Comparative Analysis of Bagging and Boosting Algorithms for Predicting Protein-Protein Interactions Using Learned Embeddings

Sini S Raj; Vinod Chandra S S

doi:10.55006/biolsciences.2026.6102

Authors

Sini S Raj Machine Intelligence Research Lab, Department of Computer Science, University of Kerala, Thiruvananthapuram, Kerala, India https://orcid.org/0000-0001-8701-7224
Vinod Chandra S S Machine Intelligence Research Lab, Department of Computer Science, University of Kerala, Thiruvananthapuram, Kerala, India

DOI:

https://doi.org/10.55006/biolsciences.2026.6102

Keywords:

Viral infections, Protein-Protein Interactions (PPIs), Word2Vec embedding, Learned embeddings, Ensemble learning

Abstract

Viral infections are a major global health concern, as evidenced by the rapid spread of SARS-CoV-2, leading to a worldwide pandemic. Viruses can manipulate host cell machinery by integrating their genetic material into the host genome, a process facilitated by Protein-Protein Interactions (PPIs). Identifying PPIs between humans and viruses is essential for understanding the mode of infection and host immune responses and developing effective treatment regimes. Although experimental methods like mass spectrometry-based proteomics and yeast two-hybrid assays are widely employed to identify human-virus PPIs they are often time-consuming, expensive, and labor-intensive. Here, we propose an alternative method that overcomes technical limitations by leveraging machine learning models to predict human-virus PPIs with enhanced accuracy and efficiency, emphasizing the role of automatic feature extraction and ensemble learning techniques in driving superior prediction performance. Protein sequences are analyzed using Word2Vec embeddings to automatically extract complex features, offering a significant advantage over manual feature engineering. The study employs two ensemble learning approaches, boosting and bagging, to train predictive models on the extracted features. Among these, XGBoost, a boosting algorithm, demonstrated superior predictive performance compared to bagging models. Our findings highlight the potential of combining automated feature extraction with advanced ensemble learning methods to improve the efficiency and accuracy of PPI prediction. This approach enhances our understanding of protein sequences and their interactions and holds promise for accelerating the development of effective antiviral therapies.

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