Publications

Please see my Google Scholar Profile for an up-to-date list.

(*) denotes equal contribution

2024

Mitigating Heterogeneity in Federated Multimodal Learning with Biomedical Vision-Language Pre-training
Zitao Shuai, Liyue Shen.
ArXiv Preprint, 2024.

Part-aware Personalized Segment Anything Model for Patient-Specific Segmentation
Chenhui Zhao, Liyue Shen.
ArXiv Preprint, 2024.

Solving Inverse Problems with Latent Diffusion Models via Hard Data Consistency
Bowen Song*, Soo Min Kwon*, Zecheng Zhang, Xinyu Hu, Qing Qu, Liyue Shen.
International Conference on Learning Representations (ICLR), 2024. (Spotlight)
[code]

2023

The Emergence of Reproducibility and Consistency in Diffusion Models
Huijie Zhang, Jinfan Zhou, Yifu Lu, Minzhe Guo, Liyue Shen, Qing Qu.
Neural Information Processing Systems (NeurIPS), Diffusion Models Workshop, 2023. (Best Paper Award)

Poisson-Gaussian Holographic Phase Retrieval with Score-based Image Prior
Zongyu Li, Jason Hu, Xiaojian Xu, Liyue Shen, Jeffrey A. Fessler.
Neural Information Processing Systems (NeurIPS), Deep Learning and Inverse Problems Workshop, 2023.

Volumetric MRI with Sparse Sampling for MR-guided 3D Motion Tracking via Sparse Prior-augmented Implicit Neural Representation Learning
Lianli Liu, Liyue Shen, Adam Johansson, James M Balter, Yue Cao, Lucas Vitzthum, Lei Xing.
Medical Physics, 2023.

Super-resolution Biomedical Imaging via Reference-free Statistical Implicit Neural Representation
Siqi Ye, Liyue Shen, Md Tauhidul Islam, Lei Xing.
Physics in Medicine and Biology (PMB), 2023.

PINER: Prior-Informed Implicit Neural Representation Learning for Test-Time Adaptation in Sparse-View CT Reconstruction
Bowen Song, Liyue Shen*, Lei Xing*.
IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), 2023.
[code]

Label-Efficient Self-Supervised Federated Learning for Tackling Data Heterogeneity in Medical Imaging
Rui Yan, Liangqiong Qu, Qingyue Wei, Shih-Cheng Huang, Liyue Shen, Daniel Rubin, Lei Xing, Yuyin Zhou.
IEEE Transactions on Medical Imaging (TMI), 2023.
[code]

Patient-specific Auto-segmentation on Daily kVCT Images for Adaptive Radiotherapy
Yizheng Chen, Michael F Gensheimer, Hilary P Bagshaw, Santino Butler, Lequan Yu, Yuyin Zhou, Liyue Shen, Nataliya Kovalchuk, Murat Surucu, Daniel T Chang, Lei Xing, Bin Han.
International Journal of Radiation Oncology* Biology* Physics, 2023.

Modeling Linear Accelerator (Linac) Beam Data by Implicit Neural Representation Learning for Commissioning and Quality Assurance Applications
Lianli Liu, Liyue Shen, Yong Yang, Emil Schüler, Wei Zhao, Gordon Wetzstein, Lei Xing.
Medical Physics, 2023.

Before 2022

NeRP: Implicit Neural Representation Learning with Prior Embedding for Sparsely Sampled Image Reconstruction
Liyue Shen, John Pauly, Lei Xing.
IEEE Transactions on Neural Networks and Learning Systems (TNNLS), 2022.
[code]

Solving Inverse Problems in Medical Imaging with Score-Based Generative Models
Yang Song*, Liyue Shen*, Lei Xing, Stefano Ermon.
International Conference on Learning Representations (ICLR), 2022.
[code]

Leveraging Data-driven Self-consistency for High-fidelity Gene Expression Recovery
Md Tauhidul Islam, Jen-Yeu Wang, Hongyi Ren, Xiaomeng Li, Masoud Badiei Khuzani, Shengtian Sang, Lequan Yu, Liyue Shen, Wei Zhao, Lei Xing.
Nature Communications, 2022.

A Geometry-Informed Deep Learning Framework for Ultra-Sparse Computed Tomography (CT) Imaging
Liyue Shen, Wei Zhao, Dante Capaldi, John Pauly, Lei Xing.
Computers in Biology and Medicine (CIBM), 2022.

Real Time Volumetric MRI for 3D Motion Tracking via Geometry-Informed Deep Learning
Lianli Liu, Liyue Shen, Adam Johansson, James M Balter, Yue Cao, Lei Xing.
Medical Physics, 2022.

Implicit Neural Representation for Radiation Therapy Dose Distribution
Varun Vasudevan, Liyue Shen, Charles Huang, Cynthia F Chuang, Md Tauhidul Islam, Hongyi Ren, Yong Yang, Peng Dong, Lei Xing.
Physics in Medicine and Biology (PMB), 2022.

Attention-Guided Deep Learning for Gestational Age Prediction using Fetal Brain MRI
Liyue Shen*, Jimmy Zheng*, Edward Lee, Michelle Han, Katie Shpanskaya, Emily McKenna, Dinko Plasto, Courtney Mitchell, Lillian Lai, Carolina Guimaraes, Hisham Dahmoush, Jane Chueh, Safwan Halabi, John Pauly, Lei Xing, Quin Lu, Ozgur Oztekin, Beth Kline-Fath, Kristen Yeom.
Scientific Reports, 2022.
[dataset]

Novel-View X-ray Projection Synthesis through Geometry-Integrated Deep Learning
Liyue Shen, Lequan Yu, Wei Zhao, John Pauly, Lei Xing.
Medical Image Analysis (MedIA), 2021.

GLoRIA: A Multimodal Global-Local Representation Learning Framework for Label-efficient Medical Image Recognition
Shih-Cheng Huang*, Liyue Shen*, Matthew Lungren, Serena Yeung.
International Conference on Computer Vision (ICCV), 2021.
[code]

Artificial Intelligence in Image-guided Radiotherapy: A Review of Treatment Target Localization
Wei Zhao, Liyue Shen, Md Tauhidul Islam, Wenjian Qin, Zhicheng Zhang, Xiaokun Liang, Gaolong Zhang, Shouping Xu, Xiaomeng Li.
Quantitative Imaging in Medicine and Surgery (QIMS), 2021.

Deep Neural Network with Consistency Regularization of Multi-Output Channels for Improved Tumor Detection and Delineation
Hyunseok Seo, Lequan Yu, Hongyi Ren, Xiaomeng Li, Liyue Shen, Lei Xing.
IEEE Transactions on Medical Imaging (TMI), 2021.

Multi-Domain Image Completion for Random Missing Input Data
Liyue Shen, Wentao Zhu, Xiaosong Wang, Lei Xing, John Pauly, Daguang Xu.
IEEE Transactions on Medical Imaging (TMI), 2020.

A Mean-Field Theory for Kernel Alignment with Random Features in Generative Adversarial Networks
Masoud Badiei Khuzani*, Liyue Shen*, Shahin Shahrampour, Lei Xing.
Journal of Machine Learning Research (JMLR) (under revision), 2019.

Patient-Specific Reconstruction of Volumetric Computed Tomography Images from a Single Projection View via Deep Learning
Liyue Shen*, Wei Zhao*, Lei Xing.
Nature Biomedical Engineering, 2019.
[code]

Markerless Pancreatic Tumor Target Localization Enabled by Deep Learning
Wei Zhao, Liyue Shen, Bin Han, Yong Yang, Kai Cheng, Diego AS Toesca, Albert C Koong, Daniel T Chang, Lei Xing.
International Journal of Radiation Oncology Biology Physics, 2019.

A Deep Learning Approach for Dual-Energy CT Imaging Using a Single-Energy CT Data
Wei Zhao, Tianling Lv, Peng Gao, Liyue Shen, Xianjin Dai, Kai Cheng, Mengyu Jia, Yang Chen, Lei Xing.
International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine, 2019.

Harnessing the Power of Deep Learning for Volumetric CT Imaging with Single or Limited Number of Projections
Liyue Shen, Wei Zhao, Lei Xing.
SPIE Medical Imaging, 2019. (Oral)

Automatic Marker-Free Target Positioning and Tracking for Image-Guided Radiotherapy and Interventions
Wei Zhao, Liyue Shen, Yan Wu, Bin Han, Yong Yang, Lei Xing.
SPIE Medical Imaging, 2019. (Oral)

Deep Learning with Attention to Predict Gestational Age of the Fetal Brain
Liyue Shen, Katie Shpanskaya, Edward Lee, Emily McKenna, Maryam Maleki, Quin Lu, Safwan Halabi, John Pauly, Kristen Yeom.
Neural Information Processing Systems (NeurIPS), Machine Learning for Health (ML4H) Workshop, 2018. (Spotlight)
International Society for Magnetic Resonance in Medicine (ISMRM), 2019. (Oral)

Scaling Human-Object Interaction Recognition through Zero-Shot Learning
Liyue Shen, Serena Yeung, Judy Hoffman, Greg Mori, Li Fei-Fei.
IEEE Winter Conference on Applications of Computer Vision (WACV), 2018.

Learning to Learn from Noisy Web Videos
Serena Yeung, Vignesh Ramanathan, Olga Russakovsky, Liyue Shen, Greg Mori, Li Fei-Fei.
IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2018.

Scalable Person Re-identification: A Benchmark
Liang Zheng*, Liyue Shen*, Lu Tian*, Shengjin Wang, Jingdong Wang, Qi Tian.
International Conference on Computer Vision (ICCV), 2015.
[project page] [code] [data]