[R] kernlab's ksvm method freeze

[Heiko Strathmann]

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
> >>
> >>
> > 
> > ______________________________________________
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> > and provide commented, minimal, self-contained, reproducible code.