Feb 13, 2023
Ontologies are increasingly being used to provide background knowledge in machine learning models. We provide an introduction to different methods that use ontologies in machine learning models. We will start the tutorial by introducing semantic similarity measures that rely on axioms in ontologies to compare domain entities. From semantic similarity, we will develop and discuss unsupervised machine learning methods that can “embed” ontologies in vector spaces to allow comparison of domain entities based on similarity in these spaces. We will introduce mOWL, a software library for machine learning with ontologies, based on which the methods we discuss can be implemented. mOWL is freely available at https://github.com/bio-ontology-research-group/mowl. Throughout the tutorial, we will use biomedical examples for hands-on tasks. 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.
Since 2008, the SWAT4(HC)LS Workshop has provided a platform for the presentation and discussion of the benefits and limits of applying Web-based information systems and semantic technologies in the domains of health care and life sciences. Growing steadily each year as Semantic Web applications become more widespread, SWAT4LS has been in Edinburgh (2008), Amsterdam (2009), Berlin (2010), London (2011), Paris (2012), Aveiro (SWAT4LS School organized in 2012), Edinburgh (2013) and Berlin (2014). Since 2015, SWAT4LS changed format and has been organized as a 2 day conference, preceded by a tutorial day and followed by a hackathon day (Cambridge, 2015, and Amsterdam, 2016). SWAT4(HC)LS aims at providing an open and stimulating environment that brings together researchers, both developers and users, from areas as diverse as eHealth, medical and clinical informatics, bioinformatics, cheminformatics, drug discovery, drug safety, systems biology, medical physics, data science, and biocomputing, to discuss goals, current limits and real experiences in the application of Semantic Web and Linked Data technologies to challenges in health care and life sciences. The meetings are typically very interactive and are accompanied by tutorials and a hackathon.
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