N-fold way simulated tempering for pairwise interaction point processes

Pairwise interaction point processes with strong interaction are usually difficult to sample. We discuss how Besag lattice processes can be used in a simulated tempering MCMC scheme to help with the simulation of such processes. We show how the N-fold way algorithm can be used to sample the lattice processes efficiently and introduce the N-fold way algorithm into our simulated tempering scheme. To calibrate the simulated tempering scheme we use the Wang-Landau algorithm

A Dominated Coupling From The Past algorithm for the stochastic simulation of networks of biochemical reactions

<p>Abstract</p> <p>Background</p> <p>In recent years, stochastic descriptions of biochemical reactions based on the Master Equation (ME) have become widespread. These are especially relevant for models involving gene regulation. Gillespie’s Stochastic Simulation Algorithm (SSA) is the most widely used method for the numerical evaluation of these models. The SSA produces exact samples from the distribution of the ME for finite times. However, if the stationary distribution is of interest, the SSA provides no information about convergence or how long the algorithm needs to be run to sample from the stationary distribution with given accuracy. </p> <p>Results</p> <p>We present a proof and numerical characterization of a Perfect Sampling algorithm for the ME of networks of biochemical reactions prevalent in gene regulation and enzymatic catalysis. Our algorithm combines the SSA with Dominated Coupling From The Past (DCFTP) techniques to provide guaranteed sampling from the stationary distribution. The resulting DCFTP-SSA is applicable to networks of reactions with uni-molecular stoichiometries and sub-linear, (anti-) monotone propensity functions. We showcase its applicability studying steady-state properties of stochastic regulatory networks of relevance in synthetic and systems biology.</p> <p>Conclusion</p> <p>The DCFTP-SSA provides an extension to Gillespie’s SSA with guaranteed sampling from the stationary solution of the ME for a broad class of stochastic biochemical networks.</p

A gradient field approach to modelling fibre-generated spatial point processes

A new non-parametric model is introduced for point processes that are clustered along curves or fibres, with additional background noise. The model identifies random curves as integral lines of a gradient field. In principle this enables the inclusion of all possible non-self-intersecting curves with one underlying smoothness constraint. Markov chain Monte Carlo is combined with Empirical Bayes to provide a practical estimation procedure for properties of the underlying fibre distribution, based on the observed point pattern data. Comparisons are made with other techniques in the literature. Illustrations of the methodology include applications to fingerprints, earthquakes and galaxies

Fibre-generated point processes and fields of orientations

This paper introduces a new approach to analyzing spatial point data clustered along or around a system of curves or "fibres." Such data arise in catalogues of galaxy locations, recorded locations of earthquakes, aerial images of minefields and pore patterns on fingerprints. Finding the underlying curvilinear structure of these point-pattern data sets may not only facilitate a better understanding of how they arise but also aid reconstruction of missing data. We base the space of fibres on the set of integral lines of an orientation field. Using an empirical Bayes approach, we estimate the field of orientations from anisotropic features of the data. We then sample from the posterior distribution of fibres, exploring models with different numbers of clusters, fitting fibres to the clusters as we proceed. The Bayesian approach permits inference on various properties of the clusters and associated fibres, and the results perform well on a number of very different curvilinear structures

Inference on point processes with unobserved one-dimensional reference structure

We present a novel approach to examining local anisotropy in planar point processes. Our method is based on a kernel Principal Component Analysis and produces a tensor field that describes local orientation. The approach is illustrated on an example examining pore patterns in ink fingerprints

A Bayesian approach to inferring vascular tree structure from 2D imagery

We describe a method for inferring tree-like vascular structures from 2D imagery. A Markov Chain Monte Carlo (MCMC) algorithm is employed to sample from the posterior distribution given local feature estimates, derived from likelihood maximisation for a Gaussian intensity profile. A multiresolution scheme, in which coarse scale estimates are used to initialise the algorithm for finer scales, has been implemented and used to model retinal images. Results are presented to show the effectiveness of the method