Comparative Analysis of Quantum Support Vector Machines and Variational Quantum Classifiers for B-cell Epitope Prediction in Vaccine Design

Abstract: Quantum computing offers new opportunities for addressing complex classification tasks in biomedical applications. This study investigates two quantum machine learning models-the Quantum Support Vector Machine (QSVM) and the Variational Quantum Classifier (VQC)-in the context of B-cell epitope prediction, a key step in modern vaccine design. QSVM builds upon the classical SVM framework by using quantum circuits to encode nonlinear kernel computations, while VQC replaces the entire classification pipeline with trainable quantum circuits optimized variationally. A benchmark dataset from the Immune Epitope Database (IEDB) is used for model evaluation. Each epitope is represented by 10 physicochemical features, and dimensionality reduction via Principal Component Analysis (PCA) is applied to assess model performance across different feature spaces. We also examine the effect of sample size on prediction outcomes. Experimental results show that QSVM performs well under limited data conditions, while VQC achieves higher accuracy in larger datasets. These findings highlight the potential of quantum-enhanced models for bioinformatics tasks, particularly in supporting efficient and scalable epitope-based vaccine development.