Feature selection

Genomics

Biology

Discriminative model

Gene

Machine learning

Epigenomics

Gene expression

Genome

Artificial intelligence

DNA methylation

Computer science

Unsupervised learning

Biochemistry

Selection (genetic algorithm)

Nature Reviews Genetics

Machine learning methods are becoming increasingly important in the analysis of large-scale genomic, epigenomic, proteomic and metabolic data sets. In this Review, the authors consider the applications of supervised, semi-supervised and unsupervised machine learning methods to genetic and genomic studies. They provide general guidelines for the selection and application of algorithms that are best suited to particular study designs. The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in the analysis of large, complex data sets. Here, we provide an overview of machine learning applications for the analysis of genome sequencing data sets, including the annotation of sequence elements and epigenetic, proteomic or metabolomic data. We present considerations and recurrent challenges in the application of supervised, semi-supervised and unsupervised machine learning methods, as well as of generative and discriminative modelling approaches. We provide general guidelines to assist in the selection of these machine learning methods and their practical application for the analysis of genetic and genomic data sets.

Machine learning applications in genetics and genomics