Chen Li

PhD candidate
TopoXLab
Dept of Biomedical Informatics
Stony Brook University

I am currently a PhD Candidate at the Department of Biomedical Informatics at Stony Brook University, advised by Prof.Chao Chen. During my PhD, I have also worked closely with Dr.Xiaoling Hu.

Before that, I obtained my master and bachelor degrees from Stony Brook University and Jilin University, respectively.

Research Interests: My research focuses on developing reliable and data-efficient AI through uncertainty estimation and generative modeling, with applications in biomedical imaging, and large language models. In particular, I am interested in:

  1. Uncertainty Estimation
  2. Semi-supervised learning
  3. Diffusion models
  4. Large language models
    5.
Email Address: li.chen.8 at stonybrook dot edu

CV / Scholar / Github

Publications

ORCE: Order-Aware Alignment of Verbalized Confidence in Large Language Models
Chen Li, Xiaoling Hu, Songzhu Zheng, Jiawei Zhou, Chao Chen
ArXiv preprint, 2026
Paper

Multi-Channel Uncertainty-Weighted Score Matching for Conditional Diffusion in Medical UDA
Chen Li, Meilong Xu, Xiaoling Hu, Weimin Lyu, Chao Chen
European Conference on Computer Vision (ECCV), 2026
Paper Code

Topology-Based Biomarkers Accurately Predict Breast Cancer Outcome and Survival
Sandeep Singhal*, Chen Li*, Andrew Aukerman, Mathieu Carrière, Michael L Miller, Hanina Hibshoosh, Jasmine A McDonald, Joy R Winfield, Sai Tun Hein Aung, Gustavo Martinez-Delgado, Ziv Frankenstein, Young-Ho Lee, Raul Rabadan, Joel Saltz, Chao Chen, Kevin Gardner
* Equal contribution. Cancer Research, 2026
Paper Code

MATCH: Multi-faceted Adaptive Topo-Consistency for Semi-Supervised Histopathology Segmentation
Meilong Xu, Xiaoling Hu, Shahira Abousamra, Chen Li, Chao Chen
Advances in Neural Information Processing Systems (NeurIPS), 2025
Paper Code

TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model
Meilong Xu, Saumya Gupta, Xiaoling Hu, Chen Li, Shahira Abousamra, Dimitris Samaras, Prateek Prasanna, Chao Chen
Conference on Computer Vision and Pattern Recognition (CVPR), 2025
Paper Code

Spatial diffusion for cell layout generation
Chen Li, Xiaoling Hu, Shahira Abousamra, Meilong Xu, Chao Chen
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2024
Paper Code

Calibrating Uncertainty for Semi-Supervised Crowd Counting
Chen Li, Xiaoling Hu, Shahira Abousamra, Chao Chen
International Conference on Computer Vision (ICCV), 2023
Paper Code

Confidence Estimation Using Unlabeled Data
Chen Li, Xiaoling Hu, Chao Chen
International Conference on Learning Representations (ICLR), 2023
Paper OpenReview Code Poster

Spatial Transcriptomic Analysis Reveals Associations between Genes and Cellular Topology in Breast and Prostate Cancers
Alsaleh, Lujain and Li, Chen and Couetil, Justin L and Ye, Ze and Huang, Kun and Zhang, Jie and Chen, Chao and Johnson, Travis S
Cancers, 2022
Paper