Publications

(Updated June 2024)

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,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 Transactions on Pattern Analysis and Machine Intelligence (TPAMI), 2024
[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 (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


[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

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,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,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] 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] 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,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. 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.

2. 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.

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

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

5. 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.