Shuaike Shen 「沈帅克」

I am a first-year PhD student at the Computational Biology Department, part of the School of Computer Science at Carnegie Mellon University, where I work on AI for Science and Computational Biology.

Previously, I completed my undergraduate studies at Mixed Class of Chu Kochen Honors College , Zhejiang University and received an honors degree in Computer Science and Technology in 2025. My advisors are Prof. Chunhua Shen and Hao Chen, who are affiliated to State Key Lab of CAD & CG, Zhejiang University.

Before becoming a PhD student, I had a wonderful research experience at University ofIllinois at Urbana-Champaign and was honored to work with Prof. Ge Liu.

Email  /  Scholar  /  Twitter  /  LinkedIn  /  Github  /  CV (Oct 2025)

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Research Interests

I am keenly interested in research topics associated with AI for Science and various Generative Models. My prior research experience encompasses protein design, molecule design, crystal models and advanced generative models. If you are interested in my research, please feel free to email me at shenshuaike256 at gmail dot com or shuaikes at cs dot cmu dot edu


Publications & Preprints

* denotes equal contribution and † denotes corresponding author.

Research Experience

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Computational Biology Department , Carnegie Mellon University, Pittsburgh, U.S.

Research Assistant
(Aug.2025 - Present), Advisors: Prof. Jian Ma , Prof. Lei Li and Prof. Olexandr Isayev
Working on AI/ML for scientific discovery and computational biology.

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AI for Science Center, Shanghai AI Lab, Shanghai, China

Research Intern
(May.2025 - Aug.2025), Advisors: Dr. Biqing Qi & Dr. Yuqiang Li
Working on LLM for molecular spectra and molecular foundation model.

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Computer Science & Biochemistry, University of Illinois at Urbana-Champaign, Urbana, U.S.

Research Intern
(May.2024 - Mar.2025), Advisors: Prof. Ge Liu & Prof. Nicholas Ching Hai Wu
Working on protein co-design and developing online Reinforcement Learning algorithm for Flow Matching models.

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State Key Lab of CAD & CG, Zhejiang University, Hangzhou, China

Research Assistant
(Oct.2022 - May.2024), Advisors: Prof. Chunhua Shen & Prof. Hao Chen
Working on protein design, biomolecules interaction and material science.

Education

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PhD Student, Carnegie Mellon University

(Aug.2025 - Present)
Computational Biology, Computational Biology Department, School of Computer Science
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Bachelor of Engineering with Honors, Zhejiang University

(Sep.2021 - June.2025)
Computer Science and Technology, Mixed Class of Chu Kochen Honors College

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