Quantum Convolutional HLA Immunogenic Peptide Prediction (Q-CHIPP): Next-Generation Neoantigen Prediction with Quantum Neural Networks

The immune system is an intricately evolved series of cellular and protein-protein interactions, which defend the body against pathogens and abnormal cells such as cancer. A key player in the immunologic recognition of non-self is the immune synapse, where T cell receptors (TCRs) scan peptides presented on major histocompatibility complex (MHC) molecules to detect and eliminate cells displaying non-self antigens. While this interaction is vital for vaccine and immunotherapy success, the underlying rules of TCR recognition remain poorly understood. This is only further challenged as the application of predictive models is very limited due to small training datasets. While traditional machine learning models excel at predicting neoantigen binding to MHC, they often struggle to accurately predict immunogenicity. To address these challenges, we developed a quantum computing approach using Quantum Convolutional Neural Networks (QCNNs). Here we present Quantum Convolutional Human Leukocyte Antigen (HLA) Immunogenic Peptide Prediction (Q-CHIPP), the first application of quantum hardware based on training/predicting both MHC binding and immunogenicity in a combinatorial approach. Additionally, we present a large scale use of quantum hardware at scale with 46 qubits. This study underscores how quantum technology can be used for biological modeling and presents a scalable QCNN design with the potential to overcome current computational bottlenecks as quantum hardware advances.