Yuan He's Wiki

Yuan He (In Chinese: 何源)

Department of Computer Science

University of Oxford

Hi! I am Yuan He, a PhD candidate in Computer Science, supervised by Professor Ian Horrocks, Professor Bernardo Cuenca Grau, and Dr. Jiaoyan Chen at the University of Oxford. My primary research interests lie in the area of neural-symbolic AI, especially knowledge representation (KR) and natural language processing (NLP). In my PhD (DPhil), I have been working on adapting language models (LMs) to a range of ontology engineering tasks including ontology alignment, completion, embeddings, and more. I am also interested in geometric embeddings and their use in addressing the limitations of LMs and representing logics.

I am developing and maintaining DeepOnto, a Python package for ontology engineering with deep learning and particularly language models.

Google Scholar

Events (recent two years)

{Oct 2023} Won the Best Resource Paper Runner-Up in CIKM-2023. [certificate]
{Sep 2023} One poster paper accepted at ISWC-2023.
{Aug 2023} Two papers accepted at CIKM-2023.
{Aug 2023} Joined the Program Committee of AAAI-2024.
{Jun 2023} Joined the Program Committee of CIKM-2023.
{May 2023} Paper accepted in Findings of ACL-2023.
{Mar 2023} Paper accepted in WWW journal.
{Jan 2023} Teaching KRR classes.
{Jan 2023} Rebuild DeepOnto.
{Oct 2022} Nominated as Best Resource Paper candidate in ISWC-2022. [nomination]
{Oct 2022} Organising the Bio-ML track of OAEI. [track]
{Sep 2022} Paper accepted in DL4KG@ISWC-2022 workshop.
{Aug 2022} Joined the Program Committee of AAAI-2023.
{Jul 2022} Joined the Program Committee of ISWC-2022.
{Jul 2022} Paper accepted at ISWC-2022. [arxiv]
{Jul 2022} Won the Best Research Report Award in ISWS-2022. [certificate]
{Jul 2022} Attending International Semantic Web Summer School (ISWS-2022). [website]
{Feb 2022} Presenting the paper accepted in AAAI-2022. [slides][video]
{Jan 2022} Teaching classes for the Knowledge Representation & Reasoning (KRR) course at Oxford.

Events (past)

{Dec 2021} Started to develop DeepOnto. [repository]
{Dec 2021} Paper accepted in AAAI-2022. [arxiv]
{Dec 2021} Passed the Transfer of Status (for Oxford PhD).
{Oct 2021} Presentation for the paper accepted in OM@ISWC-2021 workshop. [slides]
{Aug 2021} Paper accepted in OM@ISWC-2021 workshop.
{Jan 2021} Started the project: Oxford-SRUK Ontology Alignment.
{Dec 2020} Presentation for the paper accepted in AACL-2020. [slides][video]
{Nov 2020} Teaching Support for MAT Marking at Oxford.

Education

{Oct 2020 - Present}

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

{Sep 2016 - Jul 2020}

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

Publications

Preprint

Yuan He, Jiaoyan Chen, Hang Dong, Ian Horrocks, Carlo Allocca, Taehun Kim, Brahmananda Sapkota. DeepOnto: A Package for Ontology Engineering with Deep Learning. arXiv preprint arXiv:2307.03067 (2023). [preprint]

Conference Paper

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: Proceedings of 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]

Journal Paper

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 111.6 (2023), pp. 653–685. doi: 10.1109/JPROC.2023.3279374. [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 Journal. [preprint][paper]

Workshop Paper

Pour, M. A. N., Algergawy, A., Buche, P., Castro, L. J., Chen, J., Dong, H., Fallatah, O., Faria, D., Fundulaki, I., Hertling, S., He, Y., Horrocks, I., Huschka, M., Ibanescu, L., Ernesto Jiménez-Ruiz, Karam, N., Laadhar, A., Lambrix, P., Li, H., … Zhou, L. Results of the Ontology Alignment Evaluation Initiative 2022. In: The 17th International Workshop on Ontology Matching (OM@ISWC-2022). [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]

Google Scholar

Semantic Scholar

DBLP

Professional Services

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

ACL Rolling Review (ARR)
European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD-2022)

Journal Reviewer

Journal of Bioinformatics.
Journal of Biomedical Semantics.
Journal of Web Semantics .

Organiser

OAEI Bio-ML Track (collocated at ISWC)

Selected Awards

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]

Amateur Works

[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.

Contact

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