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 not a R-workspace, but my zipped working directory.
The file I run is parameterSearch.R.
The freeze happens more or less late in the search, but not at a fixed
point.
Heiko
Am Dienstag, den 01.12.2009, 10:25 +0100 schrieb Uwe
Ligges:>
> Heiko Strathmann wrote:
> > Hello again,
> >
> > i got this message from the maintainer:
>
> And which part is from the maintainer?
>
> Uwe
>
>
>
> >
> > 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
> >> <ligges at 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.
> >>
> >> Please report your findings to the package maintainer who
> >> might be able to debug this under Linux (probably easier
than
> >> under Windows).
> >>
> >> Best,
> >>
> >>
> >> Uwe Ligges
> >>
> >>
> >>
> >>
> >>
> >>
> >> Heiko Strathmann wrote:
> >> 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
> >>
> >>
> >>
______________________________________________
> >> 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.
> >>
> >>
> >>
> >>
> >
> >