arXiv AI By Hamed Babaei Giglou, S\"oren Auer, Jennifer D'Souza

When Does Bigger Help? A Controlled Study of LLM Scale for Ontology Learning

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arXiv AI
Oct 2

LLM-Assisted Discovery of Typed Semantic Links for Ontology Network Construction

The paper presents an automated framework for building ontology networks by discovering typed semantic links between concepts across domains. It uses domain‑adapted DistilBERT embeddings, clustering to prune candidates, and GPT‑4o for generating interpretable relationships, reducing 800k raw pairs to 95k high‑quality candidates. Human validation on 429 links shows an 80.19% precision and 0.890 F1, outperforming five similarity‑based baselines and demonstrating the need for LLM reasoning in ontology link construction.

By Nouha Hayouni, Sheeba Samuel, Alsayed Algergawy
arXiv Computation and Language
Sep 10

OntologyAligner: Ontology-Aligned Retrieval and Hierarchy-Guided Large Language Model Reranking for Biomedical Ontology Normalization

arXiv:2609.10055v1 Announce Type: cross Abstract: Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical dat...

By Jie Song, Zhichuan Xu, Ziyu Lu, Meng Xiao, Cheng Bi, Yuxin Zhang, Xin Zheng, Xiaoran Li, Qiongfang Cao, Hao Yang, Bairong Shen
arXiv Machine Learning
Nov 2

Peeling the Matryoshka: Extracting Ontological Structure from Retrieval Embeddings

The paper demonstrates that Matryoshka Representation Learning (MRL) embeddings contain a natural coarse‑to‑fine hierarchy, with prefix length aligning to gold taxonomy granularity. By training a simple order‑embedding probe called PEEL on these frozen embeddings, the authors can recover high‑fidelity taxonomic DAGs from a concept vocabulary alone, achieving strong results on two OLLM benchmarks and transferring to new domains without target‑edge supervision. The study shows that pre‑trained retrieval embeddings encode a decodable granularity gradient, enabling a minimal probe to extract explicit parent‑child (is‑a) structure.

By Eunchan Kim, Inwhee Joe
arXiv AI
Oct 31

Can LLMs Faithfully Solve Ontology Engineering Tasks? A Mechanistic Interpretability Study

The paper introduces MIOE, a causal‑abstraction benchmark designed to probe how large language models (LLMs) handle ontology engineering tasks such as entity typing and subsumption prediction. Using this benchmark, the authors evaluate several mechanistic interpretability methods—including SAE, DBM, and DAS—on Qwen3‑8B and Qwen3‑4B models, finding that distributed subspace interventions perform best but still mix with auxiliary class‑specific information. The study shows that while ontological predictions are accessible at a mechanistic level, current techniques do not yet isolate a clean, disentangled causal mechanism for ontological knowledge.

By Bohui Zhang, Albert Mero\~no-Pe\~nuela, Elena Simperl