Zijie Fang
PhD Student in Bioengineering The Hong Kong University of Science and Technology
I am currently working towards a PhD degree in Bioengineering (Scientific Computation Concentration) since 2025.09 at the Hong Kong University of Science and Technology (HKUST), supervised by Prof. Jiguang Wang. I am currently working on computational biology, with a particular focus on agentic reasoning large language models (LLMs).
Before that, I received my Master degree in Computer Technology at Tsinghua Shenzhen International Graduate School, Tsinghua University (THU) in 2025, supervised by Prof. Zhi Wang and co-supervised by Prof. Yongbing Zhang from Harbin Institute of Technology (Shenzhen). Besides, I obtained my BS degree in Software Engineering from Nanjing University of Information Science and Technology (NUIST) in 2022.
Email: [email protected]
Homepage: www.vison307.cn
Github: github.com/Vison307
Winned Competitions
STP Open Challenge
1st Place
In this challenge, participants are given paired spatial transcriptomics and spatial proteomics datasets measured on adjacent tissue sections of glioma patients. The goal is to build models that predict spatial pro expression profiles from spatial gene expression profiles. This task evaluates a model's ability to learn transcript-protein relationships while preserving spatial context and tissue architecture.
WSSS4LUAD @ ISICDM 2021
3rd Place (Bonus Winner)
The participants are required to develop machine learning algorithms where only image-level annotations are given for algorithm training. And pixel-level ground truth is utilized for validation and testing.
LEOPARD @ MICCAI 2024
3rd Place (Bonus Winner)
The goal of this challenge is to yield top-performance deep learning solutions to predict the time to biochemical recurrence from H&E-stained histopathological tissue sections, i.e. based on morphological features.
Selected Publications
For the full paper list please click here.
Weakly-Supervised Semantic Segmentation for Histopathology Images Based on Dataset Synthesis and Feature Consistency Constraint
Accepted by AAAI 2023 (Oral)
Zijie Fang, Yang Chen, Yifeng Wang, Zhi Wang, Xiangyang Ji, Yongbing Zhang
HisynSeg: Weakly-Supervised Histopathological Image Segmentation via Image-Mixing Synthesis and Consistency Regularization
Accepted by IEEE Transactions on Medical Imaging (IEEE TMI)
Zijie Fang, Yifeng Wang, Peizhang Xie, Zhi Wang, Yongbing Zhang
MamMIL: Multiple Instance Learning for Whole Slide Images with State Space Models
Accepted by IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM)
Zijie Fang, Yifeng Wang, Ye Zhang, Zhi Wang, Jian Zhang, Xiangyang Ji, Yongbing Zhang
A Multi-Perspective Self-Supervised Generative Adversarial Network for FS to FFPE Stain Transfer
Accepted by IEEE Transactions on Medical Imaging (IEEE TMI)
Yiyang Lin, Yifeng Wang, Zijie Fang (Co-first), Zexin Li, Xianchao Guan, Danling Jiang, Yongbing Zhang
Multi-Beholder: Biomarker Prediction for Low-Grade Glioma with Multiple Instance Learning and One-Class Classification
Submitted to IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE/ACM TCBB)
Zijie Fang, Yihan Liu, Yifeng Wang, Xiangyang Zhang, Yang Chen, Changjing Cai, Yiyang Lin, Ying Han, Zhi Wang, Shan Zeng, Jun Tan, Yongbing Zhang, Hong Shen
Honors & Awards
- Outstanding Graduates of Beijing (2025) 北京市优秀毕业生
- THU Second-Class Scholarship (2023 & 2024) 清华校二等奖学金
- Outstanding Undergraduate Graduation Thesis (Project) of Jiangsu Province, Second Prize (2022) 江苏省普通高等学校本专科优秀毕业论文（设计）二等奖
- Outstanding Graduates of Jiangsu Province (2022) 江苏省普通高校省级优秀毕业生
- Merit Student of Jiangsu Province (2021) 江苏省级三好学生
- President's Scholarship of NUIST (top 0.1%) (2020) 南京信息工程大学校长奖学金（前0.1%）
- National Scholarship (2020) 国家奖学金
Discipline Competitions
- The Lanqiao Programming Competition in Jiangsu Province (C/C++ groups), First Prize (2019 ~ 2021) 蓝桥杯程序设计大赛江苏省赛（C/C++组），一等奖
- The National Finals of Lanqiao Programming Competition (C/C++ groups), Second Prize (2020 & 2021) 蓝桥杯程序设计大赛全国总决赛（C/C++组），二等奖
- The 11th May Day Mathematical Contest in Modeling of Jiangsu Province, Third Prize (2020) 第十一届江苏省五一数学建模竞赛，三等奖
Services
Reviewer of IEEE Transactions on Pattern Analysis and Machine Intelligence (T-PAMI), IEEE Journal of Biomedical and Health Informatics (IEEE JBHI), AIM-FM Workshop @ NeurIPS'24, Neurocomputing, IJCNN, The Journal of Supercomputing, Computing, and Computer Communications.