Nmix: a hybrid deep learning model for precise prediction of 2’-O-methylation sites based on multi-feature fusion and ensemble learning

RNA 2'-O-methylation (Nm) is a crucial post-transcriptional modification with significant biological implications. However, experimental identification of Nm sites is challenging and resource-intensive. While multiple computational tools have been developed to identify Nm sites, their predictive performance, particularly in terms of precision and generalization capability, remains deficient. We introduced Nmix, an advanced computational tool for precise prediction of Nm sites in human RNA. We constructed the largest, low-redundancy dataset of experimentally verified Nm sites and employed an innovative multi-feature fusion approach, combining one-hot, Z-curve and RNA secondary structure encoding. Nmix utilizes a meticulously designed hybrid deep learning architecture, integrating 1D/2D convolutional neural networks, self-attention mechanism and residual connection. We implemented asymmetric loss function and Bayesian optimization-based ensemble learning, substantially improving predictive performance on imbalanced datasets. Rigorous testing on two benchmark datasets revealed that Nmix significantly outperforms existing state-of-the-art methods across various metrics, particularly in precision, with average improvements of 33.1% and 60.0%, and Matthews correlation coefficient, with average improvements of 24.7% and 51.1%. Notably, Nmix demonstrated exceptional cross-species generalization capability, accurately predicting 93.8% of experimentally verified Nm sites in rat RNA. We also developed a user-friendly web server (https://tubic.org/Nm) and provided standalone prediction scripts to facilitate widespread adoption. We hope that by providing a more accurate and robust tool for Nm site prediction, we can contribute to advancing our understanding of Nm mechanisms and potentially benefit the prediction of other RNA modification sites.