Hi Wuming, it has been a while. I was not able to fix this problem these day. Also I could not get in contact with the developer, so I switched to SHOGUN, which has an interface for R. With the SHOGUN interface to libsvm, everything worked fine. Also, its a cool package and worth that you check it out :) Cheers, Heiko
2011/12/21 Wuming Gong <gongx...@umn.edu>: > Hi Heiko, > > I run into a similar problem recently. I have a custom kernel which have > some small negative eigenvalues, possibly due to numerical error. I first > used ksvm(K, y) to train the model, but ksvm() freeze (no response to > Ctrl+c). I thought it was due to positive definiteness of the matrix, so I > used nearPD() from Matrix package to correct kernel. This sometimes solved > the freeze problem. But sometimes ksvm() still freeze even with the > corrected matrix with all positive eigenvalues. Then I checked document of > libsvm and found the following FAQ > > > Q: The training time is too long. What should I do? > For large problems, please specify enough cache size (i.e., -m). Slow > convergence may happen for some difficult cases (e.g. -c is large). You can > try to use a looser stopping tolerance with -e. If that still doesn't work, > you may train only a subset of the data. You can use the program subset.py > in the directory "tools" to obtain a random subset. > > If you have extremely large data and face this difficulty, please contact > us. We will be happy to discuss possible solutions. > > When using large -e, you may want to check if -h 0 (no shrinking) or -h 1 > (shrinking) is faster. See a related question below. > > > So I changed tor from 0.001 to 0.01 and turn off shrinking heuristic. This > seems working well for most of the other freeze problems. > > Wuming > > > On Tue, Dec 1, 2009 at 5:46 AM, Heiko Strathmann > <heiko.strathm...@googlemail.com> wrote: >> Sorry i forget to paste it. >> But it should be there in another mail. >> >> Also, the suggested trick fixes the problem in with the given workspace, >> but still fails in another one (where the kernel matrix IS positive >> definite) >> http://www-stud.uni-due.de/~sfhestra/freeze_on_pos_def_matrix.tar.gz >> >> This is not a R-workspace, but my zipped working directory. >> The file I run is parameterSearch.R. >> The freeze happens more or less late in the search, but not at a fixed >> point. >> >> >> Heiko >> >> Am Dienstag, den 01.12.2009, 10:25 +0100 schrieb Uwe Ligges: >>> >>> Heiko Strathmann wrote: >>> > Hello again, >>> > >>> > i got this message from the maintainer: >>> >>> And which part is from the maintainer? >>> >>> Uwe >>> >>> >>> >>> > >>> > Am Montag, den 30.11.2009, 11:22 +0100 schrieb Heiko Strathmann: >>> >> Ok, i reported it. >>> >> thanks for trying it out again. >>> >> >>> >> Am 30. November 2009 11:06 schrieb Uwe Ligges >>> >> <lig...@statistik.tu-dortmund.de>: >>> >> My apologies, that must have been a copy&paste error and the >>> >> essential argument got lost. I can reproduce it now under >>> >> R-2.10.0 both Windows and Linux. >>> >> >>> >> Please report your findings to the package maintainer who >>> >> might be able to debug this under Linux (probably easier than >>> >> under Windows). >>> >> >>> >> Best, >>> >> >>> >> >>> >> Uwe Ligges >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> Heiko Strathmann wrote: >>> >> I tried out the code you wrote, it also works for me, >>> >> but it lacks a >>> >> parameter i use in my code. >>> >> >>> >> The problem (at this computer) seems to be this >>> >> "cross"-parameter of >>> >> ksvm - if I, for example, add the parameter cross=10, >>> >> i get the old >>> >> problem: >>> >> >>> >> library("kernlab") >>> >> load("freeze_workspace.RDATA") >>> >> replicate(10, ksvm(kernel="matrix", kernelMatrix, >>> >> trainingDataYs, type="C-svc", C=2, cross=10)) >>> >> >>> >> gets me a frozen R process, CTRL-C does not work >>> >> anymore, and the only thing left is to kill it. >>> >> >>> >> (for cross < 4, the thing still works) >>> >> >>> >> (I also just reinstalled my Ubuntu and R) >>> >> >>> >> Heiko Strathmann >>> >> >>> >> >>> >> Am Sonntag, den 29.11.2009, 19:52 +0100 schrieb Uwe >>> >> Ligges: >>> >> Heiko Strathmann wrote: >>> >> Hello uwe, >>> >> Thanks for trying out. >>> >> the freeze happens after about 10 to >>> >> 20 iterations. Did you try as many? >>> >> I just tried again: >>> >> >>> >> library("kernlab") >>> >> load("freeze_workspace.RDATA") >>> >> replicate(100, ksvm(kernel="matrix", >>> >> kernelMatrix, trainingDataYs, type="C-svc", >>> >> C=2)) >>> >> >>> >> and everything is still fine (same on Linux). >>> >> >>> >> Uwe Ligges >>> >> >>> >> >>> >> >>> >> Am Sonntag, den 29.11.2009, 17:22 >>> >> +0100 schrieb Uwe Ligges: >>> >> I just tried >>> >> >>> >> ksvm(kernel="matrix", >>> >> kernelMatrix, trainingDataYs, >>> >> type="C-svc", cross=10, C=2) >>> >> >>> >> several times on both >>> >> workspaces and both returned >>> >> some results after a couple of >>> >> seconds under the same >>> >> versions (R version 2.10.0 and >>> >> kernlab 0.9-9.) under Windows >>> >> XP. >>> >> >>> >> There mist be something else >>> >> going on... >>> >> >>> >> Best wishes, >>> >> Uwe Ligges >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> Heiko Strathmann wrote: >>> >> Hello again, >>> >> >>> >> the freeze seems to >>> >> depend on the kernel >>> >> matrix. >>> >> With another kernel >>> >> matrix of similiar >>> >> size, gernerated with >>> >> the same >>> >> kernel, but on another >>> >> dataset, there is no >>> >> freeze. >>> >> >>> >> I have put a workspace >>> >> with the working >>> >> matrix and one with >>> >> the freezing >>> >> matrix online for >>> >> testing (see old >>> >> email) >>> >> >>> >> http://www-stud.uni-due.de/~sfhestra/ >>> >> >>> >> In my eyes this >>> >> behavior is really >>> >> strange, and i have no >>> >> clue, what to >>> >> do to solve this. >>> >> >>> >> Regards, >>> >> Heiko Strathmann >>> >> >>> >> Am Sonntag, den >>> >> 29.11.2009, 14:21 >>> >> +0100 schrieb Heiko >>> >> Strathmann: >>> >> Hello, >>> >> >>> >> I am using >>> >> kernlab to do >>> >> some binary >>> >> classification >>> >> on aminoacid >>> >> strings. >>> >> >>> >> I am using a >>> >> custom kernel, >>> >> so i use the >>> >> ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
