Open in new window / Try shogun cloud
--- Log opened Sat Jun 02 00:00:41 2012
heiko2hihi00:00
heiko2heiko300:01
heiko3heiko2: so did you submit?00:01
heiko3nips?00:01
heiko2yes00:01
heiko2its done :)00:01
heiko2lots of work00:01
heiko3congrats00:01
heiko3and exam?00:01
heiko2thanks :)00:01
heiko2exam was nice00:01
heiko2also by arthur btw :)00:01
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heiko3hahah exam by supervisor??00:01
heiko2yes, funny isnt it? :)00:01
heiko3that should be unfair a little00:01
heiko2oh, my girl just returned home, gotta go00:02
heiko3heh00:02
heiko2no, he gave me no hints ;)00:02
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n4nd0good night!01:11
blackburnnite01:12
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CIA-9shogun: Soeren Sonnenburg master * r78f9ac6 / src/configure : fix octave detection for octave 3.6.x (Closes issue #383) - http://git.io/aDihsw06:44
CIA-9shogun: Soeren Sonnenburg master * r8a15088 / src/configure : fix ruby detection in configure - http://git.io/DfZJdw06:44
CIA-9shogun: Soeren Sonnenburg master * r7344caa / (2 files in 2 dirs): add empty define for ignore in class list - http://git.io/jFNJBg06:44
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CIA-9shogun: Soeren Sonnenburg master * rb921a7d / (2 files in 2 dirs): add proper copyrights in Director* stuff - http://git.io/_GUY1g20:24
CIA-9shogun: Soeren Sonnenburg master * r80b8013 / (src/shogun/lib/Hash.cpp src/shogun/lib/Hash.h): fix compile warning in md5sum - http://git.io/gbxZXQ20:24
CIA-9shogun: Soeren Sonnenburg master * rf0a2a12 / (5 files in 3 dirs): add empty liblinear regressor - http://git.io/e6BGBA20:24
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blackburnhaha20:26
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gsomixmechanics is full of pain21:19
gsomixdepressive lagrangians, suffering hamiltonians and many integrals of fear21:21
gsomixthey come to me in dreams21:24
gsomixand organize an orgy of terror21:25
blackburn:D21:26
blackburnwell I still feel excited about Lagrange's stuff21:27
gsomixblackburn, my favorite subject is multi-dimensional oscillators21:38
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KMcQuistenAfternoon Sergey22:15
blackburnhey22:15
blackburn(its me)22:16
blackburn:)22:16
KMcQuistenI'd guessed :)22:16
KMcQuistenSo, any ideas as to what the problem is?22:16
blackburnokayy let me try to guess22:16
blackburncould you please first say what is classifier you do use?22:17
blackburnMKLRegression?22:17
KMcQuistenI'm working with the MKLRegression22:17
KMcQuistenYes22:17
blackburnlet me check the code22:17
blackburnokay and the problem appears only with combined features, right?22:18
KMcQuistenTo the best of my knowledge yes.  It worked fine when I gave a single kernel to LibSVR, but I dind't try putting a single kernel into MKLRegression22:20
blackburnlet me try to come with some reproducing example22:20
blackburnKMcQuisten: should it look similar to python_modular/kernel_combined_modular.py?22:23
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KMcQuistenYes, essentially, but using StringWordFeatures and the CommWordStringKernel in the Comined objects.22:26
blackburnI changed mkl_binclass_modular.py to regression - works22:27
blackburnlets see if stringfeatures change the game22:28
blackburnKMcQuisten: can I ask you to modify some code meanwhile? some simple thing to debug22:31
KMcQuistenSure22:31
blackburnI just want to know where it wants to stop22:31
KMcQuistenRight22:31
KMcQuistenJust let me know where I need to modify things22:32
blackburnshogun/features/StringFeatures.cpp:26422:32
blackburnreplace SG_ERROR with SG_WARNING and try to recompile22:32
blackburnah and %d after "is" word in msg (I forgot that)22:33
KMcQuistenOk, done.  Now I'll recompile22:34
blackburnthanks22:34
KMcQuistenOk, here's what I got.  It looks like we have an index issue:22:38
KMcQuistenSpectrum_MKLselect.py:66: RuntimeWarning: [WARN] Requested feature vector with index 50 while total num is 50   testsvm.train(combfeats) Traceback (most recent call last):   File "Spectrum_MKLselect.py", line 66, in <module>     testsvm.train(combfeats) SystemError: [ERROR] Trying to access string[50] but num_str=5022:38
blackburnhmm22:40
blackburnonly 50, but no more, right?22:40
KMcQuistenYes.  I only put in 50 data points as a toy set.  Let me check with the whole dataset22:40
blackburnwait wait22:40
blackburnERROR is raised somewhere22:41
KMcQuistenYes.  I think it's trying to access index 50 on a vector that's 0 indexed with 50 items in ti22:41
blackburnno, that can go for bigger values (it stopped because of the SG_ERROR)22:42
KMcQuistenHow is that possible?  If you have a vector of length 50 its highest index is 49.  I get the same kind of error with the full set of 2430 sequences22:44
blackburnI mean it can go for 51, etc22:44
KMcQuistenSystemError: [ERROR] Trying to access string[2430] but num_str=243022:45
KMcQuistenRIght.  I know i'm not limited to 50 data points22:45
blackburnok let me find this ERROR22:45
blackburnI tried to combine string and real features btw22:45
blackburnworks22:45
blackburnKMcQuisten: could you please replace SG_ERROR with SG_WARNING at line 348 too?22:48
KMcQuistensure22:51
KMcQuistenI will also try and comine the real and the StringWord22:51
KMcQuistenand see if it works for me too22:51
blackburnwhat do you combine?22:52
blackburnstring and string?22:52
KMcQuistenStringWord and StringWord.   DNA sequences mapped into the unsigned 16bit integers.  In python, it's StringWordFeatures, but in the C++ it's StringFeatures<uint_16>22:53
KMcQuistennot StringFeatures<char>22:53
blackburnok22:54
blackburnKMcQuisten: okay I managed to reproduce22:56
blackburntwo StringWord feautres22:56
KMcQuistendoes it work for you?22:59
blackburnno dies on the same error22:59
KMcQuistenThat makes me a happy cmaper22:59
KMcQuistencamper22:59
KMcQuistenat least it's reproduceable23:00
blackburnyeah I'll try to figure out what is wrong23:00
KMcQuistenthanks so much!23:00
KMcQuistenI've got plenty of other work and writing to do, so i'll just camp here for a while23:01
blackburnok sure23:01
blackburnI'll let you know on any progress23:02
KMcQuistenThank you23:02
gsomixgood night guys23:11
blackburnKMcQuisten: hmm as I thought it stopped at 18323:23
blackburn92*223:23
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KMcQuistenWhat does that indicate?23:26
blackburnsome code adds number of feature vectors somehow I guess23:28
blackburnbut it is really strange23:28
KMcQuistenWhat's the significance of the 92 * 2?23:28
blackburnnumber of feature vectors in test example is 9223:28
KMcQuistenAh23:29
blackburnand two string word features23:29
blackburnKMcQuisten: good thing I detected a bug :D23:30
KMcQuistenIndeed.  I changed that error to a warning as you asked before and recompiled, got the following:23:31
KMcQuistenSpectrum_MKLselect.py:66: RuntimeWarning: [WARN] Requested feature vector with index 2430 while total num is 243023:32
KMcQuistenSpectrum_MKLselect.py:66: RuntimeWarning: [WARN] Requested feature vector with index 2431 while total num is 243023:32
KMcQuistenSpectrum_MKLselect.py:66: RuntimeWarning: [WARN] Requested feature vector with index 2432 while total num is 243023:32
KMcQuistenSpectrum_MKLselect.py:66: RuntimeWarning: [WARN] Trying to access string[2432] but num_str=243023:32
KMcQuistenSegmentation fault (core dumped)23:33
KMcQuistenDoes the Combinedfeats object adress all the features as thogh they are one long list?23:33
blackburnsomething like that but I do not understand what is the difference between real+string and string+string23:34
CIA-9shogun: Sergey Lisitsyn master * r3e1dc47 / src/shogun/regression/svr/SVRLight.cpp : Fixed wrong free in SVRLight - http://git.io/n7oILw23:37
blackburnKMcQuisten: okay I'm pretty near I think23:57
blackburnsvr bug23:57
--- Log closed Sun Jun 03 00:00:41 2012