About

• I am a postdoctoral researcher at The Chinese University of Hong Kong (CUHK). Prior to this, I obtained my PhD degree from the University of Science and Technology of China (USTC) in 2026 and master degree from Institute of Computing Technology (ICT, Chinese Academy of Sciences (CAS)) and University of Chinese Academy of Sciences (UCAS) in 2023, where I was advised by Prof. Shaohua Kevin Zhou. In 2020, I obtained my bachelor degree from USTC, majoring in Computer Science and Technology. I have had the privilege of collaborating with Prof. Peng Xiong, Prof. Yefeng Zheng.
• My research centers on AI biology, with focus on fundamental challenges in RNA modeling and molecular design, including:
  • Structure and function prediction.
  • Multimodal biological foundation model
  • Unified molecular design
• I am always welcoming discussions and collaborative opportunities, please feel free to contact me via email. :)

News

• 05/2026:   Honored to be awarded the Chinese Academy of Sciences, President’s Excellent Award.
• 03/2026:   Honored to be awarded as the Outstanding Graduate of USTC and Anhui Provincial Outstanding Graduate (Ph.D., Class of 2026).
• 01/2026:   NC-Bench (bioRxiv, code) has been accepted by ICLR 2026.
• 08/2025:   We release structRFM (bioRxiv, code), a structure-guided RNA foundation model for structural and functional inference.
• 07/2025:   BPfold has been published in Nature Communications.
• 10/2024:   We release BPfold (bioRxiv, code), an effective tool for RNA secondary structure prediction.

Publications

(#: equal contribution, *: corresponding author. Selected publications | Google Scholar)

RNA Foundation Model

• A fully open structure-guided RNA foundation model for robust structural and functional inference
  Heqin Zhu, Ruifeng Li, Feng Zhang, Fenghe Tang, Tong Ye, Xin Li, Yunjie Gu, Peng Xiong*, S. Kevin Zhou*  [code][PyPI]

RNA Structure Prediction

• NC-Bench and NCfold for RNA non-canonical base pair prediction
  Heqin Zhu#, Ruifeng Li#, Ao Chang, Mingqian Li, Hongyang Chen*, Peng Xiong*, S. Kevin Zhou*  [code][page]

• Deep generalizable prediction of RNA secondary structure via base pair motif energy
  Heqin Zhu, Fenghe Tang, Quan Quan, Ke Chen, Peng Xiong*, S. Kevin Zhou*  [code][PyPI][poster][poster2]

RNA Function Prediction

• IRESeek: Structure-informed deep learning method for accurate identification of internal ribosome entry sites in circular RNAs
  Feng Zhang#, Heqin Zhu#, Jie Hu, Jiayin Gao, Ke Chen, S. Kevin Zhou*, and Peng Xiong*  [code]

Universal Model & Domain Adaptation

• UOD: universal oneshot detection of anatomical landmark  (Early Accept)
  Heqin Zhu, Quan Quan, Qingsong Yao, Zaiyi Liu, S. Kevin Zhou   [code][poster]
• Learning to localize cross-anatomy landmarks in x-ray images with a universal model
  Heqin Zhu, Qingsong Yao, Li Xiao, S. Kevin Zhou   [code]
• You Only Learn Once: Universal Anatomical Landmark Detection
  Heqin Zhu, Qingsong Yao, Li Xiao, S. Kevin Zhou   [code]

Unsupervised & Self-supervised & Few-shot learning

• Which images to label for few-shot medical image analysis?
  Quan Quan#, Qingsong Yao#, Heqin Zhu, Qiyuan Wang, S. Kevin Zhou   [code]
• IGU-Aug: Information-guided unsupervised augmentation and pixel-wise contrastive learning for medical image analysis
  Quan Quan#, Qingsong Yao#, Heqin Zhu, S. Kevin Zhou   [code]
• Slide-SAM: medical SAM meets sliding window
  Quan Quan#, Fenghe Tang#, Zikang Xu, Heqin Zhu, S. Kevin Zhou   [code]
• Hyspark: Hybrid sparse masking for large scale medical image pre-training
  Fenghe Tang, Ronghao Xu, Qingsong Yao, Xueming Fu, Quan Quan, Heqin Zhu, Zaiyi Liu, S. Kevin Zhou   [code]

Honors and Awards

• 2026, President’s Excellent Award, CAS
• 2026, Provincial Outstanding Graduate (Ph.D., Class of 2026), Anhui Province
• 2026, Outstanding Graduate (Ph.D., Class of 2026), USTC
• 2025, National Scholarship for Doctoral Students, Chinese Ministry of Education
• 2025, Suzhou Industrial Park Scholarship, USTC
• 2020-2025, Graduate Academic Scholarship, UCAS & ICT & USTC
• 2023, Merit Student Award, UCAS & ICT
• 2018-2019, Outstanding Student Award, USTC
• 2017, Institute of Chemistry Excellence Scholarship, USTC

Educations

• 09/2023 - 06/2026, Ph.D. student of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China (USTC), Suzhou, China
• 09/2020 - 06/2023, Master of Computer Science and Technology, University of Chinese Academy of Sciences (UCAS) & Institute of Computing Technology (ICT), CAS, Beijing, China
• 09/2016 - 06/2020, Bachelor of Computer Science and Technology, University of Science and Technology of China (USTC), Hefei, China
  • Hua Xia Talent Program in Computer Science and Technology

Work Experiences

• 07/2021 - 11/2021, Research Intern, Tencent JARVIS Lab, Shenzhen, China
• 09/2019 - 04/2020, Research Intern, Z2sky, Suzhou, China

Professional Services

• Journal Reviewers
  • TCSVT: IEEE Transactions on Circuits and Systems for Video Technology
• Conference Reviewers
  • MICCAI: International Conference on Medical Image Computing and Computer-Assisted Intervention
  • Neurips: Conference on Neural Information Processing Systems
• Teaching Assistants
  • Spring 2024, Teaching Assistant: Biomolecular structure prediction and modeling, USTC
  • Fall 2023, Teaching Assistant: Electronic information openness practices, USTC
• Volunteer Experiences
  • 2024, Volunteer: Medical Augmented Reality Summer School, Suzhou
  • 2023, Volunteer: Dushu Lake Forum Dushu Lake Symposium on Medical lmage Computing, Suzhou

Invited Talks

• Structure-centric AI for RNA modeling
  • 12/2025, Course on Digital Healthcare Technology and Applications, USTC
• Deep generalizable prediction of RNA secondary structure via base pair motif energy
  • 05/2025, The 3rd National Conference on Biomolecular Structure Prediction and Simulation.
• Universal one-shot detection of anatomical landmarks
  • 03/2023, Academic Forum for Graduates, Institute of Computing Technology.