Terminal view

Ziqian LIN

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

Hong Kong SAR, China

Email: linzq.gm [AT] gmail.com  ·  GitHub: Lim-ZQ  ·  Group GitHub: ml4bio  ·  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.

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: 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: 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

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)
• CSCI-5640, Natural Language Processing (2025)
• ENGG-1110, Problem Solving By Programming (2024)