Machine learning in plant–pathogen interactions: empowering biological predictions from field scale to genome scale

Summary: Machine learning (ML) encompasses statistical methods that learn to identify patterns in complex datasets. Here, I review application areas in plant–pathogen interactions that have recently benefited from ML, such as disease monitoring, the discovery of gene regulatory networks, genomic selection for disease resistance and prediction of pathogen effectors. However, achieving robust performance from ML is not trivial and requires knowledge of both the methodology and the biology. I discuss common pitfalls and challenges in using ML approaches. Finally, I highlight future opportunities for ML as a tool for dissecting plant–pathogen interactions using high-throughput data, for example, through integration of diverse data sources and the analysis with higher resolution, such as from individual cells or on elaborate spatial and temporal scales.