--- Log opened Tue Apr 17 00:00:09 2012 | ||
--- Day changed Tue Apr 17 2012 | ||
emrecelikten | and get accepted to a conference? | 00:00 |
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emrecelikten | No guidance from anyone whatsoever | 00:00 |
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emrecelikten | Apparently no :P | 00:46 |
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CIA-64 | shogun: Josh Klontz master * rb8bec85 / (5 files in 5 dirs): added basic CMake project files - http://git.io/hMwTwg | 09:06 |
CIA-64 | shogun: Soeren Sonnenburg master * rce82cc1 / (5 files in 5 dirs): | 09:06 |
CIA-64 | shogun: Merge pull request #461 from jklontz/master | 09:06 |
CIA-64 | shogun: Remove some deprecated function calls and add cmake project files. - http://git.io/OpDwww | 09:06 |
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sonne|work | pluskid: what is the lasso parameter doing in CLARS? | 09:24 |
pluskid | sonne|work: you mean the regularization coefficient? | 09:25 |
sonne|work | the parameter in the constructor | 09:25 |
sonne|work | it can be true or false | 09:25 |
pluskid | \\\\\\\\\\\\\\\\\\ | 09:25 |
pluskid | oops, cat on keyboard | 09:25 |
pluskid | when it is true, it runs the LASSO | 09:25 |
pluskid | when false, it runs LARS | 09:26 |
pluskid | the LARS algorithm has a modification, which could give us a LASSO solution | 09:26 |
pluskid | when passed true in the constructor, this modification is turned on | 09:27 |
pluskid | I think the most case we use LARS is to get the LASSO solution (instead of the original LARS), so I made that parameter default to true | 09:27 |
pluskid | sonne|work: am I clear? | 09:27 |
sonne|work | yes | 09:29 |
sonne|work | that was just missing from the doc | 09:30 |
CIA-64 | shogun: Soeren Sonnenburg master * r879ba9e / src/shogun/regression/LARS.h : fix doxygen warning in lars - http://git.io/-3TFeQ | 09:30 |
sonne|work | however I still don't know what the difference between LASSO / LARS is | 09:30 |
pluskid | sonne|work: thanks for the fix of doxygen | 09:31 |
pluskid | in my understanding, LARS is a stagewise variable selection algorithm | 09:32 |
pluskid | LASSO in its general meaning corresponds the the linear regression with L1-regularization | 09:33 |
pluskid | the original LARS algorithm doesn't corresponds to any objective function though | 09:33 |
pluskid | but when the *lasso modification* is enabled in the LARS algorithm, it will provide the solution for the LASSO problem | 09:34 |
pluskid | when referring LASSO, we generally mean the problem | 09:34 |
pluskid | and there are many different algorithms for solving LASSO | 09:34 |
pluskid | sonne|work: that's my understanding, if you have interest, you may refer to the paper for more details :) www.stanford.edu/~hastie/Papers/LARS/LeastAngle_2002.pdf | 09:36 |
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sonne|work | pluskid: ok I will have to read that | 09:47 |
sonne|work | pluskid: I understand the problem with multiclass/kernel machine | 09:47 |
sonne|work | one cannot set a multiclass machine as constraint generator | 09:49 |
sonne|work | there is a separate multiclass mkl for that | 09:49 |
sonne|work | so you should be fine | 09:49 |
pluskid | sonne|work: that's nice, so we would be safe to simply remove the (currently) commented out code in GUIClassifier | 09:54 |
uricamic | hi there | 10:26 |
uricamic | I have some problems with git push | 10:26 |
uricamic | I have committed changes to my branch, followed instructions from http://article.gmane.org/gmane.comp.ai.machine-learning.shogun/2537 and when I try to git push origin my_branch it results in this error: failed to push some refs to 'git@github.com:uricamic/shogun.git' | 10:28 |
pluskid | uricamic: what is the detailed output of git? | 10:40 |
uricamic | pluskid: you mean after that push? | 10:40 |
uricamic | To git@github.com:uricamic/shogun.git ! [rejected] GSKRR -> GSKRR (non-fast-forward) error: failed to push some refs to 'git@github.com:uricamic/shogun.git' To prevent you from losing history, non-fast-forward updates were rejected Merge the remote changes (e.g. 'git pull') before pushing again. See the 'Note about fast-forwards' section of 'git push --help' for details. | 10:41 |
pluskid | uricamic: it seems you have rebased your local branch, isn't it? | 10:42 |
pluskid | one simple solution is to first delete your remote branch, and then push again | 10:42 |
pluskid | something like | 10:42 |
pluskid | git push origin :branch-name | 10:42 |
pluskid | and then | 10:42 |
uricamic | pluskid: yes, I have followed this link: http://article.gmane.org/gmane.comp.ai.machine-learning.shogun/2537 | 10:42 |
pluskid | git push origin branch-name | 10:42 |
uricamic | delete my remote branch? | 10:43 |
pluskid | yes, try the command I mentioned above | 10:43 |
uricamic | how can I delete my remote branch? | 10:44 |
pluskid | git push origin :branch-name | 10:44 |
pluskid | note the colon (:) before the branch name | 10:44 |
uricamic | ok, I will try this | 10:44 |
uricamic | pluskid: thanks, it seems that this worked | 10:45 |
pluskid | although it seems you can also solve this problem by using git pull, but that will introduce an empty commit for merging, so I think the method here is more cleaner | 10:45 |
shogun-buildbot | build #477 of ruby_modular is complete: Success [build successful] Build details are at http://www.shogun-toolbox.org/buildbot/builders/ruby_modular/builds/477 | 10:46 |
pluskid | uricamic: then you should be able to push your branch to origin now :) | 10:46 |
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uricamic | pluskid: ok, I think the pushed worked, but now when I have already some opened pull request for this, should I close it and do a pull request again? | 10:48 |
uricamic | *push | 10:49 |
pluskid | uricamic: you have to create multiple branches to make multiple pull request | 10:49 |
pluskid | I think the pull request are to be closed by the maintainers when they merged your commits to the official shogon repo | 10:50 |
pluskid | *shogun | 10:50 |
uricamic | pluskid: yes, I already know this :) the question is, if I have to do the pull request again, or if the changes which I have pushed right now will appear in the original pull request | 10:50 |
pluskid | uricamic: OK, I see, as long as the branch name does not change, your new commits will be automatically "merged" into the pull request | 10:51 |
pluskid | uricamic: you can look at the pull request you originally opened, navigate to "commits" tab, and see your new commits there | 10:51 |
uricamic | pluskid: ok, thanks again :) | 10:52 |
pluskid | uricamic: u r wel~ :) | 10:53 |
n4nd0 | hey guys | 10:55 |
n4nd0 | so now you were talking about the topic | 10:55 |
n4nd0 | if a pull request is already opened | 10:55 |
n4nd0 | is there any danger to rebase with the changes added to remote master since that pull request was opened? | 10:56 |
pluskid | n4nd0: I don't think so | 10:57 |
pluskid | actually, rebasing is always encouraged , I think | 10:58 |
n4nd0 | ok, so I can just go to my master | 10:58 |
n4nd0 | rebase upstream/master | 10:58 |
n4nd0 | push origin master | 10:58 |
n4nd0 | go to my branch | 10:58 |
n4nd0 | rebase master | 10:58 |
n4nd0 | and later commit and push the new changes to the branch to update the pull request | 10:59 |
pluskid | what github do is simply keeping a reference to the branch name you are using for that pull request | 10:59 |
n4nd0 | aham | 10:59 |
pluskid | when your branch changes (i.e. new commits are added), the pull request updates automatically | 10:59 |
n4nd0 | but I am afraid that the changes that enter in my branch when doing rebasing | 10:59 |
n4nd0 | the ones that are not mine | 10:59 |
n4nd0 | are introduced in the pull request as mine | 11:00 |
pluskid | rebasing is inserting changes *before* your branch commits | 11:00 |
pluskid | so when you run git rebase master | 11:00 |
n4nd0 | yeah | 11:01 |
pluskid | it takes those commits in master that happens *after* you create the branch, | 11:01 |
n4nd0 | but now we are talking about changes that happened *after* the first changes in that pull request | 11:01 |
pluskid | yes | 11:01 |
pluskid | those commits are inserted *before* the first commit in your branch | 11:01 |
n4nd0 | that makes sense | 11:02 |
n4nd0 | :) | 11:02 |
pluskid | however, we do have problem pushing to remote branch when we do rebasing | 11:02 |
pluskid | if we have already pushed parts of our branch to origin | 11:03 |
pluskid | we get non-fast-forward error | 11:03 |
pluskid | you have encountered this error before, IIRC :) | 11:03 |
pluskid | you solved it with git pull | 11:03 |
pluskid | which produce an empty commit of merging | 11:03 |
pluskid | My solution is to delete the remote branch first and push again | 11:04 |
pluskid | which would be cleaner in my view | 11:04 |
n4nd0 | yeah, I think I had an error related to this before | 11:04 |
n4nd0 | but I think it was because I didn't push to origin master after rebasing | 11:05 |
pluskid | oh, maybe | 11:05 |
n4nd0 | I will try it soon and let you know | 11:05 |
n4nd0 | I agree, to delete the remote branch looks cleaner | 11:05 |
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Marina | Hi, I have the same problem with poims like Ralf Anders: http://article.gmane.org/gmane.comp.ai.machine-learning.shogun/2536/match= can anyone help me | 12:13 |
n4nd0 | Marina: I have no experience in that part of the project but I can take it a look | 12:15 |
Marina | that would be great | 12:16 |
n4nd0 | Marina: so you get an error with a python script right? | 12:18 |
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Marty28 | hi | 12:18 |
n4nd0 | Marina: in that case, can you please tell me the name of that file if included in shogun or give me a pointer to it? | 12:18 |
Marty28 | hi marina | 12:19 |
Marty28 | Marina: I guess I just wrote you an email, right? | 12:20 |
Marina | I got your email. | 12:21 |
Marty28 | fine :) | 12:22 |
Marina | the name of the file is poim.py | 12:26 |
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Marty28 | Easysvm has some POIM. | 12:28 |
Marty28 | http://people.tuebingen.mpg.de/vipin/www.fml.tuebingen.mpg.de/raetsch//projects/easysvm/ | 12:30 |
n4nd0 | Marty28, Marina: I don't know if you already solved this issue or not | 12:30 |
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Marina | no i didn't | 12:37 |
Marina | I made poims with poim.py half a year before and now it doesn't work anymore.... | 12:38 |
n4nd0 | Marina: all right | 12:38 |
n4nd0 | Marina: so where is this poim.py? | 12:39 |
Marty28 | It is in the easysvm package. It uses shogun-content. | 12:40 |
n4nd0 | ok found it | 12:40 |
n4nd0 | applications/easysvm/esvm/poim.py | 12:40 |
Marina | can I send it to you per email? | 12:40 |
Marina | a yes that's it | 12:40 |
n4nd0 | Marina: ok, so can you tell me exactly how to reproduce the error? | 12:41 |
* n4nd0 is afk | 12:42 | |
* n4nd0 is back | 12:44 | |
n4nd0 | wiking: around? | 12:45 |
Marty28 | My code here: | 12:46 |
Marty28 | print "Loading kernel" | 12:46 |
Marty28 | k1 = rdata.dataio.load_kernel(basename + ".kernel.dat",True) | 12:46 |
Marty28 | print "Loading SVM" | 12:46 |
Marty28 | svm1 = rdata.dataio.loadbz2(basename + ".svm.bz2") | 12:46 |
Marty28 | # POIM stuff | 12:47 |
Marty28 | print "Computing POIMs" | 12:47 |
Marty28 | from poim import compute_poims | 12:47 |
Marty28 | poimdegree = 5 | 12:47 |
Marty28 | max_len = 2 | 12:47 |
Marty28 | # | 12:47 |
Marty28 | print "Trying to POIM..." | 12:47 |
Marty28 | poim, max_poim, diff_poim, poim_totalmass = compute_poims(svm1, k1, poimdegree, max_len) | 12:47 |
* Marty28 tries to remember IRC... | 12:47 | |
wiking | ? | 12:48 |
wiking | n4nd0: sup? | 12:48 |
n4nd0 | wiking: git support ... as usual :P | 12:48 |
wiking | lol | 12:48 |
n4nd0 | wiking: I don't know if you read my conv with pluskid before, it is about that | 12:48 |
n4nd0 | wiking: I can make a summary otherwise | 12:48 |
wiking | sorry was away :( | 12:48 |
n4nd0 | wiking: ok so I openend a pull request | 12:49 |
n4nd0 | didn't work on it for a couple of days | 12:49 |
n4nd0 | now I am back | 12:49 |
n4nd0 | I rebased my origin master with upstream master, push to origin master | 12:49 |
n4nd0 | back in my branch where I do the work | 12:49 |
n4nd0 | I do some commits | 12:49 |
n4nd0 | rebase master | 12:50 |
n4nd0 | and when I try to push, the usual error | 12:50 |
n4nd0 | git push origin jlcovertree | 12:50 |
n4nd0 | To git@github.com:iglesias/shogun.git ! [rejected] jlcovertree -> jlcovertree (non-fast-forward) | 12:50 |
n4nd0 | error: failed to push some refs to 'git@github.com:iglesias/shogun.git' | 12:50 |
Marina | and if you use exactly the code from https://github.com/shogun-toolbox/shogun/blob/master/applications/easysvm/esvm/poim.py you get the error: TypeError: WeightedDegreePositionStringKernel_prepare_POIM2() takes exactly 4 arguments (2 given) | 12:50 |
n4nd0 | To prevent you from losing history, non-fast-forward updates were rejected | 12:50 |
n4nd0 | Merge the remote changes (e.g. 'git pull') before pushing again. See the | 12:50 |
n4nd0 | 'Note about fast-forwards' section of 'git push --help' for details. | 12:50 |
Marty28 | compute_poims does distr = ones((max_len,4))/4 ; | 12:50 |
Marty28 | then kernel.prepare_POIM2(distr, poimdegree, max_len) | 12:50 |
wiking | n4nd0: and after doing a git pull? | 12:50 |
n4nd0 | wiking: I didn't pull yet because as far as I remember | 12:51 |
n4nd0 | wiking: last time I did that | 12:51 |
Marty28 | The error is only about the distr (numpy.ones generated it) | 12:51 |
n4nd0 | wiking: and my commits entered twice in the branch | 12:51 |
Marina | So I have write kernel.prepare_POIM2(distr) to kernel.prepare_POIM2(distr, poimdegree, max_len) like you | 12:51 |
Marina | and than I get the same error | 12:51 |
wiking | n4nd0: mmm that's interesting | 12:51 |
Marina | TypeError: in method 'WeightedDegreePositionStringKernel_prepare_POIM2', argument 2 of type 'float64_t *' | 12:51 |
Marty28 | The error is only about the type of dist. | 12:52 |
wiking | afaik a git pull would try to do a merge basically | 12:52 |
n4nd0 | wiking: I will pull and push and see what happens | 12:52 |
wiking | pull will do you a merge thing | 12:52 |
wiking | or at least will try | 12:52 |
n4nd0 | wiking: in any case, pluskid suggested to delete the remote branch doing git push :branch | 12:52 |
wiking | since what it'll try to do | 12:52 |
wiking | is to sync your remote repo with your local changes | 12:52 |
wiking | hehehe | 12:53 |
wiking | that's another option of course | 12:53 |
n4nd0 | wiking: if I remove the remote branch, the pull request will disappear as well or not? | 12:53 |
wiking | it's more brute force solution | 12:53 |
wiking | but it'll solve your thing | 12:53 |
wiking | yes | 12:53 |
wiking | itshould | 12:53 |
Marty28 | So probably either WeightedDegreePositionStringKernel.prepare_POIM2 was changed or numpy.ones (improbable) | 12:53 |
wiking | since that commit only exist in that branch | 12:53 |
wiking | afaik | 12:54 |
wiking | but i'm not 100% sure of github internals | 12:54 |
wiking | so maybe they do save somewhere the pull requested commits | 12:54 |
wiking | i wouldn't do but who knows | 12:54 |
Marina | Marty28: yes I think so too | 12:54 |
wiking | maybe for some caching purposes or something they'd do it | 12:54 |
n4nd0 | Marina, Marty28: mm I can execute poim.py without problems, maybe I am trying exactly what fails for you | 12:55 |
n4nd0 | maybe I am not, sorry | 12:55 |
n4nd0 | wiking: I am going to pull and push | 12:55 |
Marty28 | numpy.ones gives <type 'numpy.ndarray'> | 12:55 |
n4nd0 | wiking: hopefully the commits won't be duplicated | 12:55 |
wiking | hehehe | 12:55 |
Marty28 | prepare_POIM2 needs float64_t * | 12:55 |
wiking | well that happens when rebase/merge fails | 12:56 |
wiking | but it's not a real duplication... | 12:56 |
n4nd0 | wiking: git pull origin branch right? | 12:56 |
wiking | yep the remote branch... | 12:56 |
n4nd0 | wiking: mmm, I got some conflicts :( | 12:57 |
wiking | so the merge was not possible | 12:57 |
wiking | i mean automatically | 12:57 |
wiking | what are you conflict files? | 12:57 |
Marty28 | n4nd0: Of what type is your "dist" (1st parameter of prepare_POIM2)? | 12:57 |
n4nd0 | wiking: is there a way to indicate to accept my local version? | 12:58 |
wiking | n4nd0: you'll have to fix it by yourself by hand | 12:58 |
n4nd0 | wiking: all right | 12:58 |
wiking | n4nd0: check the git status | 12:58 |
wiking | and you'll see the conflicted files | 12:58 |
wiking | there go in edit them as you please | 12:58 |
wiking | and then do a git commit -a | 12:58 |
wiking | thus you'll have the merge done | 12:58 |
n4nd0 | ok | 12:58 |
n4nd0 | Marty28: I am taking a closer look to poim.py | 12:59 |
n4nd0 | Marty28: I can just see method definitions there | 13:00 |
Marty28 | print "TYPE(distr): " + str(type(distr)) gives <type 'numpy.ndarray'> for me | 13:00 |
Marina | yes right | 13:00 |
Marty28 | prepare_POIM2 needs 'float64_t *' | 13:01 |
n4nd0 | Marty28: yeah but what do you want me to execute? | 13:03 |
n4nd0 | Marty28: I mean, there must be another script making use of the functions in poim.py | 13:04 |
n4nd0 | Marty28: is it what you pasted above? | 13:04 |
Marina | but if I make print distr.dtype than the answer is float64 | 13:04 |
Marty28 | Our own? | 13:05 |
Marina | no I've found it on http://www.scipy.org/Tentative_NumPy_Tutorial | 13:05 |
Marty28 | n4nd0: poim.compute_poims is used | 13:06 |
n4nd0 | Marty28: from where? | 13:06 |
Marty28 | From my script | 13:08 |
Marty28 | n4nd0: poim, max_poim, diff_poim, poim_totalmass = compute_poims(svm1, k1, poimdegree, max_len) | 13:08 |
n4nd0 | Marty28: yeah but ... how I can execute your script? | 13:08 |
Marty28 | Of course the script needs an svm and a kernel. | 13:09 |
n4nd0 | Marty28: so do you have all the code for me to reproduce the error in one file or in several files? | 13:09 |
Marty28 | I would have to prepare that, mom | 13:09 |
n4nd0 | http://snipt.org | 13:10 |
n4nd0 | you can paste your code there if so | 13:10 |
n4nd0 | wiking: :O it went pretty bad | 13:25 |
n4nd0 | wiking: I pull, solved the conflict | 13:25 |
n4nd0 | wiking: commit the merge | 13:25 |
n4nd0 | wiking: push all the changes and look | 13:26 |
n4nd0 | https://github.com/shogun-toolbox/shogun/pull/455/commits | 13:26 |
n4nd0 | in my pull request the commits appear twice and I have even got commits not done by me | 13:26 |
wiking | ihhhh | 13:26 |
wiking | :( | 13:27 |
sonne|work | n4nd0: you forgot a rebase | 13:27 |
n4nd0 | sonne|work: really? in my branch or where? | 13:29 |
sonne|work | n4nd0: at some point you did a git pull | 13:30 |
sonne|work | and then a git push | 13:30 |
n4nd0 | summary of what I did | 13:30 |
sonne|work | which will make all the commits you did before the pull not to appear on top | 13:30 |
sonne|work | but before that | 13:30 |
sonne|work | so things look cluttered | 13:30 |
n4nd0 | the pull request was opened from the other day | 13:31 |
n4nd0 | git checkout master | 13:31 |
n4nd0 | git fetch upstream | 13:31 |
n4nd0 | git rebase upstream/master | 13:31 |
n4nd0 | git push origin master | 13:31 |
n4nd0 | git checkout <my branch> | 13:31 |
n4nd0 | git rebase master | 13:31 |
n4nd0 | some new commits | 13:32 |
n4nd0 | I couldn't push for the error ^ | 13:32 |
n4nd0 | git pull | 13:32 |
n4nd0 | fix conflicts | 13:32 |
n4nd0 | git commit (commit for the merge) | 13:32 |
n4nd0 | git push origin <my branch> | 13:32 |
n4nd0 | what should I have done? | 13:32 |
sonne|work | the last git pull should have been a git pull --rebase | 13:32 |
n4nd0 | it was git pull origin <my branch> | 13:33 |
n4nd0 | I should have done then git pull --rebase origin < my branch > | 13:33 |
n4nd0 | ?? | 13:33 |
wiking | mmm we don't have a structural solver out of box right? :) | 13:33 |
sonne|work | wiking, after the end of gsoc | 13:33 |
wiking | hehehe who's doing it? | 13:33 |
sonne|work | we will see :) | 13:33 |
wiking | ah ok shit yeah | 13:34 |
wiking | no decision yet | 13:34 |
wiking | :))) | 13:34 |
wiking | anyhow i'll put one now in | 13:34 |
wiking | some hackstuff based on libqp | 13:34 |
sonne|work | n4nd0: I don't know how you work but I ususally keep master in sync with origin/master | 13:34 |
Marty28 | ok | 13:34 |
sonne|work | n4nd0: so I would have done git checkout master; git pull --rebase ; git checkout <my branch> ; git rebase master ; ... | 13:35 |
n4nd0 | how would you have solved my situation then? | 13:36 |
n4nd0 | there was a branch | 13:36 |
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n4nd0 | with a pull request issued | 13:37 |
n4nd0 | where I wanted to make new changes | 13:37 |
Marty28 | http://snipt.org/uhggf0 | 13:37 |
n4nd0 | but also to bring in there the changes from master | 13:37 |
Marty28 | kernel_weighted_degree_position_string_modular is from shogun examples | 13:37 |
Marty28 | Data is shogun data | 13:38 |
rico | hi there | 13:38 |
n4nd0 | Marty28: ok, let me try to make it work :) | 13:38 |
sonne|work | n4nd0: via git checkout master; git pull --rebase ; git checkout <my branch> ; git rebase master ; git push | 13:38 |
Marty28 | Just a type error, it says. | 13:38 |
n4nd0 | sonne|work: and after that start the new work | 13:40 |
n4nd0 | sonne|work: maybe it was that, I should have pushed changes from master before commiting my own changes | 13:40 |
rico | I am working on action recognition using opencv (mostly in c++) | 13:40 |
rico | I am looking for code example which shows use of libshogun on opencv data structure. | 13:40 |
sonne|work | I don't understand - I thought the new work was already committed? | 13:40 |
rico | maybe a way to convert SGMatrix to opencv matrix ? | 13:40 |
Marty28 | n4nd0: thanks :) | 13:41 |
sonne|work | rico: SGMatrix is just a ptr to some values, i.e. double* | 13:41 |
n4nd0 | sonne|work: no, the new work was still to be done | 13:41 |
Marina | n4nd0: many thanks :) | 13:41 |
sonne|work | n4nd0: then branch off from master, do the new work and push | 13:42 |
n4nd0 | sonne|work: mmm I think there's a missunderstanding here | 13:44 |
n4nd0 | sonne|work: the branch already existed, I did some work, commit, ..., pull request and fine | 13:44 |
n4nd0 | sonne|work: after a couple of days, I want to continue with my work in that branch | 13:45 |
n4nd0 | sonne|work: but sync it with master too | 13:45 |
rico | sonne|work: float64_t don't match with opencv's double, is there any issue already reported ? | 13:46 |
n4nd0 | that branch had a pull request open | 13:46 |
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sonne|work | n4nd0: yes I understand that is why I am saying that you should do git checkout master; git pull --rebase ; git checkout <my branch> ; git rebase master to be in sync again | 14:04 |
sonne|work | rico - it is just a double | 14:04 |
n4nd0 | sonne|work: ok, for the moment I will delete the pull request since it has got quite dirty | 14:05 |
gsomix | hello | 14:12 |
gsomix | it's seems I will be an optician :) | 14:13 |
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Marty28 | sonne: Hi! Do you know who takes care of WeightedDegreePositionStringKernel.compute_POIM2 etc. in the shogun team? Is this the most modern method for POIMs? | 14:34 |
sonne|work | I should but don't have time currently | 14:43 |
n4nd0 | sonne|work: it looks like it is a problem with the typemaps | 14:44 |
n4nd0 | sonne|work: my guess is that to change the type of the argument to an SGVector should make it work | 14:45 |
n4nd0 | sonne|work: what do you think? | 14:45 |
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sonne|work | n4nd0: sounds likely | 14:45 |
n4nd0 | sonne|work: I am working on it | 14:46 |
wiking | haha anybody up for extending the HKM? http://www.vlfeat.org/~vedaldi/assets/pubs/sreekanth10generalized.pdf | 14:48 |
blackburn | hey there | 14:48 |
n4nd0 | blackburn: hey! | 14:48 |
blackburn | wiking: I told you they had rbf stuff! | 14:49 |
wiking | :)) | 14:49 |
wiking | when? | 14:49 |
wiking | they even have this now: http://www.vlfeat.org/~vedaldi/assets/pubs/vedaldi12sparse.pdf | 14:49 |
blackburn | wiking: before :D | 14:49 |
wiking | ah ok | 14:49 |
blackburn | hmm last one is quite interesting | 14:50 |
wiking | yeps | 14:52 |
sonne|work | what? how do they do it for gaussian kernels? | 14:53 |
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blackburn | sonne|work: magic | 14:55 |
sonne|work | black or white? | 14:56 |
blackburn | sonne|work: just some fourier stuff | 14:57 |
blackburn | as in HIK and JS | 14:57 |
sonne|work | so gaussians become polynomials? | 14:57 |
blackburn | sonne|work: I am not sure what you mean | 14:58 |
blackburn | using bochner's theorem they obtain spectrum of kernel usually | 14:58 |
blackburn | so they just construct features from spectrum | 14:59 |
Marina | n4nd0 : have you found the "poim - problem? | 15:24 |
n4nd0 | Marina: it looks like there is class that is not up to date | 15:25 |
n4nd0 | Marina: I am working on it | 15:25 |
Marina | thank you!!!!! | 15:26 |
blackburn | Marina: are you able to validate the fix? | 15:28 |
blackburn | we have not much expertise in that stuff but there are some pitfalls I'd like to avoid | 15:30 |
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n4nd0 | Marty28: about the parameter poimdegree | 15:38 |
n4nd0 | Marty28: you gave it the value of 5 in your example | 15:38 |
n4nd0 | Marty28: I think that makes the program break a bit later | 15:39 |
Marty28 | I just used some number, AFAIK. | 15:39 |
n4nd0 | aham, all right | 15:39 |
n4nd0 | it looks like it cannot be any number | 15:39 |
Marty28 | use 1 | 15:40 |
n4nd0 | no | 15:40 |
n4nd0 | I mean, it breaks too | 15:40 |
Marty28 | easysvm.py poim 10 6 wd 10 2 arff testmotif1.arff poims.png dna R | 15:41 |
Marty28 | easysvm.py poim 10 6 wd 10 2 fasta testmotifpos.fasta testmotifneg.fasta poims.png dna R | 15:41 |
n4nd0 | ok | 15:41 |
Marty28 | This is an application of POIM functionality. | 15:41 |
n4nd0 | what you tell me the values then? | 15:41 |
n4nd0 | for poimdegree and max_len | 15:42 |
n4nd0 | 10 and 6? | 15:42 |
Marty28 | esvm/experiment.py | 15:43 |
Marty28 | There svm_poim | 15:43 |
Marty28 | so it is the 6 in the example | 15:43 |
Marty28 | usage: %s poim C poimdegree wd [kernelparameters] [arff|fasta] inputfiles poim.png [dna|protein] non(nucleotide|amino)converter | 15:44 |
n4nd0 | what about max_len? | 15:44 |
Marty28 | I guess it is about the motifs. | 15:44 |
Marty28 | Maybe start with 5. | 15:44 |
n4nd0 | 6 for poimdegree and 5 for max_len fails | 15:46 |
Marty28 | max_len 2? | 15:46 |
n4nd0 | 6 and 23 made it work | 15:47 |
n4nd0 | ok | 15:47 |
Marty28 | len(examples[0]) | 15:47 |
n4nd0 | yeah ... | 15:47 |
n4nd0 | but examples was? | 15:47 |
n4nd0 | anyway, that is solved now | 15:48 |
Marty28 | hehe | 15:48 |
n4nd0 | so now you script executes without problems | 15:48 |
Marty28 | I guess 92, but I do not know exactly. | 15:48 |
Marty28 | fine, thanks! | 15:48 |
n4nd0 | blackburn: should we modify the whole class first? | 15:49 |
n4nd0 | all the float64_t* to SG_Vector or SGMatrix? | 15:50 |
blackburn | n4nd0: yes float64_t* won't work at all | 15:50 |
n4nd0 | blackburn: ok, I will do that and prepare a pull request so you can check it | 15:51 |
blackburn | n4nd0: I am worried they do some tricks there (like different real and efficient shapes of matrices) | 15:51 |
Marty28 | (if you succeed please also think about WeightedDegreeStringKernel, which has similar functionality. s?ren ought to know.) | 15:53 |
sonne|work | n4nd0: that is legacy code - the remainders of the double* -> SGVector migration we started changing last gsoc | 15:59 |
n4nd0 | sonne|work: yeah, it looks like that | 15:59 |
blackburn | legacy shit | 16:00 |
n4nd0 | :D | 16:00 |
Marty28 | sonne: So is there a more modern version for WD and POIMs? Or any string kernels which are even better for the purpose? | 16:02 |
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Marty28 | Still changing the data type of a simple 1d-array ought to be easy, I suppose | 16:07 |
tom__ | Is there an implementation of substring kernels in libshogun ? | 16:07 |
n4nd0 | Marty28: yeah, it is probably easy, I am a slow guy though :) | 16:08 |
Marty28 | Learning curves are exponential :D | 16:08 |
blackburn | Marty28: you are always welcome to fix things by yourself :P | 16:09 |
Marty28 | Just a computational biologist. I can invent new applications and promote your stuff, though :) | 16:12 |
tom__ | Is there an implementation of substring kernels in libshogun ? Thanks. | 16:13 |
n4nd0 | tom__: I don't really know if we have what you are looking for | 16:15 |
n4nd0 | tom__: you can take a look here and check if any of these would serve you | 16:15 |
n4nd0 | http://www.shogun-toolbox.org/doc/en/current/dir_00ae96b5ce7201865cb2972b4a123693.html | 16:15 |
blackburn | or https://github.com/shogun-toolbox/shogun/tree/master/src/shogun/kernel | 16:15 |
n4nd0 | yeah, better try the second link, documentation may not be updated | 16:16 |
n4nd0 | blackburn: thanks ;) | 16:16 |
sonne|work | n4nd0: actually no new string kernel for a few years now - I guess we have them all :D | 16:23 |
Marty28 | :) | 16:24 |
tom__ | sonne|work: n4nd0: thx, great works btw. | 16:25 |
Marina | I get the same float64 error if I used : maxlen = 23 and poimdegree = 6... whats my mistake? | 16:26 |
Marty28 | Marina: I guess it only works for a new version he made. | 16:26 |
blackburn | Marina: the problem is in old typemaps we have abandoned | 16:27 |
blackburn | it was (float64_t*, int, int) or so | 16:27 |
blackburn | and now it should be SGMatrix | 16:27 |
blackburn | the only issue with it is a proper shapes handling | 16:28 |
n4nd0 | Marty28, Marina: the thing is that not only the couple of changes that I made to make your script work are necessary to fix all the class | 16:29 |
n4nd0 | and it will take some time to have it ready | 16:29 |
Marina | ah ok... | 16:30 |
Marina | but how coud I used the SGMatrix? | 16:30 |
blackburn | Marina: you don't have to it is just dev issue | 16:30 |
Marina | :-) | 16:32 |
Marty28 | n4nd0: Ok. Yet I think it will be worth it, the functionality sounds interesting :) | 16:33 |
n4nd0 | I have to go now | 16:45 |
n4nd0 | I will continue to work on this later | 16:45 |
n4nd0 | hopefully it will be ready soon | 16:45 |
n4nd0 | bye! | 16:45 |
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Marty28 | thanks :) | 16:47 |
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pluskid | n4nd0, deleting the remote branch won't make your pull request disappear | 16:51 |
pluskid | as long as you push again the branch to remote | 16:51 |
pluskid | I have done this multiple times | 16:52 |
blackburn | hmm nice idea | 16:52 |
pluskid | n4nd0's solution: git pull and merge, will cause duplicated commits as he said | 16:53 |
pluskid | so this would be a better solution | 16:53 |
pluskid | if there's any wiki for shogun, I think we can write something about our git work flow | 16:54 |
blackburn | pluskid: README.developer? | 16:54 |
blackburn | there is some mentioning of git workflow | 16:55 |
blackburn | please add | 16:55 |
pluskid | ok | 16:55 |
blackburn | pluskid: btw if you want to update chinese doc - feel free :) however I bet you won't like it (I wouldn't) | 16:59 |
pluskid | coz you don't know Chinese :p | 17:00 |
pluskid | BTW: why are there English and Chinese doc in the homepage? | 17:00 |
pluskid | I mean, no other languages? | 17:00 |
blackburn | pluskid: soeren wanted me to do russian but I was lazy and didn't | 17:01 |
pluskid | haha | 17:01 |
blackburn | but actually does it make sense? | 17:01 |
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pluskid | what? | 17:01 |
blackburn | I see no reason to use any other lang | 17:01 |
pluskid | what make sense? | 17:01 |
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pluskid | hmm, English is almost universal | 17:01 |
pluskid | I'm just curious to see only Chinese there :p | 17:02 |
blackburn | it is obvious that machine learners can read and write in english | 17:02 |
pluskid | yes, that's almost true | 17:02 |
pluskid | and some can read english but might prefer other (native) language when available | 17:02 |
blackburn | it is a nightmare to support | 17:03 |
pluskid | but sync is a headache, when one has multiple translation | 17:03 |
pluskid | yes | 17:03 |
pluskid | I agree with you on this point | 17:03 |
blackburn | once some X language speaker leaves | 17:03 |
Marina | can I use an older shogun version to make poims work now? | 17:03 |
blackburn | you have nothing to do with that translation | 17:03 |
blackburn | Marina: what stops you? | 17:04 |
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pluskid | btw: I'll travel with the family tomorrow and be back the day after tomorrow | 17:04 |
pluskid | not sure whether there will be internet access during the trip | 17:05 |
blackburn | that's ok and thanks for notifying | 17:05 |
pluskid | hope I won't miss some important thing | 17:05 |
blackburn | no most important is 23, April | 17:05 |
pluskid | :) | 17:05 |
blackburn | pluskid: I guess it would be kind of morning for you when gsocers are announced? | 17:06 |
pluskid | not sure about the exact time | 17:06 |
blackburn | 21 UTC afaik | 17:06 |
pluskid | not good at counting numbers :p, but most of the time when friends in the US send me emails, I got them in the morning | 17:08 |
blackburn | hard to believeheh | 17:08 |
pluskid | 21 + 8 % 24 = 5, seems so | 17:08 |
pluskid | early in the morning if I'm not counting wrong :p | 17:08 |
Marina | i get still the error TypeError: in method 'WeightedDegreePositionStringKernel_prepare_POIM2', argument 2 of type 'float64_t *' | 17:08 |
blackburn | pluskid: however that could be a great moment and you shall be here :) | 17:09 |
blackburn | Marina: still? | 17:09 |
Marina | yes | 17:09 |
@sonney2k | blackburn, did anyone merge a fix? | 17:09 |
blackburn | sonney2k: no, fix is not ready yet | 17:09 |
blackburn | Marina: what do you mean saying still? | 17:09 |
pluskid | blackburn, I'll try to be there, if necessary :) | 17:10 |
@sonney2k | then I don't understand | 17:10 |
@sonney2k | why try again if there is no fix yet? | 17:10 |
blackburn | sonney2k: no idea | 17:10 |
blackburn | sonney2k: please let n4ndo know about shapes of matrices there if would you have time | 17:12 |
Marina | ignore still ... I get the error and don't know what to do | 17:12 |
blackburn | non-trivial sometimes | 17:12 |
blackburn | Marina: do you want all the fixes get merged in a minute? :) | 17:12 |
Marina | :) sometimes | 17:14 |
@sonney2k | hah! | 17:14 |
blackburn | Marina: I am not able to fix things now so you have to wait a little this time | 17:14 |
Marina | ok, thanks! | 17:15 |
blackburn | this could be a day though ;) | 17:15 |
* sonney2k attempts to do a quick fix | 17:15 | |
@sonney2k | (within the next 2 train stations) | 17:16 |
blackburn | sonney2k: good luck ;) | 17:17 |
blackburn | see you all | 17:17 |
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CIA-64 | shogun: Soeren Sonnenburg master * r8436b0a / (2 files): convert get_POIM2 to user SGVector - http://git.io/M4v28A | 17:19 |
@sonney2k | Marina, try again | 17:19 |
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n4nd0 | sonney2k: I can do a pull request for the changes I have done so far | 17:22 |
n4nd0 | sonney2k: it might be ok as quick fix | 17:22 |
n4nd0 | right now it compiles correctly and the script Marty28 sent me works well | 17:23 |
shogun-buildbot | build #725 of libshogun is complete: Failure [failed compile] Build details are at http://www.shogun-toolbox.org/buildbot/builders/libshogun/builds/725 blamelist: sonne@debian.org | 17:25 |
pluskid | updated README.developer for some notes on git | 17:33 |
pluskid | and opened a new pull request | 17:34 |
pluskid | btw, n4nd0, have you got our previous conversation just now? you can safely delete your remote branch without affecting your pull request | 17:34 |
n4nd0 | oh yes pluskid I just read it in the logs :) | 17:35 |
n4nd0 | it is a good plan then | 17:35 |
n4nd0 | so I just have to delete the branch and it later push again? | 17:35 |
pluskid | I think better delete *the moment* before you would push again | 17:36 |
pluskid | not sure what github will show when someone go and look at the pull request, and find there's no such branch :p | 17:36 |
pluskid | however, there's a "force" option for pushing, which could ignore the non-fast-forward error, but I haven't tried this | 17:37 |
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n4nd0 | wiking suggested me once not to force the push | 17:37 |
pluskid | yes, that's sounds horrible | 17:38 |
pluskid | I'd rather not try | 17:38 |
pluskid | though I guess the underlying thing is the same as deleting and pushing again | 17:39 |
Marina | sonney2k: I reinstall shogun now, right? | 17:39 |
pluskid | Marina, maybe have to reinstall from the latest git repo | 17:40 |
Marina | thanks i do so | 17:41 |
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Marina | I get the error: WeightedDegreePositionStringKernel.cpp:1861: error: prototype for ?shogun::SGMatrix<double> shogun::CWeightedDegreePositionStringKernel::get_POIM2()? does not match any in class ?shogun::CWeightedDegreePositionStringKernel | 17:42 |
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n4nd0 | pluskid: I think that my problem is a bit worse though | 17:44 |
n4nd0 | the commit history in my branch screwed | 17:44 |
n4nd0 | https://github.com/iglesias/shogun/commits/jlcovertree | 17:44 |
n4nd0 | I have duplicated commits :S | 17:44 |
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pluskid | n4nd0, so you have merged locally? | 17:48 |
pluskid | that means those duplicated commits exists in your local branch | 17:49 |
n4nd0 | pluskid: I think so, since I couldn't push, I did git pull and solved conflicts | 17:49 |
pluskid | hmm | 17:49 |
pluskid | I have a suggestion | 17:49 |
pluskid | you might create a new branch | 17:49 |
n4nd0 | and move the files there right? | 17:49 |
pluskid | and make your changes of the current branch w.r.t. master as a patch | 17:50 |
pluskid | and apply the patch in the new branch | 17:50 |
pluskid | push the new branch to origin | 17:50 |
pluskid | update your pull request (you can edit the commit range, where you can change the branch name) | 17:50 |
pluskid | the pro is that you can avoid those duplicated commits | 17:51 |
pluskid | the cons is that you "lose" your individual commits, and merge them into one big commit | 17:51 |
pluskid | I think there's a command git-format-patch | 17:51 |
pluskid | for convenient making patches | 17:51 |
n4nd0 | mmm | 17:52 |
n4nd0 | so I should create the new branch | 17:52 |
n4nd0 | and move there the files that I have been working on | 17:52 |
n4nd0 | ? | 17:52 |
pluskid | hmm | 17:53 |
pluskid | first goto the master branch | 17:53 |
pluskid | then create a new branch (based on master) | 17:53 |
n4nd0 | ok | 17:53 |
pluskid | then goto jlcovertree branch | 17:53 |
pluskid | run git diff master > something.patch | 17:54 |
pluskid | and then goto the new branch | 17:54 |
pluskid | apply the patch | 17:54 |
n4nd0 | oh | 17:54 |
n4nd0 | I didn't know about this patches | 17:54 |
n4nd0 | can I apply the changes directly? | 17:55 |
pluskid | yes, I guess so | 17:55 |
pluskid | something like | 17:55 |
pluskid | patch -p0 < the_path_file, IIRC | 17:55 |
n4nd0 | ok | 17:56 |
n4nd0 | I will try it | 17:56 |
pluskid | try it, your work will be safe in the jlcovertree branch as long as you don't delete it | 17:56 |
n4nd0 | I need a rest but I will try it later | 17:57 |
n4nd0 | pluskid: thank you! | 17:57 |
pluskid | btw, I'm looking at the doc of git-format-patch | 17:58 |
pluskid | which might give you a better solution | 17:58 |
pluskid | which retains your individual commits | 17:58 |
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pluskid | git-format-patch master | 18:08 |
pluskid | will give you an individual patch for each of your commits | 18:08 |
pluskid | select those good ones and discard duplicated ones | 18:08 |
pluskid | and then use git-am to apply those patches | 18:08 |
pluskid | in that order | 18:09 |
pluskid | I think this seems to be a better solution, that retains your commit history | 18:09 |
pluskid | n4nd0, see above | 18:09 |
pluskid | and good night :) | 18:09 |
pluskid | hope your problem could be resolved | 18:09 |
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Marty28 | re | 18:21 |
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CIA-64 | shogun: Soeren Sonnenburg master * r2649a77 / (4 files in 2 dirs): SGVector fix for WD-kernel constructor - http://git.io/ZZCF7g | 18:42 |
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Marty28 | sounds good | 18:46 |
shogun-buildbot | build #726 of libshogun is complete: Success [build successful] Build details are at http://www.shogun-toolbox.org/buildbot/builders/libshogun/builds/726 | 18:50 |
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@sonney2k | n4nd0, pluskid yeah you should really use git format-patch - otherwise you loose all your commit messages | 19:43 |
n4nd0 | sonney2k: ok, I am watching now the video pluskid sent in the ML and I will try to fix it later in a new branch | 19:44 |
n4nd0 | sonney2k: but I have a doubt, if apply these patches in a new branch, the pull request will die right? | 19:44 |
n4nd0 | I mean that I have to do a new one | 19:46 |
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@sonney2k | n4nd0, yeah you have to do a new one | 19:56 |
@sonney2k | except if you use push --force | 19:56 |
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n4nd0 | sonney2k: I will do a new one then, if that is not a problem for you | 20:03 |
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n4nd0 | sonney2k: about the WD-kernel, are you taking care of that then? I have seen your commits | 20:30 |
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gsomix | I need more blackburn. | 21:02 |
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CIA-64 | shogun: Sergey Lisitsyn master * rb45f523 / src/shogun/multiclass/MulticlassLibLinear.cpp : SG_ADD for MC liblinear - http://git.io/jTHThw | 23:32 |
CIA-64 | shogun: Sergey Lisitsyn master * r4997875 / src/NEWS : Updated news - http://git.io/BS3Ddw | 23:32 |
@sonney2k | gsomix, for some gay games or what? | 23:32 |
blackburn | sonney2k: phew | 23:33 |
@sonney2k | n4nd0, yeah WD kernel stuff should work? | 23:33 |
@sonney2k | gsomix, how is it going - happily SGVectoring? | 23:33 |
blackburn | sonney2k: you are talking with sleeping deads probably | 23:33 |
blackburn | n4ndo is not present at all and gsomix is sleeping afaik | 23:34 |
blackburn | :) | 23:34 |
@sonney2k | blackburn, the good thing when doing that is that they cannot prove me wrong - I am always right then :) | 23:35 |
blackburn | sonney2k: yeah you may claim whatever :) | 23:35 |
-!- sonney2k is now known as sonne|god | 23:36 | |
* sonne|god == god | 23:36 | |
blackburn | lol | 23:36 |
* sonne|god shogun is my mission | 23:37 | |
* sonne|god obey! | 23:37 | |
blackburn | sonne|god: I do | 23:37 |
@sonne|god | blackburn, go review pluskids patch :) | 23:37 |
-!- sonne|god is now known as sonne|fallengod | 23:38 | |
blackburn | hehe | 23:38 |
@sonne|fallengod | blackburn, or did you do it already | 23:38 |
blackburn | sonne|fallengod: I'll merge his readme stuff for now | 23:39 |
@sonne|fallengod | blackburn, I mean the multiclass stuff? | 23:39 |
blackburn | sonne|fallengod: yes I'll get back to it once I am finished with some shity issue ;) | 23:40 |
CIA-64 | shogun: Chiyuan Zhang master * r86dce0b / src/README.developer : Added some notes of git work flow for developers. - http://git.io/DnywEw | 23:40 |
CIA-64 | shogun: Sergey Lisitsyn master * r4287096 / src/README.developer : Merge branch 'git-workflow-doc' of git://github.com/pluskid/shogun - http://git.io/MimugQ | 23:40 |
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@sonney2k | blackburn, I am looking at his MC stuff now | 23:47 |
@sonney2k | blackburn, this patch is huuuuge! | 23:53 |
blackburn | sonney2k: yes exactly | 23:53 |
@sonney2k | blackburn, problem is (as he pointed out) that we have to paths | 23:53 |
@sonney2k | one machine -> kernelmachine -> svm | 23:53 |
@sonney2k | the other: machine -> multiclassmachine -> mulitclasskernelmachine -> multiclasssvm | 23:54 |
@sonney2k | so a multiclass svm cannot be an svm any longer | 23:54 |
blackburn | sonney2k: I prefer second | 23:54 |
@sonney2k | eh? | 23:54 |
@sonney2k | we have both! | 23:54 |
@sonney2k | it is only that multiclasssvm can no longer be an svm | 23:55 |
@sonney2k | and this breaks a couple of things | 23:55 |
blackburn | sonney2k: there are a couple of reasons why multiclasssvm is not an svm | 23:56 |
@sonney2k | blackburn, yeah I am ok with that | 23:57 |
blackburn | sonney2k: C1/C2 and a lot of other things | 23:57 |
@sonney2k | blackburn, yeah but for multiclass svm he now basically needs to add all the svm relvant functions | 23:58 |
@sonney2k | like C | 23:58 |
blackburn | yes we have to.. | 23:58 |
@sonney2k | epsilon | 23:58 |
@sonney2k | etc | 23:58 |
@sonney2k | it is what he did | 23:58 |
blackburn | yes I know | 23:58 |
@sonney2k | I don't understand why he made multiclassvm a friend of svm though? | 23:58 |
@sonney2k | do you? | 23:58 |
blackburn | hmm let me check | 23:58 |
--- Log closed Wed Apr 18 00:00:19 2012 |
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