I have a numpy
array Z
with shape (k,N)
and a second array X
with shape (N,n)
.
Using numpy
broadcasting, I can easily obtain a new array H
with shape (n,k,N)
whose slices are the array Z
whose rows have been multiplied by the columns of X
:
H = Z.reshape((1, k, N)) * X.T.reshape((n, 1, N))
This works fine and is surprisingly fast. Now, X
is extremely sparse, and I want to further speed up this operation using sparse matrix operations.
However if I perform the following operations:
import scipy.sparse as sprs
spX = sprs.csr_matrix(X)
H = (Z.reshape((1,k,N))*spX.T.reshape((n,1,N))).dot(Z.T)
I get the following error:
Traceback (most recent call last):
File "<input>", line 1, in <module>
File "C:\Python27\lib\site-packages\scipy\sparse\base.py", line 126, in reshape
self.__class__.__name__)
NotImplementedError: Reshaping not implemented for csc_matrix.
Is there a way to use broadcasting with sparse scipy
matrices?
Scipy sparse matrices are limited to 2D shapes. But you can use Numpy in a "sparse" way:
H = np.zeros((n,k,N), np.result_type(Z, X))
I, J = np.nonzero(X)
Z_ = np.broadcast_to(Z, H.shape)
H[J,:,I] = Z_[J,:,I] * X[I,J,None]
Unfortunately the result H
is still a dense array.
Nb indexing with None
is a handy way to add a unit-length dimension at the desired axis. The order of the result when combining advanced indexing with slicing is explained in the docs .
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