arXiv:2609.08174v1 Announce Type: new
Abstract: We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs a...
By Xiao Yu Cindy Zhang, Wyeth Wasserman, Jian Zhu
arXiv:2610.18672v1 Announce Type: cross
Abstract: Biomedical language models (LMs) provide strong representations for clinical tasks, but they often fail to capture the hierarchical structure among m...
By Ziyang Song, Lia Shen, Yixuan Li, Qincheng Lu, Weihao Li, Haoran Xu, He Zhu, Xinyu Wang, Yue Li
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:2607. 18927v1 Announce Type: new Abstract: We present OntoBook, a method that converts medical ontology structure into pretraining signal for encoder language models.
By Rian Touchent (ALMAnaCH), \'Eric de la Clergerie (ALMAnaCH)
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
Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical va...