CLCAP: Contrastive learning improves antigenicity prediction for influenza A virus using convolutional neural networks

Influenza viruses are detected year-round over the world and the viruses will usually circulate during fall and winter, causing the seasonal flu. The growing novel variants of influenza viruses pose a significant concern to public health annually. However, the rapid mutation of the influenza viruses makes it challenging to timely track their evolution. Therefore, a fast, low-cost, and precise method to predict the antigenic variant of influenza viruses could help vaccine development and prevent viral transmission. In this study, we propose a multi-channel convolutional neural network using contrastive learning to predict the antigenicity of influenza A viruses. An integrated dataset containing antigenic data and protein sequences was collected from various public resources and literature. The experimental results on three different influenza subtypes indicate our proposed model outperforms other traditional machine learning classifiers for antigenicity prediction. In addition, it also demonstrates superior performance over several state-of-the-art approaches, with 5.18 %, 7.03 % and 7.82 % increase in accuracy compared to the best results for H1N1, H3N2 and H5N1, respectively. The proposed framework is timely and effective in influenza antigenicity prediction and can be adapted to the study of other viruses.