A population Monte Carlo scheme with transformed weights and its application to stochastic kinetic models

This paper addresses the problem of Monte Carlo approximation of posterior probability distributions. In particular, we have considered a recently proposed technique known as population Monte Carlo (PMC), which is based on an iterative importance sampling approach. An important drawback of this methodology is the degeneracy of the importance weights when the dimension of either the observations or the variables of interest is high. To alleviate this difficulty, we propose a novel method that performs a nonlinear transformation on the importance weights. This operation reduces the weight variation, hence it avoids their degeneracy and increases the efficiency of the importance sampling scheme, specially when drawing from a proposal functions which are poorly adapted to the true posterior. For the sake of illustration, we have applied the proposed algorithm to the estimation of the parameters of a Gaussian mixture model. This is a very simple problem that enables us to clearly show and discuss the main features of the proposed technique. As a practical application, we have also considered the popular (and challenging) problem of estimating the rate parameters of stochastic kinetic models (SKM). SKMs are highly multivariate systems that model molecular interactions in biological and chemical problems. We introduce a particularization of the proposed algorithm to SKMs and present numerical results.Comment: 35 pages, 8 figure

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

Approximate Bayesian computation methods can be used to evaluate posterior distributions without having to calculate likelihoods. In this paper we discuss and apply an approximate Bayesian computation (ABC) method based on sequential Monte Carlo (SMC) to estimate parameters of dynamical models. We show that ABC SMC gives information about the inferability of parameters and model sensitivity to changes in parameters, and tends to perform better than other ABC approaches. The algorithm is applied to several well known biological systems, for which parameters and their credible intervals are inferred. Moreover, we develop ABC SMC as a tool for model selection; given a range of different mathematical descriptions, ABC SMC is able to choose the best model using the standard Bayesian model selection apparatus.Comment: 26 pages, 9 figure

Robust Covariance Adaptation in Adaptive Importance Sampling

Importance sampling (IS) is a Monte Carlo methodology that allows for approximation of a target distribution using weighted samples generated from another proposal distribution. Adaptive importance sampling (AIS) implements an iterative version of IS which adapts the parameters of the proposal distribution in order to improve estimation of the target. While the adaptation of the location (mean) of the proposals has been largely studied, an important challenge of AIS relates to the difficulty of adapting the scale parameter (covariance matrix). In the case of weight degeneracy, adapting the covariance matrix using the empirical covariance results in a singular matrix, which leads to poor performance in subsequent iterations of the algorithm. In this paper, we propose a novel scheme which exploits recent advances in the IS literature to prevent the so-called weight degeneracy. The method efficiently adapts the covariance matrix of a population of proposal distributions and achieves a significant performance improvement in high-dimensional scenarios. We validate the new method through computer simulations

Continuum variational and diffusion quantum Monte Carlo calculations

This topical review describes the methodology of continuum variational and diffusion quantum Monte Carlo calculations. These stochastic methods are based on many-body wave functions and are capable of achieving very high accuracy. The algorithms are intrinsically parallel and well-suited to petascale computers, and the computational cost scales as a polynomial of the number of particles. A guide to the systems and topics which have been investigated using these methods is given. The bulk of the article is devoted to an overview of the basic quantum Monte Carlo methods, the forms and optimisation of wave functions, performing calculations within periodic boundary conditions, using pseudopotentials, excited-state calculations, sources of calculational inaccuracy, and calculating energy differences and forces

Boosting Bayesian Parameter Inference of Nonlinear Stochastic Differential Equation Models by Hamiltonian Scale Separation

Parameter inference is a fundamental problem in data-driven modeling. Given observed data that is believed to be a realization of some parameterized model, the aim is to find parameter values that are able to explain the observed data. In many situations, the dominant sources of uncertainty must be included into the model, for making reliable predictions. This naturally leads to stochastic models. Stochastic models render parameter inference much harder, as the aim then is to find a distribution of likely parameter values. In Bayesian statistics, which is a consistent framework for data-driven learning, this so-called posterior distribution can be used to make probabilistic predictions. We propose a novel, exact and very efficient approach for generating posterior parameter distributions, for stochastic differential equation models calibrated to measured time-series. The algorithm is inspired by re-interpreting the posterior distribution as a statistical mechanics partition function of an object akin to a polymer, where the measurements are mapped on heavier beads compared to those of the simulated data. To arrive at distribution samples, we employ a Hamiltonian Monte Carlo approach combined with a multiple time-scale integration. A separation of time scales naturally arises if either the number of measurement points or the number of simulation points becomes large. Furthermore, at least for 1D problems, we can decouple the harmonic modes between measurement points and solve the fastest part of their dynamics analytically. Our approach is applicable to a wide range of inference problems and is highly parallelizable.Comment: 15 pages, 8 figure

An Exact Auxiliary Variable Gibbs Sampler for a Class of Diffusions

Stochastic differential equations (SDEs) or diffusions are continuous-valued continuous-time stochastic processes widely used in the applied and mathematical sciences. Simulating paths from these processes is usually an intractable problem, and typically involves time-discretization approximations. We propose an exact Markov chain Monte Carlo sampling algorithm that involves no such time-discretization error. Our sampler is applicable to the problem of prior simulation from an SDE, posterior simulation conditioned on noisy observations, as well as parameter inference given noisy observations. Our work recasts an existing rejection sampling algorithm for a class of diffusions as a latent variable model, and then derives an auxiliary variable Gibbs sampling algorithm that targets the associated joint distribution. At a high level, the resulting algorithm involves two steps: simulating a random grid of times from an inhomogeneous Poisson process, and updating the SDE trajectory conditioned on this grid. Our work allows the vast literature of Monte Carlo sampling algorithms from the Gaussian process literature to be brought to bear to applications involving diffusions. We study our method on synthetic and real datasets, where we demonstrate superior performance over competing methods.Comment: 37 pages, 13 figure

Stochastic weighted particle methods for population balance equations

A class of stochastic algorithms for the numerical treatment of population balance equations is introduced. The algorithms are based on systems of weighted particles, in which coagulation events are modelled by a weight transfer that keeps the number of computational particles constant. The weighting mechanisms are designed in such a way that physical processes changing individual particles (such as growth, or other surface reactions) can be conveniently treated by the algorithms. Numerical experiments are performed for complex laminar premixed flame systems. Two members of the class of stochastic weighted particle methods are compared to each other and to a direct simulation algorithm. One weighted algorithm is shown to be consistently better than the other with respect to the statistical noise generated. Finally, run times to achieve fixed error tolerances for a real flame system are measured and the better weighted algorithm is found to be up to three times faster than the direct simulation algorithm

A comparison of Monte Carlo-based Bayesian parameter estimation methods for stochastic models of genetic networks

We compare three state-of-the-art Bayesian inference methods for the estimation of the unknown parameters in a stochastic model of a genetic network. In particular, we introduce a stochastic version of the paradigmatic synthetic multicellular clock model proposed by Ullner et al., 2007. By introducing dynamical noise in the model and assuming that the partial observations of the system are contaminated by additive noise, we enable a principled mechanism to represent experimental uncertainties in the synthesis of the multicellular system and pave the way for the design of probabilistic methods for the estimation of any unknowns in the model. Within this setup, we tackle the Bayesian estimation of a subset of the model parameters. Specifically, we compare three Monte Carlo based numerical methods for the approximation of the posterior probability density function of the unknown parameters given a set of partial and noisy observations of the system. The schemes we assess are the particle Metropolis-Hastings (PMH) algorithm, the nonlinear population Monte Carlo (NPMC) method and the approximate Bayesian computation sequential Monte Carlo (ABC-SMC) scheme. We present an extensive numerical simulation study, which shows that while the three techniques can effectively solve the problem there are significant differences both in estimation accuracy and computational efficiency