What's the fastest way in Python to calculate cosine similarity given sparse matrix data?

Given a sparse matrix listing, what's the best way to calculate the cosine similarity between each of the columns (or rows) in the matrix? I would rather not iterate n-choose-two times.

Say the input matrix is:

A= 
[0 1 0 0 1
 0 0 1 1 1
 1 1 0 1 0]

The sparse representation is:

A = 
0, 1
0, 4
1, 2
1, 3
1, 4
2, 0
2, 1
2, 3

In Python, it's straightforward to work with the matrix-input format:

import numpy as np
from sklearn.metrics import pairwise_distances
from scipy.spatial.distance import cosine

A = np.array(
[[0, 1, 0, 0, 1],
[0, 0, 1, 1, 1],
[1, 1, 0, 1, 0]])

dist_out = 1-pairwise_distances(A, metric="cosine")
dist_out

Gives:

array([[ 1.        ,  0.40824829,  0.40824829],
       [ 0.40824829,  1.        ,  0.33333333],
       [ 0.40824829,  0.33333333,  1.        ]])

That's fine for a full-matrix input, but I really want to start with the sparse representation (due to the size and sparsity of my matrix). Any ideas about how this could best be accomplished? Thanks in advance.

You can compute pairwise cosine similarity on the rows of a sparse matrix directly using sklearn. As of version 0.17 it also supports sparse output:

from sklearn.metrics.pairwise import cosine_similarity
from scipy import sparse

A =  np.array([[0, 1, 0, 0, 1], [0, 0, 1, 1, 1],[1, 1, 0, 1, 0]])
A_sparse = sparse.csr_matrix(A)

similarities = cosine_similarity(A_sparse)
print('pairwise dense output:\n {}\n'.format(similarities))

#also can output sparse matrices
similarities_sparse = cosine_similarity(A_sparse,dense_output=False)
print('pairwise sparse output:\n {}\n'.format(similarities_sparse))

Results:

pairwise dense output:
[[ 1.          0.40824829  0.40824829]
[ 0.40824829  1.          0.33333333]
[ 0.40824829  0.33333333  1.        ]]

pairwise sparse output:
(0, 1)  0.408248290464
(0, 2)  0.408248290464
(0, 0)  1.0
(1, 0)  0.408248290464
(1, 2)  0.333333333333
(1, 1)  1.0
(2, 1)  0.333333333333
(2, 0)  0.408248290464
(2, 2)  1.0

If you want column-wise cosine similarities simply transpose your input matrix beforehand:

A_sparse.transpose()

The following method is about 30 times faster than scipy.spatial.distance.pdist. It works pretty quickly on large matrices (assuming you have enough RAM)

See below for a discussion of how to optimize for sparsity.

# base similarity matrix (all dot products)
# replace this with A.dot(A.T).toarray() for sparse representation
similarity = numpy.dot(A, A.T)


# squared magnitude of preference vectors (number of occurrences)
square_mag = numpy.diag(similarity)

# inverse squared magnitude
inv_square_mag = 1 / square_mag

# if it doesn't occur, set it's inverse magnitude to zero (instead of inf)
inv_square_mag[numpy.isinf(inv_square_mag)] = 0

# inverse of the magnitude
inv_mag = numpy.sqrt(inv_square_mag)

# cosine similarity (elementwise multiply by inverse magnitudes)
cosine = similarity * inv_mag
cosine = cosine.T * inv_mag

If your problem is typical for large scale binary preference problems, you have a lot more entries in one dimension than the other. Also, the short dimension is the one whose entries you want to calculate similarities between. Let's call this dimension the 'item' dimension.

If this is the case, list your 'items' in rows and create A using scipy.sparse. Then replace the first line as indicated.

If your problem is atypical you'll need more modifications. Those should be pretty straightforward replacements of basic numpy operations with their scipy.sparse equivalents.