Division Of Sparse Matrix

I have a scipy.sparse matrix with 45671x45671 elements. In this matrix, some rows contain only '0' value. My question is, how to divide each row values by the row sum. Obviously, w

Solution 1:

I have an M hanging around:

In [241]: M
Out[241]: 
<6x3 sparse matrix of type'<class 'numpy.uint8'>'
    with 6 stored elements in Compressed Sparse Row format>
In [242]: M.A
Out[242]: 
array([[1, 0, 0],
       [0, 1, 0],
       [0, 0, 1],
       [0, 1, 0],
       [0, 0, 1],
       [1, 0, 0]], dtype=uint8)
In [243]: M.sum(1)            # dense matrix
Out[243]: 
matrix([[1],
        [1],
        [1],
        [1],
        [1],
        [1]], dtype=uint32)
In [244]: M/M.sum(1)      # dense matrix - full size of M
Out[244]: 
matrix([[ 1.,  0.,  0.],
        [ 0.,  1.,  0.],
        [ 0.,  0.,  1.],
        [ 0.,  1.,  0.],
        [ 0.,  0.,  1.],
        [ 1.,  0.,  0.]])

That will explain the memory error - if M is so large that M.A produces a memory error.

---

In [262]: S = sparse.csr_matrix(M.sum(1))
In [263]: S.shape
Out[263]: (6, 1)
In [264]: M.shape
Out[264]: (6, 3)
In [265]: M/S
....
ValueError: inconsistent shapes

I'm not entirely sure what is going on here.

Element wise multiplication works

In [266]: M.multiply(S)
Out[266]: 
<6x3 sparse matrix of type'<class 'numpy.uint32'>'with6 stored elements in Compressed Sparse Row format>

So it should work if I construct S as S = sparse.csr_matrix(1/M.sum(1))

If some of the rows sum to zero, you have a division by zero problem.

---

If I modify M to have 0 row

In [283]: M.A
Out[283]: 
array([[1, 0, 0],
       [0, 1, 0],
       [0, 0, 0],
       [0, 1, 0],
       [0, 0, 1],
       [1, 0, 0]], dtype=uint8)
In [284]: S = sparse.csr_matrix(1/M.sum(1))
/usr/local/bin/ipython3:1: RuntimeWarning: divide by zero encountered in true_divide
  #!/usr/bin/python3
In [285]: S.A
Out[285]: 
array([[  1.],
       [  1.],
       [ inf],
       [  1.],
       [  1.],
       [  1.]])
In [286]: M.multiply(S)
Out[286]: 
<6x3 sparse matrix of type'<class 'numpy.float64'>'
    with 5 stored elements in Compressed Sparse Row format>
In [287]: _.A
Out[287]: 
array([[ 1.,  0.,  0.],
       [ 0.,  1.,  0.],
       [ 0.,  0.,  0.],
       [ 0.,  1.,  0.],
       [ 0.,  0.,  1.],
       [ 1.,  0.,  0.]])

This isn't the best M to demonstrate this on, but it suggests a useful approach. The row sum will be dense, so you can clean up its inverse using the usual dense array approaches.