A Comparative Study of Machine Learning Models for Identification of Antiviral Peptides Using Various Encoded Features

Viruses are a significant threat to human life, as demonstrated by the global COVID-19 pandemic and the Ebola outbreak. Diseases such as smallpox, AIDS, hepatitis, liver cancer, and cervical cancer often caused by the Human Papillomavirus can lead to fatal outcomes. Over the years, extensive research has focused on developing vaccines and antiviral drugs, which have successfully contained and, in some cases, eradicated viral infections. Recently, computational techniques, particularly machine learning algorithms, have made notable progress in identifying potential Antiviral Peptides (AVPs), thereby accelerating experimental validation for therapeutic applications. This study introduces machine learning techniques and a Light Gradient Boosting Machine (LGBM) model combined with three feature-encoding methods to predict whether a protein sequence contains effective antiviral peptides. Eight machine learning algorithms were evaluated using both single-feature and combined feature encodings. Among them, the lightweight LGBM model trained on combined encoded features achieved the best performance, with an accuracy of 98%, precision of 97%, recall of 98%, F1-score of 98%, and an AUC of 1.00. Compared to existing models, the proposed approach achieved approximately 2% higher accuracy using individual encoding methods and about 3% higher accuracy with combined features. The reliability and effectiveness of the proposed model highlight its potential value for pharmaceutical development and academic research.