IPFMC: an iterative pathway fusion approach for enhanced multi-omics clustering in cancer research

Using multi-omics data for clustering (cancer subtyping) is crucial for precision medicine research. Despite numerous methods having been proposed, current approaches either do not perform satisfactorily or lack biological interpretability, limiting the practical application of these methods. Based on the biological hypothesis that patients with the same subtype may exhibit similar dysregulated pathways, we developed an Iterative Pathway Fusion approach for enhanced Multi-omics Clustering (IPFMC), a novel multi-omics clustering method involving two data fusion stages. In the first stage, omics data are partitioned at each layer using pathway information, with crucial pathways iteratively selected to represent samples. Ultimately, the representation information from multiple pathways is integrated. In the second stage, similarity network fusion was applied to integrate the representation information from multiple omics. Comparative experiments with nine cancer datasets from The Cancer Genome Atlas (TCGA), involving systematic comparisons with 10 representative methods, reveal that IPFMC outperforms these methods. Additionally, the biological pathways and genes identified by our approach hold biological significance, affirming not only its excellent clustering performance but also its biological interpretability.