(Eric) Zhang Chen

I advance AI research and build practical systems for healthcare and drug development.

I’m an AI researcher and builder. My work bridges AI research and real-world applications across healthcare and the pharmaceutical industry. I’ve authored more than 50 peer-reviewed papers and hold multiple US patents. I’ve also mentored over 20 interns, contributing to research publications and product features.

My work spans computer vision, large language and multimodal models, AI agents, and diffusion models. I apply AI to drug discovery, medical imaging, genomics, and the analysis of electronic health records (EHR) and real-world data (RWD). I received my Ph.D. in Bioinformatics from the University of Pennsylvania.

Experience

  1. Director of AI and Machine Learning

    BeOne Medicines

    2025 – PresentBoston, USA

  2. Senior Expert Research Scientist

    United Imaging Intelligence

    2023 – 2025Boston, USA

  3. Expert Research Scientist

    United Imaging Intelligence

    2019 – 2023Boston, USA

  4. Data Scientist

    Dana-Farber Cancer Institute

    2018 – 2019Boston, USA

  5. Data Scientist

    Thomas Jefferson University Hospital

    2016 – 2018Philadelphia, USA

Education

Publications

More on Google Scholar

2025

  1. Adapting vision foundation models for real-time ultrasound image segmentation

    International Conference on Medical Image Computing and Computer-Assisted InterventionPaper

    Xiaoran Zhang, Eric Z Chen, Lin Zhao, Xiao Chen, Yikang Liu, Boris Maihe, James S Duncan, Terrence Chen, Shanhui Sun

  2. Retrieval-augmented few-shot medical image segmentation with foundation models

    IEEE Transactions on Neural Networks and Learning SystemsPaper

    Lin Zhao, Xiao Chen, Eric Z Chen, Yikang Liu, Terrence Chen, Shanhui Sun

  3. Label-Efficient Data Augmentation with Video Diffusion Models for Guidewire Segmentation in Cardiac Fluoroscopy

    Proceedings of the AAAI Conference on Artificial IntelligencePaper

    Shaoyan Pan, Yikang Liu, Lin Zhao, Eric Z Chen, Xiao Chen, Terrence Chen, Shanhui Sun

  4. DiffDenoise: Self-Supervised Medical Image Denoising with Conditional Diffusion Models

    arXiv preprint arXiv:2504.00264Paper

    Basar Demir, Yikang Liu, Xiao Chen, Eric Z Chen, Lin Zhao, Boris Mailhe, Terrence Chen, Shanhui Sun

  5. Leveraging Diffusion Model and Image Foundation Model for Improved Correspondence Matching in Coronary Angiography

    arXiv preprint arXiv:2504.00191Paper

    Lin Zhao, Xin Yu, Yikang Liu, Xiao Chen, Eric Z Chen, Terrence Chen, Shanhui Sun

  6. No Annotate Again (NAA): Realistic Image and Annotation Synthesis for Multi-Contrast MRI through Diffusion without Paired Data

    ISMRM Annual Meeting, Abstract 3984Paper

    Xiao Chen, Chen Li, Eric Zhang Chen, Yikang Liu, Lin Zhao, Terrence Chen, Shanhui Sun

2024

  1. SemiHVision: Enhancing Medical Multimodal Models with a Semi-Human Annotated Dataset and Fine-Tuned Instruction Generation

    arXiv preprint arXiv:2410.14948Paper

    Junda Wang, Yujan Ting, Eric Z Chen, Hieu Tran, Hong Yu, Weijing Huang, Terrence Chen

  2. Auxiliary Input in Training: Incorporating Catheter Features into Deep Learning Models for ECG-Free Dynamic Coronary Roadmapping

    International Conference on Medical Image Computing and Computer-Assisted InterventionPaper

    Yikang Liu, Lin Zhao, Eric Z Chen, Xiao Chen, Terrence Chen, Shanhui Sun

  3. Spatiotemporal Diffusion Model with Paired Sampling for Accelerated Cardiac Cine MRI

    arXiv preprint arXiv:2403.08758Paper

    Shihan Qiu, Shaoyan Pan, Yikang Liu, Lin Zhao, Jian Xu, Qi Liu, Terrence Chen, Eric Z Chen, Xiao Chen, Shanhui Sun

  4. Federated Data Model

    arXiv preprint arXiv:2403.08887Paper

    Xiao Chen, Shunan Zhang, Eric Z Chen, Yikang Liu, Lin Zhao, Terrence Chen, Shanhui Sun

  5. Clinically Feasible Diffusion Reconstruction for Highly-Accelerated Cardiac Cine MRI

    arXiv preprint arXiv:2403.08749Paper

    Shihan Qiu, Shaoyan Pan, Yikang Liu, Lin Zhao, Jian Xu, Qi Liu, Terrence Chen, Eric Z Chen, Xiao Chen, Shanhui Sun

2023

  1. Enhancing Cardiac MRI Segmentation via Classifier-Guided Two-Stage Network and All-Slice Information Fusion Transformer

    International Workshop on Applications of Medical AIPaper

    Zihao Chen, Xiao Chen, Yikang Liu, Eric Z Chen, Terrence Chen, Shanhui Sun

  2. Computationally Efficient 3D MRI Reconstruction with Adaptive MLP

    International Conference on Medical Image Computing and Computer-Assisted InterventionPaper

    Eric Z Chen, Chi Zhang, Xiao Chen, Yikang Liu, Terrence Chen, Shanhui Sun

  3. From Compressed‐Sensing to Deep Learning MR: Comparative Biventricular Cardiac Function Analysis in a Patient Cohort

    Journal of Magnetic Resonance ImagingPaper

    Xianghu Yan, Yi Luo, Xiao Chen, Eric Z Chen, Qi Liu, Lixian Zou, Yuwei Bao, Lu Huang, Liming Xia

  4. An unsupervised framework for joint mri super resolution and gibbs artifact removal

    International Conference on Information Processing in Medical ImagingPaper

    Yikang Liu, Eric Z Chen, Xiao Chen, Terrence Chen, Shanhui Sun

  6. Dynamic MLP for MRI Reconstruction

    arXiv preprint arXiv:2301.08868Paper

    Chi Zhang, Eric Z Chen, Xiao Chen, Yikang Liu, Terrence Chen, Shanhui Sun

  7. Holistic Multi-Slice Framework for Dynamic Simultaneous Multi-Slice MRI Reconstruction

    arXiv preprint arXiv:2301.01355Paper

    Daniel H Pak, Xiao Chen, Eric Z Chen, Yikang Liu, Terrence Chen, Shanhui Sun

  8. Deep learning acceleration and reconstruction for single-channel signals

    the annual meeting of ISMRM. Toronto, ON, Canada.[Google Scholar]Paper

    Yongquan Ye, Zhongqi Zhang, Eric Z Chen, Xiao Chen, Shanhui Sun, Jian Xu

  9. Real-time MRI using deep learning in gastroesophageal reflux disease: a feasibility study

    ISMRM Annual Meeting, Abstract 0505Paper

    Qing Liu, Qi Liu, Jing Li, Eric Z Chen, Zhongqi Zhang, Xiao Chen, Shanhui Sun, Jian Xu, Haoran Sun

2022

  1. Robust Landmark-Based Stent Tracking in X-ray Fluoroscopy

    European Conference on Computer VisionPaper

    Luojie Huang, Yikang Liu, Li Chen, Eric Z Chen, Xiao Chen, Shanhui Sun

  2. JoJoNet: Joint-contrast and Joint-sampling-and-reconstruction Network for Multi-contrast MRI

    arXiv preprint arXiv:2210.12548Paper

    Lin Zhao, Xiao Chen, Eric Z Chen, Yikang Liu, Dinggang Shen, Terrence Chen, Shanhui Sun

  3. Flow-Based Visual Quality Enhancer for Super-Resolution Magnetic Resonance Spectroscopic Imaging

    MICCAI Workshop on Deep Generative ModelsPaper

    Siyuan Dong, Gilbert Hangel, Eric Z Chen, Shanhui Sun, Wolfgang Bogner, Georg Widhalm, Chenyu You, John A Onofrey, Robin de Graaf, James S Duncan

  4. Invertible sharpening network for MRI reconstruction enhancement

    International Conference on Medical Image Computing and Computer-Assisted InterventionPaper

    Siyuan Dong, Eric Z Chen, Lin Zhao, Xiao Chen, Yikang Liu, Terrence Chen, Shanhui Sun

  5. Deep Statistic Shape Model for Myocardium Segmentation

    arXiv preprint arXiv:2207.10607Paper

    Xiaoling Hu, Xiao Chen, Yikang Liu, Eric Z Chen, Terrence Chen, Shanhui Sun

  6. Toward clinically applicable 3-dimensional tooth segmentation via deep learning

    Journal of dental researchPaper

    J Hao, W Liao, YL Zhang, J Peng, Z Zhao, Z Chen, BW Zhou, Y Feng, B Fang, ZZ Liu, ZH Zhao

  7. Pyramid convolutional RNN for MRI image reconstruction

    IEEE Transactions on Medical ImagingPaper

    Eric Z Chen, Puyang Wang, Xiao Chen, Terrence Chen, Shanhui Sun

  8. Cascaded parallel imaging for 3D deep learning reconstruction

    ISMRMPaper

    Jingyuan Lyu, Yongquan Ye, Zhongqi Zhang, Jian Xu, Xiao Chen, Terrence Chen, Shanhui Sun, Eric Z Chen

  9. Accelerated Multiband Cine Cardiac Magnetic Resonance Imaging using Deep Learning

    ISMRMPaper

    Xiao Chen, Yuan Zheng, Eric Z Chen, Zhongqi Zhang, Yu Ding, Jian Xu, Terrence Chen, Shanhui Sun

2021

  1. Accelerating 3D MULTIPLEX MRI Reconstruction with Deep Learning

    arXiv preprint arXiv:2105.08163Paper

    Eric Z Chen, Yongquan Ye, Xiao Chen, Jingyuan Lyu, Zhongqi Zhang, Yichen Hu, Terrence Chen, Jian Xu, Shanhui Sun

  2. Cardiac Functional Analysis with Cine MRI via Deep Learning Reconstruction

    arXiv preprint arXiv:2105.08157Paper

    Eric Z Chen, Xiao Chen, Jingyuan Lyu, Qi Liu, Zhongqi Zhang, Yu Ding, Shuheng Zhang, Terrence Chen, Jian Xu, Shanhui Sun

  3. Multi-scale neural odes for 3d medical image registration

    Medical Image Computing and Computer Assisted Intervention–MICCAI 2021: 24th International Conference, Strasbourg, France, September 27–October 1, 2021, Proceedings, Part IV 24Paper

    Junshen Xu, Eric Z Chen, Xiao Chen, Terrence Chen, Shanhui Sun

  4. Evaluation of the robustness of learned MR image reconstruction to systematic deviations between training and test data for the models from the fastMRI challenge

    Machine Learning for Medical Image Reconstruction: 4th International Workshop, MLMIR 2021, Held in Conjunction with MICCAI 2021, Strasbourg, France, October 1, 2021, Proceedings 4Paper

    Patricia M Johnson, Geunu Jeong, Kerstin Hammernik, Jo Schlemper, Chen Qin, Jinming Duan, Daniel Rueckert, Jingu Lee, Nicola Pezzotti, Elwin De Weerdt, Sahar Yousefi, Mohamed S Elmahdy, Jeroen Hendrikus Franciscus Van Gemert, Christophe Schülke, Mariya Doneva, Tim Nielsen, Sergey Kastryulin, Boudewijn PF Lelieveldt, Matthias JP Van Osch, Marius Staring, Eric Z Chen, Puyang Wang, Xiao Chen, Terrence Chen, Vishal M Patel, Shanhui Sun, Hyungseob Shin, Yohan Jun, Taejoon Eo, Sewon Kim, Taeseong Kim, Dosik Hwang, Patrick Putzky, Dimitrios Karkalousos, Jonas Teuwen, Nikita Miriakov, Bart Bakker, Matthan Caan, Max Welling, Matthew J Muckley, Florian Knoll

  5. Measure Anatomical Thickness from Cardiac MRI with Deep Neural Networks

    Statistical Atlases and Computational Models of the Heart. M&Ms and EMIDEC Challenges: 11th International Workshop, STACOM 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 4, 2020, Revised Selected Papers 11Paper

    Qiaoying Huang, Eric Z Chen, Hanchao Yu, Yimo Guo, Terrence Chen, Dimitris Metaxas, Shanhui Sun

2020

  1. Clinically applicable system for 3D teeth segmentation in intraoral scans using deep learning

    Paper

    Jin Hao, Wen Liao, Yueling Zhang, Peilin Li, Jianru Yi, Jerry Peng, Zeu Zhao, Zhang Chen, Wenxuan Shi, Tingyu Chen, Bowen Zhou, Yang Feng, Bing Fang, Haoji Hu, Howard Yang, Erping Li, Zuozhu Liu, Zhihe Zhao

  2. Mitochondrial dysfunction in inflammatory bowel disease alters intestinal epithelial metabolism of hepatic acylcarnitines

    The Journal of Clinical InvestigationPaper

    Sarah A Smith, Sayaka A Ogawa, Lillian Chau, Kelly A Whelan, Kathryn E Hamilton, Jie Chen, Lu Tan, Eric Z Chen, Sue Keilbaugh, Franz Fogt, Meenakshi Bewtra, Jonathan Braun, Ramnik J Xavier, Clary B Clish, Barry Slaff, Aalim M Weljie, Frederic D Bushman, James D Lewis, Hongzhe Li, Stephen R Master, Michael J Bennett, Hiroshi Nakagawa, Gary D Wu

  3. Anatomy-Aware Cardiac Motion

    Machine Learning in Medical Imaging: 11th International Workshop, MLMI 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 4, 2020, ProceedingsPaper

    Pingjun Chen, Xiao Chen, Eric Z Chen, Hanchao Yu

  4. Anatomy-aware cardiac motion estimation

    International workshop on machine learning in medical imagingPaper

    Pingjun Chen, Xiao Chen, Eric Z Chen, Hanchao Yu, Terrence Chen, Shanhui Sun

  5. Real-Time Cardiac Cine MRI with Residual Convolutional Recurrent Neural Network

    arXiv preprint arXiv:2008.05044; ISMRMPaper

    Eric Z Chen, Xiao Chen, Jingyuan Lyu, Yuan Zheng, Terrence Chen, Jian Xu, Shanhui Sun

  6. MRI image reconstruction via learning optimization using neural ODEs

    Medical Image Computing and Computer Assisted Intervention–MICCAI 2020: 23rd International Conference, Lima, Peru, October 4–8, 2020, Proceedings, Part II 23Paper

    Eric Z Chen, Terrence Chen, Shanhui Sun

2019

  1. Pyramid convolutional RNN for MRI reconstruction

    arXiv preprint arXiv:1912.00543Paper

    Puyang Wang, Eric Z Chen, Terrence Chen, Vishal M Patel, Shanhui Sun

  2. Skin Lesion Segmentation with C-UNet

    2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)Paper

    Junyan Wu, Eric Z Chen, Ruichen Rong, Xiaoxiao Li, Dong Xu, Hongda Jiang

  3. From Deep Learning Towards Finding Skin Lesion Biomarkers

    2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)Paper

    Xiaoxiao Li, Junyan Wu, Eric Z Chen, Hongda Jiang

  4. Lesion Attributes Segmentation for Melanoma Detection with Multi-Task U-Net

    2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)PaperCode

    Eric Z Chen, Xu Dong, Xiaoxiao Li, Hongda Jiang, Ruichen Rong, Junyan Wu

  5. Weakly-and semi-supervised graph CNN for identifying basal cell carcinoma on pathological images

    Graph Learning in Medical Imaging: First International Workshop, GLMI 2019, Held in Conjunction with MICCAI 2019, Shenzhen, China, October 17, 2019, Proceedings 1Paper

    Junyan Wu, Jia-Xing Zhong, Eric Z Chen, Jingwei Zhang, Jay J Ye, Limin Yu

  6. Graph Learning in Medical Imaging

    Paper

    Junyan Wu, Jia-Xing Zhong, Eric Z Chen, Jingwei Zhang, Jay J Ye, Limin Yu

2018

  1. What evidence does deep learning model use to classify Skin Lesions?

    arXiv preprint arXiv:1811.01051Paper

    Xiaoxiao Li, Junyan Wu, Eric Z Chen, Hongda Jiang

  2. Skin Lesion Classification Via Combining Deep Learning Features and Clinical Criteria Representations

    bioRxivPaper

    Xiaoxiao Li, Junyan Wu, Hongda Jiang, Eric Z Chen, Xu Dong, Ruichen Rong

  3. Skin Lesion Segmentation with Improved C-UNet Networks

    bioRxivPaper

    Hongda Jiang, Ruichen Rong, Junyan Wu, Xiaoxiao Li, Xu Dong, Eric Z Chen

  4. Lesion Attributes Segmentation for Melanoma Detection with Deep Learning

    bioRxivPaper

    Eric Z Chen, Xu Dong, Junyan Wu, Hongda Jiang, Xiaoxiao Li, Ruichen Rong

2017

  1. A role for bacterial urease in gut dysbiosis and Crohn’s disease

    Science Translational MedicinePaper

    Josephine Ni, Ting-Chin David Shen, Eric Z Chen, Kyle Bittinger, Aubrey Bailey, Manuela Roggiani, Alexandra Sirota-Madi, Elliot S Friedman, Lillian Chau, Andrew Lin, Ilana Nissim, Justin Scott, Abigail Lauder, Christopher Hoffmann, Gloriany Rivas, Lindsey Albenberg, Robert N Baldassano, Jonathan Braun, Ramnik J Xavier, Clary B Clish, Marc Yudkoff, Hongzhe Li, Mark Goulian, Frederic D Bushman, James D Lewis, Gary D Wu

  2. A model-based approach for species abundance quantification based on shotgun metagenomic data

    Statistics in biosciencesPaperCode

    Eric Z Chen, Frederic D Bushman, Hongzhe Li

2016

  2. Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production

    GutPaper

    Gary D Wu, Charlene Compher, Eric Z Chen, Sarah A Smith, Rachana D Shah, Kyle Bittinger, Christel Chehoud, Lindsey G Albenberg, Lisa Nessel, Erin Gilroy, Julie Star, Aalim M Weljie, Harry J Flint, David C Metz, Michael J Bennett, Hongzhe Li, Frederic D Bushman, James D Lewis

2015

  1. Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

    Cell Host & MicrobePaperCode

    James D Lewis, Eric Z Chen, Robert N Baldassano, Anthony R Otley, Anne M Griffiths, Dale Lee, Kyle Bittinger, Aubrey Bailey, Elliot S Friedman, Christian Hoffmann, Lindsey Albenberg, Rohini Sinha, Charlene Compher, Erin Gilroy, Lisa Nessel, Amy Grant, Christel Chehoud, Hongzhe Li, Gary D Wu, Frederic D Bushman

  2. Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease

    Inflammatory bowel diseasesPaper

    Dale Lee, Robert N Baldassano, Anthony R Otley, Lindsey Albenberg, Anne M Griffiths, Charlene Compher, Eric Z Chen, Hongzhe Li, Erin Gilroy, Lisa Nessel, Amy Grant, Christel Chehoud, Frederic D Bushman, Gary D Wu, James D Lewis

  3. Genome Wide Nucleosome Mapping for HSV-1 Shows Nucleosomes Are Deposited at Preferred Positions during Lytic Infection.

    PloS onePaper

    J Oh, IF Sanders, EZ Chen, H Li, JW Tobias, RB Isett, S Penubarthi, H Sun, DA Baldwin, NW Fraser

2012

  1. Genome-wide roles of Foxa2 in directing liver specification

    Journal of molecular cell biologyPaper

    Chenhuan Xu, Xiaowen Lu, Eric Z Chen, Zhiying He, Borjigin Uyunbilig, Guangpeng Li, Yue Ma, Lijian Hui, Bin Xie, Yuan Gao, Xiaoyan Ding, Yiping Hu, Ping Hu, Jing-Dong J Han, Xin Wang

  2. Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: a transplantation model

    Clinical chemistryPaper

    Yama WL Zheng, KC Allen Chan, Hao Sun, Peiyong Jiang, Xiaoxi Su, Eric Z Chen, Fiona MF Lun, Emily CW Hung, Vincent Lee, John Wong, Paul BS Lai, Chi-Kong Li, Rossa WK Chiu, YM Dennis Lo

  3. A Novel YY1-miR-1 Regulatory Circuit in Skeletal Myogenesis Revealed by Genome-Wide Prediction of YY1-miRNA Network

    PLoS ONEPaper

    Leina Lu, Liang Zhou, Eric Z Chen, Kun Sun, Peiyong Jiang, Lijun Wang, Xiaoxi Su, Hao Sun, Huating Wang

2011

  1. Genome-wide identification of TF-miRNA regulatory networks in myogenesis

    2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)Paper

    Leina Lu, Liang Zhou, Eric Z Chen, Kun Sun, Peiyong Jiang, Susie Su, Lijun Wang, Hao Sun, Huating Wang

  2. Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing

    PloS onePaper

    Eric Z Chen, Rossa WK Chiu, Hao Sun, Ranjit Akolekar, KC Allen Chan, Tak Y Leung, Peiyong Jiang, Yama WL Zheng, Fiona MF Lun, Lisa YS Chan, Yongjie Jin, Attie TJI Go, Elizabeth T Lau, William WK To, Wing C Leung, Rebecca YK Tang, Sidney KC Au-Yeung, Helena Lam, Yu Y Kung, Xiuqing Zhang, John MG van Vugt, Ryoko Minekawa, Mary HY Tang, Jun Wang, Cees BM Oudejans, Tze K Lau, Kypros H Nicolaides, YM Dennis Lo

  3. SFRS7-mediated splicing of tau exon 10 is directly regulated by STOX1A in glial cells

    PloS onePaper

    Daan Van Abel, Dennis R Hölzel, Shushant Jain, Fiona MF Lun, Yama WL Zheng, Eric Z Chen, Hao Sun, Rossa WK Chiu, YM Dennis Lo, Marie Van Dijk, Cees BM Oudejans

2010

  1. Methy-Pipe: an integrated bioinformatics data analysis pipeline for whole genome methylome analysis

    2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)Paper

    Peiyong Jiang, Xiaoxi Sun, Eric Z Chen, Kun Sun, Rossa WK Chiu, YM Dennis Lo, Hao Sun

  2. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus

    Science Translational MedicinePaper

    YM Dennis Lo, KC Allen Chan, Hao Sun, Eric Z Chen, Peiyong Jiang, Fiona MF Lun, Yama W Zheng, Tak Y Leung, Tze K Lau, Charles R Cantor, Rossa WK Chiu

  3. Genome-wide mapping of SMAD target genes reveals the role of BMP signaling in embryonic stem cell fate determination

    Genome researchPaper

    Teng Fei, Kai Xia, Zhongwei Li, Bing Zhou, Shanshan Zhu, Hua Chen, Jianping Zhang, Zhang Chen, Huasheng Xiao, Jing-Dong J Han, Ye-Guang Chen

2008

  1. Developmental systems biology flourishing on new technologies

    Journal of Genetics and GenomicsPaper

    Jing-Dong J Han, Yi Liu, Huiling Xue, Kai Xia, Hong Yu, Shanshan Zhu, Zhang Chen, Wei Zhang, Zheng Huang, Chunyu Jin, Bo Xian, Jing Li, Lei Hou, Yixing Han, Chaoqun Niu, Timothy C Alcon