Hello uwe, Thanks for trying out. the freeze happens after about 10 to 20 iterations. Did you try as many?
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 kernel="matrix" option of the > >> ksvm method. > >> > >> My (normalized) kernel matrix is of size 1309*1309, my results vector > >> has the same length. > >> > >> I am using C-svc. > >> > >> My kernlab call is something similiar to this: > >> > >> ksvm(kernel="matrix", kernelMatrix, trainingDataYs, type="C-svc", > >> cross=10, C=2) > >> > >> To this point, everything works fine. > >> > >> But now, i want to do a search for a good C Parameter, so I call the > >> ksvm method multiple times in a loop, with changing parameters. > >> This loop freezes after a few iterations. > >> > >> > >> The following simple example also freezes after few iterations (the > >> number varies). See that the ksvm call is always the same in every > >> iteration: > >> > >> for (i in c(1:20)) { > >> print(i) > >> ksvm(kernel="matrix", kernelMatrix, trainingDataYs, > >> type="C-svc", > >> cross=10, C=2) > >> } > >> > >> > >> Does anybody have an idea what causes this? I am new to R and kernlab, > >> perhaps i missed something? > >> > >> I put my workspace online, which contains the kernel matrix and the > >> training labels. Simply load workspace, kernlab library and paste the > >> example code to reproduce: > >> http://www-stud.uni-due.de/~sfhestra/ > >> > >> I am using R version 2.10.0 and kernlab 0.9-9. > >> > >> Thanks for your help! > >> > >> Regards, > >> Heiko Strathmann > >> > >> > > > > ______________________________________________ > > 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. ______________________________________________ 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.
