Evolutionary Multi-Objective Optimization in Searching for Various Antimicrobial Peptides [Feature]

Antimicrobial peptides (AMPs), which are parts of the innate immune response found among all classes of life, are promising in broad-spectrum antibiotics and drug-resistant infection treatments. Although AMPs effectively kill bacteria, numerous AMPs widely distributed in the sequence space remain unknown to humans. Therefore, the de novo design of AMPs involves the exploration of vast sequence space to identify peptides with high antimicrobial activity and good diversity among the known AMPs. Computational intelligence approaches have successfully identified some AMPs; however, most of them fail to address the diversity of the obtained AMPs. This paper reports an evolutionary multi-objective approach for AMP design to optimize both the antimicrobial activity and diversity among identified AMPs. Our approach employs a deep learning model to predict a peptide’s antimicrobial activity and a niche sharing method to estimate a peptide’s density. Then, an evolutionary multi-objective algorithm is presented to simultaneously optimize the objectives of antimicrobial activity and diversity. The algorithm takes the advantage of a decomposition-based framework to search for AMPs with good diversity. These AMPs are collected by an elite archive during the evolution process. Moreover, a local search strategy is applied to enhance the quality of the identified AMPs. The experimental results show that the proposed approach outperforms the state-of-the-art designs in searching for various AMPs. The AMPs generated by the proposed approach have high antimicrobial activities and are distinct from each other and among the AMPs in the datasets.