Question: I have two sparse matrices A and B where A and B have the same number of columns (but potentially different numbers of rows). I'm trying to get a sparse matrix C with elements c_ij = sum_j min(a_ij,b_ji), where a_ij and b_ij are elements of A and B, respectively. Can this be done efficiently, and ideally sparsely? Even densely would be okay, but the matrices involved will be huge (tens of thousands of rows) and very sparse. Details: The analogy is with standard (mathematical) matrix multiplication, but instead of summing the product of elements, I want to sum the minimum of elements. An example will help. Using standard matrix multiplication A * B gives elements c_ij = sum_j a_ij * b_ji for elements a_ij in A and b_ij in B with i and j as row and column indices, respectively. For example, import numpy as np from scipy.sparse import csr_matrix A = csr_matrix([[1, 2, 0], [0, 0, 3], [4, 0, 5]]) B = csr_matrix([[2, 0, 0], [0, 0, 3], [6, 0, 0]]) C = A * B print(f"\nC = A * B = \n{C}")  gives >>> C = A * B = (0, 2) 6 (0, 0) 2 (1, 0) 18 (2, 0) 38  where c_31 = 38 = sum_j ( a_3j * b_j1 ) = 4 * 2 + 0 * 0 + 5 * 6 = 38. For each element of C, I want the sum of minimums min(a_ij * b_ji) instead of the sum of products a_ij * b_ji: c_31 = sum_j min(a_3j,b_j1) = min(4,2) + min(0,0) + min(5,6) = 7.

Answer: In normal dense arrays this would be done more easily with a three-dimensional array, but those are unavailable in sparse form. Instead, import numpy as np from scipy.sparse import csr_array, coo_array # If you're able to start in COO format instead of CSR format, it will make the code below simpler A = csr_array([ [1, 2, 0], [0, 0, 3], [4, 0, 5], [4, 0, 5], [1, 1, 6], ]) B = csr_array([ [2, 0, 0, 8], [0, 0, 3, 2], [6, 0, 0, 4], ]) m, n = A.shape n, p = B.shape # first min argument based on A a_coo = A.tocoo(copy=False) a_row_idx = ((a_coo.col + a_coo.row*(n*p))[None, :] + np.arange(0, n*p, n)[:, None]).ravel() a_min = coo_array(( np.broadcast_to(A.data, (p, A.size)).ravel(), # data: row-major repeat ( a_row_idx, # row indices np.zeros_like(a_row_idx), # column indices ), ), shape=(m*n*p, 2)) # test; deleteme a_min_dense = np.zeros((m*n*p, 2), dtype=int) a_min_dense[:, 0] = np.repeat(A.toarray(), p, axis=0).ravel() assert np.allclose(a_min_dense, a_min.toarray()) # second min argument based on B b_coo = B.tocoo(copy=False) b_row_idx = ((b_coo.row + b_coo.col*n)[None, :] + np.arange(0, m*n*p, n*p)[:, None]).ravel() b_min = coo_array(( np.broadcast_to(B.data, (m, B.size)).ravel(), # data: row-major repeat ( b_row_idx, # row indices np.ones_like(b_row_idx), # column indices ), ), shape=(m*n*p, 2)) # test; deleteme b_min_dense = np.zeros((m*n*p, 2), dtype=int) b_min_dense[:, 1] = np.tile(B.T.toarray().ravel(), (1, m)).ravel() assert np.allclose(b_min_dense, b_min.toarray()) # Alternative to this: use two one-dimensional columns and hstack ab = (a_min + b_min).min(axis=1) addend = ab.reshape((-1, n)) # scipy sparse summation input is sparse, but output is NOT SPARSE. It's an np.matrix. # If that matters, you need to run a more complex operation on 'ab' that manipulates indices. # deleteme total = addend.sum(axis=1).reshape((m, p)) # Example true sparse sum separators = np.insert( np.nonzero(np.diff(addend.row))[0] + 1, 0, 0, ) sparse_total = coo_array(( np.add.reduceat(addend.data, separators), ( addend.row[separators], np.zeros_like(separators), ) ), shape=(m*p, 1)).reshape((m, p)) # test; deleteme ab_dense = (a_min_dense + b_min_dense).min(axis=1) sum_dense = ab_dense.reshape((-1, n)).sum(axis=1).reshape((m, p)) assert np.allclose(ab.toarray().ravel(), ab_dense) assert np.allclose(sum_dense, total) assert np.allclose(sum_dense, sparse_total.toarray()) print(sum_dense)  Other notes: don't use _matrix; it's deprecated in favour of _array. The above operates on different example matrices from yours, deliberately, because it's impossible to reliably develop array manipulation code when all of the dimensions are of the same size. However, when I modify them to be the same as your original arrays, I get [[1 0 2] [3 0 0] [7 0 0]]