Machine learning for single cell genomics data analysis

Félix Merlin Angelo Philippe Raimundo
Laetitia Papaxanthos
Celine Vallot
Jean-Philippe Vert
Current Opinion in Systems Biology, 26(2021), pp. 64-71


Single-cell omics technologies produce large quantities of data describing the genomic, transcriptomic or epigenomic profiles of many individual cells in parallel. In order to infer biological knowledge and develop predictive models from these data, machine learning (ML)-based model are increasingly used due to their flexibility, scalability and impressive success in other fields. In recent years, we have seen a surge of new ML-based method development for low-dimensional representations of single-cell omics data, batch normalisation, cell type classification, trajectory inference, gene regulatory network inference or multimodal data integration. To help readers navigate this fast-moving literature, we survey in this review recent advances in ML approaches developed to analyse single-cell omics data, focusing mainly on articles published in the last two years (2019–2020).