Chenyu You
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Publications

(Updated Jul 2025)

For the complete list of publications, please visit Google Scholar, DBLP, and arXiv.

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

* indicates equal contribution.   ** indicates alphabetic author order.   ‡ indicates authors working closely with me.

Selected Publications

2025

    [ML] Beyond Matryoshka: Revisiting Sparse Coding for Adaptive Representation
    Tiansheng Wen*, Yifei Wang*, Zequn Zeng, Zhong Peng, Yudi Su, Xinyang Liu, Bo Chen, Hongwei Liu, Stefanie Jegelka, Chenyu You
    ICML 2025 / Paper / Code / Hugging Face Blog / X (Formerly Twitter)
    Oral Presentation 

    [ML,BI] OTSurv: A Novel Multiple Instance Learning Framework for Survival Prediction with Heterogeneity-aware Optimal Transport
    Qin Ren, Yifan Wang, Ruogu Fang, Haibin Ling, Chenyu You
    MICCAI 2025 / Paper / Code / Hugging Face Collection

    [ML] Why Prompt Design Matters and Works: A Complexity Analysis of Prompt Search Space in LLMs
    Xiang Zhang, Juntai Cao, Jiaqi Wei, Chenyu You, Dujian Ding
    ACL 2025 / Paper / Code / 机器之心

    [ML] UniHGKR: Unified Instruction-aware Heterogeneous Knowledge Retrievers
    Dehai Min, Zhiyang Xu, Guilin Qi, Lifu Huang, Chenyu You
    NAACL 2025 / Paper / Code
    Oral Presentation

    [ML] Uncovering Memorization Effect in the Presence of Spurious Correlations
    Chenyu You*, Haocheng Dai*, Yifei Min*, Jasjeet S. Sekhon, Sarang Joshi, James S. Duncan
    Nature Communications 2025 / Paper / Code

    [ML,BI] Application of Large Language Models in Medicine
    Fenglin Liu, Hongjian Zhou, Boyang Gu, ... Chenyu You, Xian Wu, Yefeng Zheng, Lei Clifton, Zheng Li, Jiebo Luo, David A Clifton
    Nature Reviews Bioengineering 2025 / Paper

    [ML,BI] A Flow-based Truncated Denoising Diffusion Model for Super-resolution Magnetic Resonance Spectroscopic Imaging
    Siyuan Dong*, Zhuotong Cai*, ... Chenyu You, ... Robin A de Graaf, James S Duncan
    Medical Image Analysis 2025 / Paper / Code

    [ML,BI] Style Mixup Enhanced Disentanglement Learning for Unsupervised Domain Adaptation in Medical Image Segmentation
    Zhuotong Cai, Jingmin Xin, Chenyu You, Peiwen Shi, Siyuan Dong, Nicha C Dvornek, Nanning Zheng, James S Duncan
    Medical Image Analysis 2025 / Paper

    [ML,BI] Cross-Modal Conditioned Reconstruction for Language-guided Medical Image Segmentation
    Xiaoshuang Huang‡, Hongxiang Li‡, Meng Cao‡, Long Chen, Chenyu You, Dong An
    IEEE Transactions on Medical Imaging 2025 / Paper / Code

    [ML] Rethinking and Improving Natural Language Generation with Layer-Wise Multi-View Decoding
    Fenglin Liu‡*, Xuancheng Ren*, Guangxiang Zhao, Chenyu You, Xuewei Ma, Xian Wu, Wei Fan, Xu Sun
    ACM Transactions on Knowledge Discovery from Data 2025 / Paper

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
    CVPR 2024 / Paper / Code

    [ML,BI] Segment Anything in Medical Images
    Jun Ma‡, Yuting He‡, Feifei Li‡, Lin Han‡, Chenyu You, Bo Wang
    Nature Communications 2024 / Paper / Code / Highlight Page
    Highlight  / ESI - Top 1% highly cited papers

    [ML,BI] 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 TPAMI 2024 / Paper / Code

    [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 2024 / Paper

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

    [ML,BI] Heteroscedastic Uncertainty Estimation Framework for Unsupervised Registration
    Xiaoran Zhang‡, Daniel H Pak, Shawn S Ahn, Xiaoxiao Li, Chenyu You, Lawrence Staib, Albert J Sinusas, Alex Wong, James S Duncan
    MICCAI 2024 / Paper / Project Page / Code

    [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
    WACV 2024 / Paper

    [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
    WACV 2024 / Paper

    [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
    BMVC 2024 / Paper

    [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
    SaTML 2024 / Paper

    [ML] Multi-Relational Structural Entropy
    Yuwei Cao‡, Hao Peng, Angsheng Li, Chenyu You, Zhifeng Hao, Philip S Yu
    UAI 2024 / Paper

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
    NeurIPS 2023 / Paper / Code / News

    [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
    NeurIPS 2023 / Paper / Code

    [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
    MICCAI 2023 / Paper / Code
    Early Accept 

    [ML,BI] Implicit Anatomical Rendering for Medical Image Segmentation with Stochastic Experts
    Chenyu You, Weicheng Dai, Yifei Min, Lawrence Staib, James S Duncan
    MICCAI 2023 / Paper / Code
    Early Accept 

    [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
    MICCAI 2023 / Paper / Code

    [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
    MICCAI 2023 / Paper

    [ML,BI] Pre-trained Diffusion Models for Plug-and-Play Medical Image Enhancement
    Jun Ma‡, Yuanzhi Zhu, Chenyu You, Bo Wang
    MICCAI 2023 / Paper / Code

    [ML,BI] Bootstrapping Semi-supervised Medical Image Segmentation with Anatomical-aware Contrastive Distillation
    Chenyu You, Weicheng Dai, Yifei Min, Lawrence Staib, James S. Duncan
    IPMI 2023 / Paper / 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
    RecSys 2023 / Paper

    [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
    CIKM 2023 / Paper

    [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
    WACV 2023 / Paper

    [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
    WACV 2023 / Paper

    [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
    BIBM 2023 / Paper

    [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
    MICCAI 2023 / Paper
    Early Accept 

    [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
    MICCAI Workshop 2023 / Paper

    [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
    ACL Findings 2023 / Paper

    [ML] Large Language Models Are Partially Primed in Pronoun Interpretation
    Suet-Ying Lam*, Qingcheng Zeng*‡, Kexun Zhang, Chenyu You, Rob Voigt
    ACL Findings 2023 / Paper

    [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
    Nature Digital Medicine 2023 / Paper

    [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 / Paper

    [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 / Paper

    [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 / Paper

2022

    [ML,BI] Class-Aware Adversarial Transformers for Medical Image Segmentation
    Chenyu You, Ruihan Zhao, Fenglin Liu, Siyuan Dong, Sandeep Chinchali, Ufuk Topcu, Lawrence Staib, James S. Duncan
    NeurIPS 2022 / Paper / News (Chinese)

    [ML,BI] SimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation
    Chenyu You, Weicheng Dai, Yifei Min, Lawrence Staib, James S. Duncan
    IEEE Transactions on Medical Imaging 2022 / Paper

    [ML] KerGNNs: Interpretable Graph Neural Networks with Graph Kernels
    Aosong Feng, Chenyu You, Shiqiang Wang, Leandros Tassiulas
    AAAI 2022 / Paper

    [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
    NeurIPS 2022 / Paper

    [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
    KDD 2022 / Paper

    [ML] End-to-end Spoken Conversational Question Answering: Task, Dataset and Model
    Chenyu You‡, Nuo Chen‡, Fenglin Liu, Shen Ge, Xian Wu, Yuexian Zou
    NAACL Findings 2022 / Paper / 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
    MICCAI 2022 / Paper
    Early Accept 

    [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
    MICCAI 2022 / Paper

    [ML] Sparse Logits Suffice to Fail Knowledge Distillation
    Haoyu Ma, Yifan Huang, Hao Tang, Chenyu You, Deying Kong, Xiaohui Xie
    ICLR Workshop 2022 / Paper

    [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
    MICCAI Workshop 2022 / Paper

    [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
    MICCAI Workshop 2022 / Paper

    [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
    MICCAI Workshop 2022 / Paper

    [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
    WACV 2022 / Paper

2021

    [ML] Self-supervised Contrastive Cross-Modality Representation Learning for Spoken Question Answering
    Chenyu You*, Nuo Chen‡*, Fenglin Liu, Shen Ge, Xian Wu, Yuexian Zou
    EMNLP Findings 2021 / Paper / Code

    [ML] Adaptive Bi-Directional Attention: Exploring Multi-Granularity Representations for Machine Reading Comprehension
    Nuo Chen‡, Fenglin Liu‡, Chenyu You, Peilin Zhou, Yuexian Zou
    ICASSP 2021 / Paper

    [ML] Knowledge Distillation for Improved Accuracy in Spoken Question Answering
    Chenyu You*, Nuo Chen‡*, Yuexian Zou
    ICASSP 2021 / Paper / Code

    [ML] Self-supervised Dialogue Learning for Spoken Conversational Question Answering
    Nuo Chen*, Chenyu You*, Yuexian Zou
    Interspeech 2021 / Paper / Code

    [ML,BI] Auto-Encoding Knowledge Graph for Unsupervised Medical Report Generation
    Fenglin Liu‡, Chenyu You, Xian Wu, Shen Ge, Sheng Wang, Xu Sun
    NeurIPS 2021 / Paper

    [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 2021 / Paper

    [ML] Undistillable: Making A Nasty Teacher That CANNOT teach students
    Haoyu Ma, Tianlong Chen, Ting-Kuei Hu, Chenyu You, Xiaohui Xie, Zhangyang Wang
    ICLR 2021 / Paper / Code
    Spotlight 

    [ML] MRD-Net: Multi-Modal Residual Knowledge Distillation for Spoken Question Answering
    Chenyu You*, Nuo Chen*, Yuexian Zou
    IJCAI 2021 / Paper / Code

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

    [ML] Contextualized Attention-based Knowledge Transfer for Spoken Conversational Question Answering
    Chenyu You*, Nuo Chen*, Yuexian Zou
    Interspeech 2021 / Paper / 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 2020 / Paper / Code
    ESI - Top 1% highly cited papers

    [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 / Paper / Code

    [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
    SPIE Medical Imaging 2020 / Paper

    [ML,BI] Unsupervised Wasserstein Distance Guided Domain Adaptation for 3D Multi-Domain Liver Segmentation
    Chenyu You*, Junlin Yang*, Julius Chapiro, James S Duncan
    MICCAI Workshop 2020 / Paper

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
    SPIE Optical Engineering + Applications 2019 / Paper

    [ML,BI] Super-resolution MRI and CT through GAN-CIRCLE
    Qing Lyu*, Chenyu You*, Hongming Shan, Yi Zhang, Ge Wang
    SPIE Optical Engineering + Applications 2019 / Paper

    [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 / Paper

    [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 2019 / Paper

Preprints


  1. Efficient Interactive 3D Multi-Object Removal
    Jingcheng Ni‡*, Weiguang Zhao*, Daniel Wang, Ziyao Zeng, Chenyu You, Alex Wong, Kaizhu Huang
    arXiv:2501.17636

  2. CoMA: Compositional Human Motion Generation with Multi-modal Agents
    Shanlin Sun‡*, Gabriel De Araujo‡*, Jiaqi Xu‡*, Shenghan Zhou‡*, Hanwen Zhang‡, Ziheng Huang, Chenyu You, Xiaohui Xie
    arXiv:2412.07320 / Project Page / Code

  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

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