Gabriel Stoltz

Julien Roussel, Gabriel Stoltz

We prove the consistency of Galerkin methods to solve Poisson equations where the differential operator under consideration is the generator of the Langevin dynamics. We show in particular how the hypocoercive nature of this operator can be used at the discrete level to first prove the invertibility of the rigidity matrix, and next provide error bounds on the approximation of the solution of the Poisson equation. We present general convergence results in an abstract setting, as well as explicit convergence rates for a simple one-dimensional example discretized using a tensor basis. Our theoretical findings are illustrated by numerical simulations.

Tony Lelièvre, Geneviève Robin, Inass Sekkat et al.

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.

Max Fathi, Gabriel Stoltz

The discretization of overdamped Langevin dynamics, through schemes such as the Euler-Maruyama method, can be corrected by some acceptance/rejection rule, based on a Metropolis-Hastings criterion for instance. In this case, the invariant measure sampled by the Markov chain is exactly the Boltzmann-Gibbs measure. However, rejections perturb the dynamical consistency of the resulting numerical method with the reference dynamics. We present in this work some modifications of the standard correction of discretizations of overdamped Langevin dynamics on compact spaces by a Metropolis-Hastings procedure, which allow us to either improve the strong order of the numerical method, or to decrease the bias in the estimation of transport coefficients characterizing the effective dynamical behavior of the dynamics. For the latter approach, we rely on modified numerical schemes together with a Barker rule for the acceptance/rejection criterion.

Max Fathi, A. -A. Homman, G. Stoltz

We consider in this work the numerical computation of transport coefficients for Brownian dynamics. We investigate the discretization error arising when simulating the dynamics with the Smart MC algorithm (also known as Metropolis-adjusted Langevin algorithm). We prove that the error is of order one in the time step, when using either the Green-Kubo or the Einstein formula to estimate the transport coefficients. We illustrate our results with numerical simulations.

Noe Blassel, Louis Carillo, Shiva Darshan et al.

We review various numerical approaches to compute transport coefficients in molecular dynamics. These approaches can be broadly classified into three groups: (i) nonequilibrium methods based on applying an external driving field to the system, measuring the average response in the system, and evaluating the related linear response coefficient; (ii) approaches reformulating the transport coefficient of interest through a time correlation function for the equilibrium dynamics (the most popular instances being Green--Kubo and Einstein formulas); (iii) transient techniques, where the transport coefficient can be computed by monitoring the return to the steady state of a dynamics perturbed off its stationary distribution. For all three classes of methods, we provide elements of numerical analysis, allowing to estimate or at least quantify the level of numerical errors in the estimator of the transport coefficient; and also briefly present recent attempts to more efficiently compute transport coefficients with variance reduction approaches such as control variates, importance sampling and coupling methods. The computation of transport coefficients remains nonetheless challenging and will continue requiring research efforts in the foreseeable future.

Inass Sekkat, Gabriel Stoltz

Bayesian inference allows to obtain useful information on the parameters of models, either in computational statistics or more recently in the context of Bayesian Neural Networks. The computational cost of usual Monte Carlo methods for sampling posterior 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, Gaussian minibatching noise), which are not satisfied in typical models of Bayesian inference, and quantify the bias induced by minibatching in this case. We also suggest a possible extension of AdL to further reduce the bias on the posterior distribution, by considering a dynamical friction depending on the current value of the parameter to sample.

Zineb Belkacemi, Paraskevi Gkeka, Tony Lelièvre et al.

Free energy biasing methods have proven to be powerful tools to accelerate the simulation of important conformational changes of molecules by modifying the sampling measure. However, most of these methods rely on the prior knowledge of low-dimensional slow degrees of freedom, i.e. Collective Variables (CV). Alternatively, such CVs can be identified using machine learning (ML) and dimensionality reduction algorithms. In this context, approaches where the CVs are learned in an iterative way using adaptive biasing have been proposed: at each iteration, the learned CV is used to perform free energy adaptive biasing to generate new data and learn a new CV. In this paper, we introduce a new iterative method involving CV learning with autoencoders: Free Energy Biasing and Iterative Learning with AutoEncoders (FEBILAE). Our method includes a reweighting scheme to ensure that the learning model optimizes the same loss at each iteration, and achieves CV convergence. Using the alanine dipeptide system and the solvated chignolin mini-protein system as examples, we present results of our algorithm using the extended adaptive biasing force as the free energy adaptive biasing method.

Grégoire Ferré, Gabriel Stoltz

We consider the numerical analysis of the time discretization of Feynman-Kac semigroups associated with diffusion processes. These semigroups naturally appear in several fields, such as large deviation theory, Diffusion Monte Carlo or non-linear filtering. We present errors estimates a la Talay-Tubaro on their invariant measures when the underlying continuous stochastic differential equation is discretized; as well as on the leading eigenvalue of the generator of the dynamics, which corresponds to the rate of creation of probability. This provides criteria to construct efficient integration schemes of Feynman-Kac dynamics, as well as a mathematical justification of numerical results already observed in the Diffusion Monte Carlo community. Our analysis is illustrated by numerical simulations.