I suppose that you are using numpy for matrix computations, aren't you ? What's the content of the matrices, real numbers ? I think it would be helpful if you post a short working example of a too long computation which you would like to speed up.
Gribouillis
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Are you using numpy/scipy/matlab for yor data?
pyTony
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If you are using dictionaries, there is little doubt that your code could be speeded up. For example you could still use dictionaries to map your own keys to integer indexes and use numpy matrices to actually store and manipulate the data. Again, a typical example of what you are doing would help.
Gribouillis
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