GLaMoR: Consistency Checking of OWL Ontologies using Graph Language Models

--Semantic reasoning aims to infer new knowledge from existing knowledge, with OWL ontologies serving as a standardized framework for organizing information. A key challenge in semantic reasoning is verifying ontology consistency. However, state-of-the-art reasoners are computationally expensive, and their efficiency decreases as ontology sizes grow. While classical machine learning models have been explored for consistency checking, they struggle to capture complex relationships within ontologies. Large language models (LLMs) have shown promising results for simple reasoning tasks but perform poorly on structured reasoning. The recently introduced Graph Language Model (GLM) offers a way to simultaneously process graph-structured data and text. This paper proposes GLaMoR (Graph Language Model for Reasoning), a reasoning pipeline that transforms OWL ontologies into graph-structured data and adapts the GLM architecture for consistency checking. We evaluate GLaMoR on ontologies from the NCBO BioPortal repository, converting them into triples suitable for model input. Our results show that the GLM outperforms all baseline models, achieving 95% accuracy while being 20 times faster than classical reasoners. With the increasing complexity of knowledge representation and reasoning systems, ontologies play a vital role in structuring domain knowledge across various fields, e. g., biomedical expert knowledge. OWL provides a stable foundation for diverse tasks based on ontologies. OWL 2 [1] is based on the SROIQ [2] description logic, which supports complex reasoning while maintaining logical consistency. To derive additional knowledge from these ontologies, semantic reasoners are employed to infer new facts through logical entailment. These reasoners are critical in supporting key tasks such as classification, query answering, and consistency checking by leveraging formal logic systems for precise and reliable inference. A prominent example is HermiT [3], an OWL 2-compliant reasoner that uses hyper-tableau calculus to perform reasoning tasks efficiently.