About

• I am a Ph.D. candidate at the University of Science and Technology of China (USTC), fortunately supervised by Prof. Shaohua Kevin Zhou and Dr. Peng Xiong. Prior to this, I received my bachelor degree from USTC in 2020 and obtained my master degree from Institute of Computing Technology (ICT) and University of Chinese Academy of Sciences (UCAS) in 2023.
• My research centers on AI biology, with focus on fundamental challenges in RNA modeling and design, including:
  • Structure and function prediction.
  • Multimodal biological foundation model
  • Drug discovery and RNA design for therapeutics.
  • Exploration of functional RNA motifs within non-coding genomic regions.
• I am always welcoming discussions and collaborative opportunities, please feel free to contact me via email. :)

News

• 2026-03:   Honored to be awarded as the Outstanding Graduate of USTC and Anhui Provincial Outstanding Graduate (Ph.D., Class of 2026).
• 2026-01:   NC-Bench (bioRxiv, code) has been accepted by ICLR 2026.
• 2025-08:   We release structRFM (bioRxiv, code), a structure-guided RNA foundation model for structural and functional inference.
• 2025-07:   BPfold has been published in Nature Communications.
• 2024-10:   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, 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

• 2023-09 - present, Ph.D. student of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China (USTC), Suzhou, China
• 2020-09 - 2023-06, Master of Computer Science and Technology, University of Chinese Academy of Sciences (UCAS) & Institute of Computing Technology (ICT), CAS, Beijing, China
• 2016-09 - 2020-06, 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

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

Professional Services

• Journal Reviewers
  • IEEE Transactions on Circuits and Systems for Video Technology (TCSVT)
• Conference Reviewers
  • International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)
• 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
  • 2025-12, Course on Digital Healthcare Technology and Applications, USTC
• Deep generalizable prediction of RNA secondary structure via base pair motif energy
  • 2025-05, The 3rd National Conference on Biomolecular Structure Prediction and Simulation.
• Universal one-shot detection of anatomical landmarks
  • 2023-03, Academic Forum for Graduates, Institute of Computing Technology.