HIV-1 protease cleavage sites detection with a Quantum convolutional neural network algorithm

Abstract: In this study, we propose a quantum convolutional neural network (QCNN)-based framework with the neural quantum embedding (NQE) to predict HIV-1 protease cleavage sites in amino acid sequences from viral and human proteins. To assess the effectiveness and robustness of our framework, we compared the classification performance against classical neural networks under both noiseless and noisy simulations. Among experimental conditions, the QCNN with the angle and amplitude encoding NQE conditions consistently outperformed classical counterparts in both the similar trainable parameter scale and the different number of qubits (the averaged performance of the 4-qubits and 8-qubits QCNN: 0.9146 and 0.8929 / the averaged performance of the classical neural network: 0.6125 and 0.8278). The QCNN with the NQE showed stable performance under the quantum hardware noise, confirming its applicability to biomedical data analysis with the noise intermediate-scale quantum (NISQ) hardware. This study presents the first application of NQE-augmented QCNNs for HIV-1 cleavage site classification, providing new insights into scalable and noise-resilient quantum machine learning for biomedical data.