photo taken by Brittany Fasy
  

Chao Chen   

Postdoctoral fellow
Computational Biomedicine Imaging and Modeling Center
Department of Computer Science
Rutgers University, Piscataway, NJ 08854

I am currently working with Prof. Dimitris Metaxas at Computational Biomedicine Imaging and Modeling Center , Rutgers University . From 2009 to 2012, I worked with Prof. Herbert Edelsbrunner at Institute of Science and Technology Austria. I obtained my Ph.D. degree from Rensselaer Polytechnic Institute in 2009 (advised by Prof. Daniel Freedman).

Research Interests

  • Designing algorithms and models for topological data analysis.
  • Data analytics with a focus on biomedical informatics.
  • A very interdisciplinary research in between biomedical informatics, machine learning and computational topology.

I am currently on the job market. Here is my CV.


Publications

Conferences and Workshops
  • Chao Chen, Han Liu, Dimitris Metaxas, Tianqi Zhao: "Mode Estimation for High Dimensional Discrete Tree Graphical Models", in Advances in Neural Information Processing Systems (NIPS), 2014 (Spotlight oral, acceptance rate ~5%, pdf, technical report available soon)
  • Chao Chen, Han Liu, Dimitris Metaxas, Tianqi Zhao: "Identifying Sub-Networks of Functional Connectivity Using Modes of Distributions", in the 4th NIPS Workshop on Machine Learning and Interpretation in Neuroimaging (MLINI), 2014 (pdf available soon)
  • Mustafa Uzunbas, Chao Chen, Dimitris Metaxas: "Optree: a Learning-Based Adaptive Watershed Algorithm for Neuron Segmentation", in the 17th Annual International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2014. (Early acceptance rate ~10%, pdf)
  • Mingchen Gao, Chao Chen, Shaoting Zhang, Zhen Qian, Mani Vannan, Sarah Rinehart, Dimitris Metaxas, Leon Axel: "Morphological analysis of the papillary muscles and the trabaculae", in International Symposium on Biomedical Imaging (ISBI), 2014 (pdf)
  • Mustafa Uzunbas, Chao Chen, Shaoting Zhang, Kilian Pohl, Kang Li, Dimitris Metaxas: "Collaborative multi organ segmentation by integrating deformable and graphical models", in International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2013 (pdf)
  • Mingchen Gao *, Chao Chen *, Shaoting Zhang, Zhen Qian, Dimitris Metaxas, Leon Axel: "Segmenting the papillary muscles and the trabeculae from high resolution cardiac CT through restoration of topological handles", in International Conference on Information Processing in Medical Imaging (IPMI), 2013 (pdf) (* contributed equally)
  • Chao Chen, Vladimir Kolmogorov, Yan Zhu, Dimitris Metaxas, Christoph Lampert: "Computing the M most probable modes of a graphical model", in International Conference on Artificial Intelligence and Statistics (AISTATS), 2013 (Oral presentation, acceptance rate ~11% pdf, supplemental material)
  • Novi Quadrianto, Chao Chen, Christoph Lampert: "The most persistent soft-clique in a set of sampled graphs", in International Conference on Machine Learning (ICML), 2012 (pdf)
  • Oleksiy Busaryev, Sergio Cabello, Chao Chen, Tamal K. Dey, Yusu Wang: "Annotating simplices with a homology basis and its applications", in Scandinavian Symposium and Workshops on Algorithm Theory (SWAT), 2012 (pdf)
  • Chao Chen, Herbert Edelsbrunner: "Diffusion runs low on persistence fast", in IEEE International Conference on Computer Vision (ICCV), 2011 (Acceptance rate 23.7%, pdf, poster, code)
  • Chao Chen, Daniel Freedman, Christoph H. Lampert: "Enforcing topological constraints in random field image segmentation", in IEEE Computer Vision and Pattern Recognition (CVPR), 2011 (pdf, technical report, poster, code)
  • Chao Chen, Michael Kerber: "An output-sensitive algorithm for persistent homology", in Annual Symposium on Computational Geometry (SoCG), 2011 (pdf)
  • Hubert Wagner, Chao Chen, Erald Vuçini: "Efficient computation of persistent homology for cubical data", in Proceedings of the 4th Workshop on Topology-based Methods in Data Analysis and Visualization (TopoInVis), 2011 (Best paper runner-up, pdf)
  • Chao Chen, Michael Kerber: "Persistent homology computation with a twist", in European Workshop on Computational Geometry (EuroCG), 2011 (pdf)
  • Chao Chen, Daniel Freedman: "Topology noise removal for curve and surface evolution", in Proceedings of the Medical Computer Vision Workshop (MCV) (in conjunction with MICCAI), 2010 (pdf)
  • Chao Chen, Daniel Freedman: "Hardness results for homology localization", in Proceedings of the Twenty-First Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), 2010 (pdf)
  • Chao Chen, Daniel Freedman: "Quantifying homology classes", in Annual Symposium on Theoretical Aspects of Computer Science (STACS), 2008 (pdf)
    Note: Proofs of the NP-hardness results in this paper are available in "Quantifying homology classes II: localization and stability".
  • Chao Chen, Ho-Lun Cheng: "Superimposing voronoi complexes for shape deformation", in International Symposium on Algorithms and Computation (ISAAC), 2004
Journals and Book Chapters
  • Chao Chen, Michael Kerber: “An output-sensitive algorithm for persistent homology”, in Computational Geometry: Theory and Applications (CGTA) 46 (4) pp. 435-447 - Special Issue on the 27th Annual Symposium on Computational Geometry, 2013 (pdf)
  • Yu Sheng, Barbara Cutler, Chao Chen, Joshua Nasman: "Perceptual global illumination cancellation in complex projection environments", in Computer Graphics Forum, Volume 30, Issue 4, Eurographics Symposium on Rendering (EGSR), 2011 (pdf)
  • Daniel Freedman, Chao Chen: "Algebraic topology for computer vision", Chapter 5 of Computer Vision, 239-268, Ed. Sota R. Yoshida, Nova Science Pub. Inc., Hauppauge, New York, 2011 (pdf)
  • Chao Chen, Daniel Freedman: "Hardness results for homology localization", in Discrete & Computational Geometry (DCG) 45(3): 425-448, 2011 (pdf)
  • Chao Chen, Daniel Freedman: "Measuring and computing natural generators for homology groups", in Computational Geometry: Theory and Applications (CGTA) 43(2): 169-181, 2010 (pdf)
  • Chao Chen, Ho-Lun Cheng: "Superimposing voronoi complexes for shape deformation", in International Journal of Computational Geometry and Applications (IJCGA) 16(2-3): 159-174 2006

 Last modified: Nov. 2014