Qinze Yu(余沁泽)   Ph.D. candidate Department of Computer Science and Engineering CUHK Email: qinze979ATgmail.com ORCID

Biography

I am currently a Ph.D. candidate at the Department of Computer Science and Engineering, The Chinese University of Hong Kong (CUHK), supervised by Prof. Yu Li. Before that, I obtained my Bachelor's degree from UESTC in 2022, supervised by Prof. Xucheng Luo.

Research Interests

AI for Drug Discovery, Molecular Modeling, Deep Learning, Bioinformatics.

Selected Awards

2019 National Scholarship of China

Publications (*equal contribution, ^#corresponding)

10. Uncovering evolutionarily remote and highly potent antimicrobial peptides with protein language models
    Q.Yu*, H. Liu*, H. Shi*, Y. Abdrakhmanov, J. Shen, C. Zhang, Z. Dong, L. Zong, L. Si, L. Dai^#, Y. Li^#
    Nature Biomedical Engineering, 2025.[Accepted]
11. Exploring Functional Insights into the Human Gut Microbiome via the Structural Proteome
    H. Liu*, J. Shen*, Z. Zhang*, J. Wang*, C. Zhang*, L. Zheng, H. Ni, L. Hong, J. Zhang, D. Xue, J. Chen, Q.Yu, Z. Qu, Y. Ma, T. Si, L. Zheng, S. Wang, C. Jiang, Y. Li^#, K. Wang^#, L. Dai^#
    Cell Host & Microbe, 2025.[Full text]
12. GS-DTI: A Graph-Structure-Aware Framework Leveraging Large Language Models for Drug–Target Interaction Prediction
    Q.Yu, C. Zhou, J. Jiang, X. Shi, Y. Li^#
    Bioinformatics, 2025.[Full text]
13. The MEFIER Score—A Risk Score to Stratify Infective Endocarditis in Patients With Enterococcus faecalis Bacteremia Based on an 11-Year Territory-Wide Cohort
    C.K.C. Lai^#, E. Leung, A.L.H. Lee, Q.Yu, Y. He, Y. Li, R.K.K. Leung, G.C.Y. Lui, T.C.F. Yip, G.L.H. Wong, A.P.W. Lee, R.H.L. Wong, M. Ip
    Open Forum Infectious Diseases, 2025.[Full text]
14. Deep generative design of RNA aptamers using structural predictions
    F.Wong, D.He, A.Krishnan, L.Hong, A.Z.Wang, J.Wang, Z.Hu, S.Omori, A.Li, J.Rao, Q.Yu, W.Jin, T.Zhang, K.Ilia, J.X.Chen, S.Zheng, I.King, Y.Li^#, J.J.Collins^#
    Nature Computational Science, 2024.[Full text]
15. Revisiting the Epitaxial Growth Mechanism of 2D TMDC Single Crystals
    C.Li, F.Zheng, J.Min, N.Yang, Y.Chang, H.Liu, Y.Zhang, P.Yang, Q.Yu, Y.Li, Z.Luo, A.Alijarb, K.Shih, J.Huang, L.Li^#, Y.Wan^#
    Advanced Materials, 2024.[Full text]
16. A machine learning-based risk score for prediction of infective endocarditis among patients with Staphylococcus aureus bacteraemia - The SABIER score
    C.Lai^#, E.Leung, Y.He, C-C.Cheung, O.Mui, Q.Yu, T.Li, A.Lee, Y.Li, C-Y.Lui
    The Journal of Infectious Diseases, 2024.[Full text]
17. Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model
    J.Shen*, Q.Yu*, S.Chen*, Q.Tan, J.Li, Y.Li^#
    Nature Computational Science, 2023.[Full text]
18. Drug Synergistic Combinations Predictions via Large-Scale Pre-Training and Graph Structure Learning
    Z.Hu*, Q.Yu*, Y.Guo, T.Wang, I.King, X.Gao^#, L.Song^#, Y.Li^#
    RECOMB, 2023.[Full text]
19. Session-based Recommendation Via Contrastive Learning On Heterogeneous Graph
    H.Li, X.Luo^#, Q.Yu, H.Wang
    IEEE Bigdata, 2021.[Full text]

Intern & Work Experience

• Fall, 2024 Research Intern at RIKEN, Yokohama, Japan
  Advisor: Chung-Chau Hon and Ramzan Umarov
• Fall, 2021 Research Assistant at CUHK, Hong Kong, China
  Advisor: Yu Li
• Summer, 2021 Research Assistant at CUHK SZRI, Shenzhen, China
  Advisor: Yu Li

Teaching

TA - BMEG3105: Data analytics for personalized genomics and precision medicine, Fall 2022, Fall 2023, Fall 2024
TA - CSCI3320: Fundamentals of Machine Learning, Spring 2023
TA - ENGG2020: Digital Logic and Systems, Spring 2024