Biological network analysis with deep learning

• Published in: Briefings in bioinformatics Vol. 22; no. 2; pp. 1515 - 1530
• Main Authors: Muzio, Giulia, O’Bray, Leslie, Borgwardt, Karsten
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 22.03.2021; Oxford Publishing Limited (England)
• Subjects: Algorithms; Bioinformatics; Biological activity; Chemical bonds; Chemical compounds; Computational Biology - methods; Computer applications; Deep Learning; Drug Discovery; Gene Regulatory Networks; Graph neural networks; Humans; Machine learning; Network analysis; Neural networks; Neural Networks, Computer; Predictions; Proteins; Software; drug development; deep learning; drug-target prediction; protein function prediction; protein interaction prediction; biological networks
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbaa257

Abstract Recent advancements in experimental high-throughput technologies have expanded the availability and quantity of molecular data in biology. Given the importance of interactions in biological processes, such as the interactions between proteins or the bonds within a chemical compound, this data is often represented in the form of a biological network. The rise of this data has created a need for new computational tools to analyze networks. One major trend in the field is to use deep learning for this goal and, more specifically, to use methods that work with networks, the so-called graph neural networks (GNNs). In this article, we describe biological networks and review the principles and underlying algorithms of GNNs. We then discuss domains in bioinformatics in which graph neural networks are frequently being applied at the moment, such as protein function prediction, protein–protein interaction prediction and in silico drug discovery and development. Finally, we highlight application areas such as gene regulatory networks and disease diagnosis where deep learning is emerging as a new tool to answer classic questions like gene interaction prediction and automatic disease prediction from data.