Email, GitHub, Google Scholar, LinkedIn
PhD in Computational Physics, University of Illinois at Urbana-Champaign; 2020
BS in Physics, Nanjing University; 2014
University of Chicago (Chicago, IL), PhD Researcher; 08/2018-07/2020
Created a deep learning-based model using Keras/TensorFlow to extract hierarchical slow modes from time-series data, achieving O(N) space and O(N) time complexity, as opposed to O(N^2) space and O(N^3) time complexity required by the state-of-the-art kernel-based model
Derived and proved theoretical bounds for time-lagged autoencoders for stationary processes, providing theoretical insights for future machine learning method development
Qulab Inc. (Los Angeles, CA), Research Intern; 06/2019-08/2019
Built machine learning-based adaptive sampling and Markov model analysis pipelines, successfully identifying sampling bottlenecks and help computational drug design
Implemented and tested a reinforcement learning-based sampling algorithm
University of Illinois at Urbana-Champaign (Urbana, IL), PhD Researcher and Teaching Assistant; 08/2014-07/2018
Applied data-augmented autoencoders to discover important collective variables for molecular systems
Developed an enhanced sampling framework for molecular simulations, enabling 1-2 orders of magnitude faster sampling than conventional techniques
Built a neural network-based force plugin for simulation with native CUDA support and contributed its variant to a general-purpose package widely used by simulation community
Taught lab and discussion sections for university physics courses for more than 400 engineering students in total, awarded “Excellent Teacher” 4 times out of 6 semesters
Served as the mentor teaching assistant for one semester, organized peer evaluation and offered post-lecture feedback for new TAs
Python, C/C++, Git, Machine Learning/Deep Learning, Software Testing/Continuous Integration, CUDA C/C++, SQL
H. Sidky, W. Chen, and A.L. Ferguson “Molecular latent space simulators” Chemical Science 11 (35), 9459-9467
H. Sidky, W. Chen, and A.L. Ferguson “Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation” Molecular Physics 118 (5), e1737742 (Invited New Views article in Molecular Physics)
The PLUMED Consortium (M. Bonomi, G. Bussi, C. Camilloni, G.A. Tribello, P. Banáš, A. Barducci, M. Bernetti, P.G. Bolhuis, S. Bottaro, D. Branduardi, R. Capelli, P. Carloni, M. Ceriotti, A. Cesari, H. Chen, W. Chen, F. Colizzi, S. De, M. De La Pierre, D. Donadio, V. Drobot, B. Ensing, A.L. Ferguson, M. Filizola, J.S. Fraser, H. Fu, P. Gasparotto, F. Luigi Gervasio, F. Giberti, A. Gil-Ley, T. Giorgino, G.T. Heller, G.M. Hocky, M. Iannuzzi, M. Invernizzi, K.E. Jelfs, A. Jussupow, E. Kirilin, A. Laio, V. Limongelli, K. Lindorff-Larsen, T. Löhr, F. Marinelli, L. Martin-Samos, M. Masetti, R. Meyer, A. Michaelides, C. Molteni, T. Morishita, M. Nava, C. Paissoni, E. Papaleo, M. Parrinello, J. Pfaendtner, P. Piaggi, G. Piccini, A. Pietropaolo, F. Pietrucci, S. Pipolo, D. Provasi, D. Quigley, P. Raiteri, S. Raniolo, J. Rydzewski, M. Salvalaglio, G. Cesare Sosso, V. Spiwok, J. Šponer, D.W.H. Swenson, P. Tiwary, O. Valsson, M. Vendruscolo, G.A. Voth, and A. White) “A community effort to promote transparency and reproducibility in enhanced molecular simulations” Nature Methods 16, 670 (2019)
H. Sidky, W. Chen, and A.L. Ferguson “High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnets” J. Phys. Chem. B 123 38 7999-8009 (2019)
W. Chen, H. Sidky, and A.L. Ferguson “Capabilities and limitations of time-lagged autoencoders for slow mode discovery in dynamical systems” J. Chem. Phys. 151 064123 (2019)
W. Chen, H. Sidky, and A.L. Ferguson “Nonlinear discovery of slow molecular modes using state-free reversible VAMPnets” J. Chem. Phys. 150 214114 (2019) (Selected as J. Chem. Phys. “Editor’s Pick”)
W. Chen, A.R. Tan, and A.L. Ferguson “Collective variable discovery and enhanced sampling using autoencoders: Innovations in network architecture and error function design” J. Chem. Phys. 149 072312 (2018) (Invited Submission to the “Enhanced Sampling for Molecular Simulations” Issue)
W. Chen and A.L. Ferguson “Molecular enhanced sampling with autoencoders: On-the-fly nonlinear collective variable discovery and accelerated free energy landscape exploration” J. Comput. Chem. 39 25 2079-2102 (2018)
Kuck Computational Science & Engineering Scholarship, UIUC (≤ 4 recipients); 07/2019
List of Teachers Ranked Excellent by Students, UIUC; 12/2014, 05/2015, 12/2015, 05/2017
China Electric Power Research 14th Institute Scholarship; 11/2013
Third Grade Award, 16th Forum of Sciences and Arts of Nanjing University (with Article Titled Aharonov-Bohm Effect); 05/2013
National Scholarship; 11/2012
Second Grade Award, 15th Forum of Sciences and Arts of Nanjing University (with Article Titled Solar Neutrino Problem); 05/2012