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Multidimensional Scaling + PyTables

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Multidimensional Scaling + PyTables

Postby NoExiT » Fri May 16, 2014 13:52

Hi everyone,

I have a huge (200,000x200,000) distance matrix (RMSD between protein structures) stored in a hdf5 file. And I want to know if I can use the Orange.projection.mds.MDS module on it directly ?

Maybe, it is not feasible ... or between with less datas. I don't know.

Thanks for your response.

Re: Multidimensional Scaling + PyTables

Postby Ales » Fri May 16, 2014 14:02

No that is not feasible without a significant amount of RAM. Orange.projection.mds.MDS works on an in memory matrix representation.

Re: Multidimensional Scaling + PyTables

Postby NoExiT » Fri May 16, 2014 14:20

Yeah ... unfortunately that's what I thought ...
Is there a alternative method to represent relationship between datas ?

Thank you !

p.s. for the information, I can have an access to a computer with at least 96GB of RAM.


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