Ontology-to-tools compilation for executable semantic constraint enforcement in LLM agents
This addresses the problem of integrating generative models with symbolic constraints for researchers and practitioners in knowledge graph ecosystems, though it appears incremental as an extension of existing frameworks.
The paper tackles the problem of coupling large language models (LLMs) with formal domain knowledge by introducing ontology-to-tools compilation, which enforces semantic constraints during generation rather than through post-hoc validation, reducing manual schema and prompt engineering in an illustrative case of metal-organic polyhedra synthesis literature.
We introduce ontology-to-tools compilation as a proof-of-principle mechanism for coupling large language models (LLMs) with formal domain knowledge. Within The World Avatar (TWA), ontological specifications are compiled into executable tool interfaces that LLM-based agents must use to create and modify knowledge graph instances, enforcing semantic constraints during generation rather than through post-hoc validation. Extending TWA's semantic agent composition framework, the Model Context Protocol (MCP) and associated agents are integral components of the knowledge graph ecosystem, enabling structured interaction between generative models, symbolic constraints, and external resources. An agent-based workflow translates ontologies into ontology-aware tools and iteratively applies them to extract, validate, and repair structured knowledge from unstructured scientific text. Using metal-organic polyhedra synthesis literature as an illustrative case, we show how executable ontological semantics can guide LLM behaviour and reduce manual schema and prompt engineering, establishing a general paradigm for embedding formal knowledge into generative systems.