Shuaike Shen

Shuaike Shen

Zhejiang University

🧑🏻‍💻 About me

I am currently a junior undergraduate student from Mixed Class, Chu Kochen Honors College of Zhejiang University, majoring in Computer Science and Technology. My advisors are professor Chunhua Shen and Hao Chen who are affiliated to State Key Lab of CAD & CG, Zhejiang University.

I am keenly interested in research topics associated with Artificial Intelligence assisted Biomolecule Design, Materials&Drug Discovery, and Diffusion Models. My prior research experience encompasses protein design and the prediction of crystal structures and properties. Currently, I am engaged in exploring diverse areas, including co-designing protein structures and sequences, utilizing diffusion models for the creation of innovative crystal structures, protein motif scaffolding, and the design of protein binders.

I am looking for PhD position for Fall 2025 intake, if you have any clues please feel free to contact me.

🔥 News

  • 2024.05:  🎉🎉 One paper has been accepted by ICML’2024
  • 2024.01:  🎉🎉 The first paper I participated in was accepted by ICLR’2024.

📝 Publications

ICML'2024
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Floating Anchor Diffusion Model for Multi-motif Scaffolding

Ke Liu, Shuaike Shen, Weian Mao, Xiaoran Jiao, Zheng Sun, Hao Chen†, Chunhua Shen†

[Project Page] [Code]

Introduction

  • A method to scaffold multiple protein functional motifs without prior knowledge. FADiff is based on a diffusion process which is modified to take into account the movement of the single motifs as independent rigid bodies.
ICLR'2024 spotlight
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De novo Protein Design Using Geometric Vector Field Networks

Weian Mao*, Zheng Sun*, Muzhi Zhu*, Shuaike Shen, Lin Yuanbo Wu, Hao Chen†, Chunhua Shen†

[Code] [Project Page] [Paper]

  • The code will be released after being sorted out.

Introduction

  • We propose a novel structure graph encoder, which can address the atom representation bottleneck observed in traditional IPA encoders.

🌐 Research Interests

AI for Science

  • Protein & Antibody Design

  • AI for Drug Discovery

  • Materials discovery & properties prediction

Generative Models

  • Diffusion models

  • Flow-based models

  • Equivariant Neural Networks

🏯 Research Experience

State Key Lab of CAD & CG, Zhejiang University

Advisors: Prof. Chunhua Shen & Prof. Hao Chen (Oct.2022 - Present)

  • I contributed to a protein project by proposing a novel structure encoder, addressing the atom representation bottleneck observed in traditional IPA encoders. The introduced encoder exhibited superior designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%) compared to the previous model. In both Inverse Folding and Protein Design tasks, this innovative encoder consistently outperformed its predecessor.

📖 Educations

  • 2021.09 - 2025.6 (now), Zhejiang University, Zhejiang
  • 2018.09 - 2021.06, Urumqi No.1 Senior High School, Xinjiang