Heqin Zhu (朱河勤)

NC-Bench and NCfold: A Benchmark and Closed-Loop Framework for RNA Non-Canonical Base-Pair Prediction

Heqin Zhu#, Ruifeng Li#, Ao Chang, Mingqian Li, Hongyang Chen*, Peng Xiong*, Shaohua Kevin Zhou*

[bioRxiv] [code] [page] [poster] BibTeX

@inproceedings{NCfold,
  title={NC-Bench and NCfold: A Benchmark and Closed-Loop Framework for RNA Non-Canonical Base-Pair Prediction},
  author={Zhu, Heqin and Li, Ruifeng and Chang, Ao and Li, Mingqian and Chen, Hongyang and Xiong, Peng and Zhou, Shaohua Kevin},
  year={2026},
  booktitle={The Fourteenth International Conference on Learning Representations}
}

Deep generalizable prediction of RNA secondary structure via base pair motif energy

Heqin Zhu, Fenghe Tang, Quan Quan, Ke Chen, Peng Xiong*, Shaohua Kevin Zhou*

[paper] [code] [poster] [poster2] [PyPI] BibTeX

@article{zhu2025deep,
  title={Deep generalizable prediction of RNA secondary structure via base pair motif energy},
  author={Zhu, Heqin and Tang, Fenghe and Quan, Quan and Chen, Ke and Xiong, Peng and Zhou, Shaohua Kevin},
  journal={Nature Communications},
  volume={16},
  number={1},
  pages={5856},
  year={2025},
  publisher={Nature Publishing Group UK London}
}

A fully open structure-guided RNA foundation model for robust structural and functional inference

Heqin Zhu#, Ruifeng Li, Ao Chang, Haobin Chen, Feng Zhang, Fenghe Tang, Tong Ye, Xin Li, Yunjie Gu, Peng Xiong*, Shaohua Kevin Zhou*

[bioRxiv] [code] [PyPI] BibTeX

@article{zhu2025fully,
  title={A fully open structure-guided RNA foundation model for robust structural and functional inference},
  author={Zhu, Heqin and Li, Ruifeng and Chang, Ao and Chen, Haobin and Zhang, Feng and Tang, Fenghe and Ye, Tong and Li, Xin and Gu, Yunjie and Xiong, Peng and Zhou, Shaohua Kevin},
  journal={bioRxiv},
  pages={2025--08},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

IRESeek: structure-informed deep learning method for accurate identification of internal ribosome entry sites in circular RNAs

Feng Zhang#, Heqin Zhu#, Jiayin Gao, Jie Hu, Ke Chen, Shaohua Kevin Zhou*, Peng Xiong*

[paper] [code] BibTeX

@article{zhang2025ireseek,
  title={IRESeek: structure-informed deep learning method for accurate identification of internal ribosome entry sites in circular RNAs},
  author={Zhang, Feng and Zhu, Heqin and Gao, Jiayin and Hu, Jie and Chen, Ke and Zhou, Shaohua Kevin and Xiong, Peng},
  journal={NAR Genomics and Bioinformatics},
  volume={7},
  number={4},
  pages={lqaf210},
  year={2025},
  publisher={Oxford University Press}
}

U-Bench: A Comprehensive Understanding of U-Net through 100-Variant Benchmarking

Fenghe Tang, Chengqi Dong, Wenxin Ma, Zikang Xu, Heqin Zhu, Zihang Jiang, Rongsheng Wang, Yuhao Wang, Chenxu Wu, Shaohua Kevin Zhou

BibTeX

@article{tang2025u,
  title={U-Bench: A Comprehensive Understanding of U-Net through 100-Variant Benchmarking},
  author={Tang, Fenghe and Dong, Chengqi and Ma, Wenxin and Xu, Zikang and Zhu, Heqin and Jiang, Zihang and Wang, Rongsheng and Wang, Yuhao and Wu, Chenxu and Zhou, Shaohua Kevin},
  journal={arXiv preprint arXiv:2510.07041},
  year={2025}
}

Pele scores: pelvic x-ray landmark detection with pelvis extraction and enhancement

Zhen Huang#, Han Li#, Shitong Shao, Heqin Zhu, Huijie Hu, Zhiwei Cheng, Jianji Wang, Shaohua Kevin Zhou

BibTeX

@article{huang2024pele,
  title={Pele scores: pelvic x-ray landmark detection with pelvis extraction and enhancement},
  author={Huang, Zhen and Li, Han and Shao, Shitong and Zhu, Heqin and Hu, Huijie and Cheng, Zhiwei and Wang, Jianji and Zhou, Shaohua Kevin},
  journal={International Journal of Computer Assisted Radiology and Surgery},
  volume={19},
  number={5},
  pages={939--950},
  year={2024},
  publisher={Springer International Publishing Cham}
}

Which images to label for few-shot medical image analysis?

Quan Quan#, Qingsong Yao#, Heqin Zhu, Qiyuan Wang, Shaohua Kevin Zhou

[code] BibTeX

@article{quan2024images,
  title={Which images to label for few-shot medical image analysis?},
  author={Quan, Quan and Yao, Qingsong and Zhu, Heqin and Wang, Qiyuan and Zhou, Shaohua Kevin},
  journal={Medical Image Analysis},
  volume={96},
  pages={103200},
  year={2024},
  publisher={Elsevier}
}

Igu-aug: Information-guided unsupervised augmentation and pixel-wise contrastive learning for medical image analysis

Quan Quan#, Qingsong Yao#, Heqin Zhu, Shaohua Kevin Zhou

[arXiv] [code] BibTeX

@article{quan2024igu,
  title={Igu-aug: Information-guided unsupervised augmentation and pixel-wise contrastive learning for medical image analysis},
  author={Quan, Quan and Yao, Qingsong and Zhu, Heqin and Zhou, Shaohua Kevin},
  journal={IEEE Transactions on Medical Imaging},
  volume={44},
  number={1},
  pages={154--164},
  year={2024},
  publisher={IEEE}
}

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, Shaohua Kevin Zhou

[arXiv] [code] BibTeX

@inproceedings{tang2024hyspark,
  title={Hyspark: Hybrid sparse masking for large scale medical image pre-training},
  author={Tang, Fenghe and Xu, Ronghao and Yao, Qingsong and Fu, Xueming and Quan, Quan and Zhu, Heqin and Liu, Zaiyi and Zhou, Shaohua Kevin},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={330--340},
  year={2024},
  organization={Springer Nature Switzerland Cham}
}

SIX-Net: Spatial-Context Information miX-up for Electrode Landmark Detection

Xinyi Wang, Zikang Xu, Heqin Zhu, Qingsong Yao, Yiyong Sun, Shaohua Kevin Zhou

BibTeX

@inproceedings{wang2024six,
  title={SIX-Net: Spatial-Context Information miX-up for Electrode Landmark Detection},
  author={Wang, Xinyi and Xu, Zikang and Zhu, Heqin and Yao, Qingsong and Sun, Yiyong and Zhou, Shaohua Kevin},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={338--348},
  year={2024},
  organization={Springer Nature Switzerland Cham}
}

Uod: Universal one-shot detection of anatomical landmarks

Heqin Zhu, Quan Quan, Qingsong Yao, Zaiyi Liu, Shaohua Kevin Zhou

[paper] [arXiv] [code] [poster] BibTeX

@inproceedings{zhu2023uod,
  title={Uod: Universal one-shot detection of anatomical landmarks},
  author={Zhu, Heqin and Quan, Quan and Yao, Qingsong and Liu, Zaiyi and Zhou, Shaohua Kevin},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={24--34},
  year={2023},
  organization={Springer Nature Switzerland Cham}
}

Slide-sam: Medical sam meets sliding window

Quan Quan#, Fenghe Tang#, Zikang Xu, Heqin Zhu, Shaohua Kevin Zhou

[code] BibTeX

@article{quan2023slide,
  title={Slide-sam: Medical sam meets sliding window},
  author={Quan, Quan and Tang, Fenghe and Xu, Zikang and Zhu, Heqin and Zhou, Shaohua Kevin},
  journal={arXiv preprint arXiv:2311.10121},
  year={2023}
}

Learning to Localize Cross-Anatomy Landmarks in X-Ray Images with a Universal Model

Heqin Zhu, Qingsong Yao, Li Xiao, Shaohua Kevin Zhou

[paper] [code] BibTeX

@article{zhu2022learning,
  title={Learning to Localize Cross-Anatomy Landmarks in X-Ray Images with a Universal Model},
  author={Zhu, Heqin and Yao, Qingsong and Xiao, Li and Zhou, Shaohua Kevin},
  journal={BME Frontiers},
  volume={2022},
  pages={9765095},
  year={2022}
}

Datr: Domain-adaptive transformer for multi-domain landmark detection

Heqin Zhu, Qingsong Yao, Shaohua Kevin Zhou

BibTeX

@article{zhu2022datr,
  title={Datr: Domain-adaptive transformer for multi-domain landmark detection},
  author={Zhu, Heqin and Yao, Qingsong and Zhou, Shaohua Kevin},
  journal={arXiv preprint arXiv:2203.06433},
  year={2022}
}

DFTR: Depth-supervised hierarchical feature fusion transformer for salient object detection

Heqin Zhu, Xu Sun, Yuexiang Li, Kai Ma, Shaohua Kevin Zhou, Yefeng Zheng*

BibTeX

@article{zhu2022dftr,
  title={DFTR: Depth-supervised hierarchical feature fusion transformer for salient object detection},
  author={Zhu, Heqin and Sun, Xu and Li, Yuexiang and Ma, Kai and Zhou, Shaohua Kevin and Zheng, Yefeng},
  journal={arXiv preprint arXiv:2203.06429},
  year={2022}
}

Relative distance matters for one-shot landmark detection

Qingsong Yao, Jianji Wang, Yihua Sun, Quan Quan, Heqin Zhu, Shaohua Kevin Zhou

BibTeX

@article{yao2022relative,
  title={Relative distance matters for one-shot landmark detection},
  author={Yao, Qingsong and Wang, Jianji and Sun, Yihua and Quan, Quan and Zhu, Heqin and Zhou, Shaohua Kevin},
  journal={arXiv preprint arXiv:2203.01687},
  year={2022}
}

You only learn once: Universal anatomical landmark detection

Heqin Zhu, Qingsong Yao, Li Xiao, Shaohua Kevin Zhou

[paper] [arXiv] [code] BibTeX

@inproceedings{zhu2021you,
  title={You only learn once: Universal anatomical landmark detection},
  author={Zhu, Heqin and Yao, Qingsong and Xiao, Li and Zhou, Shaohua Kevin},
  booktitle={International conference on medical image computing and computer-assisted intervention},
  pages={85--95},
  year={2021},
  organization={Springer International Publishing Cham}
}

Deep learning to segment pelvic bones: large-scale CT datasets and baseline models

Pengbo Liu, Hu Han, Yuanqi Du, Heqin Zhu, Yinhao Li, Feng Gu, Honghu Xiao, Jun Li, Chunpeng Zhao, Li Xiao, Shaohua Kevin Zhou

BibTeX

@article{liu2021deep,
  title={Deep learning to segment pelvic bones: large-scale CT datasets and baseline models},
  author={Liu, Pengbo and Han, Hu and Du, Yuanqi and Zhu, Heqin and Li, Yinhao and Gu, Feng and Xiao, Honghu and Li, Jun and Zhao, Chunpeng and Xiao, Li and Zhou, Shaohua Kevin},
  journal={International Journal of Computer Assisted Radiology and Surgery},
  volume={16},
  number={5},
  pages={749--756},
  year={2021},
  publisher={Springer International Publishing Cham}
}

A 3 DSegNet: anatomy-aware artifact disentanglement and segmentation network for unpaired segmentation, artifact reduction, and modality translation

Yuanyuan Lyu, Haofu Liao, Heqin Zhu, Shaohua Kevin Zhou

BibTeX

@inproceedings{lyu20213,
  title={A 3 DSegNet: anatomy-aware artifact disentanglement and segmentation network for unpaired segmentation, artifact reduction, and modality translation},
  author={Lyu, Yuanyuan and Liao, Haofu and Zhu, Heqin and Zhou, Shaohua Kevin},
  booktitle={International Conference on Information Processing in Medical Imaging},
  pages={360--372},
  year={2021},
  organization={Springer International Publishing Cham}
}

Heqin Zhu (朱河勤)

Publications