Advanced parameters setting for multi‐Models

• Users, who would like to reproduce this AMR benchmarking results, are not advised to change settings in this category.
• But you can change them accordingly when you want to make use of this benchmarking workflow to explore more.
• For species related to multi-models, we have listed the possible maximum (in terms of data sets this study provides) for each setting, so you can explore as you like by reducing the species, but not by adding others on.

option	action	values ([default])
species_list_multi_antibiotics	Benchmarked species for single-species multi-antibiotic model.	Mycobacterium_tuberculosis, Escherichia_coli, Staphylococcus_aureus, Salmonella_enterica, Klebsiella_pneumoniae, Pseudomonas_aeruginosa, Acinetobacter_baumannii, Streptococcus_pneumoniae, Neisseria_gonorrhoeae
species_list_multi_species	Benchmarked species for multi-species models.	Mycobacterium_tuberculosis, Salmonella_enterica, Streptococcus_pneumoniae, Escherichia_coli, Staphylococcus_aureus, Klebsiella_pneumoniae, Acinetobacter_baumannii, Pseudomonas_aeruginosa, Campylobacter_jejuni
merge_name	Used to name the folder for multi-models. E.g. multi-models of M. tuberculosis and S. enterica will result in Mt_Se.	Mt_Se_Sp_Ec_Sa_Kp_Ab_Pa_Cj
cv_number_multiS	The value of k+1, where the k corresponds to k-fold cross-validation and 1 corresponds to the holdout test set, for multi-species models	6