[R] Re: Writing new kernel option in svm E1071

[David Meyer]

I would like to add: If your problem is specifically to deal with small
fractions of positive examples, you might consider the weighting feature
of svm.

g.
-d

David Meyer wrote:
> 
> Dear Adai,
> 
> unfortunately, you currently can't extend the kernel set at the R level
> (and due to performance issues this probably will never be possible).
> 
> (It's quite simple at the C-level, though).
> 
> But I think an option for providing the computed kernel values would be
> a useful feature easy to add; I cc: this mail to Chih-Jen Lin, the
> author of LIBSVM, perhaps he agrees.
> 
> g.,
> -d
> 
> > Adaikalavan Ramasamy wrote:
> >
> > I am trying to use the svm function in E1071 package. It does come
> > with built in kernel functions like radial, linear etc. I wish to use
> > the radial basis function but with a constant added to the diagonal of
> > the kernel (or Gram) matrix. This was the suggested method in a paper
> > UCSC-CRL-99-09 Brown et al.
> >
> > So I wrote the following code, [which works correctly if I test on two
> > vectors manually]
> >
> > kernel.new.fn <- function(u,v)
> > {   exp(-gamma*det(t(u-v)%*%(u-v), method="qr")) +
> > ifelse(identical(u, v), 0.1 ,0)    }
> >
> > But when I try to run the code, I get the following error:
> >
> > > test.svm  <- svm( X ,  Ysvm, kernel="kernel.new.fn")
> > Error in svm.default(X.complete, Ysvm[, 3], kernel = "kernel.new.fn")
> > :
> >  wrong kernel specification!
> >
> > I am guessing the problem being svm.default does not recognise
> > "kernel.new.fn".
> > svm.default calls a C file "svmtrain" to do the calculations.
> >
> > Q1: Is there an exisiting option to add a constant to the diagonal of
> > the kernel ?
> 
> no.
> 
> > Q2: Is there a way I can get svm.default to recognise there is new
> > option called kernel.new.fn externally without meddling with C
> > file which I am not so familiar with.
> 
> no.
> 
> >        [OR equivalently is there a way of feeding in the
> > computed kernel instead - I can do this manually using a loop]
> 
> again, no.
> 
> >
> > This is as much due to my lack of programming as it is to my lack of
> > experience with svm.
> >
> > Many thanks in advance, Adai.
> >
> >
> >
> >
> >
> >
> 
> --
>         Mag. David Meyer                Wiedner Hauptstrasse 8-10
> Vienna University of Technology         A-1040 Vienna/AUSTRIA
>          Department of                  Tel.: (+431) 58801/10772
> Statistics and Probability Theory       mail: david.meyer at ci.tuwien.ac.at
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-- 
	Mag. David Meyer		Wiedner Hauptstrasse 8-10
Vienna University of Technology		A-1040 Vienna/AUSTRIA
         Department of			Tel.: (+431) 58801/10772
Statistics and Probability Theory	mail: david.meyer at ci.tuwien.ac.at
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