Robert Hoehndorf, Associate Professor of Computer Science at King Abdullah University of Science and Technology (KAUST), will present "Machine learning with biomedical ontologies."
Robert Hoehndorf is an Associate Professor of Computer Science at King Abdullah University of Science and Technology (KAUST), where he is the Principal Investigator of the Bio-Ontology Research Group (BORG). His main academic interests are knowledge representation and symbolic approaches to artificial intelligence and using them to gain novel biological insights. They develop knowledge-based methods for the analysis of large, complex and heterogeneous datasets in biology, and apply them to understanding genotype-phenotype relations.
Ontologies are widely used in biological and biomedical research to formalize and constrain the relations between biomedical entities. It is critical to make use of knowledge in ontologies when building predictive models, in particular when available data is limited or the prediction problem is sufficiently complex. Ontology embeddings can be used to introduce background knowledge into machine learning models, axioms in ontologies can be used as constraints that reduce search space, and some embeddings allow neural networks to compute entailments and enable zero-shot learning. I will discuss methods for embedding Semantic Web ontologies in the Web Ontology Language (OWL), outline some of their formal properties that relate them to model theory, and show how they can be used in machine learning in the biomedical domain.
Kulmanov et al. Semantic similarity and machine learning with
ontologies. Briefings in Bioinformatics,
Kulmanov et al. EL Embeddings: Geometric Construction of Models for
the Description Logic EL++. Proceedings of IJCAI 2019,
Tang et al. FALCON: Faithful Neural Semantic Entailment over ALC
Ontologies. arXiv, 2023. https://arxiv.org/abs/2208.07628
We continue the CIRSS speaker series in Spring 2023 with a focus on “Knowledge Graphs and Semantic Computing”. We will meet on Fridays, 9-10am Central Time, on Zoom. To join a session, go to the current week’s session and click the “access” link, which will lead you to a calendar entry. There, click the “PARTICIPATE online” button to join a session. Recordings of past talks can be found next to "access" if available. The event is open to the public, and everyone is welcome to attend! This series is hosted by the Center for Informatics Research in Science and Scholarship (CIRSS). If you have any questions, please contact Jana Diesner and Halil Kilicoglu.
This event is sponsored by Center for Informatics Research in Science and Scholarship