Re: [Java-ML-support] Read MCL result from SparseMatrix representation

[Thomas A. <th...@ab...>]

Hi Chris,

I think your best bet is to go into the SparseMatrix code or into the 
MCL clustering class code.

net.sf.javaml.clustering.mcl.MCL.java has a method that extracts the 
clusters from the sparse matrix. You can check how it's done there and 
that should give you a good idea on how to do it yourself.

cheers,
Thomas



On 8/22/2012 5:47 PM, Chris Csdev wrote:
> Dear all,
>
> I am investigating java-ml for its Markov CLustering implementation.
> In my current project, I have a in-memory model of 2D adjency matrix 
> (a two-dimensional array of the double primitive type : double[][]).
>
> Note that this matrix is sparse in the sense that it is triangular 
> superior (I am using a symetric distance, hence I don't fill the 
> inferior triangle of my 2D matrix).
>
> Fortunately, I can convert it into a SparseMatrix using the associated 
> constructor and then run the MCL algorithm.
>
> The code fragment from my program is as follows.
>
> double[][] adjencyMatrix;
>
> // omitted operations to fill adjencyMatrix
>
> SparseMatrix smatrix = new SparseMatrix(adjencyMatrix);
> MarkovClustering mcl = new MarkovClustering();
> double maxResidual = 0.001;
> double gammaExp = 2.0;
> double loopGain = 0.;
> double zeroMax = 0.001;
> SparseMatrix matrix = mcl.run(smatrix, maxResidual, gammaExp, 
> loopGain, zeroMax);
>
> From this point, I understand that "matrix" helds a "sparse matrix 
> with row-major format" of my results, that is, a compressed version of 
> the traditional 2D matrix resulting from MCL. I am able to read the 
> MCL results from a traditional 2D data structure, yet I don't know to 
> grasp how to unveil clusters from the resulting SparseMatrix.
>
> I have been unable to find the proper documentation to understand the 
> SparseMatrix data structure used in java-ml. Can you point me to the 
> paper or documentation that you may have used to create the data 
> structure ? If no, is it possible to convert a SparseMatrix into a 
> double[][] (which I suspect to be performance killing) ?
>
> Thanks you in advance for any help !
>
> Best Regards,
>
> Chris
>
>
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