title: A review of supervised machine learning applied to ageing research.
abstract: Broadly speaking, supervised machine learning is the computational task of learning correlations between variables in annotated data (the training set), and using this information to create a predictive model capable of inferring annotations for new data, whose annotations are not known. Ageing is a complex process that affects nearly all animal species. This process can be studied at several levels of abstraction, in different organisms and with different objectives in mind. Not surprisingly, the diversity of the supervised machine learning algorithms applied to answer biological questions reflects the complexities of the underlying ageing processes being studied. Many works using supervised machine learning to study the ageing process have been recently published, so it is timely to review these works, to discuss their main findings and weaknesses. In summary, the main findings of the reviewed papers are: the link between specific types of DNA repair and ageing; ageing-related proteins tend to be highly connected and seem to play a central role in molecular pathways; ageing/longevity is linked with autophagy and apoptosis, nutrient receptor genes, and copper and iron ion transport. Additionally, several biomarkers of ageing were found by machine learning. Despite some interesting machine learning results, we also identified a weakness of current works on this topic: only one of the reviewed papers has corroborated the computational results of machine learning algorithms through wet-lab experiments. In conclusion, supervised machine learning has contributed to advance our knowledge and has provided novel insights on ageing, yet future work should have a greater emphasis in validating the predictions.
authors.affiliation: School of Computing, University of Kent, Canterbury, Kent, CT2 7NF, UK. ff79@kent.ac.uk.
authors.forename: Fabio
authors.identifier: 0000-0001-7159-4668
authors.initials: F
authors.lastname: Fabris
authors.affiliation: Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, UK.
authors.forename: João Pedro de
authors.initials: JP
authors.lastname: Magalhães
authors.affiliation: School of Computing, University of Kent, Canterbury, Kent, CT2 7NF, UK.
authors.forename: Alex A
authors.initials: AA
authors.lastname: Freitas
mesh_terms: D000375:Aging / Q000502:physiology*; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D008954:Models, Biological; D012107:Research Design; D000069553:Supervised Machine Learning
keywords: Ageing; Model interpretation; Supervised machine learning