David
On Nov 29, 2009, at 1:28 PM, Heiko Strathmann wrote:
> 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 at 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 at 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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT