My research interests revolve around Natural Language Processing, Knowledge Engineering, and Deep Learning, currently with the following specific topics:

• Large Language Models for Knowledge Engineering 

• Large Langauge Model Hallucinations

• Language Model Interpretability

• Embedding and Geometric Deep Learning

• Neural-Symbolic Integration

I am also the main contributor of  several packages and resources, notably: DeepOnto, OAEI Bio-ML, and HierarchyTransformers.

DPhil in Computer Science - University of Oxford - [Fully funded]

Thesis: Language Models for Ontology Engineering

Supervisor(s): Prof. Ian Horrocks,Prof. Bernardo Cuenca Grau, Dr Jiaoyan Chen

BSc (Hons) AI and Maths - University of Edinburgh - [Ranked top]

Thesis: Incorporating Phonetic Information in Model Design for Machine Transliteration

Supervisor(s): Dr. Shay Cohen

• Jiaoyan Chen, Olga Mashkova, Fernando Zhapa-Camacho, Robert Hoehndorf, Yuan He, and Ian Horrocks. Ontology Embedding: A Survey of Methods, Applications and Resources. arXiv preprint arXiv:2406.10964 (2024). [preprint]

• Yuan He, Zhangdie Yuan, Jiaoyan Chen, Ian Horrocks. Language Models as Hierarchy Encoders. arXiv preprint arXiv:2401.11374 (2024). [preprint]

• Yuan He, Jiaoyan Chen, Hang Dong, Ian Horrocks. Exploring Large Language Models for Ontology Alignment. In: Posters and Demos of the 22nd International Semantic Web Conference (ISWC-2023). [arxiv] [paper]

• Hang Dong, Jiaoyan Chen, Yuan He, and Ian Horrocks. Ontology Enrichment from Texts: A Biomedical Dataset for Concept Discovery and Placement. In: Proceedings of the 32nd ACM International Conference on Information and Knowledge Management (CIKM-2023). [preprint] [paper - Best Resource Paper Runner-Up]

• Hang Dong, Jiaoyan Chen, Yuan He, Yinan Liu, and Ian Horrocks. Reveal the Unknown: Out-of-Knowledge-Base Mention Discovery with Entity Linking. In: Proceedings of the 32nd ACM International Conference on Information and Knowledge Management (CIKM-2023). [preprint] [paper]

• Yuan He, Jiaoyan Chen, Ernesto Jiménez-Ruiz, Hang Dong, and Ian Horrocks. Language Model Analysis for Ontology Subsumption Inference. In: Findings of the Association for Computational Linguistics (ACL-2023). [preprint] [paper]

• Yuan He, Jiaoyan Chen, Hang Dong, Ernesto Jiménez-Ruiz, Ali Hadian and Ian Horrocks. Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matching. In: The 21st International Semantic Web Conference (ISWC-2022). [preprint] [paper - Best Resource Paper Candidate]

• Yuan He, Jiaoyan Chen, Denvar Antonyrajah, and Ian Horrocks. BERTMap: A BERT-based Ontology Alignment System. In: Proceedings of the 36th AAAI Conference on Artificial Intelligence (AAAI-2022). [preprint] [paper]

• Yuan He and Shay B. Cohen. English-to-Chinese Transliteration with Phonetic Auxiliary Task.  In: Proceedings of the 1st Conference of the Asia-Pacific Chapter of the Association for Computational Linguistics and the 10th International Joint Conference on Natural Language Processing (AACL-2020). [paper]

• Geyang Song, Yuan He, Brian Sheil, and James Morris. Ground settlement prediction for open caisson shafts in sand using a neural network constrained by empiricism. In: Computers and Geotechnics (2024).

• Jiaoyan Chen, Yuxia Geng, Zhuo Chen, Jeff Z. Pan, Yuan He, Wen Zhang, Ian Horrocks, and Huajun Chen. Zero-Shot and Few-Shot Learning With Knowledge Graphs: A Comprehensive Survey. In: Proceedings of the IEEE (2023). [preprint][paper]

•  Jiaoyan Chen, Yuan He, Ernesto Jiménez-Ruiz, Hang Dong and Ian Horrocks. Contextual Semantic Embeddings for Ontology Subsumption Prediction. In: World Wide Web (2023). [preprint][paper]

• Ryan Brate, Minh-Hoang Dang, Fabian Hoppe, Yuan He, Albert Meroño Peñuela, and Vijay Sadashivaiah. Improving Language Model Predictions via Prompts Enriched with Knowledge Graphs. In: Workshop on Deep Learning for Knowledge Graphs (DL4KG@ISWC-2022). [paper]

• Yuan He, Jiaoyan Chen, Denvar Antonyrajah, and Ian Horrocks. Biomedical Ontology Alignment with BERT. In: The 16th International Workshop on Ontology Matching (OM@ISWC-2021). [paper]

Program Committee Member

• Conference on Information and Knowledge Management (CIKM)

• Association for the Advancement of Artificial Intelligence (AAAI)

• International Semantic Web Conference (ISWC)

• Extended Semantic Web Conference (ESWC)

Conference Reviewer

• International Conference on Learning Representations (ICLR)

• Neural Information Processing Systems (NeurIPS)

• ACL Rolling Review (ARR for ACL, EMNLP, NAACL, etc.) 

• European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD)

Journal Reviewer

• Journal of Bioinformatics

• Journal of Biomedical Semantics

• Journal of Web Semantics

• Semantic Web Journal

• Data Mining and Knowledge Discovery

Organiser

• OAEI Bio-ML Track (collocated at ISWC)

• Best Resource Paper Runner-Up at the ACM International Conference on Information and Knowledge Management (CIKM-2023). [certificate]

• Best Resource Paper Candidate at the International Semantic Web Conference (ISWC-2022). [nomination]

• Best Research Report Award from ISWS-2022. [certificate]

• PhD Scholarship from Samsung Research UK (SRUK). [fully funded]

• Received The 2020 Joint Class Prize (Ranked Top 1) for the degree of BSc in Artificial Intelligence and Mathematics. [certificate]

• [Art] I am an amateur music composer, singer, pianist and novel/poetry/prose writer (specific to Chinese literature).

  • Please check the post here to view the links to my work if you are interested to know me beyond the academic scope. 

• [Sport] I joined the university badminton squad (OuBaC) at Oxford.