About Me

About me

My name is Xupeng Chen, born in CHINA in 1995.

I major in biology and minor in statistics in Tsinghua University during my undergraduate study. I changed my study field to EE and start my Ph.D. study in NYU Tandon School, mentored by Prof. Yao Wang in NYU Video Lab.

Resume

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Xupeng Chen

New York, NY 11201 | xupeng.chen@nyu.edu | GitHub | LinkedIn

Education

New York University — Brooklyn, NY Ph.D. in Electrical and Computer Engineering | Sep 2019 – Present

  • Advisor: Prof. Yao Wang (Video Lab)

Tsinghua University — Beijing, China B.S. in Biological Sciences (Xuetang Program), Minor in Statistics | Sep 2014 – Jul 2018

  • Advisor: Prof. Zhi Lu (Bioinformatics Division, BNRIST)

Research Experience

NYU Wireless & Video Lab, New York University — Research Assistant | Sep 2019 – Present

  • Working on deep learning for medical image segmentation problems in electron microscopy (EM) neuron images
  • Proposed a deep learning based method for synapse detection, segmentation, and partner assignment
  • Published at ISBI 2020 on synaptic partner assignment in EM images

Bioinformatics Division, Tsinghua University — Research Assistant | Sep 2016 – Jul 2018

  • Developed DeepShape: RNA structural motif finding using deep learning
  • Used variational autoencoders (VAE) and graph convolutional networks (GCN) for RNA structure analysis
  • Developed mixture models for position weight matrix (PWM) optimization
  • Contributed to eMAIZE: a comprehensive database for maize multi-omics (published in Molecular Plant)

Janelia Research Campus, HHMI — Summer Intern | Jun 2018 – Aug 2018

  • Worked on neuromuscular junction (NMJ) segmentation in electron microscopy images
  • Synaptic partner prediction using deep learning approaches
  • Synaptic cluster analysis project

Publications

  1. Xupeng Chen, Yinda Zhang, Wei Huang, Yun Wang, Yao Wang, Toufiq Parag. Synapse Detection, Segmentation, and Partner Assignment with Deep Learning. ISBI 2020.
  2. Zijian Ding, …, Xupeng Chen, et al. eMAIZE: A comprehensive database integrating genetic, genomic, and transcriptomic data for maize. Molecular Plant, 2019.

Teaching & Activities

  • 2020 — Teaching Assistant for Medical Imaging Lecturer: Prof. Jonathan Mamou — New York University
  • 2018 — Teaching Assistant for Bioinformatics Basic Course Lecturer: Prof. Zhi Lu — Tsinghua University
  • 2015-2018 — Scholarship XueTang scholarship — Tsinghua University
  • 2017 — Second prize The First National College Students’ Brain Computation and Application Competition — International
  • 2017 — First Prize eMaize Challenge: Machine learning in breeding — National
  • 2018 — Meritorious Winner Mathematical Contest in Modeling (MCM) — International
  • 2016-2018 — Xuetang Research Funding $10,000 for Research in Lu lab — Tsinghua University
  • 2016-2018 — Initiative Scientific Research Program $8,000 for Research in Biomedical Image analysis — Tsinghua University
  • 2015 — Golden Prize Social practice award for investigation on e-cycling — Tsinghua University

Skills

  • Proficient in Python, MATLAB, R, Bash, LaTeX
  • Familiar with Machine Learning, Deep Learning (Tensorflow, Keras, Pytorch), and Computer Vision tools
  • Familiar with Linux, MacOS, Windows

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