Preserved in Portico This version is not peer-reviewed
On the Inapplicability of Supervised Machine Learning to Evolutionary Studies
: Received: 8 December 2020 / Approved: 9 December 2020 / Online: 9 December 2020 (09:53:18 CET)
: Received: 28 January 2021 / Approved: 28 January 2021 / Online: 28 January 2021 (11:31:23 CET)
A peer-reviewed article of this Preprint also exists.
Journal reference: Genes 2021
Supervised machine learning (SML) is a powerful method for predicting a small number of well-defined output groups (e.g., potential buyers of a certain product) by taking as input a large number of known well-defined measurements (e.g., past purchases, income, ethnicity, gender, credit record, age, favorite color, favorite chewing gum). SML is predicated upon the existence of a training dataset in which the correspondence between the input and output is known to be true. SML has had enormous success in the world of commerce, and this success has prompted a few scientists to employ it in the study of molecular and genome evolution. Here, we list the properties of SML that make it an unsuitable tool in evolutionary studies. In particular, we argue that SML cannot be used in an evolutionary exploratory context for the simple reason that training datasets that are known to be a priori true do not exist. As a case study, we use an SML study in which it was concluded that most human genomes evolve by positive selection through soft selective sweeps (Schrider and Kern 2017). We show that in the absence of legitimate training datasets, Schrider and Kern (2017) used (1) simulations that employ many manipulatable variables and (2) a system of cherry-picking data that would put to shame most modern evangelical exegeses of the Bible. These two factors, in addition to the lack of methodological detail and the lack of either negative controls or corrections for multiple comparisons, lead us to conclude that all evolutionary inferences derived from so-called SML algorithms (e.g., discoal) should be taken with a huge shovel of salt.
machine learning; evolution; discoal; SML
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