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November 2002


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Patrick Groenen <[log in to unmask]>
Reply To:
Classification, clustering, and phylogeny estimation
Fri, 15 Nov 2002 09:27:00 +0100
text/plain (66 lines)
Neil and Dirk,

I have tried a dissimilarity matrix of 500 by 500 in SPSS Proxscal (ordinal)
and it took about 20 seconds on a pentium 4, 1.5 Ghz. Proxscal is the
program I prefer most for doing MDS at this moment.

Patrick Groenen
Prof. dr. Patrick J.F. Groenen
Econometric Institute
Erasmus University Rotterdam
Room H11.23
P.O. Box 1738, 3000 DR Rotterdam, The Netherlands
tel:    ++ 31 10 408 1281
fax:    ++ 31 10 408 9162
e-mail: [log in to unmask]

> -----Original Message-----
> From: Classification, clustering, and phylogeny estimation
> [mailto:[log in to unmask]]On Behalf Of [log in to unmask]
> Sent: Thursday 14 November 2002 18:39
> To: [log in to unmask]
> Subject:
> Dirk:
> MDS using SAS or SPSS will most likely be very slow. I have done
> MDS with SPSS and a matrix of your dimensions and 1 hour later it
> was still running.
> If performance is an issue, writting code will always run faster
> then the commercial stat packages. I use IMSL which has an MDS
> function and the runtime results were vastly superior. One reason
> is with SPSS, the GUI slows things done, their code does lots of
> memory allocation, slowing things down also.
> "Hand-Rolling" your own code with a proven MDS function (which
> are easy to find) will run much fast as you can just cache (store
> your matrix in memory) and let it fly.
> The net conclusion, unless it's a small sample size and I want to
> test my own programs... I compare my results with SPSS to affirm
> the results match. Direct programming is always much faster.
> Neil Gottlieb
> Profile Depot, Inc.
> you wrote:
> Dear Listmembers,
> I would like to do a MDS with a 400X400 square, symetric matrix of
> (dis)similaritys. Most MDS-Software is limited to a much smaller amount
> of variables though. I have been told, that SAS might be able to process
> the analyis I need, but this is quite inconvenient for me in terms of
> access to the software, hardware-requirements etc. Could anybody tell
> me, if there is a stand-alone program that can do MDS (preferably
> nonmetric) with a matrix of that size?
> Thanks a lot for your help,
> dirk
> P.S: My Matrix is not suitable for factor analysis and clustering does
> not produce the results I need.