[Numpy-discussion] performance of scipy: potential inefficiency in logsumexp and sampling from multinomial

Charles R Harris charlesr.harris@gmail....
Mon Oct 12 16:48:51 CDT 2009


On Mon, Oct 12, 2009 at 3:25 PM, per freem <perfreem@gmail.com> wrote:

> hi all,
>
> i have a piece of code that relies heavily on sampling from
> multinomial distributions and using their results to compute log
> probabilities. my code makes heavy use of 'multinomial' from scipy,
> and of 'logsumexp'.
>
> my code is unusually slow, and profiling it with Python's "cPickle"
> module reveals that most of the time is spent in the following
> functions:
>
> 479.524    0.000 code.py:211(my_func)
> 122.682    0.000
>
> /Library/Python/2.5/site-packages/scipy/maxentropy/maxentutils.py:27(logsumexp)
> 40.645    0.000
> /Library/Python/2.5/site-packages/numpy/core/numeric.py:180(asarray)
> 20.374    0.000 {method 'max' of 'numpy.ndarray' objects}
>
> (the first column represents cumulative time, the second is percall time.)
>
> my code (listed as 'my_func' above) essentially computes a list of log
> probabilities, exponentiates them and renormalizes them (using
> 'logsumexp') and then samples from a multinomial distribution using
> those probabilities as a parameter. i then check to see which object
> came up true from the multinomial sample. here's a sketch of the code:
>
> def my_func(my_list, n_items)
>    final_list = []
>    for n in xrange(n_items):
>        prob = my_dict[(my_list(n), n)]
>        final_list.append(prob)
>    final_list = final_list - logsumexp(final_list)
>    sample = multinomial(1, exp(final_list))
>    sample_index = list(sampled_reassignment).index(1)
>    return sample_index
>
> the list 'my_list' usually has around 3 to 5 elements in it, and
> 'my_dict' has about 500-1000 keys.
>
> this function gets called about 1.5 million times in my code, and it
> takes about 5 minutes, which seems very long relative to these
> operations. (i'd like to scale this up to a case where the function is
> called about 10-120 million times.)
>
> are there known efficiency issues with logsumexp? it seems like it
> should be a very cheap operation. also, 'multinomial' ought to be
> relatively cheap, i believe. does anyone have any ideas on how this
> can be optimized?  any input will be greatly appreciated.  i am also
> open to using cython if that is likely to make a significant
> improvement in this case.
>
> also, what is likely to be the origin of the call to "asarray"? (i am
> not explicitly calling that function, it must be indirectly via some
> other function.)
>
>
You are going back and forth between lists and ndarrays of pretty small
sequences of items of variable size. That is bound to be inefficient and
isn't going to get you the benefits of vectorization. Is there any way you
can do what you want using the rows in a single big array?

Chuck
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