English-to-Chinese Transliteration with Phonetic Auxiliary Task. - Yuan He 008; Shay B. Cohen (AACL/IJCNLP, 2020)

Biomedical ontology alignment with BERT. - Yuan He 008; Jiaoyan Chen 001; Denvar Antonyrajah; Ian Horrocks 001 (OM@ISWC, 2021)

Low-resource Learning with Knowledge Graphs: A Comprehensive Survey. - Jiaoyan Chen 001; Yuxia Geng; Zhuo Chen 007; Jeff Z. Pan; Yuan He 008; Wen Zhang 015; Ian Horrocks 001; Huajun Chen (CoRR, 2021)

BERTMap: A BERT-Based Ontology Alignment System. - Yuan He 008; Jiaoyan Chen 001; Denvar Antonyrajah; Ian Horrocks 001 (AAAI, 2022)

Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching. - Yuan He 008; Jiaoyan Chen 001; Hang Dong 002; Ernesto Jiménez-Ruiz; Ali Hadian 001; Ian Horrocks 001 (ISWC, 2022)

Results of the Ontology Alignment Evaluation Initiative 2022. - Mina Abd Nikooie Pour; Alsayed Algergawy; Patrice Buche; Leyla Jael Castro; Jiaoyan Chen 001; Hang Dong 002; Omaima Fallatah; Daniel Faria; Irini Fundulaki; Sven Hertling; Yuan He 008; Ian Horrocks 001; et al. (OM@ISWC, 2022)

Contextual Semantic Embeddings for Ontology Subsumption Prediction. - Jiaoyan Chen 001; Yuan He 008; Ernesto Jiménez-Ruiz; Hang Dong 002; Ian Horrocks 001 (CoRR, 2022)

Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching. - Yuan He 008; Jiaoyan Chen 001; Hang Dong 002; Ernesto Jiménez-Ruiz; Ali Hadian 001; Ian Horrocks 001 (Zenodo, 2022)

Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching. - Yuan He 008; Jiaoyan Chen 001; Hang Dong 002; Ernesto Jiménez-Ruiz; Ali Hadian 001; Ian Horrocks 001 (Zenodo, 2022)

Language Model Analysis for Ontology Subsumption Inference. - Yuan He 008; Jiaoyan Chen 001; Ernesto Jiménez-Ruiz; Hang Dong 002; Ian Horrocks 001 (ACL (Findings), 2023)

Ontology Enrichment from Texts: A Biomedical Dataset for Concept Discovery and Placement. - Hang Dong 002; Jiaoyan Chen 001; Yuan He 008; Ian Horrocks 001 (CIKM, 2023)

Reveal the Unknown: Out-of-Knowledge-Base Mention Discovery with Entity Linking. - Hang Dong 002; Jiaoyan Chen 001; Yuan He 008; Yinan Liu 001; Ian Horrocks 001 (CIKM, 2023)

Results of the Ontology Alignment Evaluation Initiative 2023. - Mina Abd Nikooie Pour; Alsayed Algergawy; Patrice Buche; Leyla Jael Castro; Jiaoyan Chen 001; Adrien Coulet; Julien Cufi; Hang Dong 002; Omaima Fallatah; Daniel Faria; Irini Fundulaki; Sven Hertling; et al. (OM@ISWC, 2023)

Exploring Large Language Models for Ontology Alignment. - Yuan He 008; Jiaoyan Chen 001; Hang Dong 002; Ian Horrocks 001 (ISWC (Posters/Demos/Industry), 2023)

OntoLAMA: LAnguage Model Analysis for Ontology Subsumption Inference. - Yuan He 008; Jiaoyan Chen 001; Ernesto Jiménez-Ruiz; Hang Dong 002; Ian Horrocks 001 (Zenodo, 2023)

Ontology Enrichment from Texts (OET): A Biomedical Dataset for Concept Discovery and Placement. - Hang Dong 002; Jiaoyan Chen 001; Yuan He 008; Ian Horrocks 001 (Zenodo, 2023)

Ontology Enrichment from Texts (OET): A Biomedical Dataset for Concept Discovery and Placement. - Hang Dong 002; Jiaoyan Chen 001; Yuan He 008; Ian Horrocks 001 (Zenodo, 2023)

Zero-Shot and Few-Shot Learning With Knowledge Graphs: A Comprehensive Survey. - Jiaoyan Chen 001; Yuxia Geng; Zhuo Chen 007; Jeff Z. Pan; Yuan He 008; Wen Zhang 015; Ian Horrocks 001; Huajun Chen (Proc. IEEE, 2023)

Bio-ML: Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching. - Yuan He 008; Jiaoyan Chen 001; Hang Dong 002; Ernesto Jiménez-Ruiz; Ali Hadian 001; Ian Horrocks 001 (Zenodo, 2023)

Ontology Enrichment from Texts (OET): A Biomedical Dataset for Concept Discovery and Placement. - Hang Dong 002; Jiaoyan Chen 001; Yuan He 008; Ian Horrocks 001 (Zenodo, 2023)

Datasets for Out-of-KB Mention Discovery with Entity Linking. - Hang Dong 002; Jiaoyan Chen 001; Yuan He 008; Yinan Liu 001; Ian Horrocks 001 (Zenodo, 2023)

Contextual semantic embeddings for ontology subsumption prediction. - Jiaoyan Chen 001; Yuan He 008; Yuxia Geng; Ernesto Jiménez-Ruiz; Hang Dong 002; Ian Horrocks 001 (World Wide Web (WWW), 2023)

Ontology Enrichment from Texts (OET): A Biomedical Dataset for Concept Discovery and Placement. - Hang Dong 002; Jiaoyan Chen 001; Yuan He 008; Ian Horrocks 001 (Zenodo, 2023)

A Language Model Based Framework for New Concept Placement in Ontologies. - Hang Dong 002; Jiaoyan Chen 001; Yuan He 008; Yongsheng Gao 005; Ian Horrocks 001 (ESWC (1), 2024)

Language Models as Hierarchy Encoders. - Yuan He 008; Moy Yuan; Jiaoyan Chen 001; Ian Horrocks 001 (NeurIPS, 2024)

Results of the Ontology Alignment Evaluation Initiative 2024. - Mina Abd Nikooie Pour; Alsayed Algergawy; Eva Blomqvist; Patrice Buche; Jiaoyan Chen 001; Adrien Coulet; Julien Cufi; Hang Dong 002; Daniel Faria; Lucas Ferraz; Pedro Giesteira Cotovio; Yuan He 008; et al. (OM@ISWC, 2024)

Language Models as Hierarchy Encoders. - Yuan He 008; Zhangdie Yuan; Jiaoyan Chen 001; Ian Horrocks 001 (CoRR, 2024)

DeepOnto: A Python package for ontology engineering with deep learning. - Yuan He 008; Jiaoyan Chen 001; Hang Dong 002; Ian Horrocks 001; Carlo Allocca; Taehun Kim; Brahmananda Sapkota (Semantic Web, 2024)

Datasets for the Hierarchy Transformer Encoders (HiTs). - Yuan He 008; Zhangdie Yuan; Jiaoyan Chen 001; Ian Horrocks 001 (Zenodo, 2024)

Bio-ML: Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching. - Yuan He 008; Jiaoyan Chen 001; Hang Dong 002; Ernesto Jiménez-Ruiz; Ali Hadian 001; Ian Horrocks 001 (Zenodo, 2024)

Datasets for the Hierarchy Transformer Encoders (HiTs). - Yuan He 008; Zhangdie Yuan; Jiaoyan Chen 001; Ian Horrocks 001 (Zenodo, 2024)

Predicate-Conditional Conformalized Answer Sets for Knowledge Graph Embeddings. - Yuqicheng Zhu; Daniel Hernández 002; Yuan He 008; Zifeng Ding; Bo Xiong; Evgeny Kharlamov; Steffen Staab (ACL (Findings), 2025)

DyGMamba: Efficiently Modeling Long-Term Temporal Dependency on Continuous-Time Dynamic Graphs with State Space Models. - Zifeng Ding; Yifeng Li; Yuan He 008; Antonio Norelli; Jingcheng Wu; Volker Tresp; Michael M. Bronstein; Yunpu Ma (Trans. Mach. Learn. Res., 2025)

Supposedly Equivalent Facts That Aren't? Entity Frequency in Pre-training Induces Asymmetry in LLMs. - Yuan He 008; Bailan He; Zifeng Ding; Alisia Maria Lupidi; Yuqicheng Zhu; Shuo Chen 014; Caiqi Zhang; Jiaoyan Chen 001; Yunpu Ma; Volker Tresp; Ian Horrocks 001 (CoRR, 2025)

Evaluating Knowledge Graph Based Retrieval Augmented Generation Methods under Knowledge Incompleteness. - Dongzhuoran Zhou; Yuqicheng Zhu; Yuan He 008; Jiaoyan Chen 001; Evgeny Kharlamov; Steffen Staab (CoRR, 2025)

Distilling Tool Knowledge into Language Models via Back-Translated Traces. - Xingyue Huang; Xianglong Hu; Zifeng Ding; Yuan He 008; Rishabh; Waleed Alzarooni; Ziyu Ye; Wendong Fan; Bailan He; Haige Bo; Changran Hu; Guohao Li 001 (CoRR, 2025)

Language Models as Ontology Encoders. - Hui Yang; Jiaoyan Chen 001; Yuan He 008; Yongsheng Gao 005; Ian Horrocks 001 (CoRR, 2025)

Ontology Embedding: A Survey of Methods, Applications and Resources. - Jiaoyan Chen 001; Olga Mashkova; Fernando Zhapa-Camacho; Robert Hoehndorf; Yuan He 008; Ian Horrocks 001 (IEEE Trans. Knowl. Data Eng., 2025)

What Breaks Knowledge Graph based RAG? Empirical Insights into Reasoning under Incomplete Knowledge. - Dongzhuoran Zhou; Yuqicheng Zhu; Xiaxia Wang; Hongkuan Zhou; Yuan He 008; Jiaoyan Chen; Steffen Staab; Evgeny Kharlamov (CoRR, 2025)