Multi-level Knowledge Integration with Graph Convolutional Network for Cancer Molecular Subtype Classification

Multi-omics data provides a wealth of information concerning disease mechanisms, which benefits the exploration of the intricate molecular phenomena underlying diseases. In recent years, considerable endeavors have been directed towards the combination of graph convolutional network, which has the powerful ability to gather information, with multi-omics learning methods to obtain more reliable results. For achieving this pursuit, an essential challenge is data integration. Against this backdrop, we propose a unified framework named multi-level knowledge integration with graph convolutional network, which effectively incorporates multiple prior knowledge and omics data to learn an intrinsic representation. In specific, the model consists of two subnetworks: an attribute-level module and a sample-level module. The former firstly aggregates the knowledge given by the prior biological graphs into low-dimensional embeddings, and then maximizes the consistency between these prior views via optimizing a contrastive loss for attaining the attribute-based representations. The latter leverages an encoder to dimensionalize the original multi-omics data to attain more dominant sample knowledge, and subsequently utilizes another contrastive loss to align these representations between multiple omics for learning the global sample-level information. Comprehensive experiments are performed to show that the proposed model surpasses other state-of-the-art methods.