Comment on “Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper”

Abstract

A recent study by Faye Orcales and colleagues proposes a teaching curriculum on supervised machine learning applied to genomics data aimed at predicting antibiotic resistance. The article describes a traditional machine learning pipeline step-by-step in a way that is accessible to anyone, including novices. However, the authors provide a misleading piece of advice in the “Evaluating model performance” section, where they recommend that readers use accuracy and the F1 score for binary classification. We write this short formal comment on that article to reaffirm and explain why accuracy and the F1 score should be avoided in the evaluation of binary classification and why the Matthews correlation coefficient (MCC) should be employed instead. We also take this opportunity to warn readers about the dangers of k-fold cross-validation, which is suggested as a standard method for dividing data into training set and test set, but has several flaws and pitfalls.