Comparison of the best-performing combination (LOGIT and XGBoost) with alternative models. R1, R2 and R3 represent three repeats of retrained LOGITXGBoost models using randomly shuffled heteroresistance data. Exact P values for the comparison between LOGITXGBoost and the alternative models R1, R2 and R3 are 3.6 x 10 -18, 3.5 x 10 -20 and 3.7 x 10 -21, respectively. The average nucleotide identity (ANI)-based model quantifies genomic similarity between isolates by popANI and assigns a test isolate the same heteroresistance label as its genomically closest isolate in the training set. The phylogeny-based model places test isolates into a reconstructed phylogeny of training isolates and then performs hidden state prediction. Two-sided paired-sample t -test: exact P values are provided.
