Tutorial & Workshop on the Role of Ontologies in Biomedical AI (ROBI)

Ontologies and Linked Data resources are pervasive throughout the life sciences where hundreds of ontologies are used in almost every major biological database for the formal characterization of data and the integration of knowledge. Methods that allow incorporating the knowledge in ontologies in biomedical data analysis and particular machine learning are only now being developed. The aim of the workshop is to explore the interface between domain knowledge in biomedical ontologies and machine learning from the perspective of ontologies, their structure, and underlying conceptualization. We will discuss how ontologies can contribute to build more comprehensive AI models that utilize domain knowledge, provide explanations understandable to domain experts, and identify consistency with scientific knowledge. Of particular interest is how research on biomedical ontologies can be leveraged to improve AI.

Example questions we would like to answer in the workshop are

• Does the improvement in ontology quality in the past years reflect their impact on machine learning methods?
• How does ontology consistency impact machine learning?
• What is missing from bio-ontologies for them to have more impact on AI methods?
• How can we leverage machine learning to improve the bio-ontology ecosystem?

Topics of interest include

• ontologies, graph embeddings, ontology embeddings
• neural reasoning with biomedical ontologies
• ontologies and Natural Language Processing
• machine learning in ontology evaluation
• ontologies and explainability
• biomedical ontologies in general AI
• neuro-symbolic integration in biomedicine

Program

The workshop takes place on 25 September in the afternoon, 1:30-5:00. We will start with presentations of research and position papers, followed by a discussion session.

• 1:30 - 1:40: Opening
• 1:40 - 2:00: Knowledge graphs and Explainable AI for Drug Repurposing on Rare Diseases. Pablo Perdomo Quinteiro, Katherine Wolstencroft, Marco Roos and Núria Queralt Rosinach
• 2:00 - 2:20: Investigating Ontology Use in Artificial Intelligence and Machine Learning for Biomedical Research - A Preliminary Report from A Comprehensive Literature Review Asiyah Lin, Andrey Ibrahim Seleznev, Tianming “Danny” Ning, Paulene Grier, Lalisa Mariam Lin, Christopher Travieso, Jaleal Sanjak, Ansu Chatterjee
• 2:20 - 2:40: Testing Ontology Embedding Visualization. John Kausch
• 2:40 - 3:00: Ontology Alignment through graph projection, machine learning, and iterative inconsistency removal. Sarah Alghamdi, Fernando Zhapa-Camacho and Robert Hoehndorf.
• 3:00 - 3:15: Coffee break
• 3:15 - 4:15: Panel discussion
• 4:15: open discussion

Where and when?

The workshop will take place at the International Conference on Biological and Biomedical Ontologies (ICBO) in Ann Arbor, Michigan, USA.

Important dates:

• Submission: 30 August 2022
• Workshop date: 25 September 2022

Organizing Committee and Contact

• Robert Hoehndorf, King Abdullah University of Science and Technology
• George Gkoutos, University of Birmingham