Haifan Gong PhD, PostDoctor Researcher CBICA, Perelman School of Medicine, University of Pennsylvia, PA, USA Email: haifangong@outlook.com Google Scholar

I am currently a PostDoctor Researcher at UPenn, working with Tianyu Han at CBICA. Before that, I received my PhD degree in Computer Information Engineering at The Chinese University of Hong Kong, Shenzhen in 2025.7, supervised by Prof. Haofeng Li, Wan Xiang at SRIBD, and Prof. Dong Wang at SSE. I received my Master degree in Computer Engineering from Sun Yat-sen University (SYSU) in 2022.7, supervised by Prof. Guanbin Li at the HCP Lab.

My research interests include LLM for health, domain generalization, multi-modal learning, medical imaging analysis, and bioinformatics.

News

[10/2025] One paper was accepted to ESWA (JCR Q1)
[09/2025] One paper was accepted to NeurIPS (CCF A), while one paper was invited by Patterns (Cell Press)
[04/2025] One paper was accepted to IEEE JBHI (JCR Q1, Famous journal in medical imaging analysis)
[02/2025] One paper was accepted to IEEE TMI (JCR Q1, Top journal in medical imaging analysis)
[01/2025] One paper was accepted to AAAI (CCF A) with Oral presentation (Top 4%), another paper was accepted to ISBI also with Oral presentation (Top 15%)
[08/2024] One paper was accepted to IEEE TMI (JCR Q1, Top journal in medical imaging analysis)
[03/2024] One paper was accepted to ICME with Oral presentation (Top 15%)
[09/2023] One paper was accepted to Bioinformatics (JCR Q1, Famous journal in bioinformatics)
[06/2023] Two papers were accepted to MICCAI 2023 with one early accepted (Top 14%)
[06/2023] One paper was accepted to Nature Communications (JCR Q1, Nature subjoural)
[11/2022] One paper was accepted to Computers in Biology and Medicine (JCR Q1, IF: 7.0)
[10/2022] One paper was accepted to Cell Reports Physical Science (JCR Q1, IF: 8.9, Cell Press)
[07/2022] One paper was accepted to ACM CSUR (JCR Q1, IF: 28.0)
[06/2022] One paper was accepted to IEEE TMI (JCR Q1, Top journal in medical imaging analysis)
[05/2022] One paper was early accepted to MICCAI 2022 with Student Travel Award (Top 4%)
[11/2021] Our paper won the Best Poster Prize at ICMR 2021
[05/2021] I have joined Shanghai AI Lab as a research intern
[05/2021] We won the first prize at ImageCLEF VQA-Med-2021 challenge [Full Text]

Publications

* denotes equal contribution, # denotes corresponding author

Journals

• Costal Cartilage Segmentation with Topology Guided Deformable Mamba: Method and Benchmark
  Senmao Wang*, Haifan Gong*, Runmeng Cui, Boyao Wan, Zhonglin Hu, Haiqing Yang, Jingyang Zhou, Haiyue Jiang, and Lin Lin.
  Expert Systems With Applications, 2025
  [Full Text] [Code]

• Boundary as the Bridge: Towards Heterogeneous Partially-labeled Medical Image Segmentation and Landmark Detection
  Haifan Gong, Boyao Wan, Luoyao Kang, Xiang Wan, Lingyan Zhang, and Haofeng Li.
  IEEE Transactions on Medical Imaging (Top journal in medical image analysis), 2025
  [Full Text] [Code]

• Fetal Cerebellum Landmark Detection Based on 3D MRI: Method and Benchmark
  Haifan Gong*, Huixian Liu*, Yitao Wang, Xiaoling Liu, Xiang Wan, Qiao Shi, and Haofeng Li.
  IEEE Journal of Biomedical and Health Informatics, 2025
  [Full Text] [Code]

• BCNet: Bronchus Classification via Structure Guided Representation Learning
  Wenhao Huang*, Haifan Gong*, Huan Zhang, Yu Wang, Xiang Wan, Guanbin Li, Haofeng Li, and Hong Shen.
  IEEE Transactions on Medical Imaging (Top journal in medical image analysis), 2024
  [Full Text] [Data] [Working with InferVision]

• Unbiased Curriculum Learning Enhanced Global-Local Graph Neural Network for Protein Thermodynamic Stability Prediction
  Haifan Gong*, Yumeng Zhang*, Chenhe Dong, Yue Wang, Guanqi Chen, Bilin Liang, Haofeng Li, Lanxuan Liu, Jie Xu, Guanbin Li.
  Bioinformatics, 2023
  [Full Text] [Code]

• Bile Acid-dependent Transcription Factors and Chromatin Accessibility Determine Regional Heterogeneity of Intestinal Antimicrobial Peptides
  Yue Wang, Yanbo Yu, Lixiang Li, Mengqi Zheng, Jiawei Zhou, Haifan Gong, et al.
  Nature Communications (Nature Press), 2023
  [Full Text]

• VQAMix: Conditional Triplet Mixup for Medical Visual Question Answering
  Haifan Gong*, Guanqi Chen*, Mingzhi Mao, Zhen Li, and Guanbin Li.
  IEEE Transactions on Medical Imaging (Top journal in medical image analysis), 2022
  [Full Text] [Code]

• Thyroid Region Prior Guided Attention for Ultrasound Segmentation of Thyroid Nodules (ESI Highly Cited)
  Haifan Gong, Jiaxin Chen, Guanqi Chen, Haofeng Li, Guanbin Li and Fei Chen.
  Computers in Biology and Medicine, 2022
  [Full Text] [Code]

• Understanding the Effectiveness of Enzyme Pre-reaction State by a Quantum-based Machine Learning Model
  Shenggan Luo, Lanxuan Liu, Chu-Jun Lyu, Byuri Sim, Yihan Liu, Haifan Gong, Yao Nie, Yilei Zhao.
  Cell Reports Physical Science (Cell Press), 2022
  [Full Text]

Conferences

• Intermediate Domain Alignment and Morphology Analogy for Patent-Product Image Retrieval
  Haifan Gong*, Xuanye Zhang*, Ruifei Zhang, Yun Su, Zhuo Li, Yuhao Du, Anningzhe Gao, Xiang Wan, Haofeng Li
  Neural Information Processing Systems (NeurIPS), 2025
  [Full Text] [Code]

• Domain Generalized Medical Landmark Detection via Robust Boundary-aware Pre-training (Oral)
  Haifan Gong, Yu Lu, Xiang Wan, and Haofeng Li.
  AAAI Conference on Artificial Intelligence (AAAI), 2025
  [Full Text] [Code]

• nnMamba: 3D Biomedical Image Segmentation, Classification and Landmark Detection With State Space Model (Oral)
  Haifan Gong, Luoyao Kang, Yitao Wang, Yihan Wang, Xiang Wan, Xusheng Wu, and Haofeng Li.
  IEEE International Symposium on Biomedical Imaging (ISBI), 2025
  [Full Text] [Code]

• Intensity Confusion Matters: An Intensity-distance Guided Loss for Bronchus Segmentation (Oral)
  Haifan Gong*, Wenhao Huang*, Huan Zhang, Yu Wang, Xiang Wan, Hong Shen, Guanbin Li, and Haofeng Li.
  IEEE International Conference on Multimedia and Expo (ICME), 2024
  [Full Text] [Data] [Working with InferVision]

• ASC: Appearance and Structure Consistency for Unsupervised Domain Adaptation in Fetal Brain MRI Segmentation
  Zihang Xu*, Haifan Gong*, Xiang Wan and Haofeng Li.
  Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023
  [Full Text] [Code]

• Visual-Attribute Prompt Learning for Progressive Mild Cognitive Impairment Prediction (Early Accept)
  Luoyao Kang*, Haifan Gong*, Xiang Wan and Haofeng Li.
  Medical Image Computing and Computer Assisted Intervention (MICCAI), 2023
  [Full Text] [Code]

• Less is More: Adaptive Curriculum Learning for Thyroid Nodule Diagnosis (Student Travel Award) (Early Accept)
  Haifan Gong*, Hui Cheng*, Yifan Xie, Shuangyi Tan, Guanqi Chen, Fei Chen, Guanbin Li
  Medical Image Computing and Computer Assisted Intervention (MICCAI), 2022
  [Full Text] [Code]

• Cross-Modal Self-Attention with Multi-Task Pre-Training for Medical Visual Question Answering (Best Poster Paper)
  Haifan Gong*, Guanqi Chen*, Yizhou Yu, Guanbin Li
  ACM International Conference on Multimedia Retrieval (ICMR), 2021
  [Full Text] [Code] [中译版(非官方)]

• Multi-task Learning for Thyroid Nodule Segmentation with Thyroid Region Prior
  Haifan Gong, Guanqi Chen, Ranran Wang, Xiang Xie, Mingzhi Mao, Yizhou Yu, Fei Chen, and Guanbin Li.
  IEEE International Symposium on Biomedical Imaging (ISBI), 2021
  [Full Text] [Code]

Invited Paper and Survery

• Plug-and-play Computational Method for Advancing Natural and Biomedical Image Representation
  Haifan Gong#, Tianyu Han, Guanbin Li.
  Patterns (Cell Press), 2025
  [Full Text]

• A Survey of Natural Language Generation
  Chenhe Dong, Yinghui Li, Haifan Gong, Miaoxin Chen, Junxin Li, Ying Shen, Min Yang. (ESI Highly Cited)
  ACM Computing Surveys (ACM CSUR), 2022
  [Full Text] [Official Full Text]

Honors & Awards

• 2023 MICCAI Outstanding Reviewer Award Honerable Mentions (Top 2%) [Link]
• 2022 MICCAI Student Travel Award (Top 4%) [Link]
• 2021 ICMR Best Poster Paper Award (CCF B) [Link]
• 2021 ImageCLEF Medical VQA Competation, First Prize
• 2020 Distinguished graduates in NCU (10/10000)

Professional Activities

• Member of IEEE, ACM, AAAI, and MICCAI.
• Reviewer for npj Digital Medicine, Patterns, Artificial Intelligence in Medicine, IEEE Trans. on OE, IEEE IoT Journal, The Visual Computer, IEEE Access, Scientific Reports
• Regular Reviewer for NeurIPS, ICML, ICLR, CVPR, ICCV, AAAI, MICCAI, AISTAT, etc. since 2024.