SCONE: a subset-contrastive method for multi-omics network embedding

Network-based analyses of omics data are widely used and, while many of these methods have been adapted to single-cell scenarios, they often remain memory- and space-intensive. As a result, they are better suited to batch data or smaller datasets. Furthermore, the application of network-based methods in multi-omics often relies on similarity-based networks, which lack structurally discrete topologies. This limitation may reduce the effectiveness of graph-based methods that were initially designed for topologies with better defined structures. We propose Subset-Contrastive multi-Omics Network Embedding (SCONE), a method that employs contrastive learning techniques on large datasets through a scalable subgraph contrastive approach. By exploiting the pairwise similarity basis of many network-based omics methods, we transformed this characteristic into a strength, developing an approach that aims to achieve scalable and effective analysis. Our method demonstrates synergistic omics integration for cell type clustering in single-cell data. Additionally, we evaluate its performance in a bulk multi-omics integration scenario, where SCONE performs comparable with the state-of-the-art despite utilizing limited views of the original data. We anticipate that our findings will motivate further research into the use of subset contrastive methods for omics data.