Nonlinear Discovery of Slow Molecular Modes using State-Free Reversible
VAMPnets

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Nonlinear Discovery of Slow Molecular Modes using State-Free Reversible VAMPnets

9 February 2019

Andrew L. Ferguson

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Papers citing "Nonlinear Discovery of Slow Molecular Modes using State-Free Reversible VAMPnets"

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Title
Learning Geometrically Disentangled Representations of Protein Folding Simulations N. Joseph Tatro Payel Das Pin-Yu Chen Vijil Chenthamarakshan Rongjie Lai AI4CE 57 0 0 20 May 2022
Staying the course: Locating equilibria of dynamical systems on Riemannian manifolds defined by point-clouds J. M. Bello-Rivas Anastasia S. Georgiou J. Guckenheimer Ioannis G. Kevrekidis 34 3 0 21 Apr 2022
Characterizing metastable states with the help of machine learning P. Novelli L. Bonati Massimiliano Pontil Michele Parrinello 56 23 0 15 Apr 2022
MD-GAN with multi-particle input: the machine learning of long-time molecular behavior from short-time MD data Ryo Kawada Katsuhiro Endo Daisuke Yuhara K. Yasuoka AI4CE 51 2 0 02 Feb 2022
Chasing Collective Variables using Autoencoders and biased trajectories Zineb Belkacemi P. Gkeka T. Lelièvre G. Stoltz AI4CE 58 63 0 22 Apr 2021
Accelerated Simulations of Molecular Systems through Learning of their Effective Dynamics Pantelis R. Vlachas Julija Zavadlav M. Praprotnik Petros Koumoutsakos AI4CE 56 3 0 17 Feb 2021
Machine Learning Force Fields Oliver T. Unke Stefan Chmiela H. E. Sauceda M. Gastegger I. Poltavsky Kristof T. Schütt A. Tkatchenko K. Müller AI4CE 141 940 0 14 Oct 2020
Molecular Latent Space Simulators Hythem Sidky Wei Chen Andrew L. Ferguson AI4CE 83 34 0 01 Jul 2020
Interpretable Embeddings From Molecular Simulations Using Gaussian Mixture Variational Autoencoders Yasemin Bozkurt Varolgunes T. Bereau J. F. Rudzinski DRL 58 44 0 22 Dec 2019
Machine learning for protein folding and dynamics Frank Noé Gianni De Fabritiis C. Clementi AI4CE 121 138 0 22 Nov 2019
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 74 55 0 12 Jun 2019
Capabilities and Limitations of Time-lagged Autoencoders for Slow Mode Discovery in Dynamical Systems Wei Chen Hythem Sidky Andrew L. Ferguson 76 36 0 02 Jun 2019