Neural network-assisted RNA velocity imputation for empowering transcript dynamics-based analyses

Existing RNA velocity estimation tools often fail to calculate velocities for a substantial portion of genes due to technical limitations or model assumptions, thereby restricting downstream analyses that rely on velocity estimations. To tackle this problem, we propose NARVI (Neural Network-Assisted RNA Velocity Imputation), a deep learning framework that learns the relationship between the expression patterns and velocities of computable genes to accurately estimate velocities for otherwise incalculable genes. We evaluated the performance of NARVI across multiple single-cell transcriptome datasets and applied it to trajectory inference and marker gene analysis using the reconstituted velocities of dropped genes. This approach recovers velocities for thousands of genes that were previously impossible to estimate, thereby broadening the scope of downstream analyses and providing deeper insights into gene transcriptional dynamics.