Graph Representation Learning in Biomedicine
It addresses the problem of analyzing complex biomedical networks for researchers and practitioners, but is incremental as it synthesizes existing approaches.
The paper reviews how graph representation learning leverages systems biology principles to embed biomedical networks into vector spaces, leading to state-of-the-art improvements in domains like variant identification, single-cell analysis, and patient diagnosis.
Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence, specifically deep learning, have enabled us to model, analyze, and learn with such networked data. In this review, we put forward an observation that long-standing principles of systems biology and medicine -- while often unspoken in machine learning research -- provide the conceptual grounding for representation learning on graphs, explain its current successes and limitations, and even inform future advancements. We synthesize a spectrum of algorithmic approaches that, at their core, leverage graph topology to embed networks into compact vector spaces. We also capture the breadth of ways in which representation learning has dramatically improved the state-of-the-art in biomedical machine learning. Exemplary domains covered include identifying variants underlying complex traits, disentangling behaviors of single cells and their effects on health, assisting in diagnosis and treatment of patients, and developing safe and effective medicines.