Fast way to set many values of sparse matrix

Question

I have a sparse 5018x5018 matrix in MATLAB, which has about 100k values set to 1 (i.e., about 99.6% empty).

I'm trying to flip roughly 5% of those zeros to ones (i.e., about 1.25m entries). I have the x and y indices in the matrix I want to flip.

Here is what I have done:

sizeMat=size(network);
idxToReplace=sub2ind(sizeMat,x_idx, y_idx);
network(idxToReplace) = 1;

This is incredibly slow, in particular the last line. Is there any way to make this operation run noticeably faster, preferably without using mex files?

Answer 1

This should be faster:

idxToReplace=sparse(x_idx,y_idx,ones(size(x_idx),size(matrix,1),size(matrix,2)); % Create a sparse with ones at locations
network=network+idxToReplace; % Add the two matrices

I think your solution is very slow because you create a 1.26e6 logical array with your points and then store them in the sparse matrix. In my solution, you only create a sparse matrix and just sum the two.