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arXiv · 2107.11856

Graph Representation Learning on Tissue-Specific Multi-Omics

Amine Amor·Pietro Lio'·Vikash Singh·Ramon Viñas Torné·Helena Andres Terre
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Abstract

Combining different modalities of data from human tissues has been critical in advancing biomedical research and personalised medical care. In this study, we leverage a graph embedding model (i.e VGAE) to perform link prediction on tissue-specific Gene-Gene Interaction (GGI) networks. Through ablation experiments, we prove that the combination of multiple biological modalities (i.e multi-omics) leads to powerful embeddings and better link prediction performances. Our evaluation shows that the integration of gene methylation profiles and RNA-sequencing data significantly improves the link prediction performance. Overall, the combination of RNA-sequencing and gene methylation data leads to a link prediction accuracy of 71% on GGI networks. By harnessing graph representation learning on multi-omics data, our work brings novel insights to the current literature on multi-omics integration in bioinformatics.

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BibTeXRIS

Amine Amor, Pietro Lio', Vikash Singh, Ramon Viñas Torné, Helena Andres Terre. 2021-07-25. Graph Representation Learning on Tissue-Specific Multi-Omics. https://arxiv.org/abs/2107.11856

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