How to quickly calculate the sum of the transpose of a sparse matrix?

Dear All,

I have a very big sparse matrix A. I want to obtain the sum of its transpose of the selected columns in A. Here is my code:

B = A(:,selectedCol)';

sumA = sum(B);

I am wondering if there is a faster way to do the above calculation.

Thanks a lot in advance.

Benson

[James Tursa]

What are the actual dimensions of A and selectedCol?

Answer 1

[Matt J]

A=sprand(1e6,1e3,100/1e6);  %Example
selectedCol=1:2:100;

tic;
B=sum( A(:,selectedCol)');
toc

Elapsed time is 0.010279 seconds.

tic
B=sum( A(:,selectedCol) ,2)';
toc

Elapsed time is 0.005409 seconds.

[Benson Gou]

Hi, Matt,

Thanks a lot for your great help. I tested your code, but I found it took longer time than the original code.

Thanks a lot again.

Benson

[Matt J]

Longer on my example?

Answer 2

[Matt J]

Depening on the size of selectedCols, it may also help to cast the operation as a matrix/vector multiplication

A=sprand(1e6,1e5,100/1e6);

selectedCol=1:10:size(A,2);

tic;
B=sum( A(:,selectedCol)');
toc

Elapsed time is 0.140409 seconds.

tic
B=sum( A(:,selectedCol) ,2)';
toc

Elapsed time is 0.182437 seconds.

z=false(size(A,2),1);
tic
x=z;
x(selectedCol)=1;
B=(A*x)';
toc

Elapsed time is 0.086501 seconds.

[Benson Gou]

Hi, Matt,

Thanks a lot for your great help. I tested and compared the three sets of codes on my case. I found the original code is still little bit faster than your second code. Here is the comparison:

1. Original code: 0.393 seconds
2. Your first code: 0.521 seconds
3. Your second code: 0.424 seconds

Thanks a lot any way.

Benson

[Matt J]

But you must admit, my results show that it should be faster. Did you use the profiler to make sure that this operation was your bottleneck?

[Benson Gou]

Yes, I am using profile to find the operations which takes longer time than I can stand. The above time I compared are from profile viewer.

Another bottkeneck is find. I used find several times, but it took much longre time than other operations. I do not know if you have a faster way to replace find.

Thanks.

Benson

[Matt J]

I do not know if you have a faster way to replace find.

Yes, don't use it. Use logical indexing instead.

[Stephen23]

"I do not know if you have a faster way to replace find."

Answers and comments on your previous threads related to FIND:

https://www.mathworks.com/matlabcentral/answers/866000-how-to-run-find-function-faster#answer_734225

https://www.mathworks.com/matlabcentral/answers/861695-looking-for-a-way-faster-than-find#answer_729970

Have you considered using logical indexing?