A Graph-Based Deep Learning Framework with Gating and Omics-Linked Attention for Multi-Omics Integration and Biomarker Discovery

Integration of multi-omics data provides a comprehensive perspective on complex biological systems, facilitating advances in disease classification and biomarker discovery. However, the heterogeneity and high dimensionality of omics data present significant analytical challenges. To achieve effective and interpretable multi-omics integration, we propose a novel deep learning framework named MOGOLA(Multi-Omics integration by Gating and Omics-Linked Attention). MOGOLA consists of three core components: (1) A hybrid graph learning module that integrates Graph Convolutional Networks and Graph Attention Networks for intra-omics feature extraction. (2) A gating and confidence mechanism that adaptively weighs feature importance across different omics types. (3) A cross-omics attention-based fusion module that captures inter-omics relationships. Comprehensive evaluations on four benchmark datasets (BRCA, KIPAN, ROSMAP, and LGG) demonstrate that MOGOLA consistently outperforms eleven state-of-the-art approaches. Ablation studies further validate the contribution of each module, while biomarkers identification highlight the framework’s clinical potential. These results show that MOGOLA is a robust and interpretable approach for multi-omics data integration and a contribution to advances in computational biology and precision medicine.