Bayesian-knowledge driven ontologies: A framework for fusion of semantic knowledge under uncertainty and incompleteness

PLoS One. 2024 Mar 27;19(3):e0296864. doi: 10.1371/journal.pone.0296864. eCollection 2024.

Abstract

The modeling of uncertain information is an open problem in ontology research and is a theoretical obstacle to creating a truly semantic web. Currently, ontologies often do not model uncertainty, so stochastic subject matter must either be normalized or rejected entirely. Because uncertainty is omnipresent in the real world, knowledge engineers are often faced with the dilemma of performing prohibitively labor-intensive research or running the risk of rejecting correct information and accepting incorrect information. It would be preferable if ontologies could explicitly model real-world uncertainty and incorporate it into reasoning. We present an ontology framework which is based on a seamless synthesis of description logic and probabilistic semantics. This synthesis is powered by a link between ontology assertions and random variables that allows for automated construction of a probability distribution suitable for inferencing. Furthermore, our approach defines how to represent stochastic, uncertain, or incomplete subject matter. Additionally, this paper describes how to fuse multiple conflicting ontologies into a single knowledge base that can be reasoned with using the methods of both description logic and probabilistic inferencing. This is accomplished by using probabilistic semantics to resolve conflicts between assertions, eliminating the need to delete potentially valid knowledge and perform consistency checks. In our framework, emergent inferences can be made from a fused ontology that were not present in any of the individual ontologies, producing novel insights in a given domain.

MeSH terms

  • Bayes Theorem
  • Biological Ontologies*
  • Knowledge Bases
  • Logic
  • Semantics*
  • Uncertainty

Grants and funding

This research was supported by the Air Force Office of Scientific Research (https://www.afrl.af.mil/AFOSR/), AFOSR Grant Nos. FA9550-20-1-0032, FA9550-09-1-0716 and FA9550-07-1-0050, as well as the National Institutes of Health, (https://grants.nih.gov/) Award No. 1OT2TR003436-01. All grants were awarded to Eugene Santos. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.