Variational Encoding of Complex Dynamics

By Carlos Xavier Hernández, Hannah K. Wayment-Steele, Mohammad M. Sultan, Brooke E. Husic, Vijay S. Pande. 2017

149 citations recorded by the source corpus.

Often the analysis of time-dependent chemical and biophysical systems produces high-dimensional time-series data for which it can be difficult to interpret which individual features are most salient. While recent work from our group and others has demonstrated the utility of time-lagged covariate models to study such systems, linearity assumptions can limit the compression of inherently nonlinear dynamics into just a few characteristic components. Recent work in the field of deep learning has led to the development of the variational autoencoder (VAE), which is able to compress complex datasets into simpler manifolds. We present the use of a time-lagged VAE, or variational dynamics encoder (VDE), to reduce complex, nonlinear processes to a single embedding with high fidelity to the underlying dynamics. We demonstrate how the VDE is able to capture nontrivial dynamics in a variety of examples, including Brownian dynamics and atomistic protein folding. Additionally, we demonstrate a method for analyzing the VDE model, inspired by saliency mapping, to determine what features are selected by the VDE model to describe dynamics. The VDE presents an important step in applying techniques from deep learning to more accurately model and interpret complex biophysics.

Subfields: Artificial Intelligence, Molecular Biology, Spectroscopy

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Citations in the corpus

Deep Generative Markov State Models (2018, background): “Learning the correct long-time dynamical behavior with a generative dynamical model is difficult, as demonstrated in [8].”
Taming VAEs (2018, background): “Deep variational auto-encoders (VAEs) have made substantial progress in the last few years on modelling complex data such as images [1, 2, 3, 4, 5, 6, 7], speech synthesis [8, 9], molecular discovery [10, 11, 12], robotics [13, 14, 15] and 3d-scene understanding [16, 17, 18].”