Open in new window / Try shogun cloud
--- Log opened Fri Apr 12 00:00:27 2013
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YanglittleHey, how can I get the info of methods in detail except help , eg. shogun.Features.CombinedFeatures.append_features.obj(),06:05
YanglittleI'm reading the examples, and not know the meaning of the methods clearly.06:07
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foulwallanybody there?07:46
foulwallsonney2k: Arrange my today's work, pls07:47
foulwall...caught a bad cold... but no problem I'll try my best07:51
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@sonney2kfoulwall, then better recover before you continue08:51
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@sonney2kYanglittle, that is the part where shogun needs improvement. we have lots of methods / functions but documentation /tutorial is not as good08:53
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@sonney2kfoulwall, once you feel better we should try to get your regression demo into the shogun homepage08:54
foulwallsonney2k: maybe tomorrow?08:55
@sonney2kfoulwall, ok - please check out https://github.com/shogun-toolbox/shogun-web tomorrow - we could then under some link say /demos/regression put in the examples08:59
foulwallsonney2k: gotcha09:00
@sonney2kfoulwall, but take care health is more important!09:00
foulwallsonney2k: thanks, i will.09:00
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iglesiasgblackburn is back?10:20
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blackburniglesiasg: oops10:22
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@lisitsynI should get used to that too :D10:23
iglesiasghehe10:23
iglesiasgyou have superpowers now10:23
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lisitsynblabla10:27
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sonne|workiglesiasg: what happened to n4nd0?10:28
iglesiasgI like this nick better10:29
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iglesiasgbecause of my github identity10:29
iglesiasgI think it looks more serious :)10:29
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sonne|workiglesiasg: so you registered it?10:29
iglesiasgsonne|work: yes10:29
sonne|worklisitsyn: btw you will receive a t-shirt10:30
sonne|workbut a mentor t-shirt10:30
@lisitsynsonne|work: no, they do not ship to nigeria10:31
sonne|workand when you visit the summit you get another one10:31
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iglesiasglisitsyn: maybe you could have it shipped to Germany since you are going there for the workshop10:34
@lisitsyniglesiasg: hah well I do not care that much about it10:34
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@lisitsyniglesiasg: anyway may be it is true only for students10:35
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iglesiasglet me ask you a basic ML question regarding the classical SVM formulation for classification10:39
sonne|worklisitsyn: ship it to my address and I give it to you when you are here :D10:40
lambdayhi lisitsyn10:40
iglesiasgso the objective looks like: \min_{w, \Xi} ||w||^2 + C \sum \Xi_i10:40
iglesiasgthe regularization part, ||w||^210:41
iglesiasgI think of this part as that is the one that actually takes care of margin maximization; it can be seen equivalent to \max M where M is the margin and fixing the norm of w to 1/M10:42
@lisitsynsonne|work: makes sense - I should ask carol10:42
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@lisitsynlambday: hi10:42
@lisitsyniglesiasg: yes regularization is margin10:42
iglesiasgbut I remember once that Georg told me that it was also there because it can be proven that an arbitraly high norm of w can fit perfectly to data10:43
iglesiasgso it is there actually to avoid overfitting10:43
@lisitsyniglesiasg: yes bigger margin - less overfitting10:43
iglesiasgI guess it is another point of view of the same concept, however I think there is something that I miss10:43
@lisitsyniglesiasg: there are a few views on that10:43
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lambdayI've been trying to use SGVector constructor (data, vlen).. when I take a pointer and use new, its all fine but when I don't I'm getting a weird error...10:43
@lisitsyniglesiasg: another thing is10:43
iglesiasglisitsyn: but why arbitrarily high norm of w can perfectly fit data?10:44
@lisitsyniglesiasg: in geometrical or?10:44
@lisitsynlambday: what is the error?10:44
iglesiasglisitsyn: I don't know, in any way it can be understood - not necessarily geometrically if it cannot be seen like that10:44
@lisitsyniglesiasg: well if you don't care about margin (regularization)10:45
@lisitsyni.e. your C is low10:45
@lisitsynyou minimize the error on the training set10:45
@lisitsynw/o any restrictions10:45
@lisitsynso you fit perfectly or so10:45
iglesiasglisitsyn: mmm10:45
lambdaycorrupted double-linked list: 0x00000000017f0590 ***10:46
lambdayand then it prints the memory map10:46
@lisitsyniglesiasg: speaking geometrical margin has some other things10:46
@lisitsyniglesiasg: IIRC VC dimension has something to do with margin of a linear classifier10:46
@lisitsyniglesiasg: so it stands for complexity10:47
@lisitsyniglesiasg: the other nice view on that is10:47
@lisitsynimagine you have w = [10,0.1,0.1]10:47
iglesiasglisitsyn: ok10:47
@lisitsynand w = [2,2,2]10:47
@lisitsyniglesiasg: latter is better because the distribution of coefficients is more smooth or so10:48
@lisitsyniglesiasg: in the first case you get feature 1 *very important*10:48
iglesiasgI see10:48
@lisitsynso regularization denies one to 'overfit' like setting big coefficients to some features10:48
@lisitsyniglesiasg: w/o regularization it could get like 1003402340, -32132132, 5454510:49
@lisitsynbut it would fit the data10:49
iglesiasgthat is why I see not so clearly10:49
@lisitsynwith no real induction10:49
iglesiasgwhy bigger values fit better the data?10:49
@lisitsyniglesiasg: that's not a rule it could happen10:49
iglesiasgaham I understand10:50
@lisitsyniglesiasg: there are so many views on that10:50
iglesiasgbut say two instances of w10:51
iglesiasgboth of them of similar smoothness10:51
@lisitsyniglesiasg: if I was a physician I'd say something about fredholm equation :D10:51
iglesiasgand both of them fitting the data more or less in the same way - so with \xi_i values sort of similar10:51
@lisitsyniglesiasg: it is pretty illposed problem so would not expect that10:51
iglesiasgif one of the vectors has high values and the other one low values10:52
@lisitsyn:)10:52
iglesiasgwhy the one with low values should be preferred?10:52
@lisitsyniglesiasg: why vectors?10:52
@lisitsynare you talking about dual?10:52
iglesiasgI am calling w vector10:52
@lisitsynahh10:52
@lisitsynso you are asking why ||w|| -> min is preferred?10:52
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iglesiasgwell, because of definition ||w|| smaller implies larger margin I guess10:53
@lisitsyn1) it stands for margin (2/||w|| is the margin)10:53
@lisitsyn2) it stands for complexity (implied from margin)10:53
@lisitsyniglesiasg: it is not just implies - margin is exactly 2/||w|10:54
iglesiasgagree10:54
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@lisitsynin VC theory they kind of proved that margin is related to complexity10:54
@lisitsyniglesiasg: I like the complexity view - it unifies that framework with say decision trees10:54
@lisitsynin decision trees you have no margin but you can derive something with MDL10:55
@lisitsynminimum description length10:55
iglesiasgaham10:55
@lisitsynlike the smaller your tree is the better it is10:55
iglesiasgvery nice theory indeed10:56
@lisitsynI am wondering if some day some guy with proper brain would come with something better10:56
iglesiasgthat's why the world needs sonne|work to come back to research :)10:58
@lisitsynI am afraid there is no such person yet at all10:59
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iglesiasglisitsyn: http://abstrusegoose.com/502 probably we will never know11:06
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andrei_iusanhello, I'm a student at CS, interested in your projects, especially in BSS11:08
iglesiasghi andrei_iusan, that is good11:08
andrei_iusanI have studied linear algebra and numerical methods11:08
andrei_iusanI think those are the most relevant courses11:09
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andrei_iusanI worked with Matlab/Octave11:09
foo__Hi all11:09
foo__I am wondering if Platt's method for probabilistic output svm is implemented into shogun ? I remember a discussion on this in the forum...11:10
@lisitsynfoo__: yes11:11
@lisitsynfoo__: scores_to_probabilities method of BinaryLabels11:12
andrei_iusanI haven't studied machine learning algorithms, but I would like too, is it reallistic that I could study and learn the algorithms and technics, or I should have more knowledge for this project?11:13
iglesiasgandrei_iusan: I think it is possible to learn them11:14
@lisitsynandrei_iusan: yes sure, you don't have to be a phd in machine learning :)11:14
andrei_iusanI know matlab and played with matrices, factorizations, Jacobi, Givens, eigen-values, eigen-vectors, diagonalization, etc11:15
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@lisitsynandrei_iusan: that's cool for sure11:15
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@lisitsynandrei_iusan: you might need to consider contributing with something small though11:15
@lisitsynandrei_iusan: are you subscribed to the mailing list?11:16
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andrei_iusanno, not yet, I will subscribe now11:16
andrei_iusanok, I have subscribed11:19
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@lisitsynandrei_iusan: http://blog.gmane.org/gmane.comp.ai.machine-learning.shogun check archives (last week or so) - there is some information11:20
andrei_iusanok11:20
foo_Is probabilistic output for svm is available in shogun ?11:21
@lisitsynfoo_: scores_to_probabilities method of BinaryLabels11:21
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@lisitsyniglesiasg: ah btw that comma madness works11:24
iglesiasglisitsyn: cool11:24
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@lisitsyniglesiasg: will commit tonight if I manage to fix the last issue with default values11:24
iglesiasgI will have a look once it is up11:25
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andrei_iusanok, so what do I do next? :D11:58
andrei_iusancheck the issues on github?11:58
@lisitsynandrei_iusan: yes11:58
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andrei_iusanok12:00
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lambdayhi heiko112:15
heiko1lambday:  hi!12:15
lambdayheiko1: in the sampling gaussian unit test for dense... shall I again use fixed cov matrix12:15
heiko1lambday:  what do you mean by fixed?12:16
lambdayheiko1: not random... fixed values12:16
heiko1lambday: I see, no random is better there12:16
heiko1just compare empirical covariance with the original one12:16
lambdaythat's what I was thinking :)12:16
lambdayyes.. norm..12:17
lambdayone more thing.. as of now, i'm testing both empirical mean and cov in the same test12:17
heiko1lambday: yes, just frobenius norm or whatever12:17
heiko1lambday: thats fine12:17
lambdayheiko1: okay...12:18
lambdayheiko1: thanks man :)12:18
heiko1lambday: one more thing12:18
lambdayheiko1: yes12:18
heiko1could you add a boolean flag to the method12:18
lambdayfor?12:18
heiko1called "precision_matrix" whose default is false12:19
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heiko1and if it is true, the matrix is regarded as the inverse of the covariance matrix12:19
heiko1so for a matrix C12:19
heiko1one sometimes wants to sample N(0, C) and sometimes N(0, C^(-1))12:19
lambdayheiko1: okay...12:19
heiko1lambday: I can send you matlab code how the sampling works if needed12:20
heiko1basically just solve L\randn(...) system12:20
heiko1you can use eigen for that12:20
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lambdayheiko1: if precision_matrix is false, it would use C, otherwise it would use C_inv, in that case, it would use the cholesky factor of C_inv, right?12:21
heiko1lambday: exactly, however, do not invert the matrix (since numerical problems)12:21
heiko1just invert the cholesky instead12:21
lambdayheiko1: okay..12:22
heiko1so in anyway, you have to compute C=L*L'12:22
heiko1and then either you do L*randn(...) or (L^T )^(-1)*randn( ...)12:22
lambdayummm..12:23
lambdayyes12:23
heiko1lambday: https://gist.github.com/karlnapf/537108212:23
heiko1this is what I use in Matlab12:24
heiko1in fact, it would be great if you could also offer these standard arguments12:24
lambdayheiko1: thanks... in the current code, I took a sample from N(0,I) of size Nxdim instead (ease of use with matrix_mean and matrix_cov method in Statistics.h)..12:25
heiko1z is the standard Gaussian vector (if given, do not generate one)12:25
heiko1inds is a permutation that you want to use12:25
heiko1matrix_mean? matrix_cov?12:25
lambdayheiko1: matrix_mean for calculating empirical mean..12:26
heiko1lambday: you mean in the test?12:26
lambdayheiko1: yes ..12:26
heiko1yes, thats fine fine12:26
lambdayso, I used upper cholesky factor instead12:27
heiko1oh wait, but please test on another matrix than I12:27
heiko1identity12:27
heiko1and non-zero mean12:27
heiko1lower/upper doesnt matter12:27
heiko1as long as the samples are correct :)12:27
lambdayheiko1: hmm..12:27
lambdayheiko1: for the normal case (precision_matrix = false), current code is working fine.. the empirical and the actual mean and cov are quite close..12:28
heiko1lambday: also for non-zero, non-identity case?12:30
lambdayheiko1: yes.. :)12:30
heiko1good!12:30
heiko1if you want, we can already merge this - and then continue with the rest12:30
lambdayheiko1: few things left for the dense case..12:30
heiko1did you follow the instructions of Sergey's mail?12:30
heiko1lambday: yes?12:31
lambdayheiko1: for the gitflow?12:31
heiko1lambday: yes12:31
lambdayheiko1: watched the video link you gave.. didn't try though...12:31
lambday:(12:32
heiko1dont worry12:32
lambdayheiko1: I did all the changes locally since then12:32
heiko1ok12:32
heiko1so first of all, create a backup :)12:33
lambdayheiko1: okay..12:33
heiko1then run git flow init12:33
heiko1it will ask you a few things12:33
heiko1select develop and master for release and production12:34
heiko1and default values for the rest12:35
heiko1develop might not be in there12:35
heiko1oh and  shogun_  as version tag12:35
lambdayheiko1: shall I commit first before doing this? I am using a temporary branch locally for this..12:36
heiko1no, just make a backup12:36
heiko1you can replace the files later and commit from the new structure12:36
heiko1but make sure, things are not deleted by accident :)12:36
lambdayheiko1: alright...12:36
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heiko1lambday:  and?12:44
lambdayheiko1: I am using fedora and can't get gitflow using yum install... its not in their repo yet12:44
lambdayso, building from the source :(12:44
heiko1lambday:  uh, I see, should be fine doing this12:45
iglesiasgsonne|work: so it seems that it is Spain vs Germany in the champions league :)12:45
lambdayheiko1: argh.. I ran make install from gitflow and it asks "Run 'git submodule init && git submodule update' first."... when I do that, it says connection timed out :'(12:48
heiko1lambday: mmmh12:51
heiko1do you have checked out the submodules?12:51
heiko1it is the data folder12:51
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heiko1oh12:52
heiko1in fact, that might be the gitflow git12:52
lambdayheiko1: didn't get it :(12:53
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heiko1this git submodule is probably for the gitflow12:54
heiko1Ill download it and try to install to see what happens12:54
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heiko1lambday: the commands worked here12:55
heiko1just do "git submodule init && git submodule update" inside the gitflow folder12:55
lambdayheiko1: ya.. it shows cloning into 'shFlags' but then connection timed out..12:57
heiko1lambday: maybe re-checkout retry, its working here12:58
lambdayheiko1: okay.. i'm trying12:58
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heiko1lambday: those admin things are always annoying since they consume so much time :(13:04
lambdayheiko1: yes... :(13:05
lambdayI guess its proxy error... I have https proxy set but it uses git:// ..13:05
heiko1lambday: yes certainly13:06
heiko1works all fine here13:06
heiko1I think you can tell git the proxy13:06
heiko1saw it somewhere13:06
lambdayhmm.. i'm trying..13:08
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lambdayheiko1: finally gitflow installed... phew!13:48
lambdayheiko1: Branch name for production releases: [master] ... I'm confused.. shall i put develop here or master? and yes you were right develop isn't here.. just showing master and another branch i've created locally13:53
heiko1if develop is not there13:53
heiko1create a branch13:53
heiko1and then pull from upstream13:53
heiko1lisitsyn: right?13:53
heiko1then it is there13:54
@lisitsynheiko1: yes iirc13:54
@lisitsynit is a fork?13:54
lambdayit is a fork13:55
heiko1lisitsyn: could you guide lambday thourgh the process of creating a PR? I am going out for lunch now13:55
@lisitsynheiko1: good timing!13:56
@lisitsyn;)13:56
heiko1lambday: ask lisitsyn, I will be back in 1 hr13:56
heiko1lisitsyn: well we are trying for some time now :)13:56
lambdayheiko1: no problem.. ciao :)13:56
@lisitsynheiko1: 1 hr!13:56
@lisitsyn:D13:56
heiko1lisitsyn: + coffee :D13:56
@lisitsynit must be an elephant13:57
@lisitsynom nom13:57
@lisitsynlambday: okay let me reproduce your issue here13:57
lambday:D13:57
@lisitsynand then I'll let you know how to proceed13:57
lambdayhmm13:57
@lisitsynlambday: what does 'git remote -v' outputs?13:59
lambdayoriginhttps://github.com/lambday/shogun (fetch) originhttps://github.com/lambday/shogun (push) upstreamhttps://github.com/shogun-toolbox/shogun.git (fetch) upstreamhttps://github.com/shogun-toolbox/shogun.git (push)14:00
sonne|workheiko1: could you please register with nickserv?14:00
heiko1sonne|work: yes will do,14:00
@lisitsynlambday: please do 'git fetch upstream'14:01
@lisitsynand develop should appear14:01
sonne|workheiko1: ohh and please be a bit more positive when you reply to students on the mailinglist - your replies are usually rough german style :D14:01
lambdaylisitsyn: okay14:01
heiko1sonne|work: haha, sure! :)14:01
lambdaylisitsyn: done14:02
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lambdaylisitsyn: yes develop is there14:02
@lisitsynlambday: production releases is master14:02
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@lisitsynlambday: next version is develop14:02
@lisitsynothers are default14:02
lambdaylisitsyn: okay... let me try14:03
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lambdaylisitsyn: but when I do git flow init, it still shows master and <my-local-branch>..14:04
@lisitsynno develop?14:04
lambdaynope..14:04
@lisitsynlambday: git checkout develop14:04
@lisitsynand try again14:04
lambdayokay14:05
lambdayyes it shows now...14:05
lambdayVersion tag prefix? [] ====> shogun_ ??14:06
@lisitsynlambday: yes shogun_ but it doesn't really matter14:07
@lisitsynas you are not going to release yet :)14:07
lambdayokay14:07
lambdaylisitsyn: so, now if I want to commit, first i need to do git flow "sample_gaussian_dense" ... and then commit?14:10
lambdayi mean, git flow start "sample_gaussian_dense"14:11
lambdaythen commits and then git flow finish "sample_gaussian_dense"... and then push..14:12
@lisitsynlambday: git flow feature start sample_gaussian_dense14:15
@lisitsynsome commits14:15
@lisitsynthen git flow feature finish sample_gaussian_dense14:15
lambdaylisitsyn: alright..14:16
lambdayand then push with git push origin develop..?14:16
@lisitsynlambday: yes14:16
lambdaylisitsyn: then normal PR.. gotcha14:16
@lisitsynyes14:17
lambdaylisitsyn: thanks man :)14:17
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lambdayheiko1: hello16:42
heiko1lambday: hi!16:43
heiko1how is it going?16:43
lambdayhttps://github.com/lambday/shogun/blob/develop/src/shogun/mathematics/Statistics.cpp#L206116:43
lambdayhttps://github.com/lambday/shogun/blob/develop/tests/unit/mathematics/Statistics_unittest.cc#L10416:43
lambdayadded a unit test and the code... although.. the bool param is yet to be added16:44
lambdayfor dense matrices16:44
lambdaybut, this code gives segmentation fault for large dimensions16:44
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heiko1lambday: good!16:46
heiko1lambday: please dont do new SGMatrix, this produces a memory leak16:46
heiko1just return SGMatrix (S.data ....)16:46
lambdayheiko1: when I tried to do otherwise, it gave a weird error16:46
heiko1that does it16:46
lambdayohkay16:46
heiko1and another thing16:46
heiko1could you generate column vectors?16:47
heiko1as this is the shogun way to store them16:47
heiko1so the result matrix is DxN16:47
heiko1and set N=1 as default16:47
heiko1lambday:  you can send the PR, I will check the rest in there (easier to comment)16:48
lambdayheiko1: okay... but then matrix_mean ias to be given "col_wise = false" right?16:48
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lambdayheiko1: okay.. just fixing the "new" in SGMatrix and sending the PR16:50
lambdayheiko1: when I don't use "new", it produces an error.. :(16:56
lambdayInvalid free() / delete / delete[] / realloc()16:58
lambdaysorry my mistake17:00
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foulwalljust modified the svr demo. the dots will no longer be saved on the server, so every time enter the page the dots are prepared dots, not the dots inputed last time. And all django views are merged into one function, with only one html template, no data model needed. the demo will be very easy to merge into shogun-web.18:38
foulwallsonney2k:18:39
foulwallI'll have a look at shogun-web.18:40
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foulwallnot so late...18:40
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foulwallthere's some differences between the site in shogun-web repo and the running one.... Where's the weblog in the navigator bar?19:05
foulwall@sonney2k maybe we can add a new url router to host the django demos.19:06
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foulwallhi iglesiasg19:07
iglesiasghey foulwall19:07
iglesiasghow are you doing?19:07
iglesiasgI read in logs you were a bit sick19:07
foulwallfine!19:07
iglesiasgfeeling better?19:07
foulwallyeah. thanks for caring.19:07
iglesiasgno problem :)19:07
foulwallI've checkout the shogun-web repo19:08
iglesiasggood to hear it is better19:08
iglesiasgfoulwall: aham ok19:08
iglesiasgfoulwall: you need admin pass?19:08
foulwallaha?19:08
iglesiasgsorry?19:09
foulwallwhich admin pass?19:09
iglesiasgfor the admin interface, but if it was not that, never mind :)19:09
foulwallthe site in repo or the site running?19:09
iglesiasgfor the site in the repo I meant19:10
iglesiasgthe one you run locally for testing19:10
foulwalldemo needs no data model. so there's no need for the admin panel19:11
iglesiasgoh ok, I understand19:12
foulwallwhat i need is a url router to redirect to my demo.19:13
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iglesiasgmmm ok, I do not really understand what that means exactly honestly19:14
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foulwallmmm, just I need add rule to make a particular url, like "shogun-toolbox.org/demos/xxxx" connect with my demo19:18
foulwalliglesiasg: sorry for my poor english.19:18
iglesiasgfoulwall: It is not a problem, don't worry for that19:18
iglesiasgfoulwall: ok, I think I understand what this rule is now19:19
foulwallthat is called a url router19:19
foulwalland each request for that url is passed to their corresponding python function19:20
foulwalllate now, see you tomorrow, iglesiasg19:22
iglesiasgfoulwall: ok, see you19:23
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@lisitsynsonney2k: nice23:17
@sonney2klisitsyn, that should be enough spam23:17
@lisitsynsonney2k: who are connectionists?23:18
@sonney2klisitsyn, now we should do the workshop announcement23:18
@sonney2klisitsyn, I would rather want to do a broad announcement23:18
@sonney2klike "shogun machine learning workshop"23:18
@sonney2kand then say that it will feature general (applied) machine learning talks23:19
@sonney2kwith particular focus on the shogun machine learning toolbox23:19
@lisitsynsonney2k: makes sense23:19
@sonney2kso we could have some people just generally interested in ML23:19
@lisitsynsonney2k: I should dig into books to learn something on machine learning then!23:19
@lisitsyn:D23:19
@sonney2klisitsyn, connectionists are the root of it all23:20
@sonney2kthe neural net guys / nips roots etc23:20
@lisitsynsonney2k: I am ashamed I didn't know about that list23:20
@lisitsynsonney2k: do they have a lot of discussions there?23:20
@sonney2klisitsyn, I like ml-news better these days23:21
@lisitsynembed(...,(method=LaplacianEigenmaps,eigen_method=Randomized))23:22
@lisitsynsonney2k: ^ it works :D23:22
@sonney2k:)23:24
@sonney2kI just realize I have to write sth to gunnar23:25
@sonney2k*argh*23:25
@lisitsynsonney2k: did he agree?23:25
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@sonney2klisitsyn, chris said so23:31
@sonney2kbut that is about sth else23:31
@lisitsynsonney2k: gunnar looks like a bigger big shot than obama23:31
@sonney2kthis year gsoc is crazy - I mean it really ends late september23:32
@sonney2kand already did start now23:32
@lisitsynyees23:32
@sonney2kit is like 6 months23:32
@lisitsynI think we will all die23:32
@sonney2klisitsyn, now or never ;)23:32
@sonney2kbut ultimately I agree23:33
@lisitsynsonney2k: our students will die too23:33
@lisitsynendless summer23:34
@lisitsynsonney2k: more connectionists?23:37
@sonney2kmaybe it gives them the freedom to manage both studies & gsoc23:39
@sonney2kthis stretching reduces and increases pressure at the same time23:40
@sonney2klisitsyn, yes connectionists did not allow me to post from this address23:51
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--- Log closed Sat Apr 13 00:00:27 2013