Chao Chen


Chao Chen     

Chao Chen, Ph.D., Assistant Professor

Department of Biomedical Informatics
Computer Science Building 2313C
Stony Brook, NY 11794
Phone:  (631) 632-2593
Website (URL):


Machine learning, biomedical image analysis, topological data analysis.
Chao Chen received his Ph.D. in computer science from Rensselaer Polytechnic Institute, Master's degree from National University of Singapore and B.Sci. degree from Peking University, China. He joined the Biomedical Informatics Department in 2018. Before coming to Stony Brook, he was a faculty member in the City University of New York. 
Dr. Chao Chen's research spans machine learning, biomedical image analysis and topological data analysis. He is particularly interested in developing principled methods to characterize and regulate complex and dynamic systems arising in biomedicine and in theoretical study of deep neural networks.
Current projects:
  • Robust machine learning.
  • Image segmentation.
  • Brain image analysis and cardiac image analysis.
  • Pathology image analysis: tumor microenvironment analysis, cell detection and segmentation.

Google Scholar   |   DBLP  

Selected publications:

1. Andrew Aukerman, Mathieu Carrière, Chao Chen, Kevin Gardner, Raúl Rabadán, Rami Vanguri: "Persistent Homology Based Characterization ofthe Breast Cancer Immune Microenvironment: A Feasibility Study", in International Symposium on Computational Geometry (SoCG), 2020.

2. Shahira Abousamra, Danielle Fassler, Le Hou, Yuwei Zhang, Rajarsi Gupta, Tahsin Kurc, Luisa F. Escobar-Hoyos, Dimitris Samaras, Beatrice Knudson, Kenneth Shroyer, Joel Saltz, Chao Chen: "Weakly-Supervised Deep Stain Decomposition for Multiplex IHC Images", in IEEE International Symposium on Biomedical Imaging (ISBI), 2020

3. Ze Ye, Kin Sum Liu, Tengfei Ma, Jie Gao, Chao Chen: "Curvature Graph Network", in the Eighth International Conference on Learning Representations (ICLR), 2020.

4. Xiaoling Hu, Fuxin Li, Dimitris Samaras, Chao Chen: "Topology-Preserving Deep Image Segmentation", in the Thirty-third Conference on Neural Information Processing Systems (NeurIPS), 2019.

5. Chao Chen, Xiuyan Ni, Qinxun Bai, Yusu Wang: "A Topological Regularizer for Classifiers via Persistent Homology", in International Conference on Artificial Intelligence and Statistics (AISTATS), 2019

6. Xiuyan Ni, Zhennan Yan, Tingting Wu, Jin Fan, Chao Chen: "A Region-of-Interest-Reweight 3D Convolutional Neural Network for the Analytics of Brain Information Processing", in the 21st International Conference on Medical Image Computing & Computer Assisted Intervention (MICCAI), 2018

7. Xiuyan Ni, Novi Quadrianto, Yusu Wang, Chao Chen: "Composing Tree Graphical Models with Persistent Homology Features for Clustering Mixed-Type Data", in the 34rd International Conference on Machine Learning (ICML), 2017

8. Pengxiang Wu, Chao Chen, Yusu Wang, Shaoting Zhang, Changhe Yuan, Zhen Qian, Dimitris Metaxas, Leon Axel: "Optimal Topological Cycles and Their Application in Cardiac Trabeculae Restoration", in the 25th biennial international conference on Information Processing in Medical Imaging (IPMI), 2017

  • Data structures 
  • Machine learning and image analysis
  • Big data analytics
  • Computer Science for Biomedical Informatics