I work in cheminformatics, and wrote one of the documents cited by Sagar.

The answer is "yes and no".

My area of focus is a part of molecular similarity. The overall idea is that molecules which are similar tend to have similar functionality. There are many approximate ways to estaimte molecular similarity. The one I focus on maps chemical substructures ("features" or "descriptors") to 1 or several bits on a bitstring of length ~1024 bits, called a fingerprint.

We use Jaccard similarity (called Tanimoto similarity in my field) of two fingerprints as a proxy for molecular similarity computed as popcount(A & B) / popcount(A | B). Since popcount(A) and popcount(B) can be pre-computed, this ends up being popcount(A & B) / (popcount(A) + popcount(B) - popcount(A & B). If the fingerprints are grouped by popcount then this boils down to computing popcount(A & B), plus some tiny amount of integer math.

This can be used to find the k-nearest matches to a single query, to cluster the fingerprints, to identify diverse fingerprints, and so on.

These methods bounded by two things: 1. the time needed to compute popcount of (A & B), and 2. the memory bandwidth.

The CPU bottleneck really is the popcount calculation. At https://jcheminf.biomedcentral.com/articles/10.1186/s13321-0... I compared different popcount implementations and found POPCNT about 2-3x faster than the fastest pure-C popcount.

However, POPCNT on Intel processors isn't all that fast. Rather, when I was really focused on this 5+ years ago, Intel processors only had one execution port than could handle POPCNT, so I could only get one 8 bytes per cycle. (Some AMD processors have several such ports, but I never tried one of those CPUs.)

Instead, Wojciech Mula, Nathan Kurz and Daniel Lemire showed that AVX2 instructions were even faster than sequential POPCNT instructions because AVX2 could handle more things in parallel. See my table for numbers.

For small bitstrings (I think 512 bits was the boundary) POPCNT is still the fastest.

With AVX2 it's fast enough that memory bandwidth becomes the limiting issue, and I need to start worrying about cache locality.