Speedup math operations - Githubissues

fungs / mglex

MGLEX – A Python Package for Probabilistic Modeling and Binning of Metagenomes

GNU General Public License v3.0

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Speedup math operations #4

Open fungs opened 7 years ago

fungs commented 7 years ago

The code is currently slow, we can do much better using

removing assertions in non-debug mode
scaling data at the beginning to avoid likelihood calculations
speeding up vector arithmetics with more advanced python packages/methods
avoiding the time for parsing the data over and over again

fungs commented 6 years ago

Considerations:

numexpr, theano or numba for faster math
Cython
numpy.ascontiguousarray, numpy.vdot, numpy.memmap