Towards Ontology-Enhanced Representation Learning for Large Language Models

Abstract: Taking advantage of the widespread use of ontologies to organise and harmonize knowledge across several distinct domains, this paper proposes a novel approach to improve an embedding-LLM (embedding-LLM) of interest by infusing the knowledge formalized by a reference ontology: ontological knowledge infusion aims at boosting the ability of the considered LLM to effectively model the knowledge domain described by the infused ontology. The linguistic information (i.e. concept synonyms and descriptions) and structural information (i.e. is-a relations) formalized by the ontology are utilized to compile a comprehensive set of concept definitions, with the assistance of a powerful generative LLM (i.e. GPT-3.5-turbo). These concept definitions are then employed to fine-tune the target embedding-LLM using a contrastive learning framework. To demonstrate and evaluate the proposed approach, we utilize the biomedical disease ontology MONDO. The results show that embedding-LLMs enhanced by ontological disease knowledge exhibit an improved capability to effectively evaluate the similarity of in-domain sentences from biomedical documents mentioning diseases, without compromising their out-of-domain performance.