeren Sonnenburg :develop * fb05e45 / / (8 files): https://github.com/shogun-toolbox/shogun/commit/fb05e459d2df05cc3c5551794c662945a1932b8a17:25
shogun-notifier-shogun: Merge pull request #1651 from gsomix/feature/protobuf17:25
shogun-notifier-shogun:17:25
shogun-notifier-shogun: Protobuf based binary fileformat for reading/writing vectors/matrices with shogun17:25
shogun-notifier-shogun: Fernando Iglesias :develop * f3a668d / src/shogun/evaluation/CrossValidationOutput.h: https://github.com/shogun-toolbox/shogun/commit/f3a668dfb28d71564467bbe863245467959cacae17:26
shogun-notifier-shogun: Fix doc typo17:26
shogun-notifier-shogun: Fernando Iglesias :develop * 5445172 / doc/ipython-notebooks/metric/LMNN.ipynb: https://github.com/shogun-toolbox/shogun/commit/544517222e45c5a1d6c553a54bd70efabde113d417:26
shogun-notifier-shogun: Add multiclass classification illustration to LMNN notebook17:26
shogun-notifier-shogun: Soeren Sonnenburg :develop * 8be7bb0 / / (2 files): https://github.com/shogun-toolbox/shogun/commit/8be7bb0e6f105dfd4c84257902b082c32eb2c71d17:26
shogun-notifier-shogun: Merge pull request #1657 from iglesias/feature/lmnn17:26
shogun-notifier-shogun:17:26
shogun-notifier-shogun: Feature/lmnn17:26
shogun-buildbotbuild #2265 of deb1 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2265  blamelist: Evgeniy Andreev <gsomix@gmail.com>, Fernando Iglesias <fernando.iglesiasg@gmail.com>17:29
shogun-buildbotbuild #2266 of deb1 - libshogun is complete: Failure [failed compile]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2266  blamelist: Soeren Sonnenburg <sonne@debian.org>17:30
gsomixsonne|osx, sonne|osx sth wrong. Protobuf is in classlist.17:31
sonne|osxgsomix: ifdef HAVE_PROTOBUF?17:31
gsomixsonne|osx, yep. in *.h and *.cpp both.17:32
sonne|osxgsomix: errm cannot see it17:33
shogun-notifier-shogun: Soeren Sonnenburg :develop * 345c989 / src/shogun/base/class_list.cpp.py: https://github.com/shogun-toolbox/shogun/commit/345c989498417cd3e14768049410d4744548d89c17:34
shogun-notifier-shogun: add HAVE_PROTOBUF to classlist .py17:34
sonne|osxthat should do it17:34
sonne|osxgsomix: that is a bit tricky - the .cpp is autogenerated so that might explain it17:35
gsomixsonne|osx, ok. I'm finishing string_list stuff.17:36
sonne|osxgsomix: send a PR as soon as possible for review17:38
gsomixsonne|osx, ok, as soon as I get working unit-test.17:39
sonne|osxgsomix: ok17:39
sonne|osxgtg now17:39
sonne|osxcu17:39
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shogun-buildbotbuild #2267 of deb1 - libshogun is complete: Success [build successful]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/226717:40
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shogun-buildbotbuild #1803 of bsd1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/bsd1%20-%20libshogun/builds/1803  blamelist: Soeren Sonnenburg <sonne@debian.org>17:47
shogun-buildbotbuild #2264 of deb1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb1%20-%20libshogun/builds/2264  blamelist: Fernando Iglesias <fernando.iglesiasg@gmail.com>17:48
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travis-ci[travis-ci] it's Soeren Sonnenburg's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1168216417:55
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shogun-buildbotbuild #1535 of cyg1 - libshogun is complete: Failure [failed test]  Build details are at http://buildbot.shogun-toolbox.org/builders/cyg1%20-%20libshogun/builds/1535  blamelist: Soeren Sonnenburg <sonne@debian.org>18:12
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travis-ci[travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1168345519:00
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shogun-buildbotbuild #1884 of deb3 - modular_interfaces is complete: Failure [failed test python modular]  Build details are at http://buildbot.shogun-toolbox.org/builders/deb3%20-%20modular_interfaces/builds/1884  blamelist: Soeren Sonnenburg <sonne@debian.org>19:55
gsomixsonney2k, sonne|osx https://github.com/shogun-toolbox/shogun/pull/166720:18
wikinggsomix: u were looking for me?20:21
gsomixwiking, yep. we need enable protoc and *.cc. :)20:21
gsomixsome of code for protobuf is already in develop branch.20:22
wikingok20:22
wikingi'll give a look at it20:22
gsomix18:27 UTC. Epic fail.20:28
gsomixtime to change music in player from Om to Sunn O)))20:30
van51sonne|osx: can you also have a look here : https://github.com/shogun-toolbox/shogun/pull/1666 ?20:32
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@sonney2kgsomix, well done20:36
gsomixsonney2k, ok. fixing types20:36
@sonney2kgsomix, now all that is left after the minor fixes is sparse20:36
gsomixand sparse next, yes. it will be easy and very similar to string lists20:37
@sonney2kgsomix, lets just now discuss sparse matrices20:37
@sonney2kI think it is best if you write it out in column compressed storage http://netlib.org/linalg/html_templates/node92.html#SECTION0093120000000000000020:37
@sonney2kwhich means you have to write out 3 arrays20:38
@sonney2kgsomix, around and understood?20:40
gsomixsonney2k, yep20:40
@sonney2kit might be a bit confusing in the beginning...20:40
gsomixreading20:40
@sonney2kgsomix, basically all the nonzero entries are in the val array20:40
@sonney2kgsomix, these are the things we have in the SGSparseVectorEntry.entry's20:41
@sonney2kgsomix, actually you could do it indeed the same way like strings20:42
@sonney2kgsomix, you just have to write the values in the entry (the way you write strings) and in addition the values feat_index (also the same way you write strings)20:43
@sonney2kand then an array with the lengths of the sparse vectors (same as length of strings)20:43
gsomixsonney2k, aha, I see.20:44
@sonney2kgsomix, this is then almost the CCS format20:45
@sonney2kgsomix, basically val == array of entries20:45
@sonney2krow_ind == array of feat_index20:45
@sonney2kcol_ptr is different20:45
@sonney2kit is cumsum(sparse vector lengths)20:46
@sonney2kgsomix, does that make sense / is it clear?20:46
gsomixsonney2k, but there is one question. should I store val and row_ind in series? or I can write pairs?20:46
@sonney2kor Qs?20:46
@sonney2kgsomix, write it in series20:46
@sonney2kno pairs (slow!)20:46
gsomixI mean one data message is <<part of val array> <part of row_ind array>>20:47
gsomixor <part of val> <part of val> ... <part of row_ind> <part of row_ind> ... and so on20:47
@sonney2kgsomix, like this20:48
@sonney2krepeated int32 feat_indices;20:49
@sonney2krepeated (whatever chunk type) values;20:49
@sonney2kvan51, looks nice - but give some example with a dataset we have in data for people to try out20:49
@sonney2kvan51, maybe even create a data symlink in that application dir20:50
@sonney2kvan51, and then have it ready20:50
gsomixsonney2k, in one message? so I need add new types in Chunks, right?20:50
gsomixah, ok, it's clear20:52
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@sonney2kgsomix, no you can also do it alternating in two messages20:55
@sonney2kgsomix, I mean first indices then data20:56
votjakovrHeikoS: why can't i do something like: features.add_preprocessor(new CPruneVarSubMean()) and features.apply_preprocessor() ?21:04
@HeikoSvotjakovr: what happens? I never used preprocessors that much ...21:04
votjakovrHeikoS: it shows an exception21:05
@HeikoSwhich is?21:07
@HeikoSvotjakovr: using preprocessors would be nice, though some are not really tested and may show weird behaviour :)21:08
@HeikoSvotjakovr: you might have to debug .. :(21:08
votjakovrHeikoS: it tells [ERROR] In file /home/votjak/Projects/shogun/src/shogun/preprocessor/PruneVarSubMean.cpp line 127: assertion m_initialized failed in virtual SGMatrix<float64_t> shogun::CPruneVarSubMean::apply_to_feature_matrix(shogun::CFeatures *) file /home/votjak/Projects/shogun/src/shogun/preprocessor/PruneVarSubMean.cpp line 12721:08
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travis-ci[travis-ci] it's Heiko Strathmann's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1169201121:08
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@HeikoSvotjakovr:  ASSERT(m_initialized)21:08
@HeikoSso you will have to initialise it21:09
votjakovrHeikoS: i probably forgot about init() call21:09
@HeikoSvotjakovr: maybe a good idea to change this to required and provide an errors message if you have time21:09
votjakovrHeikoS: but is it really good idea to call init() manually?21:10
@sonney2kvotjakovr, yes - e.g.21:11
@sonney2kvotjakovr, consider you determine variance / mean on some training data21:11
@sonney2kand then you only keep a certain number of dims of you data21:11
@HeikoSvotjakovr: eating, will be back later21:11
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@sonney2kyou now want that to work on test data the very same way21:12
@sonney2kso you need to have them inited on the training data21:12
votjakovrsonney2k: oh yeah, now i see, thanks :)21:15
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gsomixsonney2k, mix of signed/unsigned in one place - pain21:26
gsomixsonney2k, https://github.com/shogun-toolbox/shogun/pull/1667 updated21:29
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travis-ci[travis-ci] it's Soeren Sonnenburg's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1169376921:30
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gsomixbtw I finally changed my gedit+nano environment to the Sublime Text 3. I'm like a hipster now.21:31
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lambdayhushell: I am really sorry have been caught up with a few things :(21:35
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travis-ci[travis-ci] it's Soeren Sonnenburg's turn to pay the next round of drinks for the massacre he caused in shogun-toolbox/shogun: http://travis-ci.org/shogun-toolbox/shogun/builds/1169378822:02
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votjakovrHeikoS: i've decided to add CWhiteningTransformation to shogun/preprocessor/22:15
@HeikoSvotjakovr: awesome!22:15
@HeikoSvotjakovr: this will be very useful for others, too22:15
@HeikoSvotjakovr: do we already have the unit variance preprocessor btw? If whitening if too expensive, that one is also useful22:16
votjakovrHeikoS: yeah22:16
votjakovrHeikoS: PruneVarSubMean22:16
@HeikoSvotjakovr: I see22:17
@HeikoSvotjakovr: maybe do a whitening and remove mean combination? its almost always used in conjunction22:17
votjakovrHeikoS: oh, yeah, this is not a problem22:18
@HeikoSvotjakovr: cool!22:18
@HeikoSvotjakovr: I like that you do that! :)22:18
* gsomix z-z-z-z22:21
@iglesiasgvotjakovr: there is something about whitening in the PCA preprocessor too22:21
@iglesiasgvotjakovr: maybe you want to check it22:22
gsomixnite guys. it seems I need sleep a little22:22
@HeikoSgsomix: night!22:22
@iglesiasgvotjakovr: I took a look yesterday but didn't find it quite similar to the whitening I learnt so... :D22:22
@HeikoSiglesiasg: PCA is very similar to whitening22:22
@iglesiasggsomix: good night proto-buffer! :P22:22
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@HeikoSbut a bit more powerful22:23
votjakovriglesiasg: oh, i saw that22:23
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shogun-notifier-shogun: Heiko Strathmann :gp_notebook * 2808d7f / doc/ipython-notebooks/gaussian_process/gaussian_process_classification.ipynb: https://github.com/shogun-toolbox/shogun/commit/2808d7f5b3affdb44d2260e40e8135d617b69f5a22:36
shogun-notifier-shogun: some more updates for likelihoods22:36
* besser82 waves22:40
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votjakovrHeikoS: btw i was thinking about mean functions... And i noticed, that it doesn't really metter what type of features we are using for zero mean function, for example22:44
@HeikoSvotjakovr: yep Zero/Constant mean is independent of the feature type22:45
@HeikoSvotjakovr: in fact mean functions should be defined on CFeatures objects22:45
@HeikoSso you could just change the interface and since we dont have other means, that change would not be a lot of work22:45
votjakovrHeikoS: yeah, that what i thought!22:45
@HeikoSvotjakovr: cool, feel free to change22:46
@HeikoSvotjakovr: what other things would have to be changed? not many I guess22:46
@HeikoSvotjakovr: Do you know if GPstuff can do GPs on non-numerical data?22:46
@HeikoSvotjakovr: I know GPML cannot22:46
@HeikoSvotjakovr: so would be very very cool to have22:46
votjakovrHeikoS: GPstuff also can't22:47
@HeikoSvotjakovr: killer feature then ;)22:47
votjakovrHeikoS: need refactor CMeanFunction a little bit to make it works22:48
votjakovrHeikoS: btw how often is GPs used in practice?22:50
votjakovrHeikoS: i've found not too much applications22:51
@HeikoSvotjakovr: ehm ...22:51
@HeikoSvotjakovr: one of the most fundamental methods in statistics ;)22:51
@HeikoSused all over the place in spatio temporal statistics22:52
@HeikoSvotjakovr: its just not that popular as SVMs, since its a bit harder to understand, but its also more powerful22:52
@HeikoSvotjakovr: in fact, there is not really a nice impleentation out there22:52
@HeikoSvotjakovr: but we changed this now partly22:52
votjakovrHeikoS: oh :)22:54
@HeikoSvotjakovr: biologists also use them very often22:56
@HeikoSvotjakovr: sometimes in different froms, but the core idea is the same22:56
@HeikoSvotjakovr: we can extend our framework to more cutting edge methods though .... the stuff in there is very fundamental but a bit old-school ;)22:56
@HeikoSvotjakovr: next thing should some some nice multiclass stuff22:56
@HeikoSvotjakovr: and then of course sparsity extensions? aka relevance vector machine22:57
@HeikoSthey scale linearly in the nubmer of training points22:57
votjakovrHeikoS: cool :)22:59
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@iglesiasgmmm I guess this week there should be weekly report mail as well, right?23:15
votjakovriglesiasg: hmm it seems nobody have sent a report23:17
@HeikoSno need for a report, send you notebooks ;)23:18
votjakovrHeikoS: notebook is still in process23:19
@iglesiasgHeikoS: all right!23:19
@HeikoSvotjakovr: looking forward to see23:19
votjakovr:)23:19
@iglesiasgI sent a new update yesterday, but I think I am going to do a small thing now before going to bed23:20
@HeikoSvotjakovr: I have written some more things, pushing now23:20
@iglesiasgHeikoS: aah true you already saw and commented what I pushed yesterday, thanks btw :)23:20
shogun-notifier-shogun: Heiko Strathmann :gp_notebook * 6fa30fc / doc/ipython-notebooks/gaussian_process/gaussian_process_classification.ipynb: https://github.com/shogun-toolbox/shogun/commit/6fa30fc22a6f8936b550e34c22211eee0d7a1cd423:20
shogun-notifier-shogun: another paragraph on inference for binary classification23:20
@HeikoSiglesiasg: welcome :)23:21
@HeikoSiglesiasg: feedback is very important for the notebooks, even more than for code23:21
@HeikoSiglesiasg: if you can give some more feedback to others, in particular those who haven't received some yet23:21
votjakovrHeikoS: oh thanks, rebasing...23:21
@iglesiasgHeikoS: all right23:22
@iglesiasgHeikoS: I started reading lambday's notebook yesterday23:22
@HeikoSiglesiasg: cool, also have a look at van51s23:23
@iglesiasgHeikoS: but I have to admit I quit after some minutes and left it for another moment23:23
@HeikoSiglesiasg: I gave lambday a *lot* of feedback already, also the stats prof here and the other mentor did23:23
@iglesiasgHeikoS: yeah, already checked van's and told him one minor thing23:23
@HeikoSiglesiasg: try to focus on having things look very cool23:24
@iglesiasgbrb23:41
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--- Log closed Tue Sep 24 00:00:12 2013