[R-pkgs] "tsne" package for t-SNE dimensionality reduction

From: Justin Donaldson <jjdonald_at_indiana.edu>
Date: Fri, 19 Feb 2010 18:10:54 -0500

I'd like to announce the availability of the "tsne" package.

It provides the T distributed Stocastic Neighbor Embedding algorithm by van der Maaten and Hinton:

  1. http://ict.ewi.tudelft.nl/~lvandermaaten/t-SNE.html


   L.J.P. van der Maaten and G.E. Hinton. Visualizing High-Dimensional Data    Using t-SNE. Journal of Machine Learning Research 9(Nov):2579-2605, 2008.    [ PDF<http://ict.ewi.tudelft.nl/%7Elvandermaaten/t-SNE_files/vandermaaten08a.pdf>] [ Supplemental

   Material<http://ict.ewi.tudelft.nl/%7Elvandermaaten/t-SNE_files/SupplementalMaterial.pdf>(24MB) ]


   L.J.P. van der Maaten. Learning a Parametric Embedding by Preserving    Local Structure. In Proceedings of the Twelfth International Conference    on Artificial Intelligence and Statistics (AISTATS), JMLR W&CP 5:384-391,    2009. [ PDF<http://ict.ewi.tudelft.nl/%7Elvandermaaten/t-SNE_files/Paper.pdf>]

It has a few utility/convenience parameters for tweaking the algorithm and providing feedback. Be sure to try the example to get an idea of how it works:


It's currently much slower than the "official" implementations by van der Maaten. If you're interested in providing some tips on optimized C/Fortan code, let me know.


Justin Donaldson
PhD Candidate, Informatics
Indiana University
aim: iujjd
twitter: jjdonald

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Received on Sun 21 Feb 2010 - 08:50:48 EST

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