A Math Puzzle

A Math Puzzle

Our reader Andrew Brommage left us with a math puzzle in the comment section -

Mathematically-minded readers may wish to try proving this as an exercise. The task is to analyse what happens to N (1 e^(-1/?N) (1 + 1/?N)) as N??

Any taker? The question is related to optimal design of hash functions.


Speaking of mathematical formula, we would like to include a separate but related derivation in this commentary. It estimates the probability of false positive of a Bloom filter.

Bloom filter is a probabilistic data structure to help us count the number of k-mers in an NGS library using less amount of RAM than hashes. It utilizes the fact that larger number of k-mers in a deep-sequenced NGS library come from sequencing errors than the underlying genome.

Bloom filter uses multiple hash functions (k) to insert each element into a bit array. It is probabilistic, because if a k-mer is found in the bit array, that k-mer may or may not be present in the data set. However, if a k-mer is not found in the bit array, it is definitely absent from the data set. You can play with a Bloom filter here to see how it works.

Bloom filter is designed based on multiple parameters, and a mathematical understanding of their relationship with false positive rate is needed for proper choice of parameters. You can find an well-explained derivation of probability of false positives here.

Written by M. //