Removing rows and columns from MATLAB matrix quickly

Question

Is there a fast way to remove rows and columns from a large matrix in MATLAB?

I have a very large (square) distance matrix, that I want to remove a number of rows/columns from.

Naively:

s = 12000;
D = rand(s);
cols = sort(randsample(s,2))
rows = sort(randsample(s,2)) 

A = D;
tic
A(rows,:) = [];
A(:,cols) = [];
toc
% Elapsed time is 54.982124 seconds.

This is terribly slow though. Oddly, this is the fastest solution suggested at the bottom here.

An improvement can be made by preallocating the array and using boolean indices

A = zeros(size(D) - [numel(rows) numel(cols)]);
r = true(size(D,1),1);
c = true(size(D,2),1);
r(rows) = false;
c(cols) = false;

tic
A = D(r,c);
toc
% Elapsed time is 20.083072 seconds.

Is there still a faster way to do this?

Answer 1

It seems like a memory bottleneck. On my feeble laptop, breaking D up and applying these operators to each part was much faster (using s=12,000 crashed my computer). Here I break it into two pieces, but you can probably find a more optimal partition.

s = 8000;
D = rand(s);

D1 = D(1:s/2,:);
D2 = D((s/2 + 1):end,:);

cols = sort(randsample(s,2));
rows = sort(randsample(s,2));

A1 = D1;
A2 = D2;

tic
A1(rows(rows <= s/2),:) = [];
A2(rows(rows > s/2) - s/2,:) = [];
A1(:,cols) = [];
A2(:,cols) = [];
toc

A = D;
tic
A(rows,:) = [];
A(:,cols) = [];
toc

Elapsed time is 2.317080 seconds.
Elapsed time is 140.771632 seconds.