CODEWITHSUNDEEP
pythonrandomsamplingdownsampling
xApple
xApple

Reputation: 6466

Python: downsample a population using frequency data

Given a data series representing frequencies of elements in a population, what would be the easiest way to downsample it ?

The following population: pop = ['a', 'b', 'a', 'c', 'c', 'd', 'c', 'a', 'a', 'b', 'a']

Can be summeriezed as: freq = {'a': 5, 'c': 3, 'b': 2, 'd': 1}

Using the simple: from collections import Counter; Counter(pop)

To randomly downsample that population to 5 individuals I can do:

>>> from random import sample
>>> from collections import Counter
>>> pop = ['a', 'b', 'a', 'c', 'c', 'd', 'c', 'a', 'a', 'b', 'a']
>>> smaller_pop = sample(pop, 5)
>>> smaller_freq = Counter(smaller_pop)
>>> print smaller_freq
Counter({'a': 3, 'c': 1, 'b': 1})

But I'm searching for a way to do this directly from the freq information without having to build the pop list. You will agree that proceeding like this should not be necessary:

>>> from random import sample
>>> from collections import Counter
>>> flatten = lambda x: [item for sublist in x for item in sublist]
>>> freq = {'a': 5, 'c': 3, 'b': 2, 'd': 1}
>>> pop = flatten([[k]*v for k,v in freq.items()])
>>> smaller_pop = sample(pop, 5)
>>> smaller_freq = Counter(smaller_pop)
>>> print smaller_freq
Counter({'a': 2, 'c': 2, 'd': 1})

For memory considerations and speed requirements, I would like to avoid placing in memory the pop list. This can surely be done using some type of weighted random generator.

Upvotes: 1

Views: 1322

Answers (1)

unutbu
unutbu

Reputation: 880079

Here is a basic algorithm that downsamples frequencies:

import random
import bisect
import collections

def downsample(freq, n):
    cumsums = []
    total = 0
    choices, weights = zip(*freq.items())
    for weight in weights:
        total += weight
        cumsums.append(total)
    assert 0 <= n <= total
    result = collections.Counter()
    for _ in range(n):
        rnd = random.uniform(0, total)
        i = bisect.bisect(cumsums, rnd)
        result[choices[i]] += 1
        cumsums = [c if idx<i else c-1 for idx, c in enumerate(cumsums)]
        total -= 1
    return result

freq = {'a': 5, 'c': 3, 'b': 2, 'd': 1}
print(downsample(freq, 5))

which prints results like

Counter({'c': 2, 'a': 1, 'b': 1, 'd': 1})

Upvotes: 1

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