Cluto Clustering Algorithm - 3D Matrix Input File

Question

[kajendiran56]

Dear All,

I have just discovered Cluto as a way of clustering data which can be presented as a matrix. The standard format is as follows:

a p1  p2  p3
b p1  p2  p3
c p1  p2  p3

where each row is an entry and each column corresponds to a parameter.

I would like to compare and cluster protein sequences, including the sequence identity between each pair and I have a need to create, rather than a 2d matrix as above, a 3 dimensional matrix e.g., element (a P1) as an object with multiple parameters.

I cannot seem to find a way of doing this and I was wondering whether such a thing is possible? Is the only option to transform the data in some way to fit a 2d matrix?

Many thanks

Answer 1

[Jean-Karim Heriche]

You can do clustering of N-way data using tensor factorization methods. See this paper for some introduction.