Ph.D. Postdoctoral Associate Weill Cornell Medicine Email: yil4033[at]med.cornell.edu

Biography

I am a Postdoctoral Associate at the Department of Population Health Sciences, Weill Cornell Medicine, under the supervision of Prof. Yifan Peng. I obtained my PhD degree at the Department of Computer Science and Engineering (CSE), The Hong Kong University of Science and Technology (HKUST), under the supervision of Prof. Hao Chen and Prof. Kwang-Ting (Tim) Cheng (IEEE Fellow). Before that, I was a full-time researcher in Jarvis Lab at Tencent directed by Dr. Yefeng Zheng (IEEE Fellow). I received my M.E. and B.E. degree from Huazhong University of Science and Technology (HUST) in 2020 and 2016 respectively, under the supervision of Prof. Xin Yang. I also served as a volunteer teacher at Laifeng Middle School Attached to CCNU in 2016-2017.

My research develops data-efficient, trustworthy, and clinically grounded AI for medical imaging and multimodal healthcare. My current interests include medical foundation models, radiology report generation, agentic clinical AI, and learning from limited or imperfect supervision.

* I am on the academic job market for tenure-track faculty positions in medical AI, AI for healthcare, and AI for science.

News

Selected Publications |

✉ indicates corresponding authorship.
Pre-Print

• Deep learning for medical image segmentation: tricks, challenges and future directions.
  Dong Zhang*, Yi Lin*, Hao Chen, Zhuotao Tian, Xin Yang, Jinhui Tang, Kwang Ting Cheng. [arXiv][code]

Journal

• Prompt-guided Foundation Model Tuning for Pathology Image Classification.
  Yi Lin*, Zhengjie Zhu*, Kwang-Ting Cheng, Hao Chen.
  Medical Image Analysis (MedIA), 2026. IF: 14.0 [paper][code]
• Rethinking Boundary Detection in Deep Learning-Based Medical Image Segmentation.
  Yi Lin*, Dong Zhang*, Xiao Fang*, Yufan Chen, Kwang-Ting Cheng, Hao Chen.
  Medical Image Analysis (MedIA), 2025. IF: 10.7 [arXiv][code]
• Boosting Convolution with Efficient MLP-Permutation for Volumetric Medical Image Segmentation.
  Yi Lin*, Xiao Fang*, Dong Zhang, Kwang-Ting Cheng, Hao Chen.
  IEEE Transactions on Medical Imaging (TMI), 2025. IF: 8.9 [arXiv][code]
• LENAS: Learning-based Neural Architecture Search and Ensemble for 3D Radiotherapy Dose Prediction.
  Yi Lin*, Yanfei Liu*, Hao Chen, Xin Yang, Kai Ma, Yefeng Zheng, Kwang-Ting Cheng.
  IEEE Transactions on Cybernetics, 2024. IF: 11.8 [arXiv][code]
  Rank 1st place in Tencent AIMIS Challenge
• BoNuS: Boundary Mining for Nuclei Segmentation with Partial Point Labels.
  Yi Lin*, Zeyu Wang, Dong Zhang, Kwang-Ting Cheng, Hao Chen.
  IEEE Transactions on Medical Imaging (TMI), 2024. IF: 10.6 [arXiv][code]
• Nuclei Segmentation with Point Annotations from Pathology Images via Self-Supervised Learning and Co-Training.
  Yi Lin*, Zhiyong Qu*, Hao Chen, Zhongke Gao, Yuexiang Li, Lili Xia, Kai Ma, Yefeng Zheng, Kwang-Ting Cheng.
  Medical image analysis (MedIA), 2023. IF: 10.9 [arXiv][code]
• Bi-modality medical image synthesis using semi-supervised sequential generative adversarial.
  Xin Yang, Yi Lin^✉, Zhiwei Wang, Xin Li, Kwang-Ting Cheng.
  IEEE Journal of Biomedical and Health Informatics (JBHI), 2019. IF: 4.098 [paper][code]
• Automatic segmentation of fat metaplasia on sacroiliac joint MRI using deep learning.
  Xin Li*, Yi Lin*, Zhuoyao Xie, Zixiao Lu, Liwen Song, Qiang Ye, Menghong Wang, Xiao Fang, Yi He, Hao Chen, Yinghua Zhao.
  Insights into Imaging, 2024. IF: 4.7 [paper][code]
• Deep learning for computational cytology: A survey.
  Hao Jiang, Yanning Zhou, Yi Lin, Ronald CK Chan, Jiang Liu, Hao Chen.
  Medical image analysis (MedIA), 2022. IF: 13.828 [arXiv]
• A Deep Learning Approach to Predict Conductive Hearing Loss in Patients With Otitis Media With Effusion Using Otoscopic Images.
  Junbo Zeng, Weibiao Kang, Suijun Chen, Yi Lin, Wenting Deng, Yajing Wang, Guisheng Chen, Kai Ma, Fei Zhao, Yefeng Zheng, Maojin Liang, Linqi Zeng, Weijie Ye, Peng Li, Yubin Chen, Guoping Chen, Jinliang Gao, Minjian Wu, Yuejia Su, Yiqing Zheng, Yuexin Cai.
  JAMA Otolaryngology–Head & Neck Surgery, 2022. IF: 8.961 [paper]
• Semi-supervised mp-MRI data synthesis with StitchLayer and auxiliary distance maximization.
  Zhiwei Wang, Yi Lin, Kwang-Ting Tim Cheng, Xin Yang.
  Medical image analysis (MedIA), 2020. IF: 8.880 [arXiv]

Conference

• MARCH: Multi-Agent Radiology Clinical Hierarchy for CT Report Generation
  Yi Lin, Yihao Ding, Yonghui Wu, Yifan Peng
  ACL, 2026. [arXiv]

• Few Shot Medical Image Segmentation with Cross Attention Transformer.
  Yi Lin*, Yufan Chen*, Kwang-Ting Cheng, Hao Chen.
  MICCAI, 2023. [arXiv][code]

• Rethinking Boundary Detection in Deep Learning Models for Medical Image Segmentation.
  Yi Lin*, Dong Zhang*, Xiao Fang, Yufan Chen, Kwang-Ting Cheng, Hao Chen.
  IPMI, 2023. [arXiv][code]

• InsMix: Towards Realistic Generative Data Augmentation for Nuclei Instance Segmentation.
  Yi Lin, Zeyu Wang, Kwang-Ting Cheng, Hao Chen.
  MICCAI, 2022. [arXiv][code]

• Seg4Reg+: Consistency Learning Between Spine Segmentation and Cobb Angle Regression.
  Yi Lin, Luyan Liu, Kai Ma, Yefeng Zheng.
  MICCAI, 2021. [arXiv][code]

• Automated pulmonary embolism detection from CTPA images using an end-to-end convolutional neural network.
  Yi Lin, Jianchao Su, Xiang Wang, Xiang Li, Jingen Liu, Kwang-Ting Cheng, Xin Yang.
  MICCAI, 2019. [paper][code]
  Student Travel Award

• Seg4Reg Networks for Automated Spinal Curvature Estimation.
  Yi Lin*, Hong-Yu Zhou*, Kai Ma, Xin Yang, Yefeng Zheng.
  MICCAI workshop, 2019. [paper][code]
  Rank 1st place in Accurate Automated Spinal Curvature Estimation Challenge (AASCE 2019)

• TIM: Temporal Decoupling with Iterative Mutual-Refinement Model for Longitudinal Radiology Report Generation.
  Yiheng Dong*, Yi Lin*, Shilong Huang, Xiyan Yang, Xin Yang
  CVPR, 2026. [paper][code]

Academic Services

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• Journal
  IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI)
  IEEE Transactions on Neural Networks and Learning Systems (TNNLS)
  IEEE Transactions on Cybernetics (TCYB)
  IEEE Transactions on Medical Imaging (TMI)
  IEEE Journal of Biomedical and Health Informatics (JBHI)
  IEEE Transactions on Biomedical Engineering (TBME)
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