Ziqian LIN

Ph.D. Candidate in Computer Science and Engineering, CUHK

Hong Kong SAR, China

Email: linzq.gm [AT] gmail.com · GitHub: Lim-ZQ · Google Scholar: profile

About Me

I am a Ph.D. candidate in the Department of Computer Science and Engineering at The Chinese University of Hong Kong, advised by Prof. Yu Li and Prof. Irwin King. My research focuses on RNA structure prediction and design, diffusion models for biomolecule generation, and biomolecule interactions.

I received my B.Eng. in Artificial Intelligence from Nanjing University, advised by Prof. Zhihua Zhou.

Research Interests

RNA structure prediction and design
Diffusion models for biomolecule generation
Biomolecule interactions

Selected Publications

Google Scholar

[RiboDiffusion] RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models

H. Huang*, Z. Lin*, D. He, L. Hong, Y. Li

ISMB / Bioinformatics, 2024. (acceptance rate 18%)

doi:10.1093/bioinformatics/btae259

Discovering reference-missing cell types in bulk transcriptomics

Y. Fan, Y. Liu, Y. Zhong, Y. Wang, K.-H. Lee, Y. Wang, X. Liu, J. Li, X. Wang, Z. Lin, L. Li, Y. Li

Bioinformatics / ECCB, 2026.

doi:10.1093/bioinformatics/btag412

[DS-ProGen] DS-ProGen: a dual-structure deep language model for functional protein design

Y. Li*, J. Jiang*, Z. Wang*, Z. Lin, D. He, Y. Shan, Y. Shao, J. Li, X. Shi, J. Wang, Y. Chen, Y. Fan, H. Li, Y. Li

AAAI, 2026.

doi:10.1609/aaai.v40i1.37037

[RMSAGen] RMSAGen: Integrating Multiple Sequence Alignment for Function RNA Design

J. Jiang, Y. Chen, Q. Zhang, J. Li, X. Shi, C. Zhou, Z. Lin, J. Wang, D. He, L. Hong, Q. Li, P. Chen, J. Chen, X. Zhang, J. Yuan, T. Zhang, Y. Li

AAAI, 2026.

doi:10.1609/aaai.v40i1.37012

Research Experience

Ph.D. Candidate, CUHK, Hong Kong SAR (Sep. 2024 – Present)

Advisors: Prof. Yu Li and Prof. Irwin King

Lead a diffusion-based RNA design pipeline with agentic orchestration.
Lead an integrative RNA 3D structure prediction tool.

Research Intern, Shanghai Academy of AI for Science, Shanghai (Aug. 2025 – Present)

Advisors: Prof. Yuan Cheng and Dr. Xvyang Liu

Develop RNA foundation models and design tooling.

Research Intern, AIH Group, The Chinese University of Hong Kong (Sep. 2023 – Aug. 2024)

Advisor: Prof. Yu Li

Developed a diffusion model for RNA inverse folding, improving recovery by 10% and diversity by 20% over prior ML methods (ISMB 2024, acceptance rate 18%).

Research Intern, LAMDA-1 Group, Nanjing University (Feb. 2022 – Sep. 2023)

Advisors: Prof. Zhihua Zhou and Prof. Shaoqun Zhang

Developed a contract-bridge AI with abductive-learning bidding and BERT-based play, outperforming Wbridge5 by 20 points on average.

Education

Ph.D. in Computer Science and Engineering, The Chinese University of Hong Kong (Sep. 2024 – Now)
B.Eng. in Artificial Intelligence, Nanjing University (Sep. 2020 – Jun. 2024)

Honors & Scholarships

2024 – Present: Postgraduate Studentship (PGS), The Chinese University of Hong Kong
2024: Outstanding graduate, University level, 10% of about 3000 graduates
2023: Outstanding Student Leader Model, University level, 1% of 13000 students
2023: Outstanding Minority Student, University level, 10 out of 1500 students
2022: National Scholarship, National level, 1 out of 97 students

Academic Service

Reviewer for journals: Science, Cell, Nature Methods, Nature Communications, Communications Biology, Bioinformatics
Reviewer for conferences: RECOMB, NeurIPS, EMNLP, ACL, AAAI

Teaching

BMEG-3105, Data Analytics for Personalized Genomics and Precision Medicine (2024–2026). The course received the Vice-Chancellor's Exemplary Teaching Award 2024, CUHK.
CSCI-5640, Natural Language Processing (2025)
ENGG-1110, Problem Solving By Programming (2024)