Publications

(Updated June 2024)

For the complete list, please see my Google Scholar, DPLB, and arXiv.
* indicates equal contribution
** indicates alphabetic author order
‡ indicates authors working closely with me

ML=Machine Learning/Statistics/Artificial Intelligence, BI=Healthcare/Biomedical Image Analysis/Biomedical Imaging/Bioinformatics, NS=Neuroscience

Selected Publications

2024

    [ML] Calibrating Multi-modal Representations: A Pursuit of Group Robustness without Annotations
    Chenyu You*, Yifei Min*, Weicheng Dai*, Jasjeet S Sekhon, Lawrence Staib, James S Duncan
    IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2024
    [code]

    [ML,BI] Segment Anything in Medical Images
    Jun Ma, Yuting He, Feifei Li, Lin Han, Chenyu You, Bo Wang
    Nature Communications, 2024
    [code]

    [ML] Multi-Relational Structural Entropy
    Yuwei Cao, Hao Peng, Angsheng Li, Chenyu You, Zhifeng Hao, Philip S Yu
    Conference on Uncertainty in Artificial Intelligence (UAI), 2024

    [ML,BI] Medical Image Registration via Neural Fields
    Shanlin Sun, Kun Han, Chenyu You, Hao Tang, Deying Kong, Junayed Naushad, Xiangyi Yan, Haoyu Ma, Pooya Khosravi, James S Duncan, Xiaohui Xie
    Medical Image Analysis (MedIA), 2024

    [NS] Rescuing Missing Data in Connectome-Based Predictive Modeling
    Qinghao Liang, ... Chenyu You, Sahand Negahban, Harrison H Zhou, Joseph Chang, Dustin Scheinost
    Imaging Neuroscience, 2024

    [ML,BI] Heteroscedastic Uncertainty Estimation for Probabilistic Unsupervised Registration of Noisy Medical Images
    Xiaoran Zhang, Daniel H Pak, Shawn S Ahn, Xiaoxiao Li, Chenyu You, Lawrence Staib, Albert J Sinusas, Alex Wong, James S Duncan
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2024

    [ML,BI] Hybrid Neural Diffeomorphic Flow for Shape Representation and Generation via Triplane
    Kun Han, Shanlin Sun, Thanh-Tung Le, Xiangyi Yan, Haoyu Ma, Chenyu You, Xiaohui Xie
    IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2024

    [ML,BI] AFTer-SAM: Adapting SAM With Axial Fusion Transformer for Medical Imaging Segmentation
    Xiangyi Yan, Shanlin Sun, Kun Han, Thanh-Tung Le, Haoyu Ma, Chenyu You, Xiaohui Xie
    IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2024

    [ML,BI] Hybrid-CSR: Coupling Explicit and Implicit Shape Representation for Cortical Surface Reconstruction
    Shanlin Sun, Thanh-Tung Le, Pooya Khosravi, Chenyu You, Kun Han, Haoyu Ma, Deying Kong, Xiangyi Yan, Xiaohui Xie
    British Machine Vision Conference (BMVC), 2024

    [ML,BI] Backdoor Attack on Unpaired Medical Image-Text Foundation Models: A Pilot Study on MedCLIP
    Ruinan Jin, Chun-Yin Huang, Chenyu You, Xiaoxiao Li
    IEEE Conference on Secure and Trustworthy Machine Learning (SaTML), 2024

2023

    [ML,BI] Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective
    Chenyu You, Weicheng Dai, Yifei Min, Fenglin Liu, David A Clifton, S Kevin Zhou, Lawrence Staib, James S Duncan
    Neural Information Processing Systems (NeurIPS), 2023
    [code]

    [ML,BI] Benchmarking Large Language Models on CMExam - A comprehensive Chinese Medical Exam Dataset
    Junling Liu, Peilin Zhou, ... Chenyu You, Zhenhua Guo, Lei Zhu, Michael Lingzhi Li
    Neural Information Processing Systems (NeurIPS Datasets and Benchmarks), 2023
    [code]

    [ML] Large Language Models Are Partially Primed in Pronoun Interpretation
    Suet-Ying Lam*, Qingcheng Zeng*, Kexun Zhang, Chenyu You, Rob Voigt
    Findings of the Association for Computational Linguistics (ACL), 2023

    [ML] Multimodal Prompt Learning for Product Title Generation with Extremely Limited Labels
    Bang Yang*, Fenglin Liu*, Zheng Li, Qingyu Yin, Chenyu You, Bing Yin, Yuexian Zou
    Findings of the Association for Computational Linguistics (ACL), 2023

    [ML,BI] ACTION++: Improving Semi-supervised Medical Image Segmentation with Adaptive Anatomical Contrast
    Chenyu You, Weicheng Dai, Yifei Min, Lawrence Staib, Jas Sekhon, James S Duncan
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023
    [code]

    [ML,BI] Implicit Anatomical Rendering for Medical Image Segmentation with Stochastic Experts
    Chenyu You, Weicheng Dai, Yifei Min, Lawrence Staib, James S Duncan
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023
    [code]

    [ML,BI] Localized Region Contrast for Enhancing Self-supervised Learning in Medical Image Segmentation
    Xiangyi Yan, Junayed Naushad, Chenyu You, Hao Tang, Shanlin Sun, Kun Han, Haoyu Ma, James S Duncan, Xiaohui Xie
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023

    [ML,BI] MedGen3D: A Deep Generative Framework for Paired 3D Image and Mask Generation
    Kun Han, Yifeng Xiong, Chenyu You, Pooya Khosravi, Shanlin Sun, Xiangyi Yan, James S Duncan, Xiaohui Xie
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023

    [ML,BI] Pre-trained Diffusion Models for Plug-and-Play Medical Image Enhancement
    Jun Ma, Yuanzhi Zhu, Chenyu You, Bo Wang
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023

    [ML,BI] Bootstrapping Semi-supervised Medical Image Segmentation with Anatomical-Aware Contrastive Distillation
    Chenyu You, Weicheng Dai, Yifei Min, Lawrence Staib, James S Duncan
    Information Processing in Medical Imaging (IPMI), 2023
    [code]

    [ML] Multi-task Item-attribute Graph Pre-training for Strict Cold-start Item Recommendation
    Yuwei Cao, Liangwei Yang, Chen Wang, Zhiwei Liu, Hao Peng, Chenyu You, Philip S Yu
    Proceedings of the 17th ACM Conference on Recommender Systems (RecSys), 2023

    [ML] Attention Calibration for Transformer-based Sequential Recommendation
    Peilin Zhou, Qichen Ye, Yueqi Xie, Jingqi Gao, Shoujin Wang, Jae Boum Kim, Chenyu You, Sunghun Kim
    Proceedings of the 32nd ACM International Conference on Information and Knowledge Management (RecSys), 2023

    [ML,BI] Diffeomorphic Image Registration With Neural Velocity Field
    Kun Han, Shanlin Sun, Xiangyi Yan, Chenyu You, Hao Tang, Junayed Naushad, Haoyu Ma, Deying Kong, Xiaohui Xie
    IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2023

    [ML,BI] Representation Recovering for Self-Supervised Pre-Training on Medical Images
    Xiangyi Yan, Junayed Naushad, Shanlin Sun, Kun Han, Hao Tang, Deying Kong, Haoyu Ma, Chenyu You, Xiaohui Xie
    IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2023

    [ML,BI] Unsupervised Domain Adaptation by Cross-Prototype Contrastive Learning for Medical Image Segmentation
    Zhuotong Cai, Jingmin Xin, Siyuan Dong, Chenyu You, Peiwen Shi, Tianyi Zeng, Jiazhen Zhang, John A Onofrey, Nanning Zheng, James S Duncan
    IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2023

    [ML,BI] Fast Reconstruction for Deep Learning PET Head Motion Correction
    Tianyi Zeng, Jiazhen Zhang, Eléonore V Lieffrig, ... Chenyu You, Mika Naganawa, Yihuan Lu, John A Onofrey
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023

    [ML,BI] Cross-Attention for Improved Motion Correction in Brain PET
    Zhuotong Cai, Tianyi Zeng, Eléonore V Lieffrig, ... Chenyu You, ... James S Duncan, John A Onofrey
    Machine Learning in Clinical Neuroimaging Workshop, MICCAI 2023

    [ML,BI] A Medical Multimodal Large Language Model for Future Pandemics
    Fenglin Liu, Tingting Zhu, Xian Wu, Bang Yang, Chenyu You, Chenyang Wang, Lei Lu, Zhangdaihong Liu, Yefeng Zheng, Xu Sun, Yang Yang, Lei Clifton, David A Clifton
    NPJ Digital Medicine, 2023

    [ML,BI] A Multiclass Radiomics Method–Based WHO Severity Scale for Improving COVID-19 Patient Assessment and Disease Characterization From CT Scans
    John Anderson Garcia Henao, ... Chenyu You, ... James S Duncan, Mauricio Reyes, Alexander Poellinger
    Investigative Radiology, 2023

    [ML,BI] MARGANVAC: Metal Artifact Reduction Method based on Generative Adversarial Network with Variable Constraints
    Guang Li, Longyin Ji, Chenyu You, Shuai Gao, Langrui Zhou, Keshu Bai, Shouhua Luo, Ning Gu
    Physics in Medicine & Biology, 2023

    [BI] A Nonconvex Model-based Combined Geometric Calibration Scheme for Micro Cone-Beam CT with Irregular Trajectories
    Guang Li, Xue Chen, Chenyu You, Xinhai Huang, Zhenhao Deng, Shouhua Luo
    Medical Physics, 2023

2022

    [ML,BI] Class-Aware Adversarial Transformers for Medical Image Segmentation
    Chenyu You, Ruihan Zhao, Fenglin Liu, Sandeep Chinchali, Ufuk Topcu, Lawrence Staib, James S Duncan
    Neural Information Processing Systems (NeurIPS), 2022
    [news]

    [ML,BI] SimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation
    Chenyu You, Yuan Zhou, Ruihan Zhao, Lawrence Staib, James S Duncan
    IEEE Transactions on Medical Imaging (TMI), 2022

    [ML] KerGNNs: Interpretable Graph Neural Networks with Graph Kernels
    Aosong Feng, Chenyu You, Shiqiang Wang, Leandros Tassiulas
    Proceedings of the 36th AAAI Conference on Artificial Intelligence (AAAI), 2022

    [ML,BI] Retrieve, Reason, and Refine: Generating Accurate and Faithful Patient Instructions
    Fenglin Liu, Bang Yang, Chenyu You, Xian Wu, Shen Ge, Zhangdaihong Liu, Xu Sun, Yang Yang, David A Clifton
    Neural Information Processing Systems (NeurIPS), 2022

    [ML,BI] Graph-in-Graph Network for Automatic Gene Ontology Description Generation
    Fenglin Liu, Bang Yang, Chenyu You, Xian Wu, Shen Ge, Adelaide Woicik, Sheng Wang
    Proceedings of the 28th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD), 2022

    [ML] End-to-end Spoken Conversational Question Answering: Task, Dataset and Model
    Chenyu You*, Nuo Chen*, Fenglin Liu, Shen Ge, Xian Wu, Yuexian Zou
    Findings of North American Chapter of the Association for Computational Linguistics (NAACL), 2022
    [code]

    [ML,BI] Momentum Contrastive Voxel-wise Representation Learning for Semi-supervised Volumetric Medical Image Segmentation
    Chenyu You, Ruihan Zhao, Lawrence Staib, James S Duncan
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2022

    [ML,BI] Multi-scale Super-Resolution Magnetic Resonance Spectroscopic Imaging with Adjustable Sharpness
    Siyuan Dong, ... Chenyu You, Robin de Graaf, John A Onofrey, James S Duncan
    Medical Image Computing and Computer Assisted Intervention (MICCAI), 2022

    [ML] Sparse Logits Suffice to Fail Knowledge Distillation
    Haoyu Ma, Yifan Huang, Hao Tang, Chenyu You, Deying Kong, Xiaohui Xie
    Privacy, Accountability, Interpretability, Robustness, Reasoning on Structured Data Workshop, ICLR 2022

    [ML,BI] Learning Correspondences of Cardiac Motion from Images Using Biomechanics-Informed Modeling
    Xiaoran Zhang, Chenyu You, Shawn Ahn, Juntang Zhuang, Lawrence Staib, James S Duncan
    Statistical Atlases and Computational Models of the Heart Workshop, MICCAI 2022

    [ML,BI] Flow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging
    Siyuan Dong, ... Chenyu You, John A Onofrey, Robin de Graaf, James S Duncan
    Deep Generative Models Workshop, MICCAI 2022

    [ML,BI] Incremental Learning Meets Transfer Learning: Application to Multi-site Prostate MRI Segmentation
    Chenyu You, Jinlin Xiang, Kun Su, Xiaoran Zhang, Siyuan Dong, John Onofrey, Lawrence Staib, James S Duncan
    Distributed, Collaborative, and Federated Learning Workshop, MICCAI 2022

    [ML] MEGAN: Memory Enhanced Graph Attention Network for Space-Time Video Super-Resolution
    Chenyu You, Lianyi Han, Aosong Feng, Ruihan Zhao, Hui Tang, Wei Fan
    IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2022

2021

    [ML] Self-supervised Contrastive Cross-Modality Representation Learning for Spoken Question Answering
    Chenyu You*, Nuo Chen*, Yuexian Zou
    Findings of Empirical Methods in Natural Language Processing (EMNLP), 2021
    [code]

    [ML] Adaptive Bi-Directional Attention: Exploring Multi-Granularity Representations for Machine Reading Comprehension
    Nuo Chen, Fenglin Liu, Chenyu You, Peilin Zhou, Yuexian Zou
    International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2021

    [ML] Knowledge Distillation for Improved Accuracy in Spoken Question Answering
    Chenyu You*, Nuo Chen*, Yuexian Zou
    International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2021
    [code]

    [ML] Self-supervised Dialogue Learning for Spoken Conversational Question Answering
    Nuo Chen*, Chenyu You*, Yuexian Zou
    Proc. Interspeech, 2021
    [code]

    [ML,BI] Auto-Encoding Knowledge Graph for Unsupervised Medical Report Generation
    Fenglin Liu, Chenyu You, Xian Wu, Shen Ge, Sheng Wang, Xu Sun
    Neural Information Processing Systems (NeurIPS), 2021

    [ML] Aligning Source Visual and Target Language Domains for Unpaired Video Captioning
    Fenglin Liu, Xian Wu, Chenyu You, Shen Ge, Yuexian Zou, Xu Sun
    IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), 2021

    [ML] Undistillable: Making A Nasty Teacher That CANNOT teach students
    Haoyu Ma, Tianlong Chen, Ting-Kuei Hu, Chenyu You, Xiaohui Xie, Zhangyang Wang
    International Conference on Learning Representations (ICLR), 2021 (Spotlight)
    [code]

    [ML] MRD-Net: Multi-Modal Residual Knowledge Distillation for Spoken Question Answering
    Chenyu You*, Nuo Chen*, Yuexian Zou
    Proc. of the 30th International Joint Conference on Artificial Intelligence (IJCAI), 2021
    [code]

    [ML] Semantic Transportation Prototypical Network for Few-Shot Intent Detection
    Weiyuan Xu, Peilin Zhou, Chenyu You, Yuexian Zou
    Proc. Interspeech, 2021

    [ML] Contextualized Attention-based Knowledge Transfer for Spoken Conversational Question Answering
    Chenyu You*, Nuo Chen*, Yuexian Zou
    Proc. Interspeech, 2021
    [code]

2020

    [ML,BI] CT super-resolution GAN constrained by the identical, residual, and cycle learning ensemble (GAN-CIRCLE)
    Chenyu You, ..., Michael W Vannier, Punam K Saha, Eric A Hoffman, Ge Wang
    IEEE Transactions on Medical Imaging (TMI), 2020
    [code]

    [ML,BI] NuSeT: A deep learning tool for reliably separating and analyzing crowded cells
    Linfeng Yang, Rajarshi P Ghosh, J Matthew Franklin, Simon Chen, Chenyu You, Raja R Narayan, Marc L Melcher, Jan T Liphardt
    PLoS Computational Biology, 2020

    [ML,BI] Deep Learning Based High-Resolution Reconstruction of Trabecular Bone Microstructures from Low-Resolution CT Scans using GAN-CIRCLE
    Indranil Guha, Syed Ahmed Nadeem, Chenyu You, Xiaoliu Zhang, Steven M Levy, Ge Wang, James C Torner, Punam K Saha
    Proc. SPIE, 2020

    [ML,BI] Unsupervised Wasserstein Distance Guided Domain Adaptation for 3D Multi-Domain Liver Segmentation
    Chenyu You*, Junlin Yang*, Julius Chapiro, James S Duncan
    Interpretable and Annotation-Efficient Learning for Medical Image Computing Workshop, MICCAI 2020

2019 and Before

    [ML,BI] Low-dose CT via deep CNN with Skip Connection and Network-in-Network
    Chenyu You, Linfeng Yang, Yi Zhang, Ge Wang
    Proc. SPIE, Developments in X-Ray Tomography XII, 2019

    [ML,BI] Super-resolution MRI and CT through GAN-CIRCLE
    Qing Lyu*, Chenyu You*, Hongming Shan, Yi Zhang, Ge Wang
    Proc. SPIE, Developments in X-Ray Tomography XII, 2019

    [BI] A Novel Calibration Method incorporating Nonlinear Optimization and Ball-bearing Markers for Cone-beam CT with a Parameterized Trajectory
    Guang Li, Shouhua Luo, Chenyu You, Matthew Getzin, Liang Zheng, Ge Wang, Ning Gu
    Medical Physics, 2019

    [ML,BI] Structurally-Sensitive Multi-Scale Deep Neural Network for Low-Dose CT Denoising
    Chenyu You, Qingsong Yang, Hongming Shan, Lars Gjesteby, Guang Li, Shenghong Ju, Zhuiyang Zhang, Zhen Zhao, Yi Zhang, Wenxiang Cong, Ge Wang
    IEEE Access, 2018

Preprints


  1. Mine yOur owN Anatomy: Revisiting Medical Image Segmentation with Extremely Limited Labels
    Chenyu You*, Weicheng Dai*, Fenglin Liu, Yifei Min, Xiaoxiao Li, David A. Clifton, Lawrence Staib, James S. Duncan
    IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), 2024 [Major Revision]

  2. LLMRec: Benchmarking Large Language Models on Recommendation Task
    Junling Liu, Chao Liu, Peilin Zhou, Qichen Ye, Dading Chong, Kang Zhou, Yueqi Xie, Yuwei Cao, Shoujin Wang, Chenyu You, Philip S.Yu, arXiv:2308.12241, 2023.

  3. Bridge the Gap between Language models and Tabular Understanding
    Nuo Chen, Linjun Shou, Ming Gong, Jian Pei, Chenyu You, Jianhui Chang, Daxin Jiang, Jia Li, arXiv:2302.09302, 2023.

  4. Exploring and Exploiting Multi-Granularity Representations for Machine Reading Comprehension
    Nuo Chen, Chenyu You, arXiv:2208.08750, 2022.

  5. Good Students Play Big Lottery Better
    Haoyu Ma, Tianlong Chen, Ting-Kuei Hu, Chenyu You, Xiaohui Xie, Zhangyang Wang, arXiv:2101.03255, 2021.

  6. Rethinking and Improving Natural Language Generation with Layer-Wise Multi-View Decoding
    Fenglin Liu, Xuancheng Ren, Guangxiang Zhao, Chenyu You, Xuewei Ma, Xian Wu, Xu Sun, arXiv:2005.08081, 2020.