Machine learning and its applications in plant molecular studies

The advent of high-throughput genomic technologies has resulted in the accumulation of massive amounts of genomic information. However, biologists are challenged with how to effectively analyze these data. Machine learning can provide tools for better and more efficient data analysis. Unfortunately, because many plant biologists are unfamiliar with machine learning, its application in plant molecular studies has been restricted to a few species and a limited set of algorithms. Thus, in this study, we provide the basic steps for developing machine learning frameworks and present a comprehensive overview of machine learning algorithms and various evaluation metrics. Furthermore, we introduce sources of important curated plant genomic data and R packages to enable plant biologists to easily and quickly apply appropriate machine learning algorithms in their research. Finally, we discuss current applications of machine learning algorithms for identifying various genes related to resistance to biotic and abiotic stress. Broad application of machine learning and the accumulation of plant sequencing data will advance plant molecular studies. The advent of high-throughput sequencing technologies has produced several large-scale data sets. This enormous amount of information enables biologists to explore topics that were once difficult or impossible to investigate, such as associations between microRNA and certain diseases, the causes of vascular inflammation and atherosclerosis in humans [1–3] and stress breeding in plants [4]. However, many challenges have also emerged. For example, the European Bioinformatics Institute now stores 273 petabytes of raw molecular data on humans, plants and animals (https://www.ebi.ac.uk/).