Comparative analysis of machine learning algorithms on the microbial strain-specific AMP prediction

Abstract

The evolution of drug-resistant pathogenic microbial species is a major global health concern. Naturally occurring, antimicrobial peptides (AMPs) are considered promising candidates to address antibiotic resistance problems. A variety of computational methods have been developed to accurately predict AMPs. The majority of such methods are not microbial strain-specific (MSS): they can predict whether a given peptide is active against some microbe, but cannot accurately calculate whether such peptide would be active against a particular microbial strain. Due to insufficient data on most microbial strains, only a few MSS predictive models have been developed so far. To overcome this problem, we developed a novel approach that allows to improve MSS predictive models (MSSPM), based on properties, computed for AMP sequences and characteristics of genomes, computed for target microbial strains. New models can perform predictions of AMPs for microbial strains that do not have data on peptides tested on them. We tested various types of feature engineering as well as different machine learning (ML) algorithms to compare the predictive abilities of resulting models. Among the ML algorithms, Random Forest and AdaBoost performed best. By using genome characteristics as additional features, the performance for all models increased significantly--on average by 7%--relative to models relying on AMP sequence-based properties only. Our novel MSS AMP predictor is freely accessible as part of DBAASP database resource at https://dbaasp.org/tools?page=genome-prediction