Hi Wuming,
it has been a while. I was not able to fix this problem these day.
Also I could not get in contact with the developer, so I switched to
SHOGUN, which has an interface for R.
With the SHOGUN interface to libsvm, everything worked fine. Also, its
a cool package and worth that you check it
Hi Heiko,
I run into a similar problem recently. I have a custom kernel which have
some small negative eigenvalues, possibly due to numerical error. I first
used ksvm(K, y) to train the model, but ksvm() freeze (no response to
Ctrl+c). I thought it was due to positive definiteness of the matrix
Sorry i forget to paste it.
But it should be there in another mail.
Also, the suggested trick fixes the problem in with the given workspace,
but still fails in another one (where the kernel matrix IS positive
definite)
http://www-stud.uni-due.de/~sfhestra/freeze_on_pos_def_matrix.tar.gz
This is n
Sorry, heres the message:
Hi
yes the freeze is rather a result of the kernelMatrix being non-positive
definite, have a look at the eigenvalues of kernelMatrix
with eigs and you will see even small negative values. This is usualy
the result of small numerical inacuracies in the computation of the
Hello again,
i got this message from the maintainer:
Am Montag, den 30.11.2009, 11:22 +0100 schrieb Heiko Strathmann:
> Ok, i reported it.
> thanks for trying it out again.
>
> Am 30. November 2009 11:06 schrieb Uwe Ligges
> :
> My apologies, that must have been a copy&paste error and t
Ok, i reported it.
thanks for trying it out again.
Am 30. November 2009 11:06 schrieb Uwe Ligges <
lig...@statistik.tu-dortmund.de>:
> My apologies, that must have been a copy&paste error and the essential
> argument got lost. I can reproduce it now under R-2.10.0 both Windows and
> Linux.
>
> Pl
My apologies, that must have been a copy&paste error and the essential
argument got lost. I can reproduce it now under R-2.10.0 both Windows
and Linux.
Please report your findings to the package maintainer who might be able
to debug this under Linux (probably easier than under Windows).
Best
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")
repl
No "freezes" on a Mac using Ligges' 100 replication script. Tried it
twice. They took around a minute each time.
--
David.
--
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
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))
a
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
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 el
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
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 s
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