A Dual Diffusion Model-Based Representation Learning Framework for AMPs Classification

Motivation The increasing prevalence of antibiotic-resistant bacteria has intensified the demand for novel antimicrobial agents. Antimicrobial peptides (AMPs) have emerged as promising alternatives, yet their identification or classification remains challenging due to the lack of multi-perspective information, insufficient feature representation learning, and monocular data modalities. Results In this paper, we propose a dual diffusion model-based representation learning framework for classifying AMPs, which effectively integrates both peptide sequence and structure information to address existing issues for the task. Specifically, our approach utilizes a multi-view feature construction module, which encodes peptide sequences and structures from distinctive perspectives, deriving initial feature representations with enriched biological semantics. To enhance representation learning, the proposed framework leverages both diffusion models for sequence and structure information respectively to effectively capture complex semantics from dual modalities. In addition, both single-modal and dual-modal contrastive learning are employed to further advance the representation learning. Results of comprehensive experiments demonstrate that our model outperforms existing methods for the task of AMPs classification, providing a feasible solution to accelerating the discovery of novel antimicrobial agents. Availability of data and codes The data and source codes are available in GitHub at https://github.com/kww567upup/DDM. Supplementary Information Supplementary data are available at Bioinformatics online.