[SciPy-user] symeig

Stuart Murdock s.e.murdock at soton.ac.uk
Wed Oct 6 04:06:04 CDT 2004


Hi
David Grant wrote:

> Would it be possible to add something like symeig to scipy?
> -------- Original Message --------
> Subject:     Re: [SciPy-user] First few eigenvectors of a numarray array
> Date:     Fri, 3 Sep 2004 17:07:06 +0200 (CEST)
> From:     p.berkes at biologie.hu-berlin.de
> Reply-To:     SciPy Users List <scipy-user at scipy.net>
> To:     SciPy Users List <scipy-user at scipy.net>
>
>
>
> Hi Stuart,
>
> in fact MDP contains a function (mdp.utils.symeig), which provides
> an interface to some LAPACK routines that are able to compute only
> the first eigenvectors of a matrix, given that it is symmetrical 
> positive definite (which should be the case, since you're doing
> PCA).
>

I have been using mdp.utils.symeig for a while now and its seems pretty 
good and reliable. I also find the sqrtm function from
MatPy pretty good, although I did have some trouble installing it with 
python 2.3 but the developers havent gotten back about that. I think 
more functions like these in scipy would give it a real cutting edge. I 
only wish I had the time / money to do it.  :-) 

Stuart

> Pietro.
>
>
> On Fri, 3 Sep 2004, Gary Ruben wrote:
>
>> Hi Stuart,
>>
>> It may well not be relevant to your needs, but since you mentioned 
>> you were doing PCA, you might want to look at the MDP package which 
>> was announced on this list a few days ago. 
>> http://mdp-toolkit.sourceforge.net/
>>
>> Gary
>>
>> ----- Original Message -----
>> From: Stuart Murdock <s.e.murdock at soton.ac.uk>
>> Date: Thu, 02 Sep 2004 19:50:57 +0000
>> To: SciPy Users List <scipy-user at scipy.net>
>> Subject: Re: [SciPy-user] First few eigenvectors of a numarray array
>>
>> > Hi Dave
>> > > David Grant wrote:
>> > > > When you say "top 10" do you mean the eigenvalues with the 
>> largest or > > smallest values?
>> > >
>> > > Primarily I would be concerned with the eigenvectors associated 
>> with the > largest eigenvalues as presently
>> > I am interested in Principal Component Analysis of biomolecular > 
>> simulation trajectories. There are ways to approximate
>> > the top eigenvector / eigenvalue, then get the next and so on but I 
>> was > wondering if there were any packages with those
>> > types of algorithms already implemented.
>> > > Thanks
>> > > Stuart
>> > > > I would also be interested in knowing if there is any 
>> mathematical way > > of doing this.  Sometimes for example in 
>> molecular simulations you > > only want to calculate the ground state 
>> energy, for example, and you > > don't care about the rest...
>> > >
>> > > Dave
>> > >
>> > >
>> > > Stuart Murdock wrote:
>> > >
>> > >> Hi
>> > >>
>> > >> I have a 10000 by 10000 square numarray array which I have 
>> obtained > >> using numarray. I need to obtain the first 10 
>> eigenvalues and
>> > >> eigenvectors of this so I dont want to have to calculate all > 
>> >> eigenvectors of the matrix. Is anyone aware of any pythonic 
>> packages > >> which
>> > >> can calculate, lets say, the 10 eigenvectors corresponding to 
>> the top > >> 10 eigenvalues of a numarray array.
>> > >>
>> > >> There are a few functions which calculate all of the 
>> eigenvectors e.g.
>> > >>
>> > >> eig
>> > >> eigenvectors
>> > >>
>> > >> but I only want to calculate the top few.
>> > >>
>> > >> Thanks
>> > >>
>> > >> Stuart
>> > >>
>> > >
>> > >
>> > >_______________________________________________
>> > >SciPy-user mailing list
>> > >SciPy-user at scipy.net
>> > >http://www.scipy.net/mailman/listinfo/scipy-user
>> > >  > >
>> > > > -- > > Stuart Murdock Ph.D,
>> > Research Fellow,
>> > Dept. of Chemistry / E-Science,
>> > University of Southampton,
>> > Highfield, Southampton,
>> > SO17 1BJ, United Kingdom
>> >  > http://www.biosimgrid.org
>> > > > > _______________________________________________
>> > SciPy-user mailing list
>> > SciPy-user at scipy.net
>> > http://www.scipy.net/mailman/listinfo/scipy-user
>>
>>
>
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-- 

Stuart Murdock Ph.D,
Research Fellow,
Dept. of Chemistry / E-Science,
University of Southampton,
Highfield, Southampton,
SO17 1BJ, United Kingdom
 
http://www.biosimgrid.org



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