Multi-Omics Analysis for Cancer Subtype Inference via Unrolling Graph Smoothness Priors

Integrating multi-omics datasets through data-driven analysis offers a comprehensive understanding of the complex biological processes underlying various diseases, particularly cancer. Graph Neural Networks (GNNs) have recently demonstrated remarkable ability to exploit relational structures in biological data, enabling advances in multi-omics integration for cancer subtype classification. Existing approaches often neglect the intricate coupling between heterogeneous omics, limiting their capacity to resolve subtle cancer subtype heterogeneity critical for precision oncology. To address these limitations, we propose a framework named Graph Transformer for Multi-omics Cancer Subtype Classification (GTMancer). This framework builds upon the GNN optimization problem and extends its application to complex multi-omics data. Specifically, our method leverages contrastive learning to embed multi-omics data into a unified semantic space. We unroll the multiplex graph optimization problem in that unified space and introduce dual sets of attention coefficients to capture structural graph priors both within and among multi-omics data. This approach enables global omics information to guide the refining of the representations of individual omics. Empirical experiments on seven real-world cancer datasets demonstrate that GTMancer outperforms existing state-of-the-art algorithms.

Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors

In recent years, Graph Convolutional Networks (GCNs) have gained popularity for their exceptional ability to process graph-structured data. Existing GCN-based approaches typically employ a shallow model architecture due to the over-smoothing phenomenon. Current approaches to mitigating over-smoothing primarily involve adding supplementary components to GCN architectures, such as residual connections and random edge-dropping strategies. However, these improvements toward deep GCNs have achieved only limited success. In this work, we analyze the intrinsic message passing mechanism of GCNs and identify a critical issue: messages originating from high-order neighbors must traverse through low-order neighbors to reach the target node. This repeated reliance on low-order neighbors leads to redundant information aggregation, a phenomenon we term over-aggregation. Our analysis demonstrates that over-aggregation not only introduces significant redundancy but also serves as the fundamental cause of over-smoothing in GCNs.