A Standardized Benchmark for Multilabel Antimicrobial Peptide Classification
Sebastian Ojeda, Rafael Velasquez, Nicolas Aparicio, Juanita Puentes, Paula Cárdenas, Nicolás Andrade, Gabriel González, Sergio Rincón, Carolina Muñoz-Camargo, Pablo Arbelaez
Antimicrobial peptides have emerged as promising molecules to combat antimicrobial resistance. However, fragmented datasets, inconsistent annotations, and the lack of standardized benchmarks hinder computational approaches and slow down the discovery of new candidates. To address these challenges, we present the Expanded Standardized Collection for Antimicrobial Peptide Evaluation (ESCAPE), an experimental framework integrating over 80.000 peptides from 27 validated repositories. Our dataset separates antimicrobial peptides from negative sequences and incorporates their functional annotations into a biologically coherent multilabel hierarchy, capturing activities across antibacterial, antifungal, antiviral, and antiparasitic classes. Building on ESCAPE, we propose a transformer-based model that leverages sequence and structural information to predict multiple functional activities of peptides. Our method achieves up to a 2.15% improvement in mean Average Precision over previous methods adapted for this task, establishing a new state-of-the-art multilabel peptide classification. ESCAPE provides a comprehensive and reproducible evaluation framework to advance AI-driven antimicrobial peptide research.