A Standardized Benchmark for Multilabel Antimicrobial Peptide Classification
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arXiv
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| Autores principales: | , , , , , , , , , |
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| Formato: | Preprint |
| Publicado: |
2025
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| _version_ | 1866914142104846336 |
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| author | Ojeda, Sebastian Velasquez, Rafael Aparicio, Nicolás Puentes, Juanita Cárdenas, Paula Andrade, Nicolás González, Gabriel Rincón, Sergio Muñoz-Camargo, Carolina Arbeláez, Pablo |
| author_facet | Ojeda, Sebastian Velasquez, Rafael Aparicio, Nicolás Puentes, Juanita Cárdenas, Paula Andrade, Nicolás González, Gabriel Rincón, Sergio Muñoz-Camargo, Carolina Arbeláez, Pablo |
| contents | 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 2.56% relative average improvement in mean Average Precision over the second-best method 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2511_04814 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | A Standardized Benchmark for Multilabel Antimicrobial Peptide Classification Ojeda, Sebastian Velasquez, Rafael Aparicio, Nicolás Puentes, Juanita Cárdenas, Paula Andrade, Nicolás González, Gabriel Rincón, Sergio Muñoz-Camargo, Carolina Arbeláez, Pablo Machine Learning Artificial Intelligence Biomolecules 68T07, 62H30, 62P10 I.2.6; I.2.1; I.5.1; I.5.2 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 2.56% relative average improvement in mean Average Precision over the second-best method 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. |
| title | A Standardized Benchmark for Multilabel Antimicrobial Peptide Classification |
| topic | Machine Learning Artificial Intelligence Biomolecules 68T07, 62H30, 62P10 I.2.6; I.2.1; I.5.1; I.5.2 |
| url | https://arxiv.org/abs/2511.04814 |