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Jiawen Li

Ph.D. Student at SIGS@THU
Tsinghua Shenzhen International Graduate School, Tsinghua University
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About Me

Hi, I am currently a Ph.D. student at the Institute of Biomedical and Health Engineering, Tsinghua Shenzhen International Graduate School (SIGS), Tsinghua University, supervised by Prof. Yonghong He. My research focuses on computational pathology, with a particular emphasis on representation and analyzing gigapixel-level whole-slide images (WSIs). I am also interested in biomedical optical imaging.

I obtained my Bachelor of Science degree from Cuiying Honors College, Lanzhou University in 2021, and obtained my Master of Engineering degree from Open FIESTA at Tsinghua SIGS in 2024. I was honored to receive the China National Scholarship in 2025.

Education

Tsinghua University
Ph.D. student in Biomedical Engineering
Aug 2024 - Present
Tsinghua University
M.E. in Biomedical Engineering
Aug 2021 - June 2024
Lanzhou University
B.S. in Mathematics
Aug 2017 - June 2021

Selected Publications

Conference Papers

E2E-ViT
Turning Pre-Trained Vision Transformers into End-to-End Histopathology Whole Slide Image Models for Survival Prediction
Jiawen Li*, Jiali Hu*, Xitong Ling*, Renao Yan, Yuxuan Chen, Tian Guan#, Yonghong He#
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)2026
Paper
StainNet
StainNet: Scaling Self-Supervised Foundation Models on Immunohistochemistry and Special Stains for Computational Pathology
Jiawen Li*, Jiali Hu*, Xitong Ling*, Yongqiang Lv, Yuxuan Chen, Yizhi Wang, Tian Guan#, Yifei Liu#, Yonghong He#
Medical Imaging with Deep Learning (MIDL)2026
Preprint
MDE-MIL
Multimodal Distillation-Driven Ensemble Learning for Long-Tailed Histopathology Whole Slide Images Analysis
Xitong Ling*, Yifeng Ping*, Jiawen Li*, Jing Peng, Yuxuan Chen, Minxi Ouyang, Yizhi Wang, Yonghong He, Tian Guan#, Xiaoping Liu#, Lianghui Zhu#
IEEE International Symposium on Biomedical Imaging (ISBI)2026
Preprint
SiMLP
Rethinking Slide-Level Adaptation of Pathology Foundation Models
Jiawen Li*, Jiali Hu*, Qiehe Sun*, Xitong Ling, Yuxuan Chen, Renao Yan, Tian Guan, Anjia Han, Chao He#, Yonghong He#
IEEE International Symposium on Biomedical Imaging (ISBI)2026
Paper
ProAlign
Cross-Modal Prototype Allocation: Unsupervised Slide Representation Learning via Patch-Text Contrast in Computational Pathology
Yuxuan Chen*, Jiawen Li*, Jiali Hu*, Xitong Ling, Tian Guan#, Anjia Han#, Yonghong He#
IEEE International Conference on Bioinformatics and Biomedicine (BIBM)2025
Paper
RetMIL
RetMIL: Retentive Multiple Instance Learning for Histopathological Whole Slide Image Classification
Hongbo Chu*, Qiehe Sun*, Jiawen Li*, Yuxuan Chen, Lizhong Zhang, Tian Guan, Anjia Han#, Yonghong He#
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)2024
Paper
WiKG
Dynamic Graph Representation with Knowledge-aware Attention for Histopathology Whole Slide Image Analysis
Jiawen Li*, Yuxuan Chen*, Hongbo Chu*, Qiehe Sun, Tian Guan, Anjia Han#, Yonghong He#
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)2024
Paper
MIL Network
Classification of Myopic Maculopathy Images with Self-supervised Driven Multiple Instance Learning Network
Jiawen Li*, Jaehyeon Soon*, Qilai Zhang*, Qifan Zhang, Yonghong He#
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)2023
Paper

Journal Articles

PathTree
Diagnostic text-guided representation learning in hierarchical classification for pathological whole slide image
Jiawen Li*, Qiehe Sun, Renao Yan, Yizhi Wang, Yuqiu Fu, Yani Wei, Tian Guan, Huijuan Shi#, Yonghong He#, Anjia Han#
Medical Image Analysis (Med. Image Anal.)2025
Paper
PathOrchestra
PathOrchestra: A comprehensive foundation model for computational pathology with over 100 diverse clinical-grade tasks
Fang Yan*#, Jianfeng Wu*, Jiawen Li*, Wei Wang*, Yirong Chen, Linda Wei, Jiaxuan Lu, Wen Chen, Zizhao Gao, Jianan Li, Heng Li, Hong Yan, Jiabo Ma, Minda Chen, Yang Lu, Qing Chen, Yizhi Wang, Xitong Ling, Xuenian Wang, Zihan Wang, Qiang Huang, Shengyi Hua, Mianxin Liu, Lei Ma, Tian Shen, Xiaofan Zhang#, Yonghong He#, Hao Chen#, Shaoting Zhang#, Zhe Wang#
NPJ Digital Medicine (NPJ Digit. Med.)2025
Paper
Dynamic Hypergraph
Dynamic hypergraph representation for bone metastasis analysis
Yuxuan Chen*, Jiawen Li*, Lianghui Zhu*, Yang Xu, Tian Guan, Huijuan Shi#, Yonghong He#, Anjia Han#
Computer Methods and Programs in Biomedicine (Comput. Methods Programs Biomed.)2025
Paper
Vectorial Adaptive Optics
Using optical skyrmions to assess vectorial adaptive optics capabilities in the presence of complex aberrations
Yifei Ma*, Zimo Zhao*, Yuanxing Shen*, Binguo Chen, An Aloysius Wang, Yuxi Cai, Ji Qin, Runchen Zhang, Yunqi Zhang, Jiahe Cui, Bangshan Sun, Jiawen Li, Yuzhu Shi, Liangyu Deng, Honghui He#, Lin Luo#, Yonghong He#, Yun Zhang, Ben Dai, Daniel J. Royston, Steve J. Elston, Stephen M. Morris, Martin J. Booth, Chao He#
Science Advances (Sci. Adv.)2025
Paper
CAMELYON+
Comprehensive benchmark dataset for pathological lymph node metastasis in breast cancer sections
Xitong Ling*, Yuanyuan Lei*, Jiawen Li*, Junru Cheng, Wenting Huang, Tian Guan, Jian Guan#, Yonghong He#
Scientific Data (Sci. Data)2025
Paper
Retarder Array
A reconfigurable arbitrary retarder array as complex structured matter
Chao He*#, Binguo Chen*, Zipei Song*, Zimo Zhao*, Yifei Ma*, Honghui He#, Lin Luo#, Tade Marozsak, An Aloysius Wang, Rui Xu, Peixiang Huang, Jiawen Li, Xuke Qiu, Yunqi Zhang, Bangshan Sun, Jiahe Cui, Yuxi Cai, Yun Zhang, Andong Wang, Mohan Wang, Patrick Salter, Julian AJ Fells, Ben Dai, Shaoxiong Liu, Limei Guo, Yonghong He, Hui Ma, Daniel J. Royston, Steve J. Elston, Qiwen Zhan, Chengwei Qiu, Stephen M. Morris, Martin J. Booth, Andrew Forbes
Nature Communications (Nat. Commun.)2025
Paper
DeepTree
DeepTree: Pathological image classification through imitating tree-like strategies of pathologists
Jiawen Li*, Junru Cheng*, Lingqin Meng, Hui Yan, Yonghong He, Huijuan Shi#, Tian Guan#, Anjia Han#
IEEE Transactions on Medical Imaging (IEEE Trans. Med. Imaging)2024
Paper

Preprints

PathFiT
Unlocking adaptive digital pathology through dynamic feature learning
Jiawen Li*, Tian Guan*, Qingxin Xia, Yizhi Wang, Xitong Ling, Jing Li, Qiang Huang, Zihan Wang, Zhiyuan Shen, Yifei Ma, Zimo Zhao, Zhe Lei, Tiandong Chen, Junbo Tan, Xueqian Wang, Xiu-Wu Bian#, Zhe Wang#, Lingchuan Guo#, Chao He#, Yonghong He#
arXiv:2412.204302024
Preprint

Experience

Algorithm Engineer · Tsinghua Research Institute
Developed deep learning algorithms for histopathology whole slide image analysis.
Begins from Jul 2023
Research Assistant · HKUST(GZ)
Conducted research on graph foundation models and multimodal LLMs in computational pathology.
Jul 2024 - Jul 2025

Teaching Assistant