| --- Log opened Thu Nov 08 00:00:17 2012 | ||
| -!- blackburn [~blackburn@188.168.13.4] has quit [Quit: Leaving.] | 01:12 | |
| -!- zxtx_ [~zv@99-7-170-103.lightspeed.sntcca.sbcglobal.net] has quit [Ping timeout: 246 seconds] | 01:59 | |
| -!- zxtx_ [~zv@ip-64-134-225-207.public.wayport.net] has joined #shogun | 02:51 | |
| -!- zxtx_ [~zv@ip-64-134-225-207.public.wayport.net] has quit [Ping timeout: 255 seconds] | 06:24 | |
| -!- zxtx_ [~zv@107.43.133.134] has joined #shogun | 07:48 | |
| -!- zxtx_ [~zv@107.43.133.134] has quit [Ping timeout: 245 seconds] | 08:03 | |
| -!- n4nd0 [~nando@s83-179-44-135.cust.tele2.se] has joined #shogun | 09:28 | |
| n4nd0 | sonney2k: hi, no news about doc camp yet? | 09:29 |
|---|---|---|
| -!- blackburn [5bdfb203@gateway/web/freenode/ip.91.223.178.3] has joined #shogun | 10:09 | |
| -!- blackburn_ [5bdfb203@gateway/web/freenode/ip.91.223.178.3] has joined #shogun | 10:12 | |
| -!- blackburn [5bdfb203@gateway/web/freenode/ip.91.223.178.3] has quit [Ping timeout: 245 seconds] | 10:15 | |
| wiking | where's heiko? :) | 10:18 |
| -!- n4nd0 [~nando@s83-179-44-135.cust.tele2.se] has quit [Quit: leaving] | 12:24 | |
| -!- zxtx_ [~zv@cpe-75-83-151-252.socal.res.rr.com] has joined #shogun | 15:50 | |
| wiking | duuuude | 16:07 |
| blackburn_ | wiking: who's that for? :) | 16:08 |
| wiking | well it's about streaming features | 16:08 |
| blackburn_ | first rule of streaming features | 16:09 |
| -!- sonne|work [~sonnenbu@194.78.35.195] has joined #shogun | 16:09 | |
| wiking | no wonder it leaks | 16:09 |
| blackburn_ | no, first rule is never talk about streaming features obviously ;) | 16:09 |
| wiking | :D | 16:09 |
| sonne|work | better leaks than GC :) | 16:09 |
| blackburn_ | really? | 16:09 |
| wiking | who's Shashwat Lal Das? | 16:10 |
| blackburn_ | our former gsoc | 16:10 |
| blackburn_ | I'd say alumni | 16:10 |
| blackburn_ | :D | 16:10 |
| wiking | :> | 16:10 |
| sonne|work | wiking: btw you can find the git tag in any shogun 2.0 .tar.bz2 in src/lib/versionstring.h | 16:10 |
| blackburn_ | wiking: if you have any questions to shashwatted code ask heiko | 16:11 |
| blackburn_ | he is shashwat now | 16:11 |
| wiking | :D | 16:12 |
| wiking | sonne|work: do u have it hand? | 16:12 |
| sonne|work | no | 16:12 |
| wiking | downloading ... | 16:12 |
| wiking | stay tuned | 16:12 |
| blackburn_ | wiking: okay joking - shashwat code is ok | 16:12 |
| blackburn_ | baozeng is not :D | 16:13 |
| blackburn_ | the-guy-who-allocates-data-on-stack | 16:13 |
| wiking | well yeah | 16:13 |
| wiking | that's another story | 16:13 |
| blackburn_ | okay time to get hooome | 16:14 |
| -!- blackburn_ [5bdfb203@gateway/web/freenode/ip.91.223.178.3] has quit [Quit: Page closed] | 16:14 | |
| wiking | sonne|work: i've downloaded tar.bz2 | 16:14 |
| wiking | sonne|work: should i build it inorder to have that src/lib/versionstring.h? | 16:15 |
| sonne|work | no | 16:16 |
| sonne|work | it is there already | 16:16 |
| wiking | i've just downloaded the tar.bz2 from the shogun site | 16:17 |
| wiking | and there's no such thing there | 16:17 |
| sonne|work | src/shogun/lib/versionstring.h | 16:17 |
| wiking | 0x9c8012f | 16:18 |
| wiking | the revision | 16:18 |
| sonne|work | yes | 16:18 |
| sonne|work | git show --pretty='format:%h'|head -1 | 16:18 |
| wiking | how do u convert that into a git commit number? | 16:18 |
| sonne|work | that's how it is created | 16:18 |
| sonne|work | just do git show 9c8012f | 16:19 |
| wiking | fatal: ambiguous argument '9c8012f': unknown revision or path not in the working tree. | 16:19 |
| sonne|work | excellent | 16:20 |
| sonne|work | something went wrong. | 16:20 |
| wiking | :( | 16:20 |
| sonne|work | wiking: does it work in your current checkout? | 16:20 |
| wiking | git show --pretty='format:%h'|head -1 ? | 16:20 |
| sonne|work | I mean the id from your current build | 16:21 |
| sonne|work | that you find in your git-master src/shogun/lib/versionstring.h | 16:21 |
| sonne|work | ? | 16:21 |
| wiking | yep | 16:21 |
| wiking | that works | 16:21 |
| sonne|work | looking at the logs I think we released 15ed29239e2f83e7cd8c5097d9180999cffeab56 | 16:23 |
| wiking | ok | 16:27 |
| wiking | let's tag that then | 16:27 |
| wiking | :D | 16:27 |
| wiking | and make a branch of it | 16:27 |
| sonne|work | we should compare it to the stuff in the tar.bz2 before we do it | 16:34 |
| sonne|work | I have no idea what could have happened ... | 16:34 |
| sonne|work | well release script needed a rewrite to work with new layout / git and we didn't release that often since then | 16:35 |
| sonne|work | so it probably still has issues | 16:35 |
| wiking | we should test it before the next release then | 16:36 |
| wiking | btw | 16:36 |
| wiking | sonne|work: https://github.com/shogun-toolbox/shogun/blob/master/src/shogun/features/streaming/StreamingFeatures.h#L88 | 16:36 |
| wiking | can we agree to throw this ctor out? | 16:36 |
| wiking | as it doesn't do anything | 16:37 |
| wiking | https://github.com/shogun-toolbox/shogun/blob/master/src/shogun/features/streaming/StreamingFeatures.cpp#L28 | 16:37 |
| wiking | sonne|work: ^ | 16:37 |
| sonne|work | huh?! | 16:38 |
| wiking | same for https://github.com/shogun-toolbox/shogun/blob/master/src/shogun/features/streaming/StreamingDotFeatures.h | 16:38 |
| wiking | sonne|work: check it out | 16:38 |
| wiking | :) | 16:38 |
| sonne|work | that oen used to do sth | 16:38 |
| sonne|work | one | 16:38 |
| sonne|work | needs more inspection - maybe some code got removed | 16:38 |
| wiking | ok i'm not going to go into that then now | 16:38 |
| sonne|work | it was used to read in files that have a label and features | 16:38 |
| wiking | sonne|work: yes but now that is moved | 16:38 |
| wiking | sonne|work: to StreamingSparseFeatures | 16:39 |
| wiking | and DenseFeatures | 16:39 |
| sonne|work | ahh ok | 16:40 |
| sonne|work | then it certainly makes sense yes | 16:40 |
| wiking | sonne|work: ok then i'll prepare now a fix | 16:41 |
| -shogungit:#shogun- [shogun] vigsterkr opened pull request #816: Fix StreamingFeatures (master...latent) https://github.com/shogun-toolbox/shogun/pull/816 | 17:04 | |
| wiking | there you go fixes | 17:06 |
| wiking | ooooh | 17:20 |
| wiking | we have a nice bug in CMulticlassLibSVM | 17:21 |
| wiking | or at least there's a problem with ./classifier_multiclasslibsvm | 17:21 |
| wiking | btw anyone tested shogun with python3.0? | 17:25 |
| wiking | :) | 17:25 |
| -!- blackburn [~blackburn@188.168.13.193] has joined #shogun | 17:48 | |
| wiking | blackburn: readlogs :) | 17:48 |
| blackburn | wiking: a lot of things, what in particular? | 17:49 |
| wiking | 7:20 < wiking> ooooh | 17:50 |
| wiking | 17:21 < wiking> we have a nice bug in CMulticlassLibSVM | 17:50 |
| wiking | 17:21 < wiking> or at least there's a problem with ./classifier_multiclasslibsvm | 17:50 |
| wiking | 17:25 < wiking> btw anyone tested shogun with python3.0? | 17:50 |
| wiking | 17:25 < wiking> :) | 17:50 |
| blackburn | wiking: what is da bug? | 17:51 |
| wiking | blackburn: try running ./classifier_multiclasslibsvm with HEAD | 17:51 |
| wiking | it fails here | 17:51 |
| wiking | multiclass/MulticlassLibSVM.cpp:190 | 17:51 |
| wiking | 190REQUIRE(set_svm(idx, svm),"SVM set failed"); | 17:51 |
| wiking | that's line 190 | 17:51 |
| wiking | idx value there is -2 | 17:51 |
| blackburn | woopie doopie | 17:51 |
| blackburn | 2 classes | 17:54 |
| blackburn | okayyyyy | 17:55 |
| blackburn | wiking: here you go | 17:56 |
| wiking | waiting :) | 17:57 |
| wiking | where r u shogungit?! :) | 17:57 |
| wiking | blackburn: and merge that PR ;) | 17:57 |
| -shogungit:#shogun- [shogun] lisitsyn pushed 1 new commit to master: https://github.com/shogun-toolbox/shogun/commit/ce7eafee615b565cdbdd091901a6d85f26525b4e | 17:57 | |
| -shogungit:#shogun- shogun/master ce7eafe Sergey Lisitsyn: Patched multiclass libsvm to support 2 classes | 17:57 | |
| blackburn | yes master | 17:57 |
| wiking | cheers | 17:57 |
| -shogungit:#shogun- [shogun] lisitsyn pushed 2 new commits to master: https://github.com/shogun-toolbox/shogun/compare/ce7eafee615b...9e87cd569db7 | 17:57 | |
| -shogungit:#shogun- shogun/master a4bc1c9 Viktor Gal: Fix StreamingFeatures... | 17:57 | |
| -shogungit:#shogun- shogun/master 9e87cd5 Sergey Lisitsyn: Merge pull request #816 from vigsterkr/latent... | 17:57 | |
| wiking | bug hunters we are :) | 18:00 |
| blackburn | bugbusters | 18:01 |
| wiking | blackburn: http://29.media.tumblr.com/tumblr_lltzgnHi5F1qzib3wo1_400.jpg | 18:04 |
| wiking | ;) | 18:04 |
| -shogungit:#shogun- [shogun] cwidmer opened pull request #817: added serialization example (master...master) https://github.com/shogun-toolbox/shogun/pull/817 | 18:26 | |
| -!- blackburn [~blackburn@188.168.13.193] has quit [Quit: Leaving.] | 18:32 | |
| -!- blackburn [~blackburn@188.168.13.193] has joined #shogun | 18:33 | |
| -shogungit:#shogun- [shogun] lisitsyn pushed 3 new commits to master: https://github.com/shogun-toolbox/shogun/compare/9e87cd569db7...ad7a0e221709 | 18:34 | |
| -shogungit:#shogun- shogun/master 5195b7f Christian Widmer: polished simple serialization example | 18:34 | |
| -shogungit:#shogun- shogun/master cfe0958 Christian Widmer: added serialization example for combined kernel consisting of spectrum and wdk kernels | 18:34 | |
| -shogungit:#shogun- shogun/master ad7a0e2 Sergey Lisitsyn: Merge pull request #817 from cwidmer/master... | 18:34 | |
| shogun-buildbot | build #628 of deb3 - modular_interfaces is complete: Failure [failed test python_modular] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/628 blamelist: Sergey Lisitsyn <lisitsyn.s.o@gmail.com>, Christian Widmer <cwidmer@tuebingen.mpg.de> | 19:17 |
| -shogungit:#shogun- [shogun] cwidmer opened pull request #818: fixed typo (master...master) https://github.com/shogun-toolbox/shogun/pull/818 | 19:27 | |
| -!- zxtx_ [~zv@cpe-75-83-151-252.socal.res.rr.com] has quit [Read error: No route to host] | 19:59 | |
| -!- zxtx [~zv@cpe-75-83-151-252.socal.res.rr.com] has joined #shogun | 20:03 | |
| -!- cwidmer [8295587b@gateway/web/freenode/ip.130.149.88.123] has joined #shogun | 20:11 | |
| wiking | cwidmer: hey | 20:14 |
| cwidmer | hi there | 20:15 |
| wiking | cwidmer: do you happen to have any DNA/gene dataset where one has to find motifs? | 20:15 |
| cwidmer | well, I can give you some splice site data... another one would be gene starts | 20:16 |
| cwidmer | what are you trying to do?# | 20:16 |
| wiking | i'm really not into this topic but | 20:17 |
| cwidmer | but? | 20:18 |
| cwidmer | you got interested ;)? | 20:18 |
| wiking | Motifs are repeated patterns in DNA sequences that are believed to have biological significance. Our dataset consists of ARSs (autonomously replicating se- quences) screened in two yeast species S. kluyveri and S. cerevisiae. Our task is to predict whether a par- ticular sequence is functional (i.e., whether they start the replication process) in S. cerevisiae and to find out the motif responsible. All the native ARSs in S. cerevisiae are labeled as pos | 20:18 |
| wiking | this is in a paper | 20:18 |
| wiking | i was wondering whether there's a similar dataset available | 20:19 |
| wiking | anywhere | 20:19 |
| cwidmer | which paper is that? | 20:19 |
| wiking | cwidmer: www.cs.cornell.edu/~cnyu/papers/icml09_latentssvm.pdf | 20:20 |
| cwidmer | I see, and i guess you've checked if their data set is available (website, supplement, ask authors)? | 20:21 |
| wiking | cwidmer: yeps | 20:22 |
| wiking | unfortunately it's not | 20:22 |
| wiking | but basically any similar problem for me would be good | 20:22 |
| wiking | cwidmer: i mean yeah i've contacted them but unfortunately this dataset in particular cannot be handed out... private etc.. | 20:22 |
| cwidmer | hmm, too bad | 20:23 |
| wiking | i've just seen your pull request | 20:23 |
| cwidmer | so they do some labeled sequence learning on motifs? | 20:23 |
| wiking | that's why i thought i give a shot to ask u something | 20:23 |
| cwidmer | heh, sure | 20:23 |
| wiking | well as much one can find out from their paper/code | 20:24 |
| wiking | their data looks something like this: some_seq:1:1:ACGTACGT | 20:25 |
| wiking | and then they try to find the starting position of the motif as well as classify it | 20:26 |
| cwidmer | I have to read the data part in detail to see what's going on | 20:27 |
| cwidmer | from glancing over it, it seems like a binary classification task | 20:27 |
| cwidmer | with latent variables | 20:27 |
| wiking | yes | 20:27 |
| cwidmer | where label is, if functional or not | 20:27 |
| cwidmer | and latent variable is motiv position | 20:28 |
| cwidmer | motif | 20:28 |
| wiking | indeed | 20:28 |
| cwidmer | I was expecting SO | 20:28 |
| wiking | yeah they didn't go that deep :) | 20:28 |
| cwidmer | hmm, ok | 20:29 |
| cwidmer | also, are they only looking for one particular motif? | 20:29 |
| wiking | yes | 20:29 |
| cwidmer | well | 20:29 |
| cwidmer | and the sequences can be of variable length? | 20:29 |
| wiking | noup | 20:29 |
| wiking | if u have anything at hand that u could share for testing shogun's machine | 20:31 |
| wiking | let me know :) | 20:31 |
| cwidmer | so you're saying all those 'autonomously replicating sequences' are of identical length? | 20:31 |
| wiking | cwidmer: well as far as i can see from the code | 20:31 |
| cwidmer | well, there is something that a colleague of mine, sebi, worked on: KIRMES | 20:31 |
| cwidmer | he is also looking at motifs in promoter sequences | 20:31 |
| cwidmer | but several | 20:31 |
| cwidmer | and he encodes their relative distances etc as features | 20:32 |
| cwidmer | and learns on that | 20:32 |
| cwidmer | http://raetschlab.org//suppl/kirmes/ | 20:32 |
| cwidmer | possibly, you can take a look at that | 20:32 |
| cwidmer | but I suspect the problem is much harder than the latent svm paper one | 20:33 |
| wiking | ok i'll check that one out | 20:34 |
| wiking | get at least an idea :) | 20:35 |
| cwidmer | just curious, what method do you want to test on this data? | 20:35 |
| wiking | simple latent svm and latent so svm | 20:36 |
| cwidmer | is the code in shogun ported from thorstens's tool or do we have a from scratch implementation? | 20:37 |
| cwidmer | it is based on the same paper at least, right? | 20:37 |
| wiking | cwidmer: we have both | 20:41 |
| wiking | i mean i have it for so | 20:41 |
| cwidmer | but what's in shogun is based on the "Learning Structural SVMs with Latent Variables" paper or something else? | 20:42 |
| wiking | cwidmer: both | 20:42 |
| wiking | cwidmer: i've tested on one dataset and the one i have from scratch implemented performs better than the algo in ""Learning Structural SVMs with Latent Variables" | 20:43 |
| cwidmer | ah nice | 20:44 |
| wiking | but i need more tests | 20:44 |
| wiking | :> | 20:44 |
| cwidmer | so what you've implemented from scratch is in libocas? | 20:45 |
| wiking | the simple latent svm is based on libocas | 20:45 |
| wiking | the latent so is based on the BMRM in shogun | 20:46 |
| wiking | and i've made it possible to work with the primal mosek solver as well | 20:46 |
| cwidmer | cool | 20:47 |
| cwidmer | i'll check it out some time, seems interesting | 20:47 |
| wiking | cwidmer: the latent so is not commited yet | 20:47 |
| wiking | it's in my git stash for a long time now | 20:49 |
| -shogungit:#shogun- [shogun] lisitsyn pushed 1 new commit to master: https://github.com/shogun-toolbox/shogun/commit/a325ca7a00a100d740afcbc0bc5d0d3a6e2bc7fb | 21:05 | |
| -shogungit:#shogun- shogun/master a325ca7 Sergey Lisitsyn: Attempted to fix strings serialization process | 21:05 | |
| -shogungit:#shogun- [shogun] lisitsyn pushed 2 new commits to master: https://github.com/shogun-toolbox/shogun/compare/a325ca7a00a1...754d81b0f0cd | 21:05 | |
| -shogungit:#shogun- shogun/master 67681ed Christian Widmer: fixed typo | 21:05 | |
| -shogungit:#shogun- shogun/master 754d81b Sergey Lisitsyn: Merge pull request #818 from cwidmer/master... | 21:05 | |
| -!- n4nd0 [~nando@s83-179-44-135.cust.tele2.se] has joined #shogun | 21:34 | |
| shogun-buildbot | build #629 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/629 | 21:53 |
| shogun-buildbot | build #630 of deb3 - modular_interfaces is complete: Failure [failed test python_modular] Build details are at http://www.shogun-toolbox.org/buildbot/builders/deb3%20-%20modular_interfaces/builds/630 blamelist: Christian Widmer <cwidmer@tuebingen.mpg.de> | 21:57 |
| -!- blackburn [~blackburn@188.168.13.193] has left #shogun [] | 22:44 | |
| -!- blackburn [~blackburn@188.168.13.193] has joined #shogun | 22:44 | |
| -!- cwidmer [8295587b@gateway/web/freenode/ip.130.149.88.123] has quit [Quit: Page closed] | 23:30 | |
| --- Log closed Fri Nov 09 00:00:17 2012 | ||
Generated by irclog2html.py 2.10.0 by Marius Gedminas - find it at mg.pov.lt!
