Semantic Apparatus – Semantic similarity and machine learning with ontologies

Cited by Lee Sonogan

A framework for unifying ontology-based semantic similarity measures: A  study in the biomedical domain - ScienceDirect

Abstract by Maxat Kulmanov, Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf

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 similarity 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

Publication: Briefings in Bioinformatics (Peer-Reviewed Journal)

Pub Date: 13, Oct 2021 Doi:

Keywords: machine learning, semantic similarity, ontology, knowledge representation, neuro-symbolic integration (Plenty more sections and references in this research article)

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.