Similarity Downselection: A Python implementation of a heuristic search algorithm for finding the set of the n most dissimilar items with an application in conformer sampling

• Main Authors: Nielson, Felicity F, Colby, Sean M, Renslow, Ryan S, Metz, Thomas O
• Format: Journal Article
• Language: English
• Published: 06.05.2021
• Subjects: Computer Science - Mathematical Software; Quantitative Biology - Biomolecules
• DOI: 10.48550/arxiv.2105.02991

Finding the set of the n items most dissimilar from each other out of a larger population becomes increasingly difficult and computationally expensive as either n or the population size grows large. Finding the set of the n most dissimilar items is different than simply sorting an array of numbers because there exists a pairwise relationship between each item and all other items in the population. For instance, if you have a set of the most dissimilar n=4 items, one or more of the items from n=4 might not be in the set n=5. An exact solution would have to search all possible combinations of size n in the population, exhaustively. We present an open-source software called similarity downselection (SDS), written in Python and freely available on GitHub. SDS implements a heuristic algorithm for quickly finding the approximate set(s) of the n most dissimilar items. We benchmark SDS against a Monte Carlo method, which attempts to find the exact solution through repeated random sampling. We show that for SDS to find the set of n most dissimilar conformers, our method is not only orders of magnitude faster, but is also more accurate than running the Monte Carlo for 1,000,000 iterations, each searching for set sizes n=3-7 out of a population of 50,000. We also benchmark SDS against the exact solution for example small populations, showing SDS produces a solution close to the exact solution in these instances.