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 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.
> >
> >
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