[R] kernlab's ksvm method freeze

Heiko Strathmann heiko.strathmann at googlemail.com
Sun Nov 29 14:51:02 CET 2009


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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