Sparse Input Data

[3bst0r]

Is there a way to input sparse data? I suspect this is not a straight-forward thing to do, because of the lack of a standard way to store sparse matrices in a text file, i.e. python probably does it different than matlab (did not check though).

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OT: I just watched a video of you presenting t-SNE at Google and I want to compliment you on your explanation skills. Very clear and understandable.

[lvdmaaten]

This is not implemented right now. Both Matlab and Numpy support compressed sparse row matrices, so it would be possible to add this.

For now, a potential way to circumvent this would be to do some kind of (logistic) PCA preprocessing in Matlab / Python and use the reduced data as input into t-SNE. (This is assuming that the full matrix is too big to keep in memory.)

[larahronn]

If I´m not mistaken, Truncated SVD is also good for preprocessing sparse data and it can work with scipy.sparse.

http://scikit-learn.org/stable/modules/generated/sklearn.decomposition.TruncatedSVD.html

(I am brand new to the field, this is my first ever comment on github - breaking the ice here ;)).