kernlab's ksvm method freeze

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