Related papers: MLIMC: Machine learning-based implicit-solvent Mon…

Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum…

Advanced algorithms are necessary to obtain faster-than-real-time dynamic simulations in a number of different physical problems that are characterized by widely disparate time scales. Recent advanced dynamic Monte Carlo algorithms that…

Purpose: Multiple Coulomb scattering (MCS) poses a challenge in proton CT (pCT) image reconstruction. The assumption of straight paths is replaced with Bayesian models of the most likely path (MLP). Current MLP-based pCT reconstruction…

Constructing unbiased estimators from Markov chain Monte Carlo (MCMC) outputs is a difficult problem that has recently received a lot of attention in the statistics and machine learning communities. However, the current unbiased MCMC…

This paper presents an efficient solution to 3D-LiDAR-based Monte Carlo localization (MCL). MCL robustly works if particles are exactly sampled around the ground truth. An inertial navigation system (INS) can be used for accurate sampling,…

A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…

Machine learning (ML) can be used to construct surrogate models for the fast prediction of a property of interest. ML can thus be applied to chemical projects, where the usual experimentation or calculation techniques can take hours or days…

Explicit machine learning-based model predictive control (explicit ML-MPC) has been developed to reduce the real-time computational demands of traditional ML-MPC. However, the evaluation of candidate control actions in explicit ML-MPC can…

Bayesian analysis is widely used in science and engineering for real-time forecasting, decision making, and to help unravel the processes that explain the observed data. These data are some deterministic and/or stochastic transformations of…

Markov chain Monte Carlo (MCMC) is widely used for Bayesian inference in models of complex systems. Performance, however, is often unsatisfactory in models with many latent variables due to so-called poor mixing, necessitating development…

In many problems, complex non-Gaussian and/or nonlinear models are required to accurately describe a physical system of interest. In such cases, Monte Carlo algorithms are remarkably flexible and extremely powerful approaches to solve such…

Modeling the response of material and chemical systems to electric fields remains a longstanding challenge. Machine learning interatomic potentials (MLIPs) offer an efficient and scalable alternative to quantum mechanical methods but do not…

We introduce Projected Latent Markov Chain Monte Carlo (PL-MCMC), a technique for sampling from the high-dimensional conditional distributions learned by a normalizing flow. We prove that a Metropolis-Hastings implementation of PL-MCMC…

Being the most classical generative model for serial data, state-space models (SSM) are fundamental in AI and statistical machine learning. In SSM, any form of parameter learning or latent state inference typically involves the computation…

Sequential Monte Carlo (SMC) methods are a widely used set of computational tools for inference in non-linear non-Gaussian state-space models. We propose a new SMC algorithm to compute the expectation of additive functionals recursively.…

Artifacts arise in the simulations of electrolytes using periodic boundary conditions (PBC). We show the origin of these artifacts are the periodic image charges and the constraint of charge neutrality inside the simulation box, both of…

Hamiltonian Monte Carlo (HMC) is a popular Markov chain Monte Carlo (MCMC) algorithm that generates proposals for a Metropolis-Hastings algorithm by simulating the dynamics of a Hamiltonian system. However, HMC is sensitive to large time…

Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…

A common way to simulate the transport and spread of pollutants in the atmosphere is via stochastic Lagrangian dispersion models. Mathematically, these models describe turbulent transport processes with stochastic differential equations…

Efficient uncertainty quantification algorithms are key to understand the propagation of uncertainty -- from uncertain input parameters to uncertain output quantities -- in high resolution mathematical models of brain physiology. Advanced…