APOLO: Automatic Prompt Optimization for Ontology Learning

Huu Tan Mai, Roman Kochnev, Cuong Xuan Chu, Lukas Lange, Heiko Paulheim +1

Ontology Learning (OL) from text has advanced with the emergence of Large Language Models (LLMs), but it remains challenging due to the limited availability of annotated training data and the difficulty of adapting LLMs to perform OL effectively. We address this via APOLO - Automatic Prompt Optimization for Ontology Learning, by casting OL as an explicit prompt optimization problem over LLM modules. To obtain training data, we employ a multi-agent system that generates text-ontology pairs from existing expert-curated ontologies. We then propose two ontology learner architectures: a greedy and an autoregressive learner, and optimize both using GEPA, a greedy evolutionary prompt optimizer built on DSPy. Experiments on two ontologies - a biomedical (DOID) and a plant ontology (PO) show consistent improvements after optimization across nearly all model and mode combinations, with autoregressive learners achieving the largest gains. Our results demonstrate that prompt optimization is a viable and lightweight alternative to fine-tuning for OL, and that the autoregressive formulation better captures ontological structure than the greedy approach.