[R] kernlab's ksvm method freeze

[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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