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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…

This is the write-up of three lectures on algorithms for dynamical fermions that were given at the ILFTN workshop 'Perspectives in Lattice QCD' in Nara during November 2005. The first lecture is on the fundamentals of Markov Chain Monte…

We introduce a dynamical fermion algorithm which is based on the hybrid Monte Carlo (HMC) algorithm, but without pseudofermions. The molecular dynamics steps in HMC are retained except the derivatives with respect to the gauge fields are…

This paper studies multi-level stochastic approximation algorithms. Our aim is to extend the scope of the multilevel Monte Carlo method recently introduced by Giles (Giles 2008) to the framework of stochastic optimization by means of…

Novel multi-step predictor-corrector numerical schemes have been derived for approximating decoupled forward-backward stochastic differential equations (FBSDEs). The stability and high order rate of convergence of the schemes are rigorously…

The Expectation-Maximization (EM) algorithm is a popular choice for learning latent variable models. Variants of the EM have been initially introduced, using incremental updates to scale to large datasets, and using Monte Carlo (MC)…

Progressive Hedging is a popular decomposition algorithm for solving multi-stage stochastic optimization problems. A computational bottleneck of this algorithm is that all scenario subproblems have to be solved at each iteration. In this…

The hybrid Monte Carlo (HMC) algorithm is applied for the Bayesian inference of the stochastic volatility (SV) model. We use the HMC algorithm for the Markov chain Monte Carlo updates of volatility variables of the SV model. First we…

In modern lattice simulations, conventional update algorithms do not allow for tunneling between topological sectors at fine lattice spacings. We compare the viability of multiple less commonly used algorithms (metadynamics, instanton…

Hamiltonian Monte Carlo (HMC) algorithms which combine numerical approximation of Hamiltonian dynamics on finite intervals with stochastic refreshment and Metropolis correction are popular sampling schemes, but it is known that they may…

This thesis is focused on the implementation and the application of a novel kind of algorithm which is expected to overcome the limitations of older schemes. This new algorithm is named Multiboson Method. It allows to simulate an arbitrary…

Stochastic gradient Markov chain Monte Carlo (SGMCMC) is a popular class of algorithms for scalable Bayesian inference. However, these algorithms include hyperparameters such as step size or batch size that influence the accuracy of…

On the base of a Feynman-Kac--type formula involving Poisson stochastic processes, recently a Monte Carlo algorithm has been introduced, which describes exactly the real- or imaginary-time evolution of many-body lattice quantum systems. We…

The R algorithm is widely used for simulating two flavours of dynamical staggered fermions. We give a simple proof that the algorithm converges to the desired probability distribution to within O(dt^2) errors, but show that the relevant…

We develop the method of stochastic modified equations (SME), in which stochastic gradient algorithms are approximated in the weak sense by continuous-time stochastic differential equations. We exploit the continuous formulation together…

The question of how to parallelize the stochastic gradient descent (SGD) method has received much attention in the literature. In this paper, we focus instead on batch methods that use a sizeable fraction of the training set at each…

We propose a modification of the Hybrid-Monte-Carlo algorithm that allows for a larger step-size of the integration scheme at constant acceptance rate. The key ingredient is the splitting of the pseudo-fermion action into two parts. We test…

A new version of the two-step multi-boson algorithm is developed with different fermion actions in the multi-boson and noisy Metropolis steps.

Parallel tempering simulates at many quark masses simultaneously, by changing the mass during the simulation while remaining in equilibrium. The algorithm is faster than pure HMC if more than one mass is needed, and works better the smaller…

There has been much recent progress in the understanding and reduction of the computational cost of the Hybrid Monte Carlo algorithm for Lattice QCD as the quark mass parameter is reduced. In this letter we present a new solution to this…