Open in new window / Try shogun cloud
--- Log opened Fri Oct 12 00:00:17 2012
wikinglol primal objective: -1000000000000000019884624838656.00000000:29
wiking:>00:29
wikingmosek mosek00:29
shogun-buildbotbuild #130 of nightly_default is complete: Failure [failed test]  Build details are at http://www.shogun-toolbox.org/buildbot/builders/nightly_default/builds/13003:31
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blackburnwiking: you've minimized it quite a lot already!15:24
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toohi there15:28
sonne|workhi there too :D15:30
tooblackburn: hi there, is that you who wrote the CAlphabet::translate_from_single_order" function ?15:30
toosonne|work: looking for some explanation about CAlphabet::translate_from_single_order15:30
sonne|worknope me15:30
sonne|workand gunnar IIRC15:31
toobitwise operations make me crazy :p15:31
sonne|worktoo efficient :DF15:31
tooindeed15:32
sonne|workyeah. idea is basically to squeeze e.g. 2 characters into one byte etc15:32
sonne|workso for DNA you need just 2 bits for A,C,G,T15:32
sonne|workso you can have 4 characters encoded in 1 byte15:33
tooI see. And max value seems to be 2^8 then alphabet of size > 256 seems not possible right now, right ?15:33
sonne|workyes it is for byte alphabets max15:34
sonne|workif you have bigger alphabets you shouldn't use StringByteFeatures but StringWordFeatures etc anyways15:35
sonne|workand then not do this kind of encoding but use the hashing trick15:35
toothe hashing trick ?15:35
sonne|workyeah, compute a hash of your n-characters15:36
sonne|workand store just that15:36
sonne|workit is good enough for any real world app and very fast15:36
toois there any example of this proc with shogun ?15:37
sonne|worktoo: use murmurhash215:38
sonne|workin lib/Hash15:38
toojust to be sure: StringWordFeatures = CStringFeatures<uint64_t> and StringByteFeatures = CStringFeatures<char> ?15:39
tootanks for advice15:43
sonne|worknot uint64_t but uint16_t15:43
sonne|workbut you can use whatever is appropriate for your alphabet15:44
tooallright, then in practice I can make shogun common string kernels work with stringfeatures from bigger alphabet (?)15:48
sonne|workdifficulty depends on kernel you need though15:52
toospectrum kernel for example15:53
sonne|workI would suggest to implement DotFeatures for your feature type - that is the fastest possible way and you can use all linear SVMs (that then train using the spectrum kernel)15:54
sonne|workthere are a couple of examples for that already Hashed* features15:55
toothanks15:57
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--- Log closed Sat Oct 13 00:00:17 2012