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 >> >> [[alternative HTML version deleted]] ______________________________________________ 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.
