Semantic similarity and machine learning with ontologies

Maxat Kulmanov, Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf
2020 Briefings in Bioinformatics  
Ontologies have long been employed in the life sciences to formally represent and reason over domain knowledge and they are employed in almost every major biological database. Recently, ontologies are increasingly being used to provide background knowledge in similarity-based analysis and machine learning models. The methods employed to combine ontologies and machine learning are still novel and actively being developed. We provide an overview over the methods that use ontologies to compute
more » ... larity and incorporate them in machine learning methods; in particular, we outline how semantic similarity measures and ontology embeddings can exploit the background knowledge in ontologies and how ontologies can provide constraints that improve machine learning models. The methods and experiments we describe are available as a set of executable notebooks, and we also provide a set of slides and additional resources at https://github.com/bio-ontology-research-group/machine-learning-with-ontologies.
doi:10.1093/bib/bbaa199 pmid:33049044 pmcid:PMC8293838 fatcat:3mqrjqnggrhdrkvsl6w4odazeu