Vectorizing multiple string comparison

Is there a way to significantly speed up this loop, perhaps by vectorizing it? Inputs in attachment. I do not have a Matlab version with "string" functions.

d = a';

for i = 1:numel(a)
    d{i} = c(strcmp(a{i}, b), :);
end

I tried working my way from the inner part with cellfun, but either I am not getting it right or it is not the good approach:

aux = cellfun(@strcmp, a, b); % does not work

[Walter Roberson]

That file is an Octave file that would take a bunch of work to read in MATLAB.

This is the wrong resource to be asking about performance improvement for Octave.

[Paolo Binetti]

You are right. R2016 does not run on the PC I mostly use, and old beast which still works perfectly, but on XP. So until I buy a new computer, I am stuck with either a much older version of Matlab or Octave, which does run on XP. I could have generated the input with my older Matlab. And your answer below gives me one more motivation to buy a new computer soon!

Answer 1

[Guillaume]

One obvious minor speed-up is to get rid of the find that serves absolutely no purpose. You can directly use the logical vector returned by strcmp:

d{i} = c(strcmp(a{i}, b)), :);

For some reason, I cannot load your mat file. I'm going to assume that a is a cell array of string, and so is b (otherwise the loop would not be needed). Assuming that there are no repeated strings in b:

assert(numel(unique(b)) == numel(b), 'This code does not work when there are duplicate values in b');
d = cell(size(a))';
[isfound, loc] = ismember(a, b);
d(isfound) = c(loc(isfound), :);

If it's guaranteed that all elements of a are found in b, then you can simplify even further to:

assert(numel(unique(b)) == numel(b), 'This code does not work when there are duplicate values in b');
[isfound, loc] = ismember(a, b);
assert(all(isfound), 'The next line only works if all elements of a are in b');
d = num2cell(c(loc, :), 2);

[Paolo Binetti]

Thank you.

• Good on you for getting rid of "find". I have edited the question accordingly.
• I am sorry that you could not download my inputs.mat file. I have uploaded it again, I have tested it and it seems to work for me.
• Nevertheless, all of your assumptions were right, except that b does actually contain repeated strings, unfortunately (if it did not, the "intersect" function would allow to vectorize).

[Guillaume]

According to Walter, your mat file is an octave file that matlab can't open.

If there are duplicate values in b, then you don't have a choice but to use a loop, either explicitly as you have done or with cellfun:

d = cellfun(@(aa) c(strcmp(aa, b), :), a, 'UniformOutput', false);

It's very possible that the cellfun may be slower than the explicit loop (due to the anonymous function call).

edit: in matlab R2016b there is a an extremely easy way to vectorise the string comparison, using the new string class:

string(a) == string(b)'

but you'd still need a loop or cellfun afterward to create the d cell array:

d = cellfun(@(r) c(r, :), num2cell(string(a) == string(b)', 1), 'UniformOutput', false)

Answer 2

[Walter Roberson]

ismember can be used between cell arrays of strings. The two-output version can be used to find the indices, which you can then use to index into c.

[Paolo Binetti]

This does not seem to work, because cell array "b" contains repeats, so a string in "a" may be have more than one match in "b", and I want all of them, not just the one with the lowest index.

[Walter Roberson]

Flip the order around, ismember(b, a) .

[Paolo Binetti]

I had a feeling I was missing an obvious point. Thank you for pointing it out! The modified code, below, runs much faster. I tried to vectorize the remainder of the loop, to no avail, but the costly string comparison at least if out of the loop.

a = { 'AAG' 'AGA' 'ATT' 'CTA' 'CTC' 'GAT' 'TAA' 'TCT' 'TTC' };
b = { 'AAG' 'AGA' 'GAT' 'ATT' 'TTC' 'TCT' 'CTC' 'TCT' 'CTA' 'TAA' 'AAG' };
c = [ 'AGA';'GAT';'ATT';'TTC';'TCT';'CTC';'TCT';'CTA';'TAA';'AAG';'AGA' ];

[temp, idx] = ismember(b, a);

d = a';

for i = 1:numel(a)
    d{i} = c(i == idx, :);
end