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My Paris colleague (and fellow-runner) Aurélien Garivier has produced an interesting comparison of 4 (or 6 if you consider scilab and octave as different from matlab) computer languages in terms of speed for producing the MLE in a hidden Markov model, using EM and the Baum-Welch algorithms. His conclusions are that

matlab is a lot faster than R and python, especially when vectorization is important : this is why the difference is spectacular on filtering/smoothing, not so much on the creation of the sample;

octave is a good matlab emulator, if no special attention is payed to execution speed…;

scilab appears as a credible, efficient alternative to matlab;

still, C is a lot faster; the inefficiency of matlab in loops is well-known, and clearly shown in the creation of the sample.

(In this implementation, R is “only” three times slower than matlab, so this is not so damning…) All the codes are available and you are free to make suggestions to improve the speed of of your favourite language!