Biography

I am a Ph.D. Student in Computer Science at University of Massachusetts Boston, working under the supervision of Professor Shichao Pei. I came from an interdisciplinary background with a broad interests in physics, bio-informatics, computer science, and deep learning. I am actively working as a backend engineer at DeepTracer lab developing machine learning approach for automated Cryo-EM protein structure modeling together with Professor Dong Si.

Interests

  • Self Supervised Multimodal Learning,
  • Knowledge & Dataset Distillation,
  • Deep Learning for Bioinformatics.

Skills

  • Python, Java, C++, PyTorch, TensorFlow,
  • Competitive Programming (TOP 0.23%).

Education

  • Ph.D. in Computer Science • Jan 2024 - Present

    University of Massachusetts Boston

  • M.S. in Data Science • Sep 2021 - May 2023

    New York University

  • B.S. in Applied Physics • Sep 2018 - June 2021

    B.S. in ACMS: Data Sci & Stat • Sep 2018 - June 2021

    University of Washington - Seattle

Experience

 
 
 
 
 

Senior Backend Algorithm Engineer

DeepTracer

Jun 2020 – Jun 2023 Seattle, WA
Develop deep learning (DL) tool for automatic protein complex structure prediction from high-dimensional microscopy images. Research computer vision algorithm for processing 3D biomedical image data.
 
 
 
 
 

Research Asistant

Dais Group

Sep 2020 – Nov 2020 Seattle, WA
Collaborated with T-Mobile telecom specialists and provided a solution for 5G telecom security. Investigate ML techniques for cybersecurity. Drafted review paper for key applications in cybersecurity.

Publications

Galaxy Dataset Distillation with Self-Adaptive Trajectory Matching
Haowen Guan* , Xuan Zhao , Zishi Wang , Zhiyang Li , Julia Kempe
Code
NeurIPS Workshop on Machine Learning and the Physical Sciences, 2023 (Accepted)
DeepTracer-Denoising: Deep Learning for 3D Electron Density Map Denoising
Haowen Guan , Dong Si*
DOI PDF Video Website
IEEE-BIBM Workshop on Machine Learning for Biological and Medical Image, 2022
Smart de novo macromolecular structure modeling from Cryo-EM Maps
Dong Si , Jason Chen , Andrew Nakamura , Luca Chang , Haowen Guan
DOI
Journal of Molecular Biology, JMB, 2023
Artificial Intelligence Advances For De Novo Molecular Structure Modeling in Cryo-Electron Microscopy
Dong Si , Andrew Nakamura , Runbang Tan , Haowen Guan , Jie Hou , Ammaar Firozi , Renzhi Cao , Kyle Hippe , Minglei Zhao
DOI
Wiley Interdisciplinary Reviews, WIREs, 2021

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