249 citations · 928 across the 13 of their papers we have counts for
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High-resolution Markov state models for the dynamics of Trp-cage miniprotein constructed over slow folding modes identified by state-free reversible VAMPnets
Hythem Sidky, Wei Chen, Andrew L. Ferguson
State-free reversible VAMPnets (SRVs) are a neural network-based framework capable of learning the leading eigenfunctions of the transfer operator of a dynamical system from trajec…
Capabilities and Limitations of Time-lagged Autoencoders for Slow Mode Discovery in Dynamical Systems
Wei Chen, Hythem Sidky, Andrew L. Ferguson
Time-lagged autoencoders (TAEs) have been proposed as a deep learning regression-based approach to the discovery of slow modes in dynamical systems. However, a rigorous analysis of…
Nonlinear Discovery of Slow Molecular Modes using State-Free Reversible VAMPnets
Wei Chen, Hythem Sidky, Andrew L Ferguson
The success of enhanced sampling molecular simulations that accelerate along collective variables (CVs) is predicated on the availability of variables coincident with the slow coll…