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March 2003

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"Classification, clustering, and phylogeny estimation" <[log in to unmask]>
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"Sirotkin, Alexander" <[log in to unmask]>
Date:
Tue, 11 Mar 2003 18:52:00 +0200
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"Classification, clustering, and phylogeny estimation" <[log in to unmask]>
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Luca I.G. Toldo wrote:



I agree fully with all the comments previously reported on the
challenging topic you raised.

You might want to have a look at the following:

- Rand index (implemented in "R" http://www.r-project.org/
<http://www.r-project.org/>  , in the package e1071 subroutine
classAgreement)
J.~Cohen. A coefficient of agreement for nominal scales. Educational and
Psychological Measurement, 20,37-46, 1960. Lawrence Hubert and Phipps
Arabie. Comparing partitions. Journal of Classification, 2, 193-218,
1985.

- Linear measure of cluster quality
Mather L.A.  JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE.
51(7):602-613,2000
- amendment of the above paper
Toldo L, JOURNAL OF THE AMERICAN SOCIETY FOR INFORMATION SCIENCE AND
TECHNOLOGY,52(7):602, 2001
-Java implementation of the linear measure of cluster quality
Toldo L, Cluster Validity Abstract # 83 Third International Meeting on
Microarray Data Standards, Annotations, Ontologies and Databases March
29-31, 2001, Stanford University

simply email me if you want a copy of the Java implementation of the
LAMCQ algorithm.

Regards
Dr. Toldo


Oops...

It appears that my mail filtering system decided that postings from that
list were SPAM and I missed the whole discussion :(
Rand index (implemented by classAgreement() in R) is exactly what I
need.
Unfortunately, because of the stupid mail filter I discovered it after I

already implemented one myself...






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