IRC logs of #shogun for Sunday, 2011-04-17

--- Log opened Sun Apr 17 00:00:36 2011
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Tanmoy@alesis00:26
Tanmoythe make is thrwoing some error00:26
Tanmoyclapack_dpotri was not declared00:27
blackburnjust do git fetch upstream & git merge upstream/master00:27
blackburnit is fixed already00:27
Tanmoyoh okie00:31
Tanmoyhmm says remote end hung up unexpectedly00:32
Tanmoyok done00:35
Tanmoythnx again blackburn00:36
blackburnnp00:36
Tanmoyneed to get some sleep00:37
Tanmoycya all00:37
blackburnsee you00:37
Tanmoyok bad stuff00:38
Tanmoythe git fetch did not work00:38
Tanmoysame error00:38
Tanmoy@blackburn did u try to check it00:41
blackburnyeap, it's working for me00:42
Tanmoyhmmm what modifications were made ?00:42
blackburnon the last commit, AveragedPerceptron stuff00:42
Tanmoyk ill probably chekc it later00:44
alesis-novikblackburn, I don't think it's properly fixed00:58
alesis-novikI submitted a pull with a fix00:58
blackburnalesis-novik: at least it's compiling now00:58
alesis-novikblackburn, do you have ATLAS?00:59
blackburnI have libatlas installed on my ubuntu, but I don't sure how sufficient it is01:00
alesis-novikThat might be it. If you have atlas, you would have compiled without any fixes01:01
alesis-novikI forgot to put checks for LAPACK and ATLAS in the first version01:01
blackburnaha01:02
Tanmoydid u just submit it now01:03
alesis-novikA few hours ago. sonney2k will probably check it tomorrow01:03
Tanmoyoh okie01:04
alesis-novikspeaking of which, I'll probably go to bed insanely early by my standards and get up as early tomorrow. I feel I won't get any work done tonight...01:04
alesis-novikTanmoy, you can always install LAPACK :D01:05
alesis-novikor rather ATLAS01:05
alesis-novikanyway, goodnight folks01:05
Tanmoyyup i did tht01:05
Tanmoyyup goodnight01:05
Tanmoynned to get some sleep01:05
Tanmoyand work on other thngs01:05
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CIA-110shogun: Sergey Lisitsyn master * rbe871a8 / src/libshogun/classifier/GaussianNaiveBayes.cpp :05:43
CIA-110shogun: Fixed destructor of GaussianNaiveBayes, fixed mistype in loop leading05:43
CIA-110shogun: to segfault in case of labels: k,k+1,...,n - http://bit.ly/hxqD6P05:43
CIA-110shogun: Soeren Sonnenburg master * r3cea610 / src/libshogun/classifier/GaussianNaiveBayes.cpp :05:43
CIA-110shogun: A number of coding style fixes like05:43
CIA-110shogun: - space between for and (05:43
CIA-110shogun: - for loops with single statement don't need brackets05:43
CIA-110shogun: etc - http://bit.ly/f3U3pD05:43
serialhex*YAY!!! it's SUNDAY!!!*06:03
@sonney2kserialhex, for several hours already :)06:03
serialhexfor me it's only been sunday for 4 mins!06:04
serialhexand only ~3,380,944.1533027566 km until 8am monday :D06:05
@bettybooyep06:06
serialhexsee!! bettyboo knows :P06:06
@bettybooserialhex: i was thinking of compiling it to a c++ dll and using that as the base. but i'd need to consult someone who knows c++ better06:06
serialhexwell dont ask me bettyboo, i dont know c++ that well06:06
@bettybooserialhex: well you can only be accepted for 1 for the summer...06:06
serialhexsonney2k: did you just wake up? or have you been up?? (the former would be better than the latter, but then what are you doing waking up at 6am on a sunday??)06:08
@sonney2kserialhex, our baby woke ab at 2:33 am ... I just managed to get her back to sleep06:08
@bettyboohi06:09
@sonney2kso I though before going to bed I review a few pull requests06:09
serialhexahh, nice.  i'm glad i dont have kids yet!06:09
serialhexi noticed the push, and i updated myself while i was still on06:09
serialhexwell hopefully you can get some rest soon06:10
@sonney2kserialhex, yeah will try now - 2 nights in a row with very little sleep are not good.... ahh and in 3 weeks we will have another child. So the situation can only improve ;-)06:12
serialhexoh niiice!!!  well g'nite sonney2k, and sleep well!06:13
serialhexi hope your newborn is strong and healthy when s/he arrives :D06:13
@sonney2kyeah cu06:13
* sonney2k is now in serialhex's timezone06:13
@sonney2khe indeed - but 3 weeks still06:14
@sonney2kanyway off to bed06:14
@sonney2kcu06:14
serialhexnite06:14
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siddharthhi all06:29
* siddharth hmm no one is here06:31
serialhexnope... no one is here at all siddharth!06:40
siddharthwhat you up to serialhex06:41
serialhexreading some blogs, learning about ruby's narray and thinking about how to use it to speed up my mendelbrodt explorer program...06:41
serialhexand i think i butchered his name... :(06:42
serialhexwhat about yourself?06:42
siddharthcool...working on integrating SGD-QN into shogun06:42
serialhexpardon my ignorance, but what is SGD-QN??06:44
serialhex<3,629,764 km until 5pm monday in berlin!!06:45
siddharthits an SVM classifier with  with stochastic gradient06:46
serialhexooh, sounds interesting!06:48
* serialhex likes stochastic things, though chaos is better :P06:49
siddharthserialhex,chaos is a new TV series :P06:50
@bettyboofunny!?!06:50
siddharthhola bettyboo06:50
serialhexreally??? i didnt know06:50
@bettyboosiddharth: How many applicants have you got so far?06:51
* serialhex dosnt watch too much tv06:51
siddharthsame here ... have watched 24 though06:52
serialhexehh, i didnt like 24 too much, though i watch ncis every so often06:53
siddharththere are many fans of Jack Bauer :P06:55
@bettyboorahaha?06:55
serialhexi know, there are a BUNCH of people who loved that show and hated to see it go off the air.07:00
siddharthyeah07:01
serialhexi have ~730,280,756 km to travel before my next birthday :(07:15
serialhexmonday is getting closer :D 3,574,047 km!!!07:16
@bettyboo;D07:16
siddharthyou going to berlin?07:18
serialhexno, just travelling though space :D07:24
serialhexi made a spiffy spaceship earth calculator in ruby and i've been playing with it ever since07:24
serialhexcode is here: https://github.com/serialhex/fun-stuff/blob/master/spaceship_earth.rb07:25
siddharthohh i see07:30
Tanmoyhi all07:30
serialhexhey Tanmoy, how are you this... morning?07:31
@bettybooho serialhex07:31
Tanmoyim doing good07:32
Tanmoyyeah its morning here07:32
siddharthyeah 11 am07:33
serialhexahh, 1:30 am here :D07:33
Tanmoywhich module r u handling07:35
serialhexare you talking to me or sidd??07:37
siddharthwell I am currently working on svm classifier07:38
Tanmoyoh i meant both :D07:38
serialhexahh... i'm (hopefully) going to be working on the ruby bindings... much to learn before then!07:40
Tanmoythe lapack issue is still not resolved right ?07:42
* serialhex is probably the oldest "student" but also the one with the least skill... he weeps because of his lack of knowlege! ;(07:42
Tanmoyhow old r u serialhex07:43
serialhex2807:43
serialhexand i'm barely an undergrad :P07:43
Tanmoyahh beat u07:43
Tanmoy2907:43
serialhexreally??07:43
Tanmoynd postgrad07:43
serialhexdammit!!!07:43
Tanmoyu at school ?07:44
serialhexyeah, i've just started back at school, after many years of goofing off and generally beeing a leech!07:44
* serialhex is technically still a leech, just a leech on the gov'ment and not his parents07:45
siddharthm doing MS07:46
Tanmoyme 207:46
siddharthya I know07:46
serialhexooh!!! competition!!!07:46
* serialhex gets som popcorn to watch the fight :P07:47
siddharthu also from IIIT :P07:47
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serialhex...even more interesting!07:47
siddharthserialhex having fun :D07:47
serialhexalways siddharth!!!!07:48
Tanmoyyup :D07:48
serialhexexcept when my cat decids to walk all over my stuff!!!  GRR!!!07:48
siddharthanother IIITian has come...07:48
siddharthakhil_ wassup07:48
Tanmoysiddharth which module u handling07:49
siddharthIntegrating SVNSGD-QN, and ollivier Primal SVM solver07:50
siddharthSVMSGDQN*07:50
siddharthwhat about u Tanmoy07:52
TanmoySVM-SO with CRF07:52
* serialhex is lost with the acronyms being thrown around...07:53
TanmoySO Structured output07:53
TanmoyCRF Conditional Random Fields07:53
serialhexahh, i see!!07:54
* serialhex is a little less confused07:54
serialhexallright, i'm off to bed all07:57
@bettyboocu07:57
siddharthgood night07:57
serialhexg'nite!  and lets hope sonney2k gets a few good nights rest also!07:57
siddharthclever bettyboo07:57
@bettyboosiddharth: is there is 13 mentors07:57
Tanmoynight07:58
serialhexshe is getting clever... a little too clever...07:58
siddharthyeah07:58
serialhexi leave you all with this:  http://xkcd.com/329/07:59
* serialhex goes to sleep, a little more afraid of bettyboo than he was before07:59
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blackburnsonney2k: thanks for style fixes10:29
blackburnthat was an awful mistype in loop10:30
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blackburnsonney2k: btw, should I make a pull request with three classes: CEvaluation and derivates CAccuracy, CMeanSquaredError?10:37
blackburnor better to implement all of these things an then pull it?10:38
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Tanmoy@sonney2k does GHMM needs to be reimplemented11:34
Tanmoybtw the Gaussian.cpp is still throwing error12:42
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alesis-novikTanmoy, it's because the patch hasn't been applied yet14:42
alesis-novikAnd good morning14:42
blackburnalesis-novik: just woked up? ;)14:43
alesis-novikMore or less14:43
alesis-novikhave been feeling broken these last few days14:43
blackburnI don't know what is the error you are talking about14:44
blackburnalesis-novik: will it appear in case of atlas is installed?14:45
alesis-novikIt will appear in case of ATLAS not being installed14:45
blackburnhmm but it compiles on my14:45
alesis-novikwhen you run configure, what do you get for the LAPACK stuff?14:46
blackburnminute..14:46
blackburnChecking for Vanilla lapack and blas support ... no (missing some features: LDA, liblinear, ...)14:47
alesis-novikah14:47
blackburnalesis-novik: this?14:47
alesis-novikso you don't have LAPACK at all14:47
blackburnaha :)14:48
alesis-novikI think it breaks for people with Vanilla, but not with ATLAS or none at all14:48
blackburnbtw, will install it :D14:48
blackburnhave installed it, now will make14:51
alesis-novikdon't forget to reconfigure :D14:51
blackburnyeap14:51
blackburnoh, I think I see now why KRR wasn't working on my shogun :D14:52
blackburnOh! it doesn't compiling now :D14:55
* blackburn said some nonsense14:56
blackburnit isn't14:56
blackburnalesis-novik: yeah, now I see the problem you talking about :D14:57
@bettybooHA14:57
alesis-novikYou could always install ATLAS :D14:58
blackburnaha, already did.14:58
alesis-novikIt does work with atlas though14:59
alesis-novikIt shouldn't produce any compilation errors if you have ATLAS installed15:00
blackburnehh15:00
blackburnah, I see15:00
blackburnsorry15:00
serialhexthats interesting... i just installed atlas & checked for blas but when i configure it tells me that neither are there15:01
alesis-novikah15:01
alesis-novikhow did you install it?15:01
blackburnbtw what is the package of atlas on ubuntu?15:01
alesis-noviklibatlas with different endings15:02
serialhexthrough synaptic...15:02
blackburnwill install all the things :D15:02
serialhexi'll tell you what packages in a min... but they were the sse2 versions15:02
blackburnserialhex: no need, I'm installing all of these *atlas now15:03
blackburnbut atlas support - no15:03
blackburnhm!15:03
alesis-novikThe thing is when you install with synaptic it adds the headers to *whatever*/include/atlas/*15:03
alesis-novikso you need to add that to the compiler include path15:03
alesis-novikotherwise it tries using #include "lapack.h" and it doesn't work, because it should be #include "atlas/lapack.h"15:04
blackburngrhh15:04
blackburnalesis-novik: seems to be as good as натягивать глаз на жопу15:06
serialhex..thats interesting, i font have a lapack.h in /usr/include or /usr/include/atlas15:06
* serialhex thinks blackburn is sending secret messages in russian :D15:07
blackburnserialhex: I don't have one too15:07
serialhex:-/15:08
blackburnserialhex: just said it is similar to pull someone's eye to his ass15:08
alesis-novikthe header file is clapack.h, if that makes any difference15:09
serialhexvery interesting imagery, i'm sure it flows better in russian, and i cant think of an equivalent we might have in english15:09
serialhexyeah, i've got that in /usr/lib/atlas15:09
serialhex& cblas.h ... so where do i tell this funky thing where to look???15:10
blackburnwhat should we do to add this folder for include?15:10
alesis-novikWell, personally since I use bash, I added this to .bashrc15:14
alesis-novikCPLUS_INCLUDE_PATH=/usr/include/atlas/15:14
alesis-novikexport CPLUS_INCLUDE_PATH15:14
alesis-novikand15:14
alesis-novikC_INCLUDE_PATH=/usr/include/atlas/15:14
alesis-novikexport C_INCLUDE_PATH15:14
serialhex:-/  maybe the configure script should be set up to look for this?15:15
alesis-novikserialhex, I prefer changing env variables, but I guess you could do that15:17
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serialhexwell if it works this way when people use synaptic to install atlas, then a dev cant expect a user to change environment variables to use their software15:18
blackburnserialhex: ./configure --enable-debug --interfaces=libshogun,python_modular --includes=/usr/include/atlas15:18
blackburnserialhex: it helped15:18
serialhexif we know there is a problem & can fix it for future people, why not just do that?15:18
blackburnbut I think somebody should fix it15:19
blackburnserialhex: yeap15:19
serialhexyeah, doing the environment variable thing worked too, compiling now...15:19
alesis-novikI see your point serialhex15:19
blackburnserialhex: I don't like this way :)15:19
Tanmoybut yeah i need to get it now15:19
Tanmoywell yeah initially i tht too i had atlas15:19
serialhex(though it never gave me the msg for vanilla lapack & blas)15:20
Tanmoyk it seems to work fine15:35
* serialhex is still compiling - 1 core @ 3ghz isnt all that fast anymore :(15:40
* blackburn too15:45
alesis-novikany idea when sonney2k will be around?15:48
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blackburnalesis-novik: I have no idea but waiting for him too :)16:18
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ZiyuanWhy CGaussianKernel is a subclass of CDotKernel but not of CDistanceKernel?17:15
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ZiyuanAnd why the "distance" and "width" in DistanceKernel.h is private?18:58
ZiyuanShouldn't it be protected?18:59
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@sonney2kback20:45
blackburnoh! nice20:46
blackburnsonney2k: if will have time please take a look on 'new' evaluation. if everything is all right will implement some more 'evaluators'20:47
@sonney2kblackburn, reading your diff20:50
blackburnsonney2k: then you could just comment it right here ;)20:51
blackburnI will have a trouble with implementing ROC and etc20:52
blackburnevaluate returns float64_t..20:53
blackburnsee..20:54
blackburnwill fix it right now20:54
blackburnsonney2k: yesterday, when testing accuracy noticed that error with gaussiannaivebayes, very sorry for missed it20:57
@sonney2kblackburn, ok kommented21:01
@sonney2kcommented that is21:02
@sonney2kblackburn, what error with GNB?21:02
blackburnsonney2k: eh.. I fixed it last night21:02
blackburnif labels was e.g. 9,10,11,..21:02
blackburnit will fail21:02
blackburnit was because for(int i= >1< instead of 0..21:04
@sonney2kok21:04
@sonney2kahh yes21:04
@sonney2kalesis-novik, pong21:05
blackburnanyway, it's working now21:05
blackburnsonney2k: using sign there won't be capability of multiclass accuracy estimation21:08
blackburnis it ok?21:09
@sonney2kblackburn, yes - that is why we need another MultiClassAccuracy ...21:09
blackburnsonney2k: okay, thank you21:09
@sonney2kif you have a better idea - let me know21:09
@sonney2k( I mean fuzzyly one could check if labels are all integers)21:09
blackburnsonney2k: SVM outputs 1.0 and -1.0?21:10
blackburnbut how I can check it?21:11
alesis-novikHello sonney2k21:11
@sonney2kblackburn, they are not +/-121:11
@sonney2kalesis-novik, hi - what's up?21:11
@sonney2kblackburn, they are in R21:11
blackburnsonney2k: ok.21:11
alesis-novikI've submitted the changes to the pull request21:11
@sonney2kbut for multiclass we know that they are alll integers >= 021:12
@sonney2kalesis-novik, ok looking into it21:12
blackburnsonney2k: what way do you prefer?21:12
alesis-novikNow working on the simple EM version. I was wondering, should I name it GMM or EMGMM and should it be under distributions or clustering? Thoughts?21:13
@sonney2kblackburn, I think having MultiClassAccuracy to is easiest21:14
@sonney2k(then your code is ok already)21:14
blackburnsonney2k: ok, will implement it21:14
@sonney2kalesis-novik, is it more clustering or distribution?21:17
blackburnsonney2k: may be sth like set_multiclass(true)?21:17
blackburnah, nevermind :)21:17
alesis-noviksonney2k, I think it's quite similar to K-Means, so clustering I guess21:18
* blackburn thinks EM is more clustering too21:18
@sonney2kok then...21:19
dvevresonney2k: hey! did you get the online features class i mailed yesterday?21:21
@sonney2kdvevre, I didn't see the pull request?!21:21
dvevresonney2k: wasn't a pull request... i sent it through email :)21:22
dvevrecan't send a pull request until i think the design's final21:22
@sonney2kalesis-novik, looks like great work21:25
alesis-novikthanks sonney2k21:26
CIA-110shogun: Alesis Novik master * r68a9604 / (3 files in 2 dirs): Changed constructor and init for PCACut, changed GUIPreProc so it would compile - http://bit.ly/frs8pL21:26
CIA-110shogun: Soeren Sonnenburg master * r47f74d3 / (6 files in 4 dirs): Merge branch 'master' of https://github.com/alesis/shogun - http://bit.ly/gm6Fez21:26
alesis-novikI was thinking of slightly changing the PDF computation to actually first compute the log-PDF21:27
blackburnsonney2k: done.21:31
blackburnsonney2k: ah, sorry, there is no '\sign' in latex21:34
blackburnsonney2k: now done truly21:37
alesis-noviksonney2k, any suggestions on what should be the GMM superclass?21:52
blackburnalesis-novik: is EM your project?21:53
alesis-novikblackburn, yes21:53
blackburnnice21:53
alesis-novikI mean hopefully :D21:54
blackburnalesis-novik: btw, you may design some hierarchy for clustering, now it seems to be not so good21:54
blackburnthe only problem - K means use CDistanceMachine just like KNN..21:55
blackburnalesis-novik: seems you have more chances than that guy ;)21:57
alesis-novikНе дели шкуру неубитого медведя. :D21:58
blackburnЯ просто хочу чтобы был ты, а не представитель одной прекрасной страны :)21:58
@bettybooyeah!21:59
alesis-novik:D /high5 bettyboo22:00
@bettybooalesis-novik: samara, or moscow, same time22:00
Ziyuansonney: I submitted a patch for Bessel kernel22:01
ZiyuanAnd how use git send-email to send patches as attachments (I don't find the option)22:02
alesis-novikZiyuan, did you submit a pull?22:04
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Ziyuansubmitted to sonney, actually...22:08
Ziyuanvia mail22:08
alesis-novikZiyuan, I think it's easier for him to comment/apply/not-loose-in-all-the-mail the patches if you submit them via pull request (unless you had some sort of arrangement)22:09
@sonney2kZiyuan, coulnd' you use jn() instead of the cyl_bessel_j ?22:11
@sonney2kthen we don't need boost22:11
@sonney2kZiyuan, btw, Tanmoy submitted a similar thing - not sure if it is correct https://github.com/shogun-toolbox/shogun/pull/48/files22:13
@sonney2kyour compute functions looks totally different22:13
ZiyuanI follow this http://crsouza.blogspot.com/2010/03/kernel-functions-for-machine-learning.html#bessel22:14
@sonney2kalesis-novik, KernelMachine or Distribution (utilizing kernel machine internally)22:15
Ziyuanand use width=1/sigma22:15
@sonney2kZiyuan, it lists 2 functions for bessel - the one that is in kernlab and another one22:15
Ziyuanto fit the intuition of width...22:15
ZiyuanSo I should point out which one I used?22:16
@sonney2kI simply don't know which one should use...22:17
@sonney2knever heard of the bessel kernel before22:17
ZiyuanI want to raise my score so picked up a kernel not yet implemented...22:20
ZiyuanI've found a paper having something to do with Bessel kernel22:26
Ziyuanhttp://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.62.788722:27
alesis-noviksonney2k, why do you say I should use KernelMachine?22:31
@sonney2kalesis-novik, sorry forget it - doesn't make sense22:36
@sonney2kZiyuan, I think your formula makes more sense (at least from the url)22:42
@sonney2kcan you pleae send a git pull request from github?22:43
@sonney2kdvevre, could you please also do it via github?22:43
dvevreokay, but now way it can be merged in this condition!22:43
@sonney2kZiyuan, ahh and please add copyright headers22:43
@sonney2kdvevre, yes but still it is easier for me22:44
ZiyuanOk22:44
blackburnsonney2k: please let me know to continue implement things in 'evaluation' or not22:44
@sonney2kblackburn, yes - it is all good now!22:44
blackburnsonney2k: should I do it in this pull?22:44
@sonney2kblackburn, I would love to replace your new code with the preivous eval functions22:45
@sonney2kin one go I am afraid.22:45
blackburneh?22:45
blackburnsorry, don't understand about replacement22:46
@sonney2kblackburn, the old PerformanceMeasures.*22:46
@sonney2kI would replace them with what you have written22:47
blackburnsonney2k: ah, you wrote vice versa :)22:47
@sonney2kwhich looks much more readable and extendible this way22:47
@sonney2kblackburn, I guess I need some sleep tonight22:47
alesis-noviksonney2k, it would kind of make sense to derive GMM from Distribution, though it still would be under clustering22:47
blackburnsonney2k: you should ;)22:47
blackburnsonney2k: so, I will make it in that pull request, right?22:48
@sonney2kalesis-novik, do as you wish - I don't have any strong preference here22:48
@sonney2kblackburn, yes22:48
blackburnsonney2k: okay, will write to you when it will be done22:48
* sonney2k yawns22:48
blackburnsonney2k: ah, I still don't know what to do with ROC22:48
@sonney2ksorry but I really need sleep22:48
blackburnsonney2k: yeap, you should22:49
blackburnwill ask you later22:49
@sonney2kblackburn, copy the code from perfmeasures22:49
@sonney2kfor now at least22:49
@sonney2kanyway22:49
* sonney2k is off to bed22:49
@sonney2kl8r22:49
blackburnsonney2k: I mean design..22:49
blackburnsee you22:49
blackburnbecause evaluate is float64_t22:49
blackburnwhatever :)22:49
alesis-novikSee you22:50
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--- Log closed Mon Apr 18 00:00:36 2011

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