MomicPred: A Cell Cycle Prediction Framework Based on Dual-Branch Multi-Modal Feature Fusion for Single-Cell Multi-Omics Data

The cell cycle plays a pivotal role in regulating cell fate and stem cell differentiation. As a rate-limiting step in differentiation, its precise regulation is essential for maintaining cellular diversity and tissue homeostasis. Recent advances in single-cell multi-omics technologies have enabled the integration of gene expression data and chromatin structural regulation, thereby enhancing the prediction of cell cycle using multi-omics approaches. However, current algorithms have yet to effectively integrate transcriptome and three-dimensional (3D) genomic data for cell cycle prediction. We propose MomicPred, an innovative dual-branch multi-modal fusion framework designed to predict cell cycle dynamics. This framework integrates transcriptome-derived gene expression data with global chromatin structural insights from 3D genome data. By leveraging the complementary nature of these multi-omics data, MomicPred extracts three core feature sets that uncover cross-layer associations and synergistic interactions between the two omics modalities, enabling high-precision cell cycle prediction. We further evaluate the framework's performance through various benchmarking strategies, demonstrating its efficiency and robustness. Furthermore, feature importance analysis reveals chromatin structural changes and key biological processes across distinct cell cycle stages, offering new perspectives for future research. MomicPred is available on GitHub at https://github.com/HaoWuLab-Bioinformatics/MomicPred.