Sparse implementations of distance computations in python / scikit-learn

Question

I have a large (100K by 30K) and (very) sparse dataset in svmlight format which I load as follows:

import numpy as np
from scipy.cluster.vq import kmeans2
f         


        

Answer 1

In scikit-learn there is a sklearn.metrics.euclidean_distances function that works both for sparse matrices and dense numpy arrays. See the reference documentation.

However non-euclidean distances are not yet implemented for sparse matrices.