Supplementary Material AStandardized Benchmark for Multilabel Antimicrobial Peptide Classification

A.1 Compilation and Standardization of Datasets We compile ESCAPE from 27 peptide databases by systematically extracting experimentally validated antimicrobial peptides annotated for antibacterial, antifungal, antiparasitic, or antiviral activity. Databases exclusively focusing on a single category, such as AVPdb [1] (antiviral), are directly mapped to one of the four target classes. Additionally, we follow the methodology outlined in TransImbAMP[6], selecting non-antimicrobial peptides from UniProt [7] by applying strict exclusion criteria. Specifically, we discard sequences containing keywords such as "membrane," "toxic," "secretory," "defensive," "antibiotic," "anticancer," "antiviral," or "antifungal" to enhance the quality of the negative class. For large and hierarchically structured databases such as DBAASP[8], DRAMP[9], dbAMP (with species-level annotations)[10], and SATPdb (which lists 38 functional categories)[11], we retain all peptides with annotations that map either directly or through hierarchical or taxonomic relationships to one of our four defined antimicrobial classes (antibacterial, antifungal, antiparasitic, antiviral).