Generative methods for sampling transition paths in molecular dynamics

Molecular systems often remain trapped for long times around some local minimum of the potential energy function, before switching to another one -- a behavior known as metastability. Simulating transition paths linking one metastable state to another one is difficult by direct numerical methods. In view of the promises of machine learning techniques, we explore in this work two approaches to more efficiently generate transition paths: sampling methods based on generative models such as variational autoencoders, and importance sampling methods based on reinforcement learning.

Removing the mini-batching error in Bayesian inference using Adaptive Langevin dynamics

The computational cost of usual Monte Carlo methods for sampling a posteriori laws in Bayesian inference scales linearly with the number of data points. One option to reduce it to a fraction of this cost is to resort to mini-batching in conjunction with unadjusted discretizations of Langevin dynamics, in which case only a random fraction of the data is used to estimate the gradient. However, this leads to an additional noise in the dynamics and hence a bias on the invariant measure which is sampled by the Markov chain. We advocate using the so-called Adaptive Langevin dynamics, which is a modification of standard inertial Langevin dynamics with a dynamical friction which automatically corrects for the increased noise arising from mini-batching. We investigate the practical relevance of the assumptions underpinning Adaptive Langevin (constant covariance for the estimation of the gradient), which are not satisfied in typical models of Bayesian inference; and show how to extend the approach to more general situations.