ulrb

Unsupervised Learning Based Definition of Microbial Rare Biosphere

Paula Branco, Catarina Magalhães, Luís Torgo, Francisco Pascoal

Last update: 17 November 2023

Copyright license: GNU General Public License

Software version identifier: 0.1.3

A tool to define rare biosphere. 'ulrb' solves the problem of the definition of rarity by replacing human decision with an unsupervised machine learning algorithm (partitioning around medoids, or k-medoids). This algorithm works for any type of microbiome data, provided there is an abundance score for each phylogenetic unit. For validation of this method to several kinds of molecular data and environments, please see Pascoal et al, 2023 (in preparation). Preliminary data suggest this method also works well for non-microbiome data, if there is a species abundance table.

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