Note: Variational Encoding of Protein Dynamics Benefits from Maximizing Latent Autocorrelation

17 Mar 2018Hannah K. Wayment-SteeleVijay S. Pande

As deep Variational Auto-Encoder (VAE) frameworks become more widely used for modeling biomolecular simulation data, we emphasize the capability of the VAE architecture to concurrently maximize the timescale of the latent space while inferring a reduced coordinate, which assists in finding slow processes as according to the variational approach to conformational dynamics. We additionally provide evidence that the VDE framework (Hern\'andez et al., 2017), which uses this autocorrelation loss along with a time-lagged reconstruction loss, obtains a variationally optimized latent coordinate in comparison with related loss functions... (read more)

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