Multidimensional integration through Markovian sampling under steered function morphing: a physical guise from statistical mechanics

We present a computational strategy for the evaluation of multidimensional integrals on hyper-rectangles based on Markovian stochastic exploration of the integration domain while the integrand is being morphed by starting from an initial appropriate profile. Thanks to an abstract reformulation of Jarzynski's equality applied in stochastic thermodynamics to evaluate the free-energy profiles along selected reaction coordinates via non-equilibrium transformations, it is possible to cast the original integral into the exponential average of the distribution of the pseudo-work (that we may term "computational work") involved in doing the function morphing, which is straightforwardly solved. Several tests illustrate the basic implementation of the idea, and show its performance in terms of computational time, accuracy and precision. The formulation for integrand functions with zeros and possible sign changes is also presented. It will be stressed that our usage of Jarzynski's equality shares similarities with a practice already known in statistics as Annealed Importance Sampling (AIS), when applied to computation of the normalizing constants of distributions. In a sense, here we dress the AIS with its "physical" counterpart borrowed from statistical mechanics.Comment: 3 figures Supplementary Material (pdf file named "JEMDI_SI.pdf"

Bayesian Methods for Exoplanet Science

Exoplanet research is carried out at the limits of the capabilities of current telescopes and instruments. The studied signals are weak, and often embedded in complex systematics from instrumental, telluric, and astrophysical sources. Combining repeated observations of periodic events, simultaneous observations with multiple telescopes, different observation techniques, and existing information from theory and prior research can help to disentangle the systematics from the planetary signals, and offers synergistic advantages over analysing observations separately. Bayesian inference provides a self-consistent statistical framework that addresses both the necessity for complex systematics models, and the need to combine prior information and heterogeneous observations. This chapter offers a brief introduction to Bayesian inference in the context of exoplanet research, with focus on time series analysis, and finishes with an overview of a set of freely available programming libraries.Comment: Invited revie

Measuring edge importance: a quantitative analysis of the stochastic shielding approximation for random processes on graphs

Mathematical models of cellular physiological mechanisms often involve random walks on graphs representing transitions within networks of functional states. Schmandt and Gal\'{a}n recently introduced a novel stochastic shielding approximation as a fast, accurate method for generating approximate sample paths from a finite state Markov process in which only a subset of states are observable. For example, in ion channel models, such as the Hodgkin-Huxley or other conductance based neural models, a nerve cell has a population of ion channels whose states comprise the nodes of a graph, only some of which allow a transmembrane current to pass. The stochastic shielding approximation consists of neglecting fluctuations in the dynamics associated with edges in the graph not directly affecting the observable states. We consider the problem of finding the optimal complexity reducing mapping from a stochastic process on a graph to an approximate process on a smaller sample space, as determined by the choice of a particular linear measurement functional on the graph. The partitioning of ion channel states into conducting versus nonconducting states provides a case in point. In addition to establishing that Schmandt and Gal\'{a}n's approximation is in fact optimal in a specific sense, we use recent results from random matrix theory to provide heuristic error estimates for the accuracy of the stochastic shielding approximation for an ensemble of random graphs. Moreover, we provide a novel quantitative measure of the contribution of individual transitions within the reaction graph to the accuracy of the approximate process.Comment: Added one reference, typos corrected in Equation 6 and Appendix C, added the assumption that the graph is irreducible to the main theorem (results unchanged

The exit problem for diffusions with time-periodic drift and stochastic resonance

Physical notions of stochastic resonance for potential diffusions in periodically changing double-well potentials such as the spectral power amplification have proved to be defective. They are not robust for the passage to their effective dynamics: continuous-time finite-state Markov chains describing the rough features of transitions between different domains of attraction of metastable points. In the framework of one-dimensional diffusions moving in periodically changing double-well potentials we design a new notion of stochastic resonance which refines Freidlin's concept of quasi-periodic motion. It is based on exact exponential rates for the transition probabilities between the domains of attraction which are robust with respect to the reduced Markov chains. The quality of periodic tuning is measured by the probability for transition during fixed time windows depending on a time scale parameter. Maximizing it in this parameter produces the stochastic resonance points.Comment: Published at http://dx.doi.org/10.1214/105051604000000530 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

A MATLAB Package for Markov Chain Monte Carlo with a Multi-Unidimensional IRT Model

Unidimensional item response theory (IRT) models are useful when each item is designed to measure some facet of a unified latent trait. In practical applications, items are not necessarily measuring the same underlying trait, and hence the more general multi-unidimensional model should be considered. This paper provides the requisite information and description of software that implements the Gibbs sampler for such models with two item parameters and a normal ogive form. The software developed is written in the MATLAB package IRTmu2no. The package is flexible enough to allow a user the choice to simulate binary response data with multiple dimensions, set the number of total or burn-in iterations, specify starting values or prior distributions for model parameters, check convergence of the Markov chain, as well as obtain Bayesian fit statistics. Illustrative examples are provided to demonstrate and validate the use of the software package.

Copulas in finance and insurance

Copulas provide a potential useful modeling tool to represent the dependence structure among variables and to generate joint distributions by combining given marginal distributions. Simulations play a relevant role in finance and insurance. They are used to replicate efficient frontiers or extremal values, to price options, to estimate joint risks, and so on. Using copulas, it is easy to construct and simulate from multivariate distributions based on almost any choice of marginals and any type of dependence structure. In this paper we outline recent contributions of statistical modeling using copulas in finance and insurance. We review issues related to the notion of copulas, copula families, copula-based dynamic and static dependence structure, copulas and latent factor models and simulation of copulas. Finally, we outline hot topics in copulas with a special focus on model selection and goodness-of-fit testing