1) Don't use loop whenever possible. Very likely there will be a function that can do the job that you want to do by using loops.
2) Stay away from cell array whenever possible. I don't understand the details, but handling cell array will take much more time than handling numbers.
3)Use faster CPU. But to my experience (though I am not quite experienced), Matlab will not use all the CPUs to do the work, even if you use a multi core cmputer.
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