Moose: Latent concept learning with reasoning-shortcut awareness in \mathcal{EL}^{++}

OWL ontologies provide a formal knowledge representation framework that enables semantic reasoning, and have been widely adopted across domains such as healthcare and bioinformatics. In practice, however, real-world ontologies are often incomplete, which pose challenges for reasoning. In this work, we focus on a fundamental subsumption reasoning problem: given an incomplete ontology and a candidate (non-entailed) subsumption, determine whether the subsumption is semantically plausible and, if so, providing a logically sound explanation containing potential missing axioms. This task unifies subsumption verification with ontology abduction, and generalizes the latter by removing the need for a predefined candidate set of missing axioms. To address this subsumption reasoning problem, we propose NeurOWL, an end-to-end neuro-symbolic framework that jointly performs verification and abduction, leveraging both formally defined semantics and textual semantics through Large Language Models and ontology embeddings. We evaluate NeurOWL on real-world ontologies across multiple domains, demonstrating strong and robust performance across different domains.

In active learning, membership queries (MQs) allow a learner to pose questions to a teacher, such as ''Is every apple a fruit?'', to which the teacher responds correctly with yes or no. These MQs can be viewed as subsumption tests with respect to the target ontology. Inspired by the standard reduction of subsumption to satisfiability in description logics, we reformulate each candidate axiom into its corresponding counter-concept and verbalise it in controlled natural language before presenting it to Large Language Models (LLMs). We introduce LLMs as a third component that provides real-world examples approximating an instance of the counter-concept. This design property ensures that only Type II errors may occur in ontology modelling; in the worst case, these errors merely delay the construction process without introducing inconsistencies. Experimental results on 13 commercial LLMs show that recall, corresponding to Type II errors in our framework, remains stable across several well-established ontologies.

Ontology learning (OL) aims to automatically construct structured knowledge models from text, yet progress remains fragmented across methods, domains, and evaluation practices. Despite decades of research, OL lacks a shared infrastructure for systematic evaluation and ontology access. This absence has hindered progress and fragmented research, leaving the central challenges of OL largely unaddressed. We introduce OntoLearner, a modular, cross-domain, and first-of-its-kind framework that unifies ontology access, large language model (LLM)-driven learning pipelines, and standardized benchmarking. OntoLearner releases 180 machine-readable ontologies spanning 22 domains and provides pipeline-ready datasets with train/dev/test splits for three core OL tasks: term typing, taxonomy discovery, and non-taxonomic relation extraction. Using this infrastructure, we conduct a large-scale empirical study of OL, evaluating 22 retrieval models and 12 LLMs across domains and tasks. The results converge on a finding that reframes the central challenge of OL: failure modes scale with ontological complexity rather than model size or architectural sophistication. The primary bottleneck is not model capability, but a structural mismatch between how models encode knowledge and how ontologies organize it. These findings establish that effective OL is reachable through the cross-domain, multi-task benchmarking enabled by OntoLearner. OntoLearner is open-source (MIT license) at https://github.com/sciknoworg/OntoLearner/.