Bayesian Inference in Hidden Markov Random Fields for Binary Data Defined on Large Lattices
Friel, N.; Pettitt, A.N.; Reeves, R.; Wit, E.
2009-01-01
Hidden Markov random fields represent a complex hierarchical model, where the hidden latent process is an undirected graphical structure. Performing inference for such models is difficult primarily because the likelihood of the hidden states is often unavailable. The main contribution of this articl
Bayesian Parameter Estimation for Latent Markov Random Fields and Social Networks
Everitt, Richard G
2012-01-01
Undirected graphical models are widely used in statistics, physics and machine vision. However Bayesian parameter estimation for undirected models is extremely challenging, since evaluation of the posterior typically involves the calculation of an intractable normalising constant. This problem has received much attention, but very little of this has focussed on the important practical case where the data consists of noisy or incomplete observations of the underlying hidden structure. This paper specifically addresses this problem, comparing two alternative methodologies. In the first of these approaches particle Markov chain Monte Carlo (Andrieu et al., 2010) is used to efficiently explore the parameter space, combined with the exchange algorithm (Murray et al., 2006) for avoiding the calculation of the intractable normalising constant (a proof showing that this combination targets the correct distribution in found in a supplementary appendix online). This approach is compared with approximate Bayesian comput...
Fusion of Hidden Markov Random Field models and its Bayesian estimation.
Destrempes, François; Angers, Jean-François; Mignotte, Max
2006-10-01
In this paper, we present a Hidden Markov Random Field (HMRF) data-fusion model. The proposed model is applied to the segmentation of natural images based on the fusion of colors and textons into Julesz ensembles. The corresponding Exploration/ Selection/Estimation (ESE) procedure for the estimation of the parameters is presented. This method achieves the estimation of the parameters of the Gaussian kernels, the mixture proportions, the region labels, the number of regions, and the Markov hyper-parameter. Meanwhile, we present a new proof of the asymptotic convergence of the ESE procedure, based on original finite time bounds for the rate of convergence. PMID:17022259
Bayesian Posterior Distributions Without Markov Chains
Cole, Stephen R.; Chu, Haitao; Greenland, Sander; Hamra, Ghassan; Richardson, David B.
2012-01-01
Bayesian posterior parameter distributions are often simulated using Markov chain Monte Carlo (MCMC) methods. However, MCMC methods are not always necessary and do not help the uninitiated understand Bayesian inference. As a bridge to understanding Bayesian inference, the authors illustrate a transparent rejection sampling method. In example 1, they illustrate rejection sampling using 36 cases and 198 controls from a case-control study (1976–1983) assessing the relation between residential ex...
Markov Random Field Surface Reconstruction
DEFF Research Database (Denmark)
Paulsen, Rasmus Reinhold; Bærentzen, Jakob Andreas; Larsen, Rasmus
2010-01-01
A method for implicit surface reconstruction is proposed. The novelty in this paper is the adaption of Markov Random Field regularization of a distance field. The Markov Random Field formulation allows us to integrate both knowledge about the type of surface we wish to reconstruct (the prior) and...
Bayesian analysis of Markov point processes
DEFF Research Database (Denmark)
Berthelsen, Kasper Klitgaard; Møller, Jesper
2006-01-01
Recently Møller, Pettitt, Berthelsen and Reeves introduced a new MCMC methodology for drawing samples from a posterior distribution when the likelihood function is only specified up to a normalising constant. We illustrate the method in the setting of Bayesian inference for Markov point processes...
Bayesian variable order Markov models: Towards Bayesian predictive state representations
C. Dimitrakakis
2009-01-01
We present a Bayesian variable order Markov model that shares many similarities with predictive state representations. The resulting models are compact and much easier to specify and learn than classical predictive state representations. Moreover, we show that they significantly outperform a more st
Energy Technology Data Exchange (ETDEWEB)
Kulkarni, Ramaprasad; Tuller, Markus; Fink, Wolfgang; Wildschild, Dorthe (Oregon State U.); (Ariz)
2012-07-27
Advancements in noninvasive imaging methods such as X-ray computed tomography (CT) have led to a recent surge of applications in porous media research with objectives ranging from theoretical aspects of pore-scale fluid and interfacial dynamics to practical applications such as enhanced oil recovery and advanced contaminant remediation. While substantial efforts and resources have been devoted to advance CT technology, microscale analysis, and fluid dynamics simulations, the development of efficient and stable three-dimensional multiphase image segmentation methods applicable to large data sets is lacking. To eliminate the need for wet-dry or dual-energy scans, image alignment, and subtraction analysis, commonly applied in X-ray micro-CT, a segmentation method based on a Bayesian Markov random field (MRF) framework amenable to true three-dimensional multiphase processing was developed and evaluated. Furthermore, several heuristic and deterministic combinatorial optimization schemes required to solve the labeling problem of the MRF image model were implemented and tested for computational efficiency and their impact on segmentation results. Test results for three grayscale data sets consisting of dry glass beads, partially saturated glass beads, and partially saturated crushed tuff obtained with synchrotron X-ray micro-CT demonstrate great potential of the MRF image model for three-dimensional multiphase segmentation. While our results are promising and the developed algorithm is stable and computationally more efficient than other commonly applied porous media segmentation models, further potential improvements exist for fully automated operation.
Limit theorems for Markov random fields
International Nuclear Information System (INIS)
Markov Random Fields (MRF's) have been extensively applied in Statistical Mechanics as well as in Bayesian Image Analysis. MRF's are a special class of dependent random variables located at the vertices of a graph whose joint distribution includes a parameter called the temperature. When the number of vertices of the graph tends to infinity, the normalized distribution of statistics based on these random variables converge in distribution. It can happen that for certain values of the temperature, that the rate of growth of these normalizing constants change drastically. This feature is generally used to explain the phenomenon of phase transition as understood by physicist. In this dissertation the author will show that this drastic change in normalizing constants occurs even in the relatively smooth case when all the random variables are Gaussian. Hence any image analytic MRF ought to be checked for such discontinuous behavior before any analysis is performed. Mixed limit theorems in Bayesian Image Analysis seek to replace intensive simulations of MRF's with limit theorems that approximate the distribution of the MRF's as the number of sites increases. The problem of deriving mixed limit theorems for MRF's on a one dimensional lattice graph with an acceptor function that has a second moment has been studied by Chow. A mixed limit theorem for the integer lattice graph is derived when the acceptor function does not have a second moment as for instance when the acceptor function is a symmetric stable density of index 0 < α < 2
Markov Model of Wind Power Time Series UsingBayesian Inference of Transition Matrix
Chen, Peiyuan; Berthelsen, Kasper Klitgaard; Bak-Jensen, Birgitte; Chen, Zhe
2009-01-01
This paper proposes to use Bayesian inference of transition matrix when developing a discrete Markov model of a wind speed/power time series and 95% credible interval for the model verification. The Dirichlet distribution is used as a conjugate prior for the transition matrix. Three discrete Markov models are compared, i.e. the basic Markov model, the Bayesian Markov model and the birth-and-death Markov model. The proposed Bayesian Markov model shows the best accuracy in modeling the autocorr...
Markov Chain Monte Carlo Bayesian Learning for Neural Networks
Goodrich, Michael S.
2011-01-01
Conventional training methods for neural networks involve starting al a random location in the solution space of the network weights, navigating an error hyper surface to reach a minimum, and sometime stochastic based techniques (e.g., genetic algorithms) to avoid entrapment in a local minimum. It is further typically necessary to preprocess the data (e.g., normalization) to keep the training algorithm on course. Conversely, Bayesian based learning is an epistemological approach concerned with formally updating the plausibility of competing candidate hypotheses thereby obtaining a posterior distribution for the network weights conditioned on the available data and a prior distribution. In this paper, we developed a powerful methodology for estimating the full residual uncertainty in network weights and therefore network predictions by using a modified Jeffery's prior combined with a Metropolis Markov Chain Monte Carlo method.
Bayesian analysis of variable-order, reversible Markov chains
Bacallado, Sergio
2011-01-01
We define a conjugate prior for the reversible Markov chain of order $r$. The prior arises from a partially exchangeable reinforced random walk, in the same way that the Beta distribution arises from the exchangeable Poly\\'{a} urn. An extension to variable-order Markov chains is also derived. We show the utility of this prior in testing the order and estimating the parameters of a reversible Markov model.
Bayesian internal dosimetry calculations using Markov Chain Monte Carlo
International Nuclear Information System (INIS)
A new numerical method for solving the inverse problem of internal dosimetry is described. The new method uses Markov Chain Monte Carlo and the Metropolis algorithm. Multiple intake amounts, biokinetic types, and times of intake are determined from bioassay data by integrating over the Bayesian posterior distribution. The method appears definitive, but its application requires a large amount of computing time. (author)
A Bayesian Markov geostatistical model for estimation of hydrogeological properties
International Nuclear Information System (INIS)
A geostatistical methodology based on Markov-chain analysis and Bayesian statistics was developed for probability estimations of hydrogeological and geological properties in the siting process of a nuclear waste repository. The probability estimates have practical use in decision-making on issues such as siting, investigation programs, and construction design. The methodology is nonparametric which makes it possible to handle information that does not exhibit standard statistical distributions, as is often the case for classified information. Data do not need to meet the requirements on additivity and normality as with the geostatistical methods based on regionalized variable theory, e.g., kriging. The methodology also has a formal way for incorporating professional judgments through the use of Bayesian statistics, which allows for updating of prior estimates to posterior probabilities each time new information becomes available. A Bayesian Markov Geostatistical Model (BayMar) software was developed for implementation of the methodology in two and three dimensions. This paper gives (1) a theoretical description of the Bayesian Markov Geostatistical Model; (2) a short description of the BayMar software; and (3) an example of application of the model for estimating the suitability for repository establishment with respect to the three parameters of lithology, hydraulic conductivity, and rock quality designation index (RQD) at 400--500 meters below ground surface in an area around the Aespoe Hard Rock Laboratory in southeastern Sweden
State-feedback stabilization of Markov jump linear systems with randomly observed Markov states
Ogura, Masaki; Cetinkaya, Ahmet
2014-01-01
In this paper we study the state-feedback stabilization of a discrete-time Markov jump linear system when the observation of the Markov chain of the system, called the Markov state, is time-randomized by another Markov chain. Embedding the Markov state into an extended Markov chain, we transform the given system with time-randomized observations to another one having the enlarged Markov-state space but with so-called cluster observations of Markov states. Based on this transformation we propo...
Illumination Invariants Based on Markov Random Fields
Czech Academy of Sciences Publication Activity Database
Vácha, Pavel; Haindl, Michal
Vukovar, Croatia : In-Teh, 2010 - (Herout, A.), s. 253-272 ISBN 978-953-7619-90-9 R&D Projects: GA MŠk 1M0572; GA ČR GA102/08/0593 Grant ostatní: GA MŠk(CZ) 2C06019 Institutional research plan: CEZ:AV0Z10750506 Keywords : illumination invariants * textural features * Markov random fields Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2010/RO/vacha-illumination invariants based on markov random fields.pdf
One-Dimensional Markov Random Fields, Markov Chains and Topological Markov Fields
Chandgotia, N; G. Han; Marcus, B; Meyerovitch, T; Pavlov, R
2014-01-01
In this paper we show that any one-dimensional stationary, finite-valued Markov Random Field (MRF) is a Markov chain, without any mixing condition or condition on the support. Our proof makes use of two properties of the support $X$ of a finite-valued stationary MRF: 1) $X$ is non-wandering (this is a property of the support of any finite-valued stationary process) and 2) $X$ is a topological Markov field (TMF). The latter is a new property that sits in between the classes of shifts of finite...
Markov Random Fields on Triangle Meshes
DEFF Research Database (Denmark)
Andersen, Vedrana; Aanæs, Henrik; Bærentzen, Jakob Andreas;
2010-01-01
In this paper we propose a novel anisotropic smoothing scheme based on Markov Random Fields (MRF). Our scheme is formulated as two coupled processes. A vertex process is used to smooth the mesh by displacing the vertices according to a MRF smoothness prior, while an independent edge process labels...
Super-Resolution Using Hidden Markov Model and Bayesian Detection Estimation Framework
Humblot, Fabrice; Mohammad-Djafari, Ali
2006-12-01
This paper presents a new method for super-resolution (SR) reconstruction of a high-resolution (HR) image from several low-resolution (LR) images. The HR image is assumed to be composed of homogeneous regions. Thus, the a priori distribution of the pixels is modeled by a finite mixture model (FMM) and a Potts Markov model (PMM) for the labels. The whole a priori model is then a hierarchical Markov model. The LR images are assumed to be obtained from the HR image by lowpass filtering, arbitrarily translation, decimation, and finally corruption by a random noise. The problem is then put in a Bayesian detection and estimation framework, and appropriate algorithms are developed based on Markov chain Monte Carlo (MCMC) Gibbs sampling. At the end, we have not only an estimate of the HR image but also an estimate of the classification labels which leads to a segmentation result.
Super-Resolution Using Hidden Markov Model and Bayesian Detection Estimation Framework
Directory of Open Access Journals (Sweden)
Humblot Fabrice
2006-01-01
Full Text Available This paper presents a new method for super-resolution (SR reconstruction of a high-resolution (HR image from several low-resolution (LR images. The HR image is assumed to be composed of homogeneous regions. Thus, the a priori distribution of the pixels is modeled by a finite mixture model (FMM and a Potts Markov model (PMM for the labels. The whole a priori model is then a hierarchical Markov model. The LR images are assumed to be obtained from the HR image by lowpass filtering, arbitrarily translation, decimation, and finally corruption by a random noise. The problem is then put in a Bayesian detection and estimation framework, and appropriate algorithms are developed based on Markov chain Monte Carlo (MCMC Gibbs sampling. At the end, we have not only an estimate of the HR image but also an estimate of the classification labels which leads to a segmentation result.
A Hidden Markov model for Bayesian data fusion of multivariate signals
Féron, O; Feron, Olivier; Mohammad-Djafari, Ali
2004-01-01
In this work we propose a Bayesian framework for data fusion of multivariate signals which arises in imaging systems. More specifically, we consider the case where we have observed two images of the same object through two different imaging processes. The objective of this work is then to propose a coherent approach to combine these data sets to obtain a segmented image which can be considered as the fusion result of these two images. The proposed approach is based on a Hidden Markov Modeling (HMM) of the images with common segmentation, or equivalently, with common hidden classification label variables which is modeled by the Potts Markov Random Field. We propose then an appropriate Markov Chain Monte Carlo (MCMC) algorithm to implement the method and show some simulation results and applications.
The ensemble of random Markov matrices
International Nuclear Information System (INIS)
The ensemble of random Markov matrices is introduced as a set of Markov or stochastic matrices with the maximal Shannon entropy. The statistical properties of the stationary distribution π, the average entropy growth rate h and the second-largest eigenvalue ν across the ensemble are studied. It is shown and heuristically proven that the entropy growth rate and second-largest eigenvalue of Markov matrices scale on average with the dimension of the matrices d as h∼log(O(d)) and |ν|∼d−1/2, respectively, yielding the asymptotic relation hτc∼1/2 between the entropy h and the correlation decay time τ = −1/log|ν|. Additionally, the correlation between h and τc is analysed; it decreases with increasing dimension d
Bayesian Smoothing Algorithms in Partially Observed Markov Chains
Ait-el-Fquih, Boujemaa; Desbouvries, François
2006-11-01
Let x = {xn}n∈N be a hidden process, y = {yn}n∈N an observed process and r = {rn}n∈N some auxiliary process. We assume that t = {tn}n∈N with tn = (xn, rn, yn-1) is a (Triplet) Markov Chain (TMC). TMC are more general than Hidden Markov Chains (HMC) and yet enable the development of efficient restoration and parameter estimation algorithms. This paper is devoted to Bayesian smoothing algorithms for TMC. We first propose twelve algorithms for general TMC. In the Gaussian case, these smoothers reduce to a set of algorithms which include, among other solutions, extensions to TMC of classical Kalman-like smoothing algorithms (originally designed for HMC) such as the RTS algorithms, the Two-Filter algorithms or the Bryson and Frazier algorithm.
Collaborative filtering via sparse Markov random fields
Tran, Truyen; Phung, Dinh; Venkatesh, Svetha
2016-01-01
Recommender systems play a central role in providing individualized access to information and services. This paper focuses on collaborative filtering, an approach that exploits the shared structure among mind-liked users and similar items. In particular, we focus on a formal probabilistic framework known as Markov random fields (MRF). We address the open problem of structure learning and introduce a sparsity-inducing algorithm to automatically estimate the interaction structures between users...
Gaussian Markov random fields theory and applications
Rue, Havard
2005-01-01
Gaussian Markov Random Field (GMRF) models are most widely used in spatial statistics - a very active area of research in which few up-to-date reference works are available. This is the first book on the subject that provides a unified framework of GMRFs with particular emphasis on the computational aspects. This book includes extensive case-studies and, online, a c-library for fast and exact simulation. With chapters contributed by leading researchers in the field, this volume is essential reading for statisticians working in spatial theory and its applications, as well as quantitative researchers in a wide range of science fields where spatial data analysis is important.
ON MARKOV CHAINS IN SPACE-TIME RANDOM ENVIRONMENTS
Institute of Scientific and Technical Information of China (English)
Hu Dihe; Hu Xiaoyu
2009-01-01
In Section 1, the authors establish the models of two kinds of Markov chains in space-time random environments (MCSTRE and MCSTRE(+)) with Abstract state space. In Section 2, the authors construct a MCSTRE and a MCSTRE(+) by an initial distribution Ф and a random Markov kernel (RMK) p(γ). In Section 3, the authors establish several equivalence theorems on MCSTRE and MCSTRE(+). Finally, the authors give two very important examples of MCMSTRE, the random walk in spce-time random environment and the Markov branching chain in space-time random environment.
Markov Model of Wind Power Time Series UsingBayesian Inference of Transition Matrix
DEFF Research Database (Denmark)
Chen, Peiyuan; Berthelsen, Kasper Klitgaard; Bak-Jensen, Birgitte;
2009-01-01
This paper proposes to use Bayesian inference of transition matrix when developing a discrete Markov model of a wind speed/power time series and 95% credible interval for the model verification. The Dirichlet distribution is used as a conjugate prior for the transition matrix. Three discrete Markov...
The Laplace Functional and Moments for Markov Branching Chains in Random Environments
Institute of Scientific and Technical Information of China (English)
HU Di-he; ZHANG Shu-lin
2005-01-01
The concepts of random Markov matrix, Markov branching chain in random environment (MBCRE) and Laplace functional of Markov branching chain in random environment (LFMBCRE) are introduced. The properties of LFMBCRE and the explicit formulas of moments of MBCRE are given.
Bayesian inference for Markov jump processes with informative observations.
Golightly, Andrew; Wilkinson, Darren J
2015-04-01
In this paper we consider the problem of parameter inference for Markov jump process (MJP) representations of stochastic kinetic models. Since transition probabilities are intractable for most processes of interest yet forward simulation is straightforward, Bayesian inference typically proceeds through computationally intensive methods such as (particle) MCMC. Such methods ostensibly require the ability to simulate trajectories from the conditioned jump process. When observations are highly informative, use of the forward simulator is likely to be inefficient and may even preclude an exact (simulation based) analysis. We therefore propose three methods for improving the efficiency of simulating conditioned jump processes. A conditioned hazard is derived based on an approximation to the jump process, and used to generate end-point conditioned trajectories for use inside an importance sampling algorithm. We also adapt a recently proposed sequential Monte Carlo scheme to our problem. Essentially, trajectories are reweighted at a set of intermediate time points, with more weight assigned to trajectories that are consistent with the next observation. We consider two implementations of this approach, based on two continuous approximations of the MJP. We compare these constructs for a simple tractable jump process before using them to perform inference for a Lotka-Volterra system. The best performing construct is used to infer the parameters governing a simple model of motility regulation in Bacillus subtilis. PMID:25720091
Ensemble bayesian model averaging using markov chain Monte Carlo sampling
Energy Technology Data Exchange (ETDEWEB)
Vrugt, Jasper A [Los Alamos National Laboratory; Diks, Cees G H [NON LANL; Clark, Martyn P [NON LANL
2008-01-01
Bayesian model averaging (BMA) has recently been proposed as a statistical method to calibrate forecast ensembles from numerical weather models. Successful implementation of BMA however, requires accurate estimates of the weights and variances of the individual competing models in the ensemble. In their seminal paper (Raftery etal. Mon Weather Rev 133: 1155-1174, 2(05)) has recommended the Expectation-Maximization (EM) algorithm for BMA model training, even though global convergence of this algorithm cannot be guaranteed. In this paper, we compare the performance of the EM algorithm and the recently developed Differential Evolution Adaptive Metropolis (DREAM) Markov Chain Monte Carlo (MCMC) algorithm for estimating the BMA weights and variances. Simulation experiments using 48-hour ensemble data of surface temperature and multi-model stream-flow forecasts show that both methods produce similar results, and that their performance is unaffected by the length of the training data set. However, MCMC simulation with DREAM is capable of efficiently handling a wide variety of BMA predictive distributions, and provides useful information about the uncertainty associated with the estimated BMA weights and variances.
Fast MCMC sampling for Markov jump processes and continuous time Bayesian networks
Rao, Vinayak
2012-01-01
Markov jump processes and continuous time Bayesian networks are important classes of continuous time dynamical systems. In this paper, we tackle the problem of inferring unobserved paths in these models by introducing a fast auxiliary variable Gibbs sampler. Our approach is based on the idea of uniformization, and sets up a Markov chain over paths by sampling a finite set of virtual jump times and then running a standard hidden Markov model forward filtering-backward sampling algorithm over states at the set of extant and virtual jump times. We demonstrate significant computational benefits over a state-of-the-art Gibbs sampler on a number of continuous time Bayesian networks.
Approximate recursive calculations of discrete Markov random fields
Arnesen, Petter
2010-01-01
In this thesis we present an approximate recursive algorithm for calculations of discrete Markov random fields defined on graphs. We write the probability distribution of a Markov random field as a function of interaction parameters, a representation well suited for approximations. The algorithm we establish is a forward-backward algorithm, where the forward part recursively decomposes the probability distribution into a product of conditional distributions. Next we establish two different ba...
Institute of Scientific and Technical Information of China (English)
LIU; Jianfeng; ZHANG; Yuan; ZHANG; Qin; WANG; Lixian; ZHANG; Jigang
2006-01-01
It is a challenging issue to map Quantitative Trait Loci (QTL) underlying complex discrete traits, which usually show discontinuous distribution and less information, using conventional statistical methods. Bayesian-Markov chain Monte Carlo (Bayesian-MCMC) approach is the key procedure in mapping QTL for complex binary traits, which provides a complete posterior distribution for QTL parameters using all prior information. As a consequence, Bayesian estimates of all interested variables can be obtained straightforwardly basing on their posterior samples simulated by the MCMC algorithm. In our study, utilities of Bayesian-MCMC are demonstrated using simulated several animal outbred full-sib families with different family structures for a complex binary trait underlied by both a QTL and polygene. Under the Identity-by-Descent-Based variance component random model, three samplers basing on MCMC, including Gibbs sampling, Metropolis algorithm and reversible jump MCMC, were implemented to generate the joint posterior distribution of all unknowns so that the QTL parameters were obtained by Bayesian statistical inferring. The results showed that Bayesian-MCMC approach could work well and robust under different family structures and QTL effects. As family size increases and the number of family decreases, the accuracy of the parameter estimates will be improved. When the true QTL has a small effect, using outbred population experiment design with large family size is the optimal mapping strategy.
Bayesian inference of BWR model parameters by Markov chain Monte Carlo
International Nuclear Information System (INIS)
In this paper, the Markov chain Monte Carlo approach to Bayesian inference is applied for estimating the parameters of a reduced-order model of the dynamics of a boiling water reactor system. A Bayesian updating strategy is devised to progressively refine the estimates, as newly measured data become available. Finally, the technique is used for detecting parameter changes during the system lifetime, e.g. due to component degradation
Infinitely dimensional control Markov branching chains in random environments
Institute of Scientific and Technical Information of China (English)
HU; Dihe
2006-01-01
First of all we introduce the concepts of infinitely dimensional control Markov branching chains in random environments (β-MBCRE) and prove the existence of such chains, then we introduce the concepts of conditional generating functionals and random Markov transition functions of such chains and investigate their branching property. Base on these concepts we calculate the moments of the β-MBCRE and obtain the main results of this paper such as extinction probabilities, polarization and proliferation rate. Finally we discuss the classification ofβ-MBCRE according to the different standards.
Random billiards with wall temperature and associated Markov chains
Cook, Scott; Feres, Renato
2012-01-01
By a random billiard we mean a billiard system in which the standard specular reflection rule is replaced with a Markov transition probabilities operator P that, at each collision of the billiard particle with the boundary of the billiard domain, gives the probability distribution of the post-collision velocity for a given pre-collision velocity. A random billiard with microstructure (RBM) is a random billiard for which P is derived from a choice of geometric/mechanical structure on the bound...
On the recurrence set of planar Markov Random Walks
Hervé, Loïc
2012-01-01
In this paper, we investigate the properties of recurrent planar Markov random walks. More precisely, we study the set of recurrent points with the use of local limit theorems. The Nagaev-Guivarc'h spectral method provides several examples for which these local limit theorems are satisfied as soon as the (standard or non-standard) central limit theorem holds.
Efficient Incorporation of Markov Random Fields in Change Detection
DEFF Research Database (Denmark)
Aanæs, Henrik; Nielsen, Allan Aasbjerg; Carstensen, Jens Michael;
2009-01-01
efficient optimization methods or numerical solvers. We here address the issue of efficient incorporation of local homogeneity constraints into change detection algorithms. We do this by exploiting recent advances in graph based algorithms for Markov Random Fields. This is combined with an IR-MAD change...
Markov Random Fields on Triangle Meshes
DEFF Research Database (Denmark)
Andersen, Vedrana; Aanæs, Henrik; Bærentzen, Jakob Andreas;
2010-01-01
In this paper we propose a novel anisotropic smoothing scheme based on Markov Random Fields (MRF). Our scheme is formulated as two coupled processes. A vertex process is used to smooth the mesh by displacing the vertices according to a MRF smoothness prior, while an independent edge process label...
Bayesian estimation for a parametric Markov Renewal model applied to seismic data
Epifani, I.; Ladelli, L.; Pievatolo, A.
2014-01-01
This paper presents a complete methodology for Bayesian inference on a semi-Markov process, from the elicitation of the prior distribution, to the computation of posterior summaries, including a guidance for its implementation. The inter-occurrence times (conditional on the transition between two given states) are assumed to be Weibull-distributed. We examine the elicitation of the joint prior density of the shape and scale parameters of the Weibull distributions, deriving a specific class of...
The construction of Markov processes in random environments and the equivalence theorems
Institute of Scientific and Technical Information of China (English)
HU Dihe
2004-01-01
In sec.1, we introduce several basic concepts such as random transition function, p-m process and Markov process in random environment and give some examples to construct a random transition function from a non-homogeneous density function. In sec.2, we construct the Markov process in random enviromment and skew product Markov process by p - m process and investigate the properties of Markov process in random environment and the original process and environment process and skew product process. In sec. 3, we give several equivalence theorems on Markov process in random environment.
Improving randomness characterization through Bayesian model selection
R., Rafael Díaz-H; Martínez, Alí M Angulo; U'Ren, Alfred B; Hirsch, Jorge G; Marsili, Matteo; Castillo, Isaac Pérez
2016-01-01
Nowadays random number generation plays an essential role in technology with important applications in areas ranging from cryptography, which lies at the core of current communication protocols, to Monte Carlo methods, and other probabilistic algorithms. In this context, a crucial scientific endeavour is to develop effective methods that allow the characterization of random number generators. However, commonly employed methods either lack formality (e.g. the NIST test suite), or are inapplicable in principle (e.g. the characterization derived from the Algorithmic Theory of Information (ATI)). In this letter we present a novel method based on Bayesian model selection, which is both rigorous and effective, for characterizing randomness in a bit sequence. We derive analytic expressions for a model's likelihood which is then used to compute its posterior probability distribution. Our method proves to be more rigorous than NIST's suite and the Borel-Normality criterion and its implementation is straightforward. We...
Braak, ter C.J.F.
2004-01-01
Differential Evolution (DE) is a simple genetic algorithm for numerical optimization in real parameter spaces. In a statistical context one would not just want the optimum but also its uncertainty. The uncertainty distribution can be obtained by a Bayesian analysis (after specifying prior and likeli
Inferring Team Strengths Using a Discrete Markov Random Field
Zech, John; Wood, Frank
2013-01-01
We propose an original model for inferring team strengths using a Markov Random Field, which can be used to generate historical estimates of the offensive and defensive strengths of a team over time. This model was designed to be applied to sports such as soccer or hockey, in which contest outcomes take value in a limited discrete space. We perform inference using a combination of Expectation Maximization and Loopy Belief Propagation. The challenges of working with a non-convex optimization p...
Linear and Parallel Learning of Markov Random Fields
Mizrahi, Yariv Dror; Denil, Misha; De Freitas, Nando
2013-01-01
We introduce a new embarrassingly parallel parameter learning algorithm for Markov random fields with untied parameters which is efficient for a large class of practical models. Our algorithm parallelizes naturally over cliques and, for graphs of bounded degree, its complexity is linear in the number of cliques. Unlike its competitors, our algorithm is fully parallel and for log-linear models it is also data efficient, requiring only the local sufficient statistics of the data to estimate par...
CHARACTERIZATION OF MARKOV-BERNOULLI GEOMETRIC DISTRIBUTION RELATED TO RANDOM SUMS
Mohamed Gharib; Ramadan, Mahmoud M.; Khaled A.H. Al-Ajmi
2014-01-01
The Markov-Bernoulli geometric distribution is obtained when a generalization, as a Markov process, of the independent Bernoulli sequence of random variables is introduced by considering the success probability changes with respect to the Markov chain. The resulting model is called the Markov- Bernoulli model and it has a wide variety of application fields. In this study, some characterizations are given concerning the Markov-Bernoulli geometric distribution as the distribution of the summati...
Multiple testing for neuroimaging via hidden Markov random field.
Shu, Hai; Nan, Bin; Koeppe, Robert
2015-09-01
Traditional voxel-level multiple testing procedures in neuroimaging, mostly p-value based, often ignore the spatial correlations among neighboring voxels and thus suffer from substantial loss of power. We extend the local-significance-index based procedure originally developed for the hidden Markov chain models, which aims to minimize the false nondiscovery rate subject to a constraint on the false discovery rate, to three-dimensional neuroimaging data using a hidden Markov random field model. A generalized expectation-maximization algorithm for maximizing the penalized likelihood is proposed for estimating the model parameters. Extensive simulations show that the proposed approach is more powerful than conventional false discovery rate procedures. We apply the method to the comparison between mild cognitive impairment, a disease status with increased risk of developing Alzheimer's or another dementia, and normal controls in the FDG-PET imaging study of the Alzheimer's Disease Neuroimaging Initiative. PMID:26012881
Dynamics of market indices, Markov chains, and random walking problem
Krivoruchenko, M I
2001-01-01
Dynamics of the major USA market indices DJIA, S&P, Nasdaq, and NYSE is analyzed from the point of view of the random walking problem with two-step correlations of the market moves. The parameters characterizing the stochastic dynamics are determined empirically from the historical quotes for the daily, weekly, and monthly series. The results show existence of statistically significant correlations between the subsequent market moves. The weekly and monthly parameters are calculated in terms of the daily parameters, assuming that the Markov chains with two-step correlations give a complete description of the market stochastic dynamics. We show that the macro- and micro-parameters obey the renorm group equation. The comparison of the parameters determined from the renorm group equation with the historical values shows that the Markov chains approach gives reasonable predictions for the weekly quotes and underestimates the probability for continuation of the down trend in the monthly quotes. The return and ...
CHARACTERIZATION OF MARKOV-BERNOULLI GEOMETRIC DISTRIBUTION RELATED TO RANDOM SUMS
Directory of Open Access Journals (Sweden)
Mohamed Gharib
2014-01-01
Full Text Available The Markov-Bernoulli geometric distribution is obtained when a generalization, as a Markov process, of the independent Bernoulli sequence of random variables is introduced by considering the success probability changes with respect to the Markov chain. The resulting model is called the Markov- Bernoulli model and it has a wide variety of application fields. In this study, some characterizations are given concerning the Markov-Bernoulli geometric distribution as the distribution of the summation index of independent randomly truncated non-negative integer valued random variables. The achieved results generalize the corresponding characterizations concerning the usual geometric distribution.
International Nuclear Information System (INIS)
We present a hierarchical Bayesian method for estimating the density and size distribution of subclad-flaws in French Pressurized Water Reactor (PWR) vessels. This model takes into account in-service inspection (ISI) data, a flaw size-dependent probability of detection (different functions are considered) with a threshold of detection, and a flaw sizing error distribution (different distributions are considered). The resulting model is identified through a Markov Chain Monte Carlo (MCMC) algorithm. The article includes discussion for choosing the prior distribution parameters and an illustrative application is presented highlighting the model's ability to provide good parameter estimates even when a small number of flaws are observed
Bayesian Lorentzian profile fitting using Markov-Chain Monte Carlo: An observer's approach
Gruberbauer, M; Weiss, W W
2008-01-01
Aims. Investigating stochastically driven pulsation puts strong requirements on the quality of (observed) pulsation frequency spectra, such as the accuracy of frequencies, amplitudes, and mode life times and -- important when fitting these parameters with models -- a realistic error estimate which can be quite different to the formal error. As has been shown by other authors, the method of fitting Lorentzian profiles to the power spectrum of time-resolved photometric or spectroscopic data via the Maximum Likelihood Estimation (MLE) procedure delivers good approximations for these quantities. We, however, intend to demonstrate that a conservative Bayesian approach allows to treat this problem in a more consistent way. Methods. We derive a conservative Bayesian treatment for the probability of Lorentzian profiles being present in a power spectrum and describe its implementation via evaluating the probability density distribution of parameters by using the Markov-Chain Monte Carlo (MCMC) technique. In addition, ...
Bayesian analysis for exponential random graph models using the adaptive exchange sampler
Jin, Ick Hoon
2013-01-01
Exponential random graph models have been widely used in social network analysis. However, these models are extremely difficult to handle from a statistical viewpoint, because of the existence of intractable normalizing constants. In this paper, we consider a fully Bayesian analysis for exponential random graph models using the adaptive exchange sampler, which solves the issue of intractable normalizing constants encountered in Markov chain Monte Carlo (MCMC) simulations. The adaptive exchange sampler can be viewed as a MCMC extension of the exchange algorithm, and it generates auxiliary networks via an importance sampling procedure from an auxiliary Markov chain running in parallel. The convergence of this algorithm is established under mild conditions. The adaptive exchange sampler is illustrated using a few social networks, including the Florentine business network, molecule synthetic network, and dolphins network. The results indicate that the adaptive exchange algorithm can produce more accurate estimates than approximate exchange algorithms, while maintaining the same computational efficiency.
Bayesian Analysis for Exponential Random Graph Models Using the Adaptive Exchange Sampler.
Jin, Ick Hoon; Yuan, Ying; Liang, Faming
2013-10-01
Exponential random graph models have been widely used in social network analysis. However, these models are extremely difficult to handle from a statistical viewpoint, because of the intractable normalizing constant and model degeneracy. In this paper, we consider a fully Bayesian analysis for exponential random graph models using the adaptive exchange sampler, which solves the intractable normalizing constant and model degeneracy issues encountered in Markov chain Monte Carlo (MCMC) simulations. The adaptive exchange sampler can be viewed as a MCMC extension of the exchange algorithm, and it generates auxiliary networks via an importance sampling procedure from an auxiliary Markov chain running in parallel. The convergence of this algorithm is established under mild conditions. The adaptive exchange sampler is illustrated using a few social networks, including the Florentine business network, molecule synthetic network, and dolphins network. The results indicate that the adaptive exchange algorithm can produce more accurate estimates than approximate exchange algorithms, while maintaining the same computational efficiency. PMID:24653788
Markov-random-field modeling for linear seismic tomography.
Kuwatani, Tatsu; Nagata, Kenji; Okada, Masato; Toriumi, Mitsuhiro
2014-10-01
We apply the Markov-random-field model to linear seismic tomography and propose a method to estimate the hyperparameters for the smoothness and the magnitude of the noise. Optimal hyperparameters can be determined analytically by minimizing the free energy function, which is defined by marginalizing the evaluation function. In synthetic inversion tests under various settings, the assumed velocity structures are successfully reconstructed, which shows the effectiveness and robustness of the proposed method. The proposed mathematical framework can be applied to inversion problems in various fields in the natural sciences. PMID:25375468
Quantitative analysis of pulmonary emphysema using isotropic Gaussian Markov random fields
Dharmagunawardhana, Chathurika; Mahmoodi, Sasan; Bennett, Michael; Niranjan, Mahesan
2014-01-01
A novel texture feature based on isotropic Gaussian Markov random fields is proposed for diagnosis and quantification of emphysema and its subtypes. Spatially varying parameters of isotropic Gaussian Markov random fields are estimated and their local distributions constructed using normalized histograms are used as effective texture features. These features integrate the essence of both statistical and structural properties of the texture. Isotropic Gaussian Markov Random Field parameter esti...
Parallel algorithms for phase unwrapping based on Markov random field models
Marroquin, Jose L.; Tapia, Maximino; Rodriguez-Vera, Ramon; Servin, Manuel
1995-12-01
A general framework is presented for the design of parallel algorithms for two-dimensional, path-independent phase unwrapping of locally inconsistent, noisy principal-value phase fields that may contain regions of invalid information. This framework is based in Bayesian estimation theory with the use of Markov random field models to construct the prior distribution, so that the solution to the unwrapping problem is characterized as the minimizer of a piecewise-quadratic functional. This method allows one to design a variety of parallel algorithms with different computational properties, which simultaneously perform the desired path-independent unwrapping, interpolate over regions with invalid data, and reduce the noise. It is also shown how this approach may be extended to the case of discontinuous phase fields, incorporating information from fringe patterns of different frequencies. Copyright (c) 1995 Optical Society of America
Recurrence and invariant measure of Markov chains in double-infinite random environments
Institute of Scientific and Technical Information of China (English)
XING; Xiusan
2001-01-01
［1］Cogburn, R., Markov chains in random environments: The case of Markovian environments, Ann. Probab., 1980, 8(3): 908—916.［2］Cogburn, R., The ergodic theory of Markov chains in random environments, Z. W., 1984, 66(2): 109—128.［3］Orey, S., Markov chains with stochastically stationary transition probabilities, Ann. Probab., 1991, 19(3): 907—928.［4］Li Yingqiu, Some notes of Markov chains in Markov environments, Advances in Mathematics(in Chinese), 1999, 28(4): 358—360.
International Nuclear Information System (INIS)
Occurrence of hazardous accident in nuclear power plants and industrial units usually lead to release of radioactive materials and pollutants in environment. These materials and pollutants can be transported to a far downstream by the wind flow. In this paper, we implemented an atmospheric dispersion code to solve the inverse problem. Having received and detected the pollutants in one region, we may estimate the rate and location of the unknown source. For the modeling, one needs a model with ability of atmospheric dispersion calculation. Furthermore, it is required to implement a mathematical approach to infer the source location and the related rates. In this paper the AERMOD software and Bayesian inference along the Markov Chain Monte Carlo have been applied. Implementing, Bayesian approach and Markov Chain Monte Carlo for the aforementioned subject is not a new approach, but the AERMOD model coupled with the said methods is a new and well known regulatory software, and enhances the reliability of outcomes. To evaluate the method, an example is considered by defining pollutants concentration in a specific region and then obtaining the source location and intensity by a direct calculation. The result of the calculation estimates the average source location at a distance of 7km with an accuracy of 5m which is good enough to support the ability of the proposed algorithm.
Random billiards with wall temperature and associated Markov chains
International Nuclear Information System (INIS)
By a random billiard we mean a billiard system in which the standard rule of specular reflection is replaced with a Markov transition probabilities operator P that gives, at each collision of the billiard particle with the boundary of the billiard domain, the probability distribution of the post-collision velocity for a given pre-collision velocity. A random billiard with microstructure, or RBM for short, is a random billiard for which P is derived from a choice of geometric/mechanical structure on the boundary of the billiard domain, as explained in the text. Such systems provide simple and explicit mechanical models of particle–surface interaction that can incorporate thermal effects and permit a detailed study of thermostatic action from the perspective of the standard theory of Markov chains on general state spaces. The main focus of this paper is on the operator P itself and how it relates to the mechanical and geometric features of the microstructure, such as mass ratios, curvatures, and potentials. The main results are as follows: (1) we give a characterization of the stationary probabilities (equilibrium states) of P and show how standard equilibrium distributions studied in classical statistical mechanics such as the Maxwell–Boltzmann distribution and the Knudsen cosine law arise naturally as generalized invariant billiard measures; (2) we obtain some of the more basic functional theoretic properties of P, in particular that P is under very general conditions a self-adjoint operator of norm 1 on a Hilbert space to be defined below, and show in a simple but somewhat typical example that P is a compact (Hilbert–Schmidt) operator. This leads to the issue of relating the spectrum of eigenvalues of P to the geometric/mechanical features of the billiard microstructure; (3) we explore the latter issue, both analytically and numerically in a few representative examples. Additionally, (4) a general algorithm for simulating the Markov chains is given based on
Energy Technology Data Exchange (ETDEWEB)
Vrugt, Jasper A [Los Alamos National Laboratory; Hyman, James M [Los Alamos National Laboratory; Robinson, Bruce A [Los Alamos National Laboratory; Higdon, Dave [Los Alamos National Laboratory; Ter Braak, Cajo J F [NETHERLANDS; Diks, Cees G H [UNIV OF AMSTERDAM
2008-01-01
Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.
International Nuclear Information System (INIS)
In this paper a novel multiresolution wavelet analysis (MWA) and non-stationary Gaussian Markov random field (GMRF) technique is introduced for the identification of microcalcifications with high accuracy. The hierarchical multiresolution wavelet information in conjunction with the contextual information of the images extracted from GMRF provides a highly efficient technique for microcalcification detection. A Bayesian teaming paradigm realized via the expectation maximization (EM) algorithm was also introduced for edge detection or segmentation of larger lesions recorded on the mammograms. The effectiveness of the approach has been extensively tested with a number of mammographic images provided by a local hospital
Directory of Open Access Journals (Sweden)
David G. Gadian
2011-10-01
Full Text Available A common feature of many magnetic resonance image (MRI data processing methods is the voxel-by-voxel (a voxel is a volume element manner in which the processing is performed. In general, however, MRI data are expected to exhibit some level of spatial correlation, rendering an independent-voxels treatment inefficient in its use of the data. Bayesian random effect models are expected to be more efficient owing to their information-borrowing behaviour. To illustrate the Bayesian random effects approach, this paper outlines a Markov chain Monte Carlo (MCMC analysis of a perfusion MRI dataset, implemented in R using the BRugs package. BRugs provides an interface to WinBUGS and its GeoBUGS add-on. WinBUGS is a widely used programme for performing MCMC analyses, with a focus on Bayesian random effect models. A simultaneous modeling of both voxels (restricted to a region of interest and multiple subjects is demonstrated. Despite the low signal-to-noise ratio in the magnetic resonance signal intensity data, useful model signal intensity profiles are obtained. The merits of random effects modeling are discussed in comparison with the alternative approaches based on region-of-interest averaging and repeated independent voxels analysis. This paper focuses on perfusion MRI for the purpose of illustration, the main proposition being that random effects modeling is expected to be beneficial in many other MRI applications in which the signal-to-noise ratio is a limiting factor.
CLOUD IMAGE DETECTION BASED ON MARKOV RANDOM FIELD
Institute of Scientific and Technical Information of China (English)
Xu Xuemei; Guo Yuanwei; Wang Zhenfei
2012-01-01
In order to overcome the disadvantages of low accuracy rate,high complexity and poor robustness to image noise in many traditional algorithms of cloud image detection,this paper proposed a novel algorithm on the basis of Markov Random Field (MRF) modeling.This paper first defined algorithm model and derived the core factors affecting the performance of the algorithm,and then,the solving of this algorithm was obtained by the use of Belief Propagation (BP) algorithm and Iterated Conditional Modes (ICM) algorithm.Finally,experiments indicate that this algorithm for the cloud image detection has higher average accuracy rate which is about 98.76％ and the average result can also reach 96.92％ for different type of image noise.
Distribution estimation of hyperparameters in Markov random field models
International Nuclear Information System (INIS)
We developed a method of distribution estimation of hyperparameters in Markov random field (MRF) models. This study was motivated by the growing quantity of image data in natural sciences owing to recent advances in measurement techniques. MRF models are used to restore images in information science, and the hyperparameters of these models can be adjusted to improve restoration performance. The parameters appearing in data analysis represent physical quantities such as diffusion coefficients. Indeed, many frameworks of hyperparameter estimation have been proposed, but most are point estimation that is susceptible to stochastic fluctuations. Distribution estimation can be used to evaluate the confidence one has in point estimates of hyperparameters, in a similar way to physicists using error bars when they evaluate important physical quantities. We use a solvable MRF model to investigate the performance of distribution estimation in simulations. (paper)
Bayesian Inference for LISA Pathfinder using Markov Chain Monte Carlo Methods
Ferraioli, Luigi; Plagnol, Eric
2012-01-01
We present a parameter estimation procedure based on a Bayesian framework by applying a Markov Chain Monte Carlo algorithm to the calibration of the dynamical parameters of a space based gravitational wave detector. The method is based on the Metropolis-Hastings algorithm and a two-stage annealing treatment in order to ensure an effective exploration of the parameter space at the beginning of the chain. We compare two versions of the algorithm with an application to a LISA Pathfinder data analysis problem. The two algorithms share the same heating strategy but with one moving in coordinate directions using proposals from a multivariate Gaussian distribution, while the other uses the natural logarithm of some parameters and proposes jumps in the eigen-space of the Fisher Information matrix. The algorithm proposing jumps in the eigen-space of the Fisher Information matrix demonstrates a higher acceptance rate and a slightly better convergence towards the equilibrium parameter distributions in the application to...
Wind Farm Reliability Modelling Using Bayesian Networks and Semi-Markov Processes
Directory of Open Access Journals (Sweden)
Robert Adam Sobolewski
2015-09-01
Full Text Available Technical reliability plays an important role among factors affecting the power output of a wind farm. The reliability is determined by an internal collection grid topology and reliability of its electrical components, e.g. generators, transformers, cables, switch breakers, protective relays, and busbars. A wind farm reliability’s quantitative measure can be the probability distribution of combinations of operating and failed states of the farm’s wind turbines. The operating state of a wind turbine is its ability to generate power and to transfer it to an external power grid, which means the availability of the wind turbine and other equipment necessary for the power transfer to the external grid. This measure can be used for quantitative analysis of the impact of various wind farm topologies and the reliability of individual farm components on the farm reliability, and for determining the expected farm output power with consideration of the reliability. This knowledge may be useful in an analysis of power generation reliability in power systems. The paper presents probabilistic models that quantify the wind farm reliability taking into account the above-mentioned technical factors. To formulate the reliability models Bayesian networks and semi-Markov processes were used. Using Bayesian networks the wind farm structural reliability was mapped, as well as quantitative characteristics describing equipment reliability. To determine the characteristics semi-Markov processes were used. The paper presents an example calculation of: (i probability distribution of the combination of both operating and failed states of four wind turbines included in the wind farm, and (ii expected wind farm output power with consideration of its reliability.
Bayesian Models of Graphs, Arrays and Other Exchangeable Random Structures.
Orbanz, Peter; Roy, Daniel M
2015-02-01
The natural habitat of most Bayesian methods is data represented by exchangeable sequences of observations, for which de Finetti's theorem provides the theoretical foundation. Dirichlet process clustering, Gaussian process regression, and many other parametric and nonparametric Bayesian models fall within the remit of this framework; many problems arising in modern data analysis do not. This article provides an introduction to Bayesian models of graphs, matrices, and other data that can be modeled by random structures. We describe results in probability theory that generalize de Finetti's theorem to such data and discuss their relevance to nonparametric Bayesian modeling. With the basic ideas in place, we survey example models available in the literature; applications of such models include collaborative filtering, link prediction, and graph and network analysis. We also highlight connections to recent developments in graph theory and probability, and sketch the more general mathematical foundation of Bayesian methods for other types of data beyond sequences and arrays. PMID:26353253
A Very Simple Safe-Bayesian Random Forest.
Quadrianto, Novi; Ghahramani, Zoubin
2015-06-01
Random forests works by averaging several predictions of de-correlated trees. We show a conceptually radical approach to generate a random forest: random sampling of many trees from a prior distribution, and subsequently performing a weighted ensemble of predictive probabilities. Our approach uses priors that allow sampling of decision trees even before looking at the data, and a power likelihood that explores the space spanned by combination of decision trees. While each tree performs Bayesian inference to compute its predictions, our aggregation procedure uses the power likelihood rather than the likelihood and is therefore strictly speaking not Bayesian. Nonetheless, we refer to it as a Bayesian random forest but with a built-in safety. The safeness comes as it has good predictive performance even if the underlying probabilistic model is wrong. We demonstrate empirically that our Safe-Bayesian random forest outperforms MCMC or SMC based Bayesian decision trees in term of speed and accuracy, and achieves competitive performance to entropy or Gini optimised random forest, yet is very simple to construct. PMID:26357350
Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks
Zhu, Shijia; Wang, Yadong
2015-12-01
Dynamic Bayesian Networks (DBN) have been widely used to recover gene regulatory relationships from time-series data in computational systems biology. Its standard assumption is ‘stationarity’, and therefore, several research efforts have been recently proposed to relax this restriction. However, those methods suffer from three challenges: long running time, low accuracy and reliance on parameter settings. To address these problems, we propose a novel non-stationary DBN model by extending each hidden node of Hidden Markov Model into a DBN (called HMDBN), which properly handles the underlying time-evolving networks. Correspondingly, an improved structural EM algorithm is proposed to learn the HMDBN. It dramatically reduces searching space, thereby substantially improving computational efficiency. Additionally, we derived a novel generalized Bayesian Information Criterion under the non-stationary assumption (called BWBIC), which can help significantly improve the reconstruction accuracy and largely reduce over-fitting. Moreover, the re-estimation formulas for all parameters of our model are derived, enabling us to avoid reliance on parameter settings. Compared to the state-of-the-art methods, the experimental evaluation of our proposed method on both synthetic and real biological data demonstrates more stably high prediction accuracy and significantly improved computation efficiency, even with no prior knowledge and parameter settings.
Bayesian Optimization in a Billion Dimensions via Random Embeddings
Wang, Ziyu; Hutter, Frank; Zoghi, Masrour; Matheson, David; De Freitas, Nando
2013-01-01
Bayesian optimization techniques have been successfully applied to robotics, planning, sensor placement, recommendation, advertising, intelligent user interfaces and automatic algorithm configuration. Despite these successes, the approach is restricted to problems of moderate dimension, and several workshops on Bayesian optimization have identified its scaling to high-dimensions as one of the holy grails of the field. In this paper, we introduce a novel random embedding idea to attack this pr...
Learning Markov Random Walks for robust subspace clustering and estimation.
Liu, Risheng; Lin, Zhouchen; Su, Zhixun
2014-11-01
Markov Random Walks (MRW) has proven to be an effective way to understand spectral clustering and embedding. However, due to less global structural measure, conventional MRW (e.g., the Gaussian kernel MRW) cannot be applied to handle data points drawn from a mixture of subspaces. In this paper, we introduce a regularized MRW learning model, using a low-rank penalty to constrain the global subspace structure, for subspace clustering and estimation. In our framework, both the local pairwise similarity and the global subspace structure can be learnt from the transition probabilities of MRW. We prove that under some suitable conditions, our proposed local/global criteria can exactly capture the multiple subspace structure and learn a low-dimensional embedding for the data, in which giving the true segmentation of subspaces. To improve robustness in real situations, we also propose an extension of the MRW learning model based on integrating transition matrix learning and error correction in a unified framework. Experimental results on both synthetic data and real applications demonstrate that our proposed MRW learning model and its robust extension outperform the state-of-the-art subspace clustering methods. PMID:25005156
IMAGE SEGMENTATION BASED ON MARKOV RANDOM FIELD AND WATERSHED TECHNIQUES
Institute of Scientific and Technical Information of China (English)
纳瑟; 刘重庆
2002-01-01
This paper presented a method that incorporates Markov Random Field(MRF), watershed segmentation and merging techniques for performing image segmentation and edge detection tasks. MRF is used to obtain an initial estimate of x regions in the image under process where in MRF model, gray level x, at pixel location i, in an image X, depends on the gray levels of neighboring pixels. The process needs an initial segmented result. An initial segmentation is got based on K-means clustering technique and the minimum distance, then the region process in modeled by MRF to obtain an image contains different intensity regions. Starting from this we calculate the gradient values of that image and then employ a watershed technique. When using MRF method it obtains an image that has different intensity regions and has all the edge and region information, then it improves the segmentation result by superimpose closed and an accurate boundary of each region using watershed algorithm. After all pixels of the segmented regions have been processed, a map of primitive region with edges is generated. Finally, a merge process based on averaged mean values is employed. The final segmentation and edge detection result is one closed boundary per actual region in the image.
Bayesian inference along Markov Chain Monte Carlo approach for PWR core loading pattern optimization
International Nuclear Information System (INIS)
Highlights: ► The BIMCMC method performs very well and is comparable to GA and PSO techniques. ► The potential of the technique is very well for optimization. ► It is observed that the performance of the method is quite adequate. ► The BIMCMC is very easy to implement. -- Abstract: Despite remarkable progress in optimization procedures, inherent complexities in nuclear reactor structure and strong interdependence among the fundamental indices namely, economic, neutronic, thermo-hydraulic and environmental effects make it necessary to evaluate the most efficient arrangement of a reactor core. In this paper a reactor core reloading technique based on Bayesian inference along Markov Chain Monte Carlo, BIMCMC, is addressed in the context of obtaining an optimal configuration of fuel assemblies in reactor cores. The Markov Chain Monte Carlo with Metropolis–Hastings algorithm has been applied for sampling variable and its acceptance. The proposed algorithm can be used for in-core fuel management optimization problems in pressurized water reactors. Considerable work has been expended for loading pattern optimization, but no preferred approach has yet emerged. To evaluate the proposed technique, increasing the effective multiplication factor Keff of a WWER-1000 core along flattening power with keeping power peaking factor below a specific limit as a first test case and flattening of power as a second test case are considered as objective functions; although other variables such as burn up and cycle length can also be taken into account. The results, convergence rate and reliability of the new method are compared to published data resulting from particle swarm optimization and genetic algorithm; the outcome is quite promising and demonstrating the potential of the technique very well for optimization applications in the nuclear engineering field.
Czech Academy of Sciences Publication Activity Database
Valečková, Markéta; Kárný, Miroslav; Sutanto, E. L.
2001-01-01
Roč. 37, č. 6 (2001), s. 1071-1078. ISSN 0005-1098 R&D Projects: GA ČR GA102/99/1564 Grant ostatní: IST(XE) 1999/12058 Institutional research plan: AV0Z1075907 Keywords : Markov chain * clustering * Bayesian mixture estimation Subject RIV: BC - Control Systems Theory Impact factor: 1.449, year: 2001
Murakami, Yohei; Takada, Shoji
2013-01-01
When exact values of model parameters in systems biology are not available from experiments, they need to be inferred so that the resulting simulation reproduces the experimentally known phenomena. For the purpose, Bayesian statistics with Markov chain Monte Carlo (MCMC) is a useful method. Biological experiments are often performed with cell population, and the results are represented by histograms. On another front, experiments sometimes indicate the existence of a specific bifurcation patt...
Time-coherency of Bayesian priors on transient semi-Markov chains for audio-to-score alignment
Cuvillier, Philippe
2014-01-01
This paper proposes a novel insight to the problem of real-time alignment with Bayesian inference. When a prior knowledge about the duration of events is available, Semi-Markov models allow the setting of individual duration distributions but give no clue about their choice. We propose a criterion of temporal coherency for such applications and show it might be obtained with the right choice of estimation method. Theoretical insights are obtained through the study of the prior state probabili...
Zhiyan Shi; Weiguo Yang
2009-01-01
We study some limit properties of the harmonic mean of random transition probability for a second-order nonhomogeneous Markov chain and a nonhomogeneous Markov chain indexed by a tree. As corollary, we obtain the property of the harmonic mean of random transition probability for a nonhomogeneous Markov chain.
Holan, S.H.; Davis, G.M.; Wildhaber, M.L.; DeLonay, A.J.; Papoulias, D.M.
2009-01-01
The timing of spawning in fish is tightly linked to environmental factors; however, these factors are not very well understood for many species. Specifically, little information is available to guide recruitment efforts for endangered species such as the sturgeon. Therefore, we propose a Bayesian hierarchical model for predicting the success of spawning of the shovelnose sturgeon which uses both biological and behavioural (longitudinal) data. In particular, we use data that were produced from a tracking study that was conducted in the Lower Missouri River. The data that were produced from this study consist of biological variables associated with readiness to spawn along with longitudinal behavioural data collected by using telemetry and archival data storage tags. These high frequency data are complex both biologically and in the underlying behavioural process. To accommodate such complexity we developed a hierarchical linear regression model that uses an eigenvalue predictor, derived from the transition probability matrix of a two-state Markov switching model with generalized auto-regressive conditional heteroscedastic dynamics. Finally, to minimize the computational burden that is associated with estimation of this model, a parallel computing approach is proposed. ?? Journal compilation 2009 Royal Statistical Society.
Segmentation of cone-beam CT using a hidden Markov random field with informative priors
Moores, M.; Hargrave, C.; Harden, F.; Mengersen, K.
2014-03-01
Cone-beam computed tomography (CBCT) has enormous potential to improve the accuracy of treatment delivery in image-guided radiotherapy (IGRT). To assist radiotherapists in interpreting these images, we use a Bayesian statistical model to label each voxel according to its tissue type. The rich sources of prior information in IGRT are incorporated into a hidden Markov random field model of the 3D image lattice. Tissue densities in the reference CT scan are estimated using inverse regression and then rescaled to approximate the corresponding CBCT intensity values. The treatment planning contours are combined with published studies of physiological variability to produce a spatial prior distribution for changes in the size, shape and position of the tumour volume and organs at risk. The voxel labels are estimated using iterated conditional modes. The accuracy of the method has been evaluated using 27 CBCT scans of an electron density phantom. The mean voxel-wise misclassification rate was 6.2%, with Dice similarity coefficient of 0.73 for liver, muscle, breast and adipose tissue. By incorporating prior information, we are able to successfully segment CBCT images. This could be a viable approach for automated, online image analysis in radiotherapy.
Posterior Mean Super-resolution with a Causal Gaussian Markov Random Field Prior
Katsuki, Takayuki; Inoue, Masato
2011-01-01
We propose a Bayesian image super-resolution (SR) method with a causal Gaussian Markov random field (MRF) prior. SR is a technique to estimate a spatially high-resolution image from given multiple low-resolution images. An MRF model with the line process supplies a preferable prior for natural images with edges. We improve the existing image transformation model, the compound MRF model, and its hyperparameter prior model. We also logically derive the optimal estimator -- not joint maximum a posteriori (MAP) or marginalized maximum likelihood (ML), but posterior mean (PM) -- from the objective function of the L2-norm (mean square error) -based peak signal-to-noise ratio (PSNR). Point estimates such as MAP and ML are generally not stable in ill-posed high-dimensional problems because of overfitting, while PM is a stable estimator because all the parameters in the model are evaluated as distributions. The estimator is numerically determined by using variational Bayes. Variational Bayes is a widely used method th...
Segmentation of cone-beam CT using a hidden Markov random field with informative priors
International Nuclear Information System (INIS)
Cone-beam computed tomography (CBCT) has enormous potential to improve the accuracy of treatment delivery in image-guided radiotherapy (IGRT). To assist radiotherapists in interpreting these images, we use a Bayesian statistical model to label each voxel according to its tissue type. The rich sources of prior information in IGRT are incorporated into a hidden Markov random field model of the 3D image lattice. Tissue densities in the reference CT scan are estimated using inverse regression and then rescaled to approximate the corresponding CBCT intensity values. The treatment planning contours are combined with published studies of physiological variability to produce a spatial prior distribution for changes in the size, shape and position of the tumour volume and organs at risk. The voxel labels are estimated using iterated conditional modes. The accuracy of the method has been evaluated using 27 CBCT scans of an electron density phantom. The mean voxel-wise misclassification rate was 6.2%, with Dice similarity coefficient of 0.73 for liver, muscle, breast and adipose tissue. By incorporating prior information, we are able to successfully segment CBCT images. This could be a viable approach for automated, online image analysis in radiotherapy.
Directory of Open Access Journals (Sweden)
Carlos Alejandro De Luna Ortega
2006-01-01
Full Text Available En este artículo se aborda el diseño de un reconocedor de voz, con el idioma español mexicano, del estado de Aguascalientes, de palabras aisladas, con dependencia del hablante y vocabulario pequeño, empleando Redes Neuronales Artificiales (ANN por sus siglas en inglés, Alineamiento Dinámico del Tiempo (DTW por sus siglas en inglés y Modelos Ocultos de Markov (HMM por sus siglas en inglés para la realización del algoritmo de reconocimiento.
Kuwatani, Tatsu; Nagata, Kenji; Okada, Masato; Toriumi, Mitsuhiro
2012-03-01
The chemical zoning profile in metamorphic minerals is often used to deduce the pressure-temperature ( P- T) history of rock. However, it remains difficult to restore detailed paths from zoned minerals because thermobarometric evaluation of metamorphic conditions involves several uncertainties, including measurement errors and geological noise. We propose a new stochastic framework for estimating precise P- T paths from a chemical zoning structure using the Markov random field (MRF) model, which is a type of Bayesian stochastic method that is often applied to image analysis. The continuity of pressure and temperature during mineral growth is incorporated by Gaussian Markov chains as prior probabilities in order to apply the MRF model to the P- T path inversion. The most probable P- T path can be obtained by maximizing the posterior probability of the sequential set of P and T given the observed compositions of zoned minerals. Synthetic P- T inversion tests were conducted in order to investigate the effectiveness and validity of the proposed model from zoned Mg-Fe-Ca garnet in the divariant KNCFMASH system. In the present study, the steepest descent method was implemented in order to maximize the posterior probability using the Markov chain Monte Carlo algorithm. The proposed method successfully reproduced the detailed shape of the synthetic P- T path by eliminating appropriately the statistical compositional noises without operator's subjectivity and prior knowledge. It was also used to simultaneously evaluate the uncertainty of pressure, temperature, and mineral compositions for all measurement points. The MRF method may have potential to deal with several geological uncertainties, which cause cumbersome systematic errors, by its Bayesian approach and flexible formalism, so that it comprises potentially powerful tools for various inverse problems in petrology.
THE DECOMPOSITION OF STATE SPACE FOR MARKOV CHAIN IN RANDOM ENVIRONMENT
Institute of Scientific and Technical Information of China (English)
Hu Dihe
2005-01-01
This paper is a continuation of [8] and [9]. The author obtains the decomposition of state space χof an Markov chain in random environment by making use of the results in [8] and [9], gives three examples, random walk in random environment, renewal process in random environment and queue process in random environment, and obtains the decompositions of the state spaces of these three special examples.
Bayesian segmentation of hyperspectral images
Mohammadpour, Adel; Mohammad-Djafari, Ali
2007-01-01
In this paper we consider the problem of joint segmentation of hyperspectral images in the Bayesian framework. The proposed approach is based on a Hidden Markov Modeling (HMM) of the images with common segmentation, or equivalently with common hidden classification label variables which is modeled by a Potts Markov Random Field. We introduce an appropriate Markov Chain Monte Carlo (MCMC) algorithm to implement the method and show some simulation results.
Bayesian segmentation of hyperspectral images
Mohammadpour, Adel; Féron, Olivier; Mohammad-Djafari, Ali
2004-11-01
In this paper we consider the problem of joint segmentation of hyperspectral images in the Bayesian framework. The proposed approach is based on a Hidden Markov Modeling (HMM) of the images with common segmentation, or equivalently with common hidden classification label variables which is modeled by a Potts Markov Random Field. We introduce an appropriate Markov Chain Monte Carlo (MCMC) algorithm to implement the method and show some simulation results.
THE CONSTRUCTION OF MULTITYPE CANONICAL MARKOV BRANCHING CHAINS IN RANDOM ENVIRONMENTS
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
The investigation for branching processes has a long history by their strong physics background, but only a few authors have investigated the branching processes in random environments. First of all, the author introduces the concepts of the multitype canonical Markov branching chain in random environment (CMBCRE) and multitype Markov branching chain in random environment (MBCRE) and proved that CMBCRE must be MBCRE, and any MBCRE must be equivalent to another CMBCRE in distribution. The main results of this article are the construction of CMBCRE and some of its probability properties.
Olivares, G.; Teferle, F. N.
2013-12-01
Geodetic time series provide information which helps to constrain theoretical models of geophysical processes. It is well established that such time series, for example from GPS, superconducting gravity or mean sea level (MSL), contain time-correlated noise which is usually assumed to be a combination of a long-term stochastic process (characterized by a power-law spectrum) and random noise. Therefore, when fitting a model to geodetic time series it is essential to also estimate the stochastic parameters beside the deterministic ones. Often the stochastic parameters include the power amplitudes of both time-correlated and random noise, as well as, the spectral index of the power-law process. To date, the most widely used method for obtaining these parameter estimates is based on maximum likelihood estimation (MLE). We present an integration method, the Bayesian Monte Carlo Markov Chain (MCMC) method, which, by using Markov chains, provides a sample of the posteriori distribution of all parameters and, thereby, using Monte Carlo integration, all parameters and their uncertainties are estimated simultaneously. This algorithm automatically optimizes the Markov chain step size and estimates the convergence state by spectral analysis of the chain. We assess the MCMC method through comparison with MLE, using the recently released GPS position time series from JPL and apply it also to the MSL time series from the Revised Local Reference data base of the PSMSL. Although the parameter estimates for both methods are fairly equivalent, they suggest that the MCMC method has some advantages over MLE, for example, without further computations it provides the spectral index uncertainty, is computationally stable and detects multimodality.
International Nuclear Information System (INIS)
A new method for the experimental determination of stopping powers based on Bayesian Inference with the Markov chain Monte Carlo (MCMC) algorithm has been devised. This method avoids the difficulties related to thin target preparation. By measuring the RBS spectra for a known material, and using the known underlying physics, the stopping powers are determined by best matching the simulated spectra with the experimental spectra. Using silicon, SiO2 and Al2O3 as test cases, good agreement is obtained between calculated and experimental data. (author)
Hierarchical Semi-Markov Conditional Random Fields for Recursive Sequential Data
Truyen, Tran The; Bui, Hung H; Venkatesh, Svetha
2010-01-01
Inspired by the hierarchical hidden Markov models (HHMM), we present the hierarchical semi-Markov conditional random field (HSCRF), a generalisation of embedded undirectedMarkov chains tomodel complex hierarchical, nestedMarkov processes. It is parameterised in a discriminative framework and has polynomial time algorithms for learning and inference. Importantly, we consider partiallysupervised learning and propose algorithms for generalised partially-supervised learning and constrained inference. We demonstrate the HSCRF in two applications: (i) recognising human activities of daily living (ADLs) from indoor surveillance cameras, and (ii) noun-phrase chunking. We show that the HSCRF is capable of learning rich hierarchical models with reasonable accuracy in both fully and partially observed data cases.
Random recurrence equations and ruin in a Markov-dependent stochastic economic environment
DEFF Research Database (Denmark)
Collamore, Jeffrey F.
2009-01-01
We develop sharp large deviation asymptotics for the probability of ruin in a Markov-dependent stochastic economic environment and study the extremes for some related Markovian processes which arise in financial and insurance mathematics, related to perpetuities and the ARCH(1) and GARCH(1,1) time...... series models. Our results build upon work of Goldie, who has developed tail asymptotics applicable for independent sequences of random variables subject to a random recurrence equation. In contrast, we adopt a general approach based on the theory of Harris recurrent Markov chains and the associated...
THE DECISION OF THE OPTIMAL PARAMETERS IN MARKOV RANDOM FIELDS OF IMAGES BY GENETIC ALGORITHM
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
This paper introduces the principle of genetic algorithm and the basic method of solving Markov random field parameters.Focusing on the shortcomings in present methods,a new method based on genetic algorithms is proposed to solve the parameters in the Markov random field.The detailed procedure is discussed.On the basis of the parameters solved by genetic algorithms,some experim ents on classification of aerial images are given.Experimental results show that the proposed method is effective and the classification results are satisfactory.
Patriche, Monica
2013-01-01
In this paper, we introduce a Bayesian abstract fuzzy economy model and we prove the Bayesian fuzzy equilibrium existence. As applications, we prove the existence of the solutions for two types of random quasi-variational inequalities with random fuzzy mappings and we also obtain random fixed point theorems.
Colonoscopy video quality assessment using hidden Markov random fields
Park, Sun Young; Sargent, Dusty; Spofford, Inbar; Vosburgh, Kirby
2011-03-01
With colonoscopy becoming a common procedure for individuals aged 50 or more who are at risk of developing colorectal cancer (CRC), colon video data is being accumulated at an ever increasing rate. However, the clinically valuable information contained in these videos is not being maximally exploited to improve patient care and accelerate the development of new screening methods. One of the well-known difficulties in colonoscopy video analysis is the abundance of frames with no diagnostic information. Approximately 40% - 50% of the frames in a colonoscopy video are contaminated by noise, acquisition errors, glare, blur, and uneven illumination. Therefore, filtering out low quality frames containing no diagnostic information can significantly improve the efficiency of colonoscopy video analysis. To address this challenge, we present a quality assessment algorithm to detect and remove low quality, uninformative frames. The goal of our algorithm is to discard low quality frames while retaining all diagnostically relevant information. Our algorithm is based on a hidden Markov model (HMM) in combination with two measures of data quality to filter out uninformative frames. Furthermore, we present a two-level framework based on an embedded hidden Markov model (EHHM) to incorporate the proposed quality assessment algorithm into a complete, automated diagnostic image analysis system for colonoscopy video.
Entropy, complexity, and Markov diagrams for random walk cancer models
Newton, Paul K.; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter
2014-12-01
The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential.
Directory of Open Access Journals (Sweden)
Giulia Carreras
2012-09-01
Full Text Available
Background: parameter uncertainty in the Markov model’s description of a disease course was addressed. Probabilistic sensitivity analysis (PSA is now considered the only tool that properly permits parameter uncertainty’s examination. This consists in sampling values from the parameter’s probability distributions.
Methods: Markov models fitted with microsimulation were considered and methods for carrying out a PSA on transition probabilities were studied. Two Bayesian solutions were developed: for each row of the modeled transition matrix the prior distribution was assumed as a product of Beta or a Dirichlet. The two solutions differ in the source of information: several different sources for each transition in the Beta approach and a single source for each transition from a given health state in the Dirichlet. The two methods were applied to a simple cervical cancer’s model.
Results : differences between posterior estimates from the two methods were negligible. Results showed that the prior variability highly influence the posterior distribution.
Conclusions: the novelty of this work is the Bayesian approach that integrates the two distributions with a product of Binomial distributions likelihood. Such methods could be also applied to cohort data and their application to more complex models could be useful and unique in the cervical cancer context, as well as in other disease modeling.
Bayesian Fine-Scale Mapping of Disease Loci, by Hidden Markov Models
Morris, A P; Whittaker, J C; Balding, D. J.
2000-01-01
We present a new multilocus method for the fine-scale mapping of genes contributing to human diseases. The method is designed for use with multiple biallelic markers—in particular, single-nucleotide polymorphisms for which high-density genetic maps will soon be available. We model disease-marker association in a candidate region via a hidden Markov process and allow for correlation between linked marker loci. Using Markov-chain–Monte Carlo simulation methods, we obtain posterior distributions...
Derivation of the Convective Dispersion Equation with Adsorption by Markov Random Ways
International Nuclear Information System (INIS)
The convective dispersion equation with adsorption is derived on the basis of the Chapman−Kolmogroff equation which expresses the statistical properties of the Markov transition probability. The acquired equation has the same expression as the one derived on the basis of the combination of both the mass balance equation and the particles retention kinetics equation. The probability variables that describe the random movement of solute particles have a definite physical significance associated with the parameters in the convective dispersion equation. The derivation confirms the validity of the Markov process to describe the particles movement in the process of convective dispersion. (fundamental areas of phenomenology (including applications))
Ryu, Duchwan
2010-09-28
We consider nonparametric regression analysis in a generalized linear model (GLM) framework for data with covariates that are the subject-specific random effects of longitudinal measurements. The usual assumption that the effects of the longitudinal covariate processes are linear in the GLM may be unrealistic and if this happens it can cast doubt on the inference of observed covariate effects. Allowing the regression functions to be unknown, we propose to apply Bayesian nonparametric methods including cubic smoothing splines or P-splines for the possible nonlinearity and use an additive model in this complex setting. To improve computational efficiency, we propose the use of data-augmentation schemes. The approach allows flexible covariance structures for the random effects and within-subject measurement errors of the longitudinal processes. The posterior model space is explored through a Markov chain Monte Carlo (MCMC) sampler. The proposed methods are illustrated and compared to other approaches, the "naive" approach and the regression calibration, via simulations and by an application that investigates the relationship between obesity in adulthood and childhood growth curves. © 2010, The International Biometric Society.
Algorithms for random generation and counting a Markov chain approach
Sinclair, Alistair
1993-01-01
This monograph studies two classical computational problems: counting the elements of a finite set of combinatorial structures, and generating them at random from some probability distribution. Apart from their intrinsic interest, these problems arise naturally in many branches of mathematics and the natural sciences.
States recognition in random walk Markov chain via binary Entropy
Directory of Open Access Journals (Sweden)
Morteza Khodabin
2013-03-01
Full Text Available In this paper, a new method for specification of recurrence or transient of states in one and two dimensional simple random walk based on upper and lower bounds of {it r}-combinations from a set of m elements $(C^{m}_{r}$ via binary entropy is introduced.
Wang, Hongyan; Zhou, Xiaobo
2013-04-01
By altering the electrostatic charge of histones or providing binding sites to protein recognition molecules, Chromatin marks have been proposed to regulate gene expression, a property that has motivated researchers to link these marks to cis-regulatory elements. With the help of next generation sequencing technologies, we can now correlate one specific chromatin mark with regulatory elements (e.g. enhancers or promoters) and also build tools, such as hidden Markov models, to gain insight into mark combinations. However, hidden Markov models have limitation for their character of generative models and assume that a current observation depends only on a current hidden state in the chain. Here, we employed two graphical probabilistic models, namely the linear conditional random field model and multivariate hidden Markov model, to mark gene regions with different states based on recurrent and spatially coherent character of these eight marks. Both models revealed chromatin states that may correspond to enhancers and promoters, transcribed regions, transcriptional elongation, and low-signal regions. We also found that the linear conditional random field model was more effective than the hidden Markov model in recognizing regulatory elements, such as promoter-, enhancer-, and transcriptional elongation-associated regions, which gives us a better choice. PMID:23237214
Weinberg, Martin D
2009-01-01
Computation of the marginal likelihood or "Bayesian Evidence" from a simulated posterior distribution is central to Bayesian model selection but is fraught with difficulty. The often-used harmonic mean approximation uses the posterior directly but is unstably sensitive to samples with anomalously small values of the likelihood and converges very slowly. The Laplace approximation is stable but makes strong, and often inappropriate, assumptions about the shape of the posterior distribution. It is useful, but not general. We need an algorithm that is general and easy to apply, like the harmonic mean approximation, but robust to sample size and multimodality. Here, I argue that the evidence can be stably computed from a posterior sample by careful attention to the numerics of the probability integral. Posing the expression for the Bayesian evidence as a Lebesgue integral, we may convert the evaluation of the sample statistic to a quadrature rule and show that the harmonic mean approximation suffers from enormous ...
Optimization by Estimation of Distribution with DEUM Framework Based on Markov Random Fields
Institute of Scientific and Technical Information of China (English)
Siddhartha Shakya; John McCall
2007-01-01
This paper presents a Markov random field (MRP) approach to estimating and sampling the probability distribution in populations of solutions. The approach is used to define a class of algorithms under the general heading distribution estimation using Markov random fields (DEUM). DEUM is a subclass of estimation of distribution algorithms (EDAs) where interaction between solution variables is represented as an undirected graph and the joint probability of a solution is factorized as a Gibbs distribution derived from the structure of the graph. The focus of this paper will be on describing the three main characteristics of DEUM framework, which distinguishes it from the traditional EDA. They are: 1) use of MRF models, 2) fitness modeling approach to estimating the parameter of the model and 3) Monte Carlo approach to sampling from the model.
Rigid Slice-To-Volume Medical Image Registration through Markov Random Fields
Porchetto, Roque; Stramana, Franco; Paragios, Nikos; Ferrante, Enzo
2016-01-01
Rigid slice-to-volume registration is a challenging task, which finds application in medical imaging problems like image fusion for image guided surgeries and motion correction for volume reconstruction. It is usually formulated as an optimization problem and solved using standard continuous methods. In this paper, we discuss how this task be formulated as a discrete labeling problem on a graph. Inspired by previous works on discrete estimation of linear transformations using Markov Random Fi...
Continuous Markov Random Fields for Robust Stereo Estimation
Yamaguchi, Koichiro; McAllester, David; Urtasun, Raquel
2012-01-01
In this paper we present a novel slanted-plane MRF model which reasons jointly about occlusion boundaries as well as depth. We formulate the problem as the one of inference in a hybrid MRF composed of both continuous (i.e., slanted 3D planes) and discrete (i.e., occlusion boundaries) random variables. This allows us to define potentials encoding the ownership of the pixels that compose the boundary between segments, as well as potentials encoding which junctions are physically possible. Our approach outperforms the state-of-the-art on Middlebury high resolution imagery as well as in the more challenging KITTI dataset, while being more efficient than existing slanted plane MRF-based methods, taking on average 2 minutes to perform inference on high resolution imagery.
Bayesian clustering of DNA sequences using Markov chains and a stochastic partition model.
Jääskinen, Väinö; Parkkinen, Ville; Cheng, Lu; Corander, Jukka
2014-02-01
In many biological applications it is necessary to cluster DNA sequences into groups that represent underlying organismal units, such as named species or genera. In metagenomics this grouping needs typically to be achieved on the basis of relatively short sequences which contain different types of errors, making the use of a statistical modeling approach desirable. Here we introduce a novel method for this purpose by developing a stochastic partition model that clusters Markov chains of a given order. The model is based on a Dirichlet process prior and we use conjugate priors for the Markov chain parameters which enables an analytical expression for comparing the marginal likelihoods of any two partitions. To find a good candidate for the posterior mode in the partition space, we use a hybrid computational approach which combines the EM-algorithm with a greedy search. This is demonstrated to be faster and yield highly accurate results compared to earlier suggested clustering methods for the metagenomics application. Our model is fairly generic and could also be used for clustering of other types of sequence data for which Markov chains provide a reasonable way to compress information, as illustrated by experiments on shotgun sequence type data from an Escherichia coli strain. PMID:24246289
Waldmann, Patrik; Hallander, Jon; Hoti, Fabian; Sillanpää, Mikko J
2008-06-01
Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general pedigrees without inbreeding. To optimize between computational time and good mixing of the Markov chain Monte Carlo (MCMC) chains, we used a hybrid Gibbs sampler that combines a single site and a blocked Gibbs sampler. The speed of the hybrid sampler and the mixing of the single-site sampler were further improved by the use of pretransformed variables. Two traits (height and trunk diameter) from a previously published diallel progeny test of Scots pine (Pinus sylvestris L.) and two large simulated data sets with different levels of dominance variance were analyzed. We also performed Bayesian model comparison on the basis of the posterior predictive loss approach. Results showed that models with both additive and dominance components had the best fit for both height and diameter and for the simulated data with high dominance. For the simulated data with low dominance, we needed an informative prior to avoid the dominance variance component becoming overestimated. The narrow-sense heritability estimates in the Scots pine data were lower compared to the earlier results, which is not surprising because the level of dominance variance was rather high, especially for diameter. In general, the hybrid sampler was considerably faster than the blocked sampler and displayed better mixing properties than the single-site sampler. PMID:18558655
Waldmann, Patrik; Hallander, Jon; Hoti, Fabian; Sillanpää, Mikko J.
2008-01-01
Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general pedigrees without inbreeding. To optimize between computational time and good mixing of the Markov chain Monte Carlo (MCMC) chains, we used a hybrid Gibbs sampler that combines a single site and a blocked Gibbs sampler. The speed of the hybrid sampler and the mixing of the single-site sampler were further improved by the use of pretransformed variables. Two traits (height and trunk diameter) from a previously published diallel progeny test of Scots pine (Pinus sylvestris L.) and two large simulated data sets with different levels of dominance variance were analyzed. We also performed Bayesian model comparison on the basis of the posterior predictive loss approach. Results showed that models with both additive and dominance components had the best fit for both height and diameter and for the simulated data with high dominance. For the simulated data with low dominance, we needed an informative prior to avoid the dominance variance component becoming overestimated. The narrow-sense heritability estimates in the Scots pine data were lower compared to the earlier results, which is not surprising because the level of dominance variance was rather high, especially for diameter. In general, the hybrid sampler was considerably faster than the blocked sampler and displayed better mixing properties than the single-site sampler. PMID:18558655
Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution
Trendelkamp-Schroer, Benjamin
2013-01-01
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the convergence of expectation values of equilibrium probabilities and expectation values of stationary quantities significantly. Unfortunately the convergence of dynamic observables such as correlation functions or timescales of conformational transitions relies on direct equilibrium simulations. Markov state models are well suited to describe both, stationary properties and properties of slow dynamical processes of a molecular system, in terms of a transition matrix for a jump process on a suitable discretiza- tion of continuous conformation space. Here, we introduce statistical estimation methods that allow a priori knowledge of equilibrium probabilities to be incorporated into the estimation of dynamical observables. Both, maximum likelihood methods and an improved Monte Carlo...
Minsley, B.J.
2011-01-01
A meaningful interpretation of geophysical measurements requires an assessment of the space of models that are consistent with the data, rather than just a single, 'best' model which does not convey information about parameter uncertainty. For this purpose, a trans-dimensional Bayesian Markov chain Monte Carlo (MCMC) algorithm is developed for assessing frequency-domain electromagnetic (FDEM) data acquired from airborne or ground-based systems. By sampling the distribution of models that are consistent with measured data and any prior knowledge, valuable inferences can be made about parameter values such as the likely depth to an interface, the distribution of possible resistivity values as a function of depth and non-unique relationships between parameters. The trans-dimensional aspect of the algorithm allows the number of layers to be a free parameter that is controlled by the data, where models with fewer layers are inherently favoured, which provides a natural measure of parsimony and a significant degree of flexibility in parametrization. The MCMC algorithm is used with synthetic examples to illustrate how the distribution of acceptable models is affected by the choice of prior information, the system geometry and configuration and the uncertainty in the measured system elevation. An airborne FDEM data set that was acquired for the purpose of hydrogeological characterization is also studied. The results compare favourably with traditional least-squares analysis, borehole resistivity and lithology logs from the site, and also provide new information about parameter uncertainty necessary for model assessment. ?? 2011. Geophysical Journal International ?? 2011 RAS.
Directory of Open Access Journals (Sweden)
Wang Kang Kang
2013-06-01
Full Text Available In this paper, our aim is to establish a class of Shannon-McMillan theorems for $m$th-order nonhomogeneous Markov information source on the generalized random selection system by constructing the consistent distribution functions. As corollaries, we obtain some Shannon-McMillan theorems for $m$th-order nonhomogeneous Markov information source and the general nonhomogeneous Markov information source. Some results which have been obtained are extended. In the proof, a new technique for studying Shannon-McMillan theorems in information theory is applied.
Theory of Distribution Estimation of Hyperparameters in Markov Random Field Models
Sakamoto, Hirotaka; Nakanishi-Ohno, Yoshinori; Okada, Masato
2016-06-01
We investigated the performance of distribution estimation of hyperparameters in Markov random field models proposed by Nakanishi-Ohno et al., http://doi.org/10.1088/1751-8113/47/4/045001" xlink:type="simple">J. Phys. A 47, 045001 (2014) when used to evaluate the confidence of data. We analytically calculated the configurational average, with respect to data, of the negative logarithm of the posterior distribution, which is called free energy based on an analogy with statistical mechanics. This configurational average of free energy shrinks as the amount of data increases. Our results theoretically confirm the numerical results from that previous study.
Statistical Shape Modelling and Markov Random Field Restoration (invited tutorial and exercise)
DEFF Research Database (Denmark)
Hilger, Klaus Baggesen
This tutorial focuses on statistical shape analysis using point distribution models (PDM) which is widely used in modelling biological shape variability over a set of annotated training data. Furthermore, Active Shape Models (ASM) and Active Appearance Models (AAM) are based on PDMs and have proven...... themselves a generic holistic tool in various segmentation and simulation studies. Finding a basis of homologous points is a fundamental issue in PDMs which effects both alignment and decomposition of the training data, and may be aided by Markov Random Field Restoration (MRF) of the correspondence...
Colour and rotation invariant textural features based on Markov random fields
Czech Academy of Sciences Publication Activity Database
Vácha, Pavel; Haindl, Michal; Suk, Tomáš
2011-01-01
Roč. 32, č. 6 (2011), s. 771-779. ISSN 0167-8655 R&D Projects: GA MŠk 1M0572; GA ČR GA102/08/0593 Grant ostatní: GA MŠk(CZ) 2C06019 Institutional research plan: CEZ:AV0Z10750506 Keywords : Image modelling * colour texture * Illumination invariance * Markov random field * rotation invariance Subject RIV: BD - Theory of Information Impact factor: 1.034, year: 2011 http://library.utia.cas.cz/separaty/2011/RO/vacha-0357314.pdf
Bidirectional Texture Function Three Dimensional Pseudo Gaussian Markov Random Field Model
Czech Academy of Sciences Publication Activity Database
Havlíček, Michal
Praha : ČVUT v Praze, 2012, s. 53-62. ISBN 978-80-01-05138-2. [Doktorandské dny 2012. Praha (CZ), 16.11.2012-23.11.2012] R&D Projects: GA ČR GA102/08/0593 Institutional support: RVO:67985556 Keywords : bidirectional texture function * texture modelling Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2013/RO/havlicek-bidirectional texture function three dimensional pseudo gaussian markov random field model.pdf
Hierarchical Markov random-field modeling for texture classification in chest radiographs
Vargas-Voracek, Rene; Floyd, Carey E., Jr.; Nolte, Loren W.; McAdams, Page
1996-04-01
A hierarchical Markov random field (MRF) modeling approach is presented for the classification of textures in selected regions of interest (ROIs) of chest radiographs. The procedure integrates possible texture classes and their spatial definition with other components present in an image such as noise and background trend. Classification is performed as a maximum a-posteriori (MAP) estimation of texture class and involves an iterative Gibbs- sampling technique. Two cases are studied: classification of lung parenchyma versus bone and classification of normal lung parenchyma versus miliary tuberculosis (MTB). Accurate classification was obtained for all examined cases showing the potential of the proposed modeling approach for texture analysis of radiographic images.
Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution
Trendelkamp-Schroer, Benjamin; Noé, Frank
2013-04-01
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the convergence of expectation values of equilibrium probabilities and expectation values of stationary quantities significantly. Unfortunately the convergence of dynamic observables such as correlation functions or timescales of conformational transitions relies on direct equilibrium simulations. Markov state models are well suited to describe both stationary properties and properties of slow dynamical processes of a molecular system, in terms of a transition matrix for a jump process on a suitable discretization of continuous conformation space. Here, we introduce statistical estimation methods that allow a priori knowledge of equilibrium probabilities to be incorporated into the estimation of dynamical observables. Both maximum likelihood methods and an improved Monte Carlo sampling method for reversible transition matrices with fixed stationary distribution are given. The sampling approach is applied to a toy example as well as to simulations of the MR121-GSGS-W peptide, and is demonstrated to converge much more rapidly than a previous approach of Noé [J. Chem. Phys. 128, 244103 (2008), 10.1063/1.2916718].
Directory of Open Access Journals (Sweden)
William A Griffin
Full Text Available Sequential affect dynamics generated during the interaction of intimate dyads, such as married couples, are associated with a cascade of effects-some good and some bad-on each partner, close family members, and other social contacts. Although the effects are well documented, the probabilistic structures associated with micro-social processes connected to the varied outcomes remain enigmatic. Using extant data we developed a method of classifying and subsequently generating couple dynamics using a Hierarchical Dirichlet Process Hidden semi-Markov Model (HDP-HSMM. Our findings indicate that several key aspects of existing models of marital interaction are inadequate: affect state emissions and their durations, along with the expected variability differences between distressed and nondistressed couples are present but highly nuanced; and most surprisingly, heterogeneity among highly satisfied couples necessitate that they be divided into subgroups. We review how this unsupervised learning technique generates plausible dyadic sequences that are sensitive to relationship quality and provide a natural mechanism for computational models of behavioral and affective micro-social processes.
Griffin, William A; Li, Xun
2016-01-01
Sequential affect dynamics generated during the interaction of intimate dyads, such as married couples, are associated with a cascade of effects-some good and some bad-on each partner, close family members, and other social contacts. Although the effects are well documented, the probabilistic structures associated with micro-social processes connected to the varied outcomes remain enigmatic. Using extant data we developed a method of classifying and subsequently generating couple dynamics using a Hierarchical Dirichlet Process Hidden semi-Markov Model (HDP-HSMM). Our findings indicate that several key aspects of existing models of marital interaction are inadequate: affect state emissions and their durations, along with the expected variability differences between distressed and nondistressed couples are present but highly nuanced; and most surprisingly, heterogeneity among highly satisfied couples necessitate that they be divided into subgroups. We review how this unsupervised learning technique generates plausible dyadic sequences that are sensitive to relationship quality and provide a natural mechanism for computational models of behavioral and affective micro-social processes. PMID:27187319
Griffin, William A.; Li, Xun
2016-01-01
Sequential affect dynamics generated during the interaction of intimate dyads, such as married couples, are associated with a cascade of effects—some good and some bad—on each partner, close family members, and other social contacts. Although the effects are well documented, the probabilistic structures associated with micro-social processes connected to the varied outcomes remain enigmatic. Using extant data we developed a method of classifying and subsequently generating couple dynamics using a Hierarchical Dirichlet Process Hidden semi-Markov Model (HDP-HSMM). Our findings indicate that several key aspects of existing models of marital interaction are inadequate: affect state emissions and their durations, along with the expected variability differences between distressed and nondistressed couples are present but highly nuanced; and most surprisingly, heterogeneity among highly satisfied couples necessitate that they be divided into subgroups. We review how this unsupervised learning technique generates plausible dyadic sequences that are sensitive to relationship quality and provide a natural mechanism for computational models of behavioral and affective micro-social processes. PMID:27187319
Wang, Kang-Ning; Sun, Zan-Dong; Dong, Ning
2015-12-01
Economic shale gas production requires hydraulic fracture stimulation to increase the formation permeability. Hydraulic fracturing strongly depends on geomechanical parameters such as Young's modulus and Poisson's ratio. Fracture-prone sweet spots can be predicted by prestack inversion, which is an ill-posed problem; thus, regularization is needed to obtain unique and stable solutions. To characterize gas-bearing shale sedimentary bodies, elastic parameter variations are regarded as an anisotropic Markov random field. Bayesian statistics are adopted for transforming prestack inversion to the maximum posterior probability. Two energy functions for the lateral and vertical directions are used to describe the distribution, and the expectation-maximization algorithm is used to estimate the hyperparameters of the prior probability of elastic parameters. Finally, the inversion yields clear geological boundaries, high vertical resolution, and reasonable lateral continuity using the conjugate gradient method to minimize the objective function. Antinoise and imaging ability of the method were tested using synthetic and real data.
A Markov random walk under constraint for discovering overlapping communities in complex networks
International Nuclear Information System (INIS)
The detection of overlapping communities in complex networks has motivated recent research in relevant fields. Aiming to address this problem, we propose a Markov-dynamics-based algorithm, called UEOC, which means 'unfold and extract overlapping communities'. In UEOC, when identifying each natural community that overlaps, a Markov random walk method combined with a constraint strategy, which is based on the corresponding annealed network (degree conserving random network), is performed to unfold the community. Then, a cutoff criterion with the aid of a local community function, called conductance, which can be thought of as the ratio between the number of edges inside the community and those leaving it, is presented to extract this emerged community from the entire network. The UEOC algorithm depends on only one parameter whose value can be easily set, and it requires no prior knowledge of the hidden community structures. The proposed UEOC has been evaluated both on synthetic benchmarks and on some real-world networks, and has been compared with a set of competing algorithms. The experimental result has shown that UEOC is highly effective and efficient for discovering overlapping communities
Directory of Open Access Journals (Sweden)
Márcio das Chagas Moura
2008-08-01
Full Text Available In this work it is proposed a model for the assessment of availability measure of fault tolerant systems based on the integration of continuous time semi-Markov processes and Bayesian belief networks. This integration results in a hybrid stochastic model that is able to represent the dynamic characteristics of a system as well as to deal with cause-effect relationships among external factors such as environmental and operational conditions. The hybrid model also allows for uncertainty propagation on the system availability. It is also proposed a numerical procedure for the solution of the state probability equations of semi-Markov processes described in terms of transition rates. The numerical procedure is based on the application of Laplace transforms that are inverted by the Gauss quadrature method known as Gauss Legendre. The hybrid model and numerical procedure are illustrated by means of an example of application in the context of fault tolerant systems.Neste trabalho, é proposto um modelo baseado na integração entre processos semi-Markovianos e redes Bayesianas para avaliação da disponibilidade de sistemas tolerantes à falha. Esta integração resulta em um modelo estocástico híbrido o qual é capaz de representar as características dinâmicas de um sistema assim como tratar as relações de causa e efeito entre fatores externos tais como condições ambientais e operacionais. Além disso, o modelo híbrido permite avaliar a propagação de incerteza sobre a disponibilidade do sistema. É também proposto um procedimento numérico para a solução das equações de probabilidade de estado de processos semi-Markovianos descritos por taxas de transição. Tal procedimento numérico é baseado na aplicação de transformadas de Laplace que são invertidas pelo método de quadratura Gaussiana conhecido como Gauss Legendre. O modelo híbrido e procedimento numérico são ilustrados por meio de um exemplo de aplicação no contexto de
Entropy and long-range memory in random symbolic additive Markov chains
Melnik, S. S.; Usatenko, O. V.
2016-06-01
The goal of this paper is to develop an estimate for the entropy of random symbolic sequences with elements belonging to a finite alphabet. As a plausible model, we use the high-order additive stationary ergodic Markov chain with long-range memory. Supposing that the correlations between random elements of the chain are weak, we express the conditional entropy of the sequence by means of the symbolic pair correlation function. We also examine an algorithm for estimating the conditional entropy of finite symbolic sequences. We show that the entropy contains two contributions, i.e., the correlation and the fluctuation. The obtained analytical results are used for numerical evaluation of the entropy of written English texts and DNA nucleotide sequences. The developed theory opens the way for constructing a more consistent and sophisticated approach to describe the systems with strong short-range and weak long-range memory.
Energy Technology Data Exchange (ETDEWEB)
Nicoulaud-Gouin, V.; Giacalone, M.; Gonze, M.A. [Institut de Radioprotection et de Surete Nucleaire-PRP-ENV/SERIS/LM2E (France); Martin-Garin, A.; Garcia-Sanchez, L. [IRSN-PRP-ENV/SERIS/L2BT (France)
2014-07-01
Calibration of transfer models according to observation data is a challenge, especially if parameters uncertainty is required, and if competing models should be decided between them. Generally two main calibration methods are used: The frequentist approach in which the unknown parameter of interest is supposed fixed and its estimation is based on the data only. In this category, least squared method has many restrictions in nonlinear models and competing models need to be nested in order to be compared. The bayesian inference in which the unknown parameter of interest is supposed random and its estimation is based on the data and on prior information. Compared to frequentist method, it provides probability density functions and therefore pointwise estimation with credible intervals. However, in practical cases, Bayesian inference is a complex problem of numerical integration, which explains its low use in operational modeling including radioecology. This study aims to illustrate the interest and feasibility of Bayesian approach in radioecology particularly in the case of ordinary differential equations with non-constant coefficients models, which cover most radiological risk assessment models, notably those implemented in the Symbiose platform (Gonze et al, 2010). Markov Chain Monte Carlo (MCMC) method (Metropolis et al., 1953) was used because the posterior expectations are intractable integrals. The invariant distribution of the parameters was performed by the metropolis-Hasting algorithm (Hastings, 1970). GNU-MCSim software (Bois and Maszle, 2011) a bayesian hierarchical framework, was used to deal with nonlinear differential models. Two case studies including this type of model were investigated: An Equilibrium Kinetic sorption model (EK) (e.g. van Genuchten et al, 1974), with experimental data concerning {sup 137}Cs and {sup 85}Sr sorption and desorption in different soils studied in stirred flow-through reactors. This model, generalizing the K{sub d} approach
International Nuclear Information System (INIS)
Calibration of transfer models according to observation data is a challenge, especially if parameters uncertainty is required, and if competing models should be decided between them. Generally two main calibration methods are used: The frequentist approach in which the unknown parameter of interest is supposed fixed and its estimation is based on the data only. In this category, least squared method has many restrictions in nonlinear models and competing models need to be nested in order to be compared. The bayesian inference in which the unknown parameter of interest is supposed random and its estimation is based on the data and on prior information. Compared to frequentist method, it provides probability density functions and therefore pointwise estimation with credible intervals. However, in practical cases, Bayesian inference is a complex problem of numerical integration, which explains its low use in operational modeling including radioecology. This study aims to illustrate the interest and feasibility of Bayesian approach in radioecology particularly in the case of ordinary differential equations with non-constant coefficients models, which cover most radiological risk assessment models, notably those implemented in the Symbiose platform (Gonze et al, 2010). Markov Chain Monte Carlo (MCMC) method (Metropolis et al., 1953) was used because the posterior expectations are intractable integrals. The invariant distribution of the parameters was performed by the metropolis-Hasting algorithm (Hastings, 1970). GNU-MCSim software (Bois and Maszle, 2011) a bayesian hierarchical framework, was used to deal with nonlinear differential models. Two case studies including this type of model were investigated: An Equilibrium Kinetic sorption model (EK) (e.g. van Genuchten et al, 1974), with experimental data concerning 137Cs and 85Sr sorption and desorption in different soils studied in stirred flow-through reactors. This model, generalizing the Kd approach, distinguishes
Local Autoencoding for Parameter Estimation in a Hidden Potts-Markov Random Field.
Song, Sanming; Si, Bailu; Herrmann, J Michael; Feng, Xisheng
2016-05-01
A local-autoencoding (LAE) method is proposed for the parameter estimation in a Hidden Potts-Markov random field model. Due to sampling cost, Markov chain Monte Carlo methods are rarely used in real-time applications. Like other heuristic methods, LAE is based on a conditional independence assumption. It adapts, however, the parameters in a block-by-block style with a simple Hebbian learning rule. Experiments with given label fields show that the LAE is able to converge in far less time than required for a scan. It is also possible to derive an estimate for LAE based on a Cramer–Rao bound that is similar to the classical maximum pseudolikelihood method. As a general algorithm, LAE can be used to estimate the parameters in anisotropic label fields. Furthermore, LAE is not limited to the classical Potts model and can be applied to other types of Potts models by simple label field transformations and straightforward learning rule extensions. Experimental results on image segmentations demonstrate the efficiency and generality of the LAE algorithm. PMID:27019491
Multilayer Markov Random Field models for change detection in optical remote sensing images
Benedek, Csaba; Shadaydeh, Maha; Kato, Zoltan; Szirányi, Tamás; Zerubia, Josiane
2015-09-01
In this paper, we give a comparative study on three Multilayer Markov Random Field (MRF) based solutions proposed for change detection in optical remote sensing images, called Multicue MRF, Conditional Mixed Markov model, and Fusion MRF. Our purposes are twofold. On one hand, we highlight the significance of the focused model family and we set them against various state-of-the-art approaches through a thematic analysis and quantitative tests. We discuss the advantages and drawbacks of class comparison vs. direct approaches, usage of training data, various targeted application fields and different ways of Ground Truth generation, meantime informing the Reader in which roles the Multilayer MRFs can be efficiently applied. On the other hand we also emphasize the differences between the three focused models at various levels, considering the model structures, feature extraction, layer interpretation, change concept definition, parameter tuning and performance. We provide qualitative and quantitative comparison results using principally a publicly available change detection database which contains aerial image pairs and Ground Truth change masks. We conclude that the discussed models are competitive against alternative state-of-the-art solutions, if one uses them as pre-processing filters in multitemporal optical image analysis. In addition, they cover together a large range of applications, considering the different usage options of the three approaches.
Perlmutter, M.
1973-01-01
Molecular diffusion through a rarefied gas is analyzed by using the theory of Markov random walks. The Markov walk is simulated on the computer by using random numbers to find the new states from the appropriate transition probabilities. As the sample molecule during its random walk passes a scoring position, which is a location at which the macroscopic diffusing flow variables such as molecular flux and molecular density are desired, an appropriate payoff is scored. The payoff is a function of the sample molecule velocity. For example, in obtaining the molecular flux across a scoring position, the random walk payoff is the net number of times the scoring position has been crossed in the positive direction. Similarly, when the molecular density is required, the payoff is the sum of the inverse velocity of the sample molecule passing the scoring position. The macroscopic diffusing flow variables are then found from the expected payoff of the random walks.
Object-oriented image coding scheme based on DWT and Markov random field
Zheng, Lei; Wu, Hsien-Hsun S.; Liu, Jyh-Charn S.; Chan, Andrew K.
1998-12-01
In this paper, we introduce an object-oriented image coding algorithm to differentiate regions of interest (ROI) in visual communications. Our scheme is motivated by the fact that in visual communications, image contents (objects) are not equally important. For a given network bandwidth budget, one should give the highest transmission priority to the most interesting object, and serve the remaining ones at lower priorities. We propose a DWT based Multiresolution Markov Random Field technique to segment image objects according to their textures. We show that this technique can effectively distinguish visual objects and assign them different priorities. This scheme can be integrated with our ROI compression coder, the Generalized Self-Similarity Tress codex, for networking applications.
The mean field theory in EM procedures for blind Markov random field image restoration.
Zhang, J
1993-01-01
A Markov random field (MRF) model-based EM (expectation-maximization) procedure for simultaneously estimating the degradation model and restoring the image is described. The MRF is a coupled one which provides continuity (inside regions of smooth gray tones) and discontinuity (at region boundaries) constraints for the restoration problem which is, in general, ill posed. The computational difficulty associated with the EM procedure for MRFs is resolved by using the mean field theory from statistical mechanics. An orthonormal blur decomposition is used to reduce the chances of undesirable locally optimal estimates. Experimental results on synthetic and real-world images show that this approach provides good blur estimates and restored images. The restored images are comparable to those obtained by a Wiener filter in mean-square error, but are most visually pleasing. PMID:18296192
Texture Analysis of the Retinal Nerve Fiber Layer in Fundus Images via Markov Random Fields
Czech Academy of Sciences Publication Activity Database
Kolář, R.; Vácha, Pavel
Heidelberg : Springer, 2009 - (Dössel, O.; Schlegel, W.), s. 247-250 ISBN 978-3-642-03890-7. [World Congress on Medical Physics and Biomedical Engineering. Munich (DE), 07.11.2009-12.11.2009] R&D Projects: GA MŠk 1M0572 Grant ostatní: GA MŠk(CZ) 2C06019 Institutional research plan: CEZ:AV0Z10750506 Keywords : glaucoma * texture analysis * fundus image Subject RIV: BD - Theory of Information http:// library .utia.cas.cz/separaty/2009/RO/vacha-texture%20analysis%20of%20the%20retinal%20nerve%20fiber%20layer%20in%20fundus%20images%20via%20markov%20random%20fields.pdf
A Markov Random Field Model-Based Approach to Natural Image Matting
Institute of Scientific and Technical Information of China (English)
Sheng-You Lin; Jiao-Ying Shi
2007-01-01
This paper proposes a Markov Random Field (MRF) model-based approach to natural image matting with complex scenes.After the trimap for matting is given manually, the unknown region is roughly segmented into several joint sub-regions.In each sub-region, we partition the colors of neighboring background or foreground pixels into several clusters in RGB color space and assign matting label to each unknown pixel.All the labels are modelled as an MRF and the matting problem is then formulated as a maximum a posteriori (MAP) estimation problem.Simulated annealing is used to find the optimal MAP estimation.The better results can be obtained under the same user-interactions when images are complex.Results of natural image matting experiments performed on complex images using this approach are shown and compared in this paper.
Markov analysis of alpha-helical, beta-sheet and random coil regions of proteins
International Nuclear Information System (INIS)
The rules up to now used to predict the spatial configuration of proteins from their primary structure are mostly based on the recurrence analysis of some doublets, triplets and so on of contiguous amino acids, but they do not take into account the correlation characteristics of the whole amino acid sequence. A statistical analysis of amino acid sequences for the alpha-helical, beta-sheet and random coil regions of about twenty proteins with known secondary structure by considering correlations effects has been carried out. The obtained results demonstrate that these sequences are at least a second-order Markov chain, i.e. they appear as if they were generated by a source that remembers at least the two aminoacids before the one being generated and that these two previous symbols influence the present choice
Face Association for Videos Using Conditional Random Fields and Max-Margin Markov Networks.
Du, Ming; Chellappa, Rama
2016-09-01
We address the video-based face association problem, in which one attempts to extract the face tracks of multiple subjects while maintaining label consistency. Traditional tracking algorithms have difficulty in handling this task, especially when challenging nuisance factors like motion blur, low resolution or significant camera motions are present. We demonstrate that contextual features, in addition to face appearance itself, play an important role in this case. We propose principled methods to combine multiple features using Conditional Random Fields and Max-Margin Markov networks to infer labels for the detected faces. Different from many existing approaches, our algorithms work in online mode and hence have a wider range of applications. We address issues such as parameter learning, inference and handling false positves/negatives that arise in the proposed approach. Finally, we evaluate our approach on several public databases. PMID:26552075
Hidaka, Shohei
2015-01-01
A Markov process, which is constructed recursively, arises in stochastic games with Markov strategies. In this study, we defined a special class of random processes called the recursive Markov process, which has infinitely many states but can be expressed in a closed form. We derive the characteristic equation which the marginal stationary distribution of an arbitrary recursive Markov process needs to satisfy.
International Nuclear Information System (INIS)
Sparsity has become a key concept for solving of high-dimensional inverse problems using variational regularization techniques. Recently, using similar sparsity-constraints in the Bayesian framework for inverse problems by encoding them in the prior distribution has attracted attention. Important questions about the relation between regularization theory and Bayesian inference still need to be addressed when using sparsity promoting inversion. A practical obstacle for these examinations is the lack of fast posterior sampling algorithms for sparse, high-dimensional Bayesian inversion. Accessing the full range of Bayesian inference methods requires being able to draw samples from the posterior probability distribution in a fast and efficient way. This is usually done using Markov chain Monte Carlo (MCMC) sampling algorithms. In this paper, we develop and examine a new implementation of a single component Gibbs MCMC sampler for sparse priors relying on L1-norms. We demonstrate that the efficiency of our Gibbs sampler increases when the level of sparsity or the dimension of the unknowns is increased. This property is contrary to the properties of the most commonly applied Metropolis–Hastings (MH) sampling schemes. We demonstrate that the efficiency of MH schemes for L1-type priors dramatically decreases when the level of sparsity or the dimension of the unknowns is increased. Practically, Bayesian inversion for L1-type priors using MH samplers is not feasible at all. As this is commonly believed to be an intrinsic feature of MCMC sampling, the performance of our Gibbs sampler also challenges common beliefs about the applicability of sample based Bayesian inference. (paper)
Infinite Structured Hidden Semi-Markov Models
Huggins, Jonathan H.; Wood, Frank
2014-01-01
This paper reviews recent advances in Bayesian nonparametric techniques for constructing and performing inference in infinite hidden Markov models. We focus on variants of Bayesian nonparametric hidden Markov models that enhance a posteriori state-persistence in particular. This paper also introduces a new Bayesian nonparametric framework for generating left-to-right and other structured, explicit-duration infinite hidden Markov models that we call the infinite structured hidden semi-Markov m...
A recursive model-reduction method for approximate inference in Gaussian Markov random fields.
Johnson, Jason K; Willsky, Alan S
2008-01-01
This paper presents recursive cavity modeling--a principled, tractable approach to approximate, near-optimal inference for large Gauss-Markov random fields. The main idea is to subdivide the random field into smaller subfields, constructing cavity models which approximate these subfields. Each cavity model is a concise, yet faithful, model for the surface of one subfield sufficient for near-optimal inference in adjacent subfields. This basic idea leads to a tree-structured algorithm which recursively builds a hierarchy of cavity models during an "upward pass" and then builds a complementary set of blanket models during a reverse "downward pass." The marginal statistics of individual variables can then be approximated using their blanket models. Model thinning plays an important role, allowing us to develop thinned cavity and blanket models thereby providing tractable approximate inference. We develop a maximum-entropy approach that exploits certain tractable representations of Fisher information on thin chordal graphs. Given the resulting set of thinned cavity models, we also develop a fast preconditioner, which provides a simple iterative method to compute optimal estimates. Thus, our overall approach combines recursive inference, variational learning and iterative estimation. We demonstrate the accuracy and scalability of this approach in several challenging, large-scale remote sensing problems. PMID:18229805
Espinoza-Molina, Daniela; Datcu, Mihai
2010-10-01
TerraSAR-X is the Synthetic Aperture Radar (SAR) German satellite which provides a high diversity of information due to its high-resolution. TerraSAR-X acquires daily a volume of up to 100 GB of high complexity, multi-mode SAR images, i.e. SpotLight, StripMap, and ScanSAR data, with dual or quad-polarization, and with different look angles. The high and multiple resolutions of the instrument (1m, 3m or 10m) open perspectives for new applications, that were not possible with past lower resolution sensors (20-30m). Mainly the 1m and 3m modes we expect to support a broad range of new applications related to human activities with relevant structures and objects at the 1m scale. Thus, among the most interesting scenes are: urban, industrial, and rural data. In addition, the global coverage and the relatively frequent repeat pass will definitely help to acquire extremely relevant data sets. To analyze the available TerrrSAR-X data we rely on model based methods for feature extraction and despeckling. The image information content is extracted using model-based methods based on Gauss Markov Random Field (GMRF) and Bayesian inference approach. This approach enhances the local adaptation by using a prior model, which learns the image structure and enables to estimate the local description of the structures, acting as primitive feature extraction method. However, the GMRF model-based method uses as input parameters the Model Order (MO) and the size of Estimation Window (EW). The appropriated selection of these parameters allows us to improve the classification and indexing results due to the number of well separated classes could be determined by them. Our belief is that the selection of the MO depends on the kind of information that the image contains, explaining how well the model can recognize complex structures as objects, and according to the size of EW the accuracy of the estimation is determined. In the following, we present an evaluation of the impact of the model
Recognition of 3-D objects based on Markov random field models
Institute of Scientific and Technical Information of China (English)
HUANG Ying; DING Xiao-qing; WANG Sheng-jin
2006-01-01
The recognition of 3-D objects is quite a difficult task for computer vision systems.This paper presents a new object framework,which utilizes densely sampled grids with different resolutions to represent the local information of the input image.A Markov random field model is then created to model the geometric distribution of the object key nodes.Flexible matching,which aims to find the accurate correspondence map between the key points of two images,is performed by combining the local similarities and the geometric relations together using the highest confidence first method.Afterwards,a global similarity is calculated for object recognition. Experimental results on Coil-100 object database,which consists of 7 200 images of 100 objects,are presented.When the numbers of templates vary from 4,8,18 to 36 for each object,and the remaining images compose the test sets,the object recognition rates are 95.75 %,99.30 %,100.0 % and 100.0 %,respectively.The excellent recognition performance is much better than those of the other cited references,which indicates that our approach is well-suited for appearance-based object recognition.
A Markov Random Field Model-Based Approach To Image Interpretation
Zhang, Jun; Modestino, James W.
1989-11-01
In this paper, a Markov random field (MRF) model-based approach to automated image interpretation is described and demonstrated as a region-based scheme. In this approach, an image is first segmented into a collection of disjoint regions which form the nodes of an adjacency graph. Image interpretation is then achieved through assigning object labels, or interpretations, to the segmented regions, or nodes, using domain knowledge, extracted feature measurements and spatial relationships between the various regions. The interpretation labels are modeled as a MRF on the corresponding adjacency graph and the image interpretation problem is formulated as a maximum a posteriori (MAP) estimation rule. Simulated annealing is used to find the best realization, or optimal MAP interpretation. Through the MRF model, this approach also provides a systematic method for organizing and representing domain knowledge through the clique functions of the pdf of the underlying MRF. Results of image interpretation experiments performed on synthetic and real-world images using this approach are described and appear promising.
Batool, Nazre; Chellappa, Rama
2014-09-01
Facial retouching is widely used in media and entertainment industry. Professional software usually require a minimum level of user expertise to achieve the desirable results. In this paper, we present an algorithm to detect facial wrinkles/imperfection. We believe that any such algorithm would be amenable to facial retouching applications. The detection of wrinkles/imperfections can allow these skin features to be processed differently than the surrounding skin without much user interaction. For detection, Gabor filter responses along with texture orientation field are used as image features. A bimodal Gaussian mixture model (GMM) represents distributions of Gabor features of normal skin versus skin imperfections. Then, a Markov random field model is used to incorporate the spatial relationships among neighboring pixels for their GMM distributions and texture orientations. An expectation-maximization algorithm then classifies skin versus skin wrinkles/imperfections. Once detected automatically, wrinkles/imperfections are removed completely instead of being blended or blurred. We propose an exemplar-based constrained texture synthesis algorithm to inpaint irregularly shaped gaps left by the removal of detected wrinkles/imperfections. We present results conducted on images downloaded from the Internet to show the efficacy of our algorithms. PMID:24968171
Medical image retrieval and analysis by Markov random fields and multi-scale fractal dimension.
Backes, André Ricardo; Gerhardinger, Leandro Cavaleri; Batista Neto, João do Espírito Santo; Bruno, Odemir Martinez
2015-02-01
Many Content-based Image Retrieval (CBIR) systems and image analysis tools employ color, shape and texture (in a combined fashion or not) as attributes, or signatures, to retrieve images from databases or to perform image analysis in general. Among these attributes, texture has turned out to be the most relevant, as it allows the identification of a larger number of images of a different nature. This paper introduces a novel signature which can be used for image analysis and retrieval. It combines texture with complexity extracted from objects within the images. The approach consists of a texture segmentation step, modeled as a Markov Random Field process, followed by the estimation of the complexity of each computed region. The complexity is given by a Multi-scale Fractal Dimension. Experiments have been conducted using an MRI database in both pattern recognition and image retrieval contexts. The results show the accuracy of the proposed method in comparison with other traditional texture descriptors and also indicate how the performance changes as the level of complexity is altered. PMID:25586375
A Joint Land Cover Mapping and Image Registration Algorithm Based on a Markov Random Field Model
Directory of Open Access Journals (Sweden)
Apisit Eiumnoh
2013-10-01
Full Text Available Traditionally, image registration of multi-modal and multi-temporal images is performed satisfactorily before land cover mapping. However, since multi-modal and multi-temporal images are likely to be obtained from different satellite platforms and/or acquired at different times, perfect alignment is very difficult to achieve. As a result, a proper land cover mapping algorithm must be able to correct registration errors as well as perform an accurate classification. In this paper, we propose a joint classification and registration technique based on a Markov random field (MRF model to simultaneously align two or more images and obtain a land cover map (LCM of the scene. The expectation maximization (EM algorithm is employed to solve the joint image classification and registration problem by iteratively estimating the map parameters and approximate posterior probabilities. Then, the maximum a posteriori (MAP criterion is used to produce an optimum land cover map. We conducted experiments on a set of four simulated images and one pair of remotely sensed images to investigate the effectiveness and robustness of the proposed algorithm. Our results show that, with proper selection of a critical MRF parameter, the resulting LCMs derived from an unregistered image pair can achieve an accuracy that is as high as when images are perfectly aligned. Furthermore, the registration error can be greatly reduced.
Automatic Lung Tumor Segmentation on PET/CT Images Using Fuzzy Markov Random Field Model
Directory of Open Access Journals (Sweden)
Yu Guo
2014-01-01
Full Text Available The combination of positron emission tomography (PET and CT images provides complementary functional and anatomical information of human tissues and it has been used for better tumor volume definition of lung cancer. This paper proposed a robust method for automatic lung tumor segmentation on PET/CT images. The new method is based on fuzzy Markov random field (MRF model. The combination of PET and CT image information is achieved by using a proper joint posterior probability distribution of observed features in the fuzzy MRF model which performs better than the commonly used Gaussian joint distribution. In this study, the PET and CT simulation images of 7 non-small cell lung cancer (NSCLC patients were used to evaluate the proposed method. Tumor segmentations with the proposed method and manual method by an experienced radiation oncologist on the fused images were performed, respectively. Segmentation results obtained with the two methods were similar and Dice’s similarity coefficient (DSC was 0.85 ± 0.013. It has been shown that effective and automatic segmentations can be achieved with this method for lung tumors which locate near other organs with similar intensities in PET and CT images, such as when the tumors extend into chest wall or mediastinum.
Medical image retrieval and analysis by Markov random fields and multi-scale fractal dimension
International Nuclear Information System (INIS)
Many Content-based Image Retrieval (CBIR) systems and image analysis tools employ color, shape and texture (in a combined fashion or not) as attributes, or signatures, to retrieve images from databases or to perform image analysis in general. Among these attributes, texture has turned out to be the most relevant, as it allows the identification of a larger number of images of a different nature. This paper introduces a novel signature which can be used for image analysis and retrieval. It combines texture with complexity extracted from objects within the images. The approach consists of a texture segmentation step, modeled as a Markov Random Field process, followed by the estimation of the complexity of each computed region. The complexity is given by a Multi-scale Fractal Dimension. Experiments have been conducted using an MRI database in both pattern recognition and image retrieval contexts. The results show the accuracy of the proposed method in comparison with other traditional texture descriptors and also indicate how the performance changes as the level of complexity is altered. (paper)
Medical image retrieval and analysis by Markov random fields and multi-scale fractal dimension
Backes, André Ricardo; Cavaleri Gerhardinger, Leandro; do Espírito Santo Batista Neto, João; Martinez Bruno, Odemir
2015-02-01
Many Content-based Image Retrieval (CBIR) systems and image analysis tools employ color, shape and texture (in a combined fashion or not) as attributes, or signatures, to retrieve images from databases or to perform image analysis in general. Among these attributes, texture has turned out to be the most relevant, as it allows the identification of a larger number of images of a different nature. This paper introduces a novel signature which can be used for image analysis and retrieval. It combines texture with complexity extracted from objects within the images. The approach consists of a texture segmentation step, modeled as a Markov Random Field process, followed by the estimation of the complexity of each computed region. The complexity is given by a Multi-scale Fractal Dimension. Experiments have been conducted using an MRI database in both pattern recognition and image retrieval contexts. The results show the accuracy of the proposed method in comparison with other traditional texture descriptors and also indicate how the performance changes as the level of complexity is altered.
MEDICAL IMAGE SEGMENTATION ON A CLUSTER OF PCS USING MARKOV RANDOM FIELDS
Directory of Open Access Journals (Sweden)
El-Hachemi Guerrout
2013-01-01
Full Text Available Medical imaging applications produce large sets of similar images. The huge amount of data makes the manual analysis and interpretation a fastidious task. Medical image segmentation is thus an important process in image processing used to partition the images into different regions (e.g. gray matter(GM, white matter(WM and cerebrospinal fluid(CSF. Hidden Markov Random Field (HMRF Model and Gibbs distributions provide powerful tools for image modeling. In this paper, we use a HMRF model to perform segmentation of volumetric medical images. We have a problem with incomplete data. We seek the segmented images according to the MAP (Maximum A Posteriori criterion. MAP estimation leads to the minimization of an energy function. This problem is computationally intractable. Therefore, optimizations techniques are used to compute a solution. We will evaluate the segmentation upon two major factors: the time of calculation and the quality of segmentation. Processing time is reduced by distributing the computation of segmentation on a powerful and inexpensive architecture that consists of a cluster of personal computers. Parallel programming was done by using the standard MPI (Message Passing Interface.
Gelman, Andrew; Stern, Hal S; Dunson, David B; Vehtari, Aki; Rubin, Donald B
2013-01-01
FUNDAMENTALS OF BAYESIAN INFERENCEProbability and InferenceSingle-Parameter Models Introduction to Multiparameter Models Asymptotics and Connections to Non-Bayesian ApproachesHierarchical ModelsFUNDAMENTALS OF BAYESIAN DATA ANALYSISModel Checking Evaluating, Comparing, and Expanding ModelsModeling Accounting for Data Collection Decision AnalysisADVANCED COMPUTATION Introduction to Bayesian Computation Basics of Markov Chain Simulation Computationally Efficient Markov Chain Simulation Modal and Distributional ApproximationsREGRESSION MODELS Introduction to Regression Models Hierarchical Linear
Analysis and Validation of Grid dem Generation Based on Gaussian Markov Random Field
Aguilar, F. J.; Aguilar, M. A.; Blanco, J. L.; Nemmaoui, A.; García Lorca, A. M.
2016-06-01
Digital Elevation Models (DEMs) are considered as one of the most relevant geospatial data to carry out land-cover and land-use classification. This work deals with the application of a mathematical framework based on a Gaussian Markov Random Field (GMRF) to interpolate grid DEMs from scattered elevation data. The performance of the GMRF interpolation model was tested on a set of LiDAR data (0.87 points/m2) provided by the Spanish Government (PNOA Programme) over a complex working area mainly covered by greenhouses in Almería, Spain. The original LiDAR data was decimated by randomly removing different fractions of the original points (from 10% to up to 99% of points removed). In every case, the remaining points (scattered observed points) were used to obtain a 1 m grid spacing GMRF-interpolated Digital Surface Model (DSM) whose accuracy was assessed by means of the set of previously extracted checkpoints. The GMRF accuracy results were compared with those provided by the widely known Triangulation with Linear Interpolation (TLI). Finally, the GMRF method was applied to a real-world case consisting of filling the LiDAR-derived DSM gaps after manually filtering out non-ground points to obtain a Digital Terrain Model (DTM). Regarding accuracy, both GMRF and TLI produced visually pleasing and similar results in terms of vertical accuracy. As an added bonus, the GMRF mathematical framework makes possible to both retrieve the estimated uncertainty for every interpolated elevation point (the DEM uncertainty) and include break lines or terrain discontinuities between adjacent cells to produce higher quality DTMs.
DEFF Research Database (Denmark)
Scholer, Marie; Irving, James; Zibar, Majken Caroline Looms;
2012-01-01
-chain-Monte-Carlo inversion approach with different priors. The ground-penetrating radar (GPR) geophysical method has the potential to provide valuable information on the hydraulic properties of the vadose zone because of its strong sensitivity to soil water content. In particular, recent evidence has suggested that the......We examined to what extent time-lapse crosshole ground-penetrating radar traveltimes, measured during a forced infiltration experiment at the Arreneas field site in Denmark, could help to quantify vadose zone hydraulic properties and their corresponding uncertainties using a Bayesian Markov......-state infiltration conditions, which represent only a small fraction of practically relevant scenarios. We explored in detail the dynamic infiltration case, specifically examining to what extent time-lapse crosshole GPR traveltimes, measured during a forced infiltration experiment at the Arreneas field site in...
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Kevin McNally
2012-01-01
Full Text Available There are numerous biomonitoring programs, both recent and ongoing, to evaluate environmental exposure of humans to chemicals. Due to the lack of exposure and kinetic data, the correlation of biomarker levels with exposure concentrations leads to difficulty in utilizing biomonitoring data for biological guidance values. Exposure reconstruction or reverse dosimetry is the retrospective interpretation of external exposure consistent with biomonitoring data. We investigated the integration of physiologically based pharmacokinetic modelling, global sensitivity analysis, Bayesian inference, and Markov chain Monte Carlo simulation to obtain a population estimate of inhalation exposure to m-xylene. We used exhaled breath and venous blood m-xylene and urinary 3-methylhippuric acid measurements from a controlled human volunteer study in order to evaluate the ability of our computational framework to predict known inhalation exposures. We also investigated the importance of model structure and dimensionality with respect to its ability to reconstruct exposure.
Expressing Bayesian Fusion as a Product of Distributions: Application to Randomized Hough Transform
Pradalier, Cédric; Colas, Francis; Bessière, Pierre
2004-04-01
Data fusion is a common issue of mobile robotics, computer assisted medical diagnosis or behavioral control of simulated character for instance. However data sources are often noisy, opinion for experts are not known with absolute precision, and motor commands do not act in the same exact manner on the environment. In these cases, classic logic fails to manage efficiently the fusion process. Confronting different knowledge in an uncertain environment can therefore be adequately formalized in the bayesian framework. Besides, bayesian fusion can be expensive in terms of memory usage and processing time. This paper precisely aims at expressing any bayesian fusion process as a product of probability distributions in order to reduce its complexity. We first study both direct and inverse fusion schemes. We show that contrary to direct models, inverse local models need a specific prior in order to allow the fusion to be computed as a product. We therefore propose to add a consistency variable to each local model and we show that these additional variables allow the use of a product of the local distributions in order to compute the global probability distribution over the fused variable. Finally, we take the example of the Randomized Hough Transform. We rewrite it in the bayesian framework, considering that it is a fusion process to extract lines from couples of dots in a picture. As expected, we can find back the expression of the Randomized Hough Transform from the literature with the appropriate assumptions.
A Hypergraph-Based Reduction for Higher-Order Binary Markov Random Fields.
Fix, Alexander; Gruber, Aritanan; Boros, Endre; Zabih, Ramin
2015-07-01
Higher-order Markov Random Fields, which can capture important properties of natural images, have become increasingly important in computer vision. While graph cuts work well for first-order MRF's, until recently they have rarely been effective for higher-order MRF's. Ishikawa's graph cut technique [1], [2] shows great promise for many higher-order MRF's. His method transforms an arbitrary higher-order MRF with binary labels into a first-order one with the same minima. If all the terms are submodular the exact solution can be easily found; otherwise, pseudoboolean optimization techniques can produce an optimal labeling for a subset of the variables. We present a new transformation with better performance than [1], [2], both theoretically and experimentally. While [1], [2] transforms each higher-order term independently, we use the underlying hypergraph structure of the MRF to transform a group of terms at once. For n binary variables, each of which appears in terms with k other variables, at worst we produce n non-submodular terms, while [1], [2] produces O(nk). We identify a local completeness property under which our method perform even better, and show that under certain assumptions several important vision problems (including common variants of fusion moves) have this property. We show experimentally that our method produces smaller weight of non-submodular edges, and that this metric is directly related to the effectiveness of QPBO [3]. Running on the same field of experts dataset used in [1], [2] we optimally label significantly more variables (96 versus 80 percent) and converge more rapidly to a lower energy. Preliminary experiments suggest that some other higher-order MRF's used in stereo [4] and segmentation [5] are also locally complete and would thus benefit from our work. PMID:26352447
IMPROVING MARKOV RANDOM FIELD BASED SUPER RESOLUTION MAPPING THROUGH FUZZY PARAMETER INTEGRATION
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D. R . Welikanna
2012-07-01
Full Text Available The objective of this study was to improve the Markov Random Field (MRF based Super Resolution Mapping (SRM technique to account for the vague land-cover interpretations (class mixture and the intermediate conditions in an urban area. The algorithm has been improved to integrate the fuzzy mean and fuzzy covariance measurements, to a MRF based SRM scheme to optimize the classification results. The technique was tested on a WORLDVIEW-2 data set, acquired over a highway construction area, in Colombo, Sri Lanka. Based on the visual interpretation of the image, three major land-cover types of this area were identified for the study; those were vegetation, soil and exposed grass and impervious surface with low medium and high albedo. The membership values for each pixel were determined from training samples through Spectral Angle Mapper (SAM technique. The compulsory fuzzy mean and the covariance measurements were derived using these membership grades, and subsequently was applied in MRF based SRM technique. The primary reference data was generated using Maximum Likelihood Classification (MLC performed on the same data which was resampled to 1m resolution. The scale factor was set to be (S = 2, to generate SRM of 1m resolution. The smoothening parameter (λ which balances the prior and likelihood energy terms were tested in the range from 0.3 to 0.9. SRM were generated using fuzzy MRF and the conventional MRF models respectively. Results suggest that the fuzzy integrated model has improved the results with an overall accuracy of 85.60% and kappa value of 0.78 between the optimal results and the reference data, while in the conventional case it was 77.81% of overall accuracy with kappa being 0.65. Among the two MRF models, fuzzy parameter integrated model shows the highest agreement with class fractions from the reference image with a smallest average _MAE (MAE, Mean Absolute Error of 0.03.
Braak, ter C.J.F.
2006-01-01
Differential Evolution (DE) is a simple genetic algorithm for numerical optimization in real parameter spaces. In a statistical context one would not just want the optimum but also its uncertainty. The uncertainty distribution can be obtained by a Bayesian analysis (after specifying prior and likeli
Directory of Open Access Journals (Sweden)
Hongqiang Liu
2016-06-01
Full Text Available A Bayesian random effects modeling approach was used to examine the influence of neighborhood characteristics on burglary risks in Jianghan District, Wuhan, China. This random effects model is essentially spatial; a spatially structured random effects term and an unstructured random effects term are added to the traditional non-spatial Poisson regression model. Based on social disorganization and routine activity theories, five covariates extracted from the available data at the neighborhood level were used in the modeling. Three regression models were fitted and compared by the deviance information criterion to identify which model best fit our data. A comparison of the results from the three models indicates that the Bayesian random effects model is superior to the non-spatial models in fitting the data and estimating regression coefficients. Our results also show that neighborhoods with above average bar density and department store density have higher burglary risks. Neighborhood-specific burglary risks and posterior probabilities of neighborhoods having a burglary risk greater than 1.0 were mapped, indicating the neighborhoods that should warrant more attention and be prioritized for crime intervention and reduction. Implications and limitations of the study are discussed in our concluding section.
Waldmann, Patrik; Hallander, Jon; Hoti, Fabian; Sillanpää, Mikko J.
2008-01-01
Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general...
Daniels, Noah M.; Hosur, Raghavendra; Berger, Bonnie; Lenore J Cowen
2012-01-01
Motivation: One of the most successful methods to date for recognizing protein sequences that are evolutionarily related has been profile hidden Markov models (HMMs). However, these models do not capture pairwise statistical preferences of residues that are hydrogen bonded in beta sheets. These dependencies have been partially captured in the HMM setting by simulated evolution in the training phase and can be fully captured by Markov random fields (MRFs). However, the MRFs can be computationa...
An Inhomogeneous Bayesian Texture Model for Spatially Varying Parameter Estimation
Dharmagunawardhana, Chathurika; Mahmoodi, Sasan; Bennett, Michael; Niranjan, Mahesan
2014-01-01
In statistical model based texture feature extraction, features based on spatially varying parameters achieve higher discriminative performances compared to spatially constant parameters. In this paper we formulate a novel Bayesian framework which achieves texture characterization by spatially varying parameters based on Gaussian Markov random fields. The parameter estimation is carried out by Metropolis-Hastings algorithm. The distributions of estimated spatially varying paramete...
Metastates in Mean-Field Models with Random External Fields Generated by Markov Chains
Formentin, M.; Külske, C.; Reichenbachs, A.
2012-01-01
We extend the construction by Külske and Iacobelli of metastates in finite-state mean-field models in independent disorder to situations where the local disorder terms are a sample of an external ergodic Markov chain in equilibrium. We show that for non-degenerate Markov chains, the structure of the theorems is analogous to the case of i.i.d. variables when the limiting weights in the metastate are expressed with the aid of a CLT for the occupation time measure of the chain. As a new phenomenon we also show in a Potts example that for a degenerate non-reversible chain this CLT approximation is not enough, and that the metastate can have less symmetry than the symmetry of the interaction and a Gaussian approximation of disorder fluctuations would suggest.
Metastates in Markov chain-driven random mean-field models
Formentin, M; Reichenbachs, A
2011-01-01
We extend the construction by Kuelske and Iacobelli of metastates in finite-state mean-field models in independent disorder to situations where the local disorder terms are realization of an external ergodic Markov chain in equilibrium. We show that for non-degenerate Markov chains, the structure of the theorems is analogous to the case of i.i.d. variables when the limiting weights in the metastate are expressed with the aid of a CLT for the occupation time measure of the chain. As a new phenomenon we also show in a Potts example that, for a degenerate non-reversible chain this CLT approximation is not enough and the metastate can have less symmetry than the symmetry of the interaction and a Gaussian approximation of disorder fluctuations would suggest.
Continuous Time Markov Networks
El-Hay, Tal; Friedman, Nir; Koller, Daphne; Kupferman, Raz
2012-01-01
A central task in many applications is reasoning about processes that change in a continuous time. The mathematical framework of Continuous Time Markov Processes provides the basic foundations for modeling such systems. Recently, Nodelman et al introduced continuous time Bayesian networks (CTBNs), which allow a compact representation of continuous-time processes over a factored state space. In this paper, we introduce continuous time Markov networks (CTMNs), an alternative representation lang...
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Feng Ding
2015-01-01
Full Text Available In order to detect the obstacle from the large amount of 3D LIDAR data in hybrid cross-country environment for unmanned ground vehicle, a new graph approach based on Markov random field was presented. Firstly, the preprocessing method based on the maximum blurred line is applied to segment the projection of every laser scan line in x-y plane. Then, based on K-means clustering algorithm, the same properties of the line are combined. Secondly, line segment nodes are precisely positioned by using corner detection method, and the next step is to take advantage of line segment nodes to build an undirected graph for Markov random field. Lastly, the energy function is calculated by means of analyzing line segment features and solved by graph cut. Two types of line mark are finally classified into two categories: ground and obstacle. Experiments prove the feasibility of the approach and show that it has better performance and runs in real time.
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Yanzi Wang
2016-01-01
Full Text Available Over the last few years; issues regarding the use of hybrid energy storage systems (HESSs in hybrid electric vehicles have been highlighted by the industry and in academic fields. This paper proposes a fuzzy-logic power management strategy based on Markov random prediction for an active parallel battery-UC HESS. The proposed power management strategy; the inputs for which are the vehicle speed; the current electric power demand and the predicted electric power demand; is used to distribute the electrical power between the battery bank and the UC bank. In this way; the battery bank power is limited to a certain range; and the peak and average charge/discharge power of the battery bank and overall loss incurred by the whole HESS are also reduced. Simulations and scaled-down experimental platforms are constructed to verify the proposed power management strategy. The simulations and experimental results demonstrate the advantages; feasibility and effectiveness of the fuzzy-logic power management strategy based on Markov random prediction.
Inferring activities from context measurements using Bayesian inference and random utility models
Hurtubia, Ricardo; Bierlaire, Michel; Flötteröd, Gunnar
2009-01-01
Smartphones collect a wealth of information about their users. This includes GPS tracks and the MAC addresses of devices around the user, and it can go as far as taking visual and acoustic samples of the user's environment. We present a framework to identify a smartphone user's activities in a Bayesian setting. As prior information, we us a random utility model that accounts for the type of activity a user is likely to perform at any given location and time; this model was estimated for the w...
Microwave imaging from experimental data within a Bayesian framework with realistic random noise
Eyraud, C.; Litman, A.; Hérique, A.; Kofman, W.
2009-02-01
This paper deals with the reconstruction of three-dimensional targets from experimental multiple-frequency data measured in the anechoic chamber of the Institut Fresnel (Marseille, France). An inverse iterative scheme is implemented with an adequate choice of the cost functional. Indeed, a Bayesian approach is considered in order to take into account the random noise which is present in the experiment. This leads to the definition of an adequate cost functional, where the weighting coefficients are changing with the frequency, the incidence angle and the receiving angle. The inversion scheme turns out to be more robust and accurate.
Microwave imaging from experimental data within a Bayesian framework with realistic random noise
International Nuclear Information System (INIS)
This paper deals with the reconstruction of three-dimensional targets from experimental multiple-frequency data measured in the anechoic chamber of the Institut Fresnel (Marseille, France). An inverse iterative scheme is implemented with an adequate choice of the cost functional. Indeed, a Bayesian approach is considered in order to take into account the random noise which is present in the experiment. This leads to the definition of an adequate cost functional, where the weighting coefficients are changing with the frequency, the incidence angle and the receiving angle. The inversion scheme turns out to be more robust and accurate
Dynkin, E B
1960-01-01
Theory of Markov Processes provides information pertinent to the logical foundations of the theory of Markov random processes. This book discusses the properties of the trajectories of Markov processes and their infinitesimal operators.Organized into six chapters, this book begins with an overview of the necessary concepts and theorems from measure theory. This text then provides a general definition of Markov process and investigates the operations that make possible an inspection of the class of Markov processes corresponding to a given transition function. Other chapters consider the more c
Rocha, G; Górski, K M; Huffenberger, K M; Lawrence, C R; Lange, A E
2009-01-01
We introduce a new method to propagate uncertainties in the beam shapes used to measure the cosmic microwave background to cosmological parameters determined from those measurements. The method, which we call Markov Chain Beam Randomization, MCBR, randomly samples from a set of templates or functions that describe the beam uncertainties. The method is much faster than direct numerical integration over systematic `nuisance' parameters, and is not restricted to simple, idealized cases as is analytic marginalization. It does not assume the data are normally distributed, and does not require Gaussian priors on the specific systematic uncertainties. We show that MCBR properly accounts for and provides the marginalized errors of the parameters. The method can be generalized and used to propagate any systematic uncertainties for which a set of templates is available. We apply the method to the Planck satellite, and consider future experiments. Beam measurement errors should have a small effect on cosmological parame...
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Alex Avilés
2016-01-01
Full Text Available The scarcity of water resources in mountain areas can distort normal water application patterns with among other effects, a negative impact on water supply and river ecosystems. Knowing the probability of droughts might help to optimize a priori the planning and management of the water resources in general and of the Andean watersheds in particular. This study compares Markov chain- (MC and Bayesian network- (BN based models in drought forecasting using a recently developed drought index with respect to their capability to characterize different drought severity states. The copula functions were used to solve the BNs and the ranked probability skill score (RPSS to evaluate the performance of the models. Monthly rainfall and streamflow data of the Chulco River basin, located in Southern Ecuador, were used to assess the performance of both approaches. Global evaluation results revealed that the MC-based models predict better wet and dry periods, and BN-based models generate slightly more accurately forecasts of the most severe droughts. However, evaluation of monthly results reveals that, for each month of the hydrological year, either the MC- or BN-based model provides better forecasts. The presented approach could be of assistance to water managers to ensure that timely decision-making on drought response is undertaken.
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Kanagi Kanapathy
2014-01-01
Full Text Available The research question is whether the positive relationship found between supplier involvement practices and new product development performances in developed economies also holds in emerging economies. The role of supplier involvement practices in new product development performance is yet to be substantially investigated in the emerging economies (other than China. This premise was examined by distributing a survey instrument (Jayaram’s (2008 published survey instrument that has been utilised in developed economies to Malaysian manufacturing companies. To gauge the relationship between the supplier involvement practices and new product development (NPD project performance of 146 companies, structural equation modelling was adopted. Our findings prove that supplier involvement practices have a significant positive impact on NPD project performance in an emerging economy with respect to quality objectives, design objectives, cost objectives, and “time-to-market” objectives. Further analysis using the Bayesian Markov Chain Monte Carlo algorithm, yielding a more credible and feasible differentiation, confirmed these results (even in the case of an emerging economy and indicated that these practices have a 28% impact on variance of NPD project performance. This considerable effect implies that supplier involvement is a must have, although further research is needed to identify the contingencies for its practices.
Energy Technology Data Exchange (ETDEWEB)
Chen, J.; Hoversten, G.M.
2011-09-15
Joint inversion of seismic AVA and CSEM data requires rock-physics relationships to link seismic attributes to electrical properties. Ideally, we can connect them through reservoir parameters (e.g., porosity and water saturation) by developing physical-based models, such as Gassmann’s equations and Archie’s law, using nearby borehole logs. This could be difficult in the exploration stage because information available is typically insufficient for choosing suitable rock-physics models and for subsequently obtaining reliable estimates of the associated parameters. The use of improper rock-physics models and the inaccuracy of the estimates of model parameters may cause misleading inversion results. Conversely, it is easy to derive statistical relationships among seismic and electrical attributes and reservoir parameters from distant borehole logs. In this study, we develop a Bayesian model to jointly invert seismic AVA and CSEM data for reservoir parameter estimation using statistical rock-physics models; the spatial dependence of geophysical and reservoir parameters are carried out by lithotypes through Markov random fields. We apply the developed model to a synthetic case, which simulates a CO{sub 2} monitoring application. We derive statistical rock-physics relations from borehole logs at one location and estimate seismic P- and S-wave velocity ratio, acoustic impedance, density, electrical resistivity, lithotypes, porosity, and water saturation at three different locations by conditioning to seismic AVA and CSEM data. Comparison of the inversion results with their corresponding true values shows that the correlation-based statistical rock-physics models provide significant information for improving the joint inversion results.
Mondal, A.
2010-03-01
In this paper, we study the uncertainty quantification in inverse problems for flows in heterogeneous porous media. Reversible jump Markov chain Monte Carlo algorithms (MCMC) are used for hierarchical modeling of channelized permeability fields. Within each channel, the permeability is assumed to have a lognormal distribution. Uncertainty quantification in history matching is carried out hierarchically by constructing geologic facies boundaries as well as permeability fields within each facies using dynamic data such as production data. The search with Metropolis-Hastings algorithm results in very low acceptance rate, and consequently, the computations are CPU demanding. To speed-up the computations, we use a two-stage MCMC that utilizes upscaled models to screen the proposals. In our numerical results, we assume that the channels intersect the wells and the intersection locations are known. Our results show that the proposed algorithms are capable of capturing the channel boundaries and describe the permeability variations within the channels using dynamic production history at the wells. © 2009 Elsevier Ltd. All rights reserved.
A Bayesian Analysis of a Random Effects Small Business Loan Credit Scoring Model
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Patrick J. Farrell
2011-09-01
Full Text Available One of the most important aspects of credit scoring is constructing a model that has low misclassification rates and is also flexible enough to allow for random variation. It is also well known that, when there are a large number of highly correlated variables as is typical in studies involving questionnaire data, a method must be found to reduce the number of variables to those that have high predictive power. Here we propose a Bayesian multivariate logistic regression model with both fixed and random effects for small business loan credit scoring and a variable reduction method using Bayes factors. The method is illustrated on an interesting data set based on questionnaires sent to loan officers in Canadian banks and venture capital companies
Patriche, Monica
2013-01-01
In this paper, we introduce an abstract fuzzy economy model with a measure space of agents which generalizes Patriche's model (2009), we obtain a theorem of fuzzy equilibrium existence and we prove the existence of the solutions for two types of random quasi-variational inequalities with random fuzzy mappings. As a consequence, we obtain random fixed point theorems.
A Bayesian decision-theoretic sequential response-adaptive randomization design.
Jiang, Fei; Jack Lee, J; Müller, Peter
2013-05-30
We propose a class of phase II clinical trial designs with sequential stopping and adaptive treatment allocation to evaluate treatment efficacy. Our work is based on two-arm (control and experimental treatment) designs with binary endpoints. Our overall goal is to construct more efficient and ethical randomized phase II trials by reducing the average sample sizes and increasing the percentage of patients assigned to the better treatment arms of the trials. The designs combine the Bayesian decision-theoretic sequential approach with adaptive randomization procedures in order to achieve simultaneous goals of improved efficiency and ethics. The design parameters represent the costs of different decisions, for example, the decisions for stopping or continuing the trials. The parameters enable us to incorporate the actual costs of the decisions in practice. The proposed designs allow the clinical trials to stop early for either efficacy or futility. Furthermore, the designs assign more patients to better treatment arms by applying adaptive randomization procedures. We develop an algorithm based on the constrained backward induction and forward simulation to implement the designs. The algorithm overcomes the computational difficulty of the backward induction method, thereby making our approach practicable. The designs result in trials with desirable operating characteristics under the simulated settings. Moreover, the designs are robust with respect to the response rate of the control group. PMID:23315678
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Regad Leslie
2010-01-01
Full Text Available Abstract Background In bioinformatics it is common to search for a pattern of interest in a potentially large set of rather short sequences (upstream gene regions, proteins, exons, etc.. Although many methodological approaches allow practitioners to compute the distribution of a pattern count in a random sequence generated by a Markov source, no specific developments have taken into account the counting of occurrences in a set of independent sequences. We aim to address this problem by deriving efficient approaches and algorithms to perform these computations both for low and high complexity patterns in the framework of homogeneous or heterogeneous Markov models. Results The latest advances in the field allowed us to use a technique of optimal Markov chain embedding based on deterministic finite automata to introduce three innovative algorithms. Algorithm 1 is the only one able to deal with heterogeneous models. It also permits to avoid any product of convolution of the pattern distribution in individual sequences. When working with homogeneous models, Algorithm 2 yields a dramatic reduction in the complexity by taking advantage of previous computations to obtain moment generating functions efficiently. In the particular case of low or moderate complexity patterns, Algorithm 3 exploits power computation and binary decomposition to further reduce the time complexity to a logarithmic scale. All these algorithms and their relative interest in comparison with existing ones were then tested and discussed on a toy-example and three biological data sets: structural patterns in protein loop structures, PROSITE signatures in a bacterial proteome, and transcription factors in upstream gene regions. On these data sets, we also compared our exact approaches to the tempting approximation that consists in concatenating the sequences in the data set into a single sequence. Conclusions Our algorithms prove to be effective and able to handle real data sets with
Monaco, James Peter; Madabhushi, Anant
2011-07-01
The ability of classification systems to adjust their performance (sensitivity/specificity) is essential for tasks in which certain errors are more significant than others. For example, mislabeling cancerous lesions as benign is typically more detrimental than mislabeling benign lesions as cancerous. Unfortunately, methods for modifying the performance of Markov random field (MRF) based classifiers are noticeably absent from the literature, and thus most such systems restrict their performance to a single, static operating point (a paired sensitivity/specificity). To address this deficiency we present weighted maximum posterior marginals (WMPM) estimation, an extension of maximum posterior marginals (MPM) estimation. Whereas the MPM cost function penalizes each error equally, the WMPM cost function allows misclassifications associated with certain classes to be weighted more heavily than others. This creates a preference for specific classes, and consequently a means for adjusting classifier performance. Realizing WMPM estimation (like MPM estimation) requires estimates of the posterior marginal distributions. The most prevalent means for estimating these--proposed by Marroquin--utilizes a Markov chain Monte Carlo (MCMC) method. Though Marroquin's method (M-MCMC) yields estimates that are sufficiently accurate for MPM estimation, they are inadequate for WMPM. To more accurately estimate the posterior marginals we present an equally simple, but more effective extension of the MCMC method (E-MCMC). Assuming an identical number of iterations, E-MCMC as compared to M-MCMC yields estimates with higher fidelity, thereby 1) allowing a far greater number and diversity of operating points and 2) improving overall classifier performance. To illustrate the utility of WMPM and compare the efficacies of M-MCMC and E-MCMC, we integrate them into our MRF-based classification system for detecting cancerous glands in (whole-mount or quarter) histological sections of the prostate
A Bayesian test for periodic signals in red noise
Vaughan, S
2009-01-01
Many astrophysical sources, especially compact accreting sources, show strong, random brightness fluctuations with broad power spectra in addition to periodic or quasi-periodic oscillations (QPOs) that have narrower spectra. The random nature of the dominant source of variance greatly complicates the process of searching for possible weak periodic signals. We have addressed this problem using the tools of Bayesian statistics; in particular using Markov chain Monte Carlo techniques to approxim...
Rocha, G.; Pagano, L.; Górski, K. M.; Huffenberger, K. M.; Lawrence, C. R.; Lange, A. E.
2010-04-01
We introduce a new method to propagate uncertainties in the beam shapes used to measure the cosmic microwave background to cosmological parameters determined from those measurements. The method, called markov chain beam randomization (MCBR), randomly samples from a set of templates or functions that describe the beam uncertainties. The method is much faster than direct numerical integration over systematic “nuisance” parameters, and is not restricted to simple, idealized cases as is analytic marginalization. It does not assume the data are normally distributed, and does not require Gaussian priors on the specific systematic uncertainties. We show that MCBR properly accounts for and provides the marginalized errors of the parameters. The method can be generalized and used to propagate any systematic uncertainties for which a set of templates is available. We apply the method to the Planck satellite, and consider future experiments. Beam measurement errors should have a small effect on cosmological parameters as long as the beam fitting is performed after removal of 1/f noise.
Adaptive Dynamic Bayesian Networks
Energy Technology Data Exchange (ETDEWEB)
Ng, B M
2007-10-26
A discrete-time Markov process can be compactly modeled as a dynamic Bayesian network (DBN)--a graphical model with nodes representing random variables and directed edges indicating causality between variables. Each node has a probability distribution, conditional on the variables represented by the parent nodes. A DBN's graphical structure encodes fixed conditional dependencies between variables. But in real-world systems, conditional dependencies between variables may be unknown a priori or may vary over time. Model errors can result if the DBN fails to capture all possible interactions between variables. Thus, we explore the representational framework of adaptive DBNs, whose structure and parameters can change from one time step to the next: a distribution's parameters and its set of conditional variables are dynamic. This work builds on recent work in nonparametric Bayesian modeling, such as hierarchical Dirichlet processes, infinite-state hidden Markov networks and structured priors for Bayes net learning. In this paper, we will explain the motivation for our interest in adaptive DBNs, show how popular nonparametric methods are combined to formulate the foundations for adaptive DBNs, and present preliminary results.
Distribusi Markov-Binomial Negatif
Widyasari, Rina
2015-01-01
The way to find a new distribution of random variables is defining the distribution which associated with Markov chain. In this research, researcher defines all the random variables identically independent distributed negative binomial distribution and form a Markov chain. Suppose that Xn is a sequence of Bernoulli trials that if 1 occurs means ”success” and 0 occurs means ”failure”. Nb(s) defined as random variables sth success in n trials. Each trial form a Markov chain, in n...
A Random Walk on WASP-12b with the Bayesian Atmospheric Radiative Transfer (BART) Code
Harrington, Joseph; Cubillos, Patricio; Blecic, Jasmina; Challener, Ryan; Rojo, Patricio; Lust, Nathaniel B.; Bowman, Oliver; Blumenthal, Sarah D.; Foster, Andrew S. D.; Foster, Austin James; Stemm, Madison; Bruce, Dylan
2016-01-01
We present the Bayesian Atmospheric Radiative Transfer (BART) code for atmospheric property retrievals from transit and eclipse spectra, and apply it to WASP-12b, a hot (~3000 K) exoplanet with a high eclipse signal-to-noise ratio. WASP-12b has been controversial. We (Madhusudhan et al. 2011, Nature) claimed it was the first planet with a high C/O abundance ratio. Line et al. (2014, ApJ) suggested a high CO2 abundance to explain the data. Stevenson et al. (2014, ApJ, atmospheric model by Madhusudhan) add additional data and reaffirm the original result, stating that C2H2 and HCN, not included in the Line et al. models, explain the data. We explore several modeling configurations and include Hubble, Spitzer, and ground-based eclipse data.BART consists of a differential-evolution Markov-Chain Monte Carlo sampler that drives a line-by-line radiative transfer code through the phase space of thermal- and abundance-profile parameters. BART is written in Python and C. Python modules generate atmospheric profiles from sets of MCMC parameters and integrate the resulting spectra over observational bandpasses, allowing high flexibility in modeling the planet without interacting with the fast, C portions that calculate the spectra. BART's shared memory and optimized opacity calculation allow it to run on a laptop, enabling classroom use. Runs can scale constant abundance profiles, profiles of thermochemical equilibrium abundances (TEA) calculated by the included TEA code, or arbitrary curves. Several thermal profile parameterizations are available. BART is an open-source, reproducible-research code. Users must release any code or data modifications if they publish results from it, and we encourage the community to use it and to participate in its development via http://github.com/ExOSPORTS/BART.This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. J. Blecic holds a NASA Earth and Space Science
Robinson, Sean; Guyon, Laurent; Nevalainen, Jaakko; Toriseva, Mervi
2015-01-01
Organotypic, three dimensional (3D) cell culture models of epithelial tumour types such as prostate cancer recapitulate key aspects of the architecture and histology of solid cancers. Morphometric analysis of multicellular 3D organoids is particularly important when additional components such as the extracellular matrix and tumour microenvironment are included in the model. The complexity of such models has so far limited their successful implementation. There is a great need for automatic, accurate and robust image segmentation tools to facilitate the analysis of such biologically relevant 3D cell culture models. We present a segmentation method based on Markov random fields (MRFs) and illustrate our method using 3D stack image data from an organotypic 3D model of prostate cancer cells co-cultured with cancer-associated fibroblasts (CAFs). The 3D segmentation output suggests that these cell types are in physical contact with each other within the model, which has important implications for tumour biology. Segmentation performance is quantified using ground truth labels and we show how each step of our method increases segmentation accuracy. We provide the ground truth labels along with the image data and code. Using independent image data we show that our segmentation method is also more generally applicable to other types of cellular microscopy and not only limited to fluorescence microscopy. PMID:26630674
International Nuclear Information System (INIS)
Brain tumors, are an abnormal growth of tissues in the brain. They may arise in people of any age. They must be detected early, diagnosed accurately, monitored carefully, and treated effectively in order to optimize patient outcomes regarding both survival and quality of life. Manual segmentation of brain tumors from CT scan images is a challenging and time consuming task. Size and location accurate detection of brain tumor plays a vital role in the successful diagnosis and treatment of tumors. Brain tumor detection is considered a challenging mission in medical image processing. The aim of this paper is to introduce a scheme for tumor detection in CT scan images using two different techniques Hidden Markov Random Fields (HMRF) and Fuzzy C-means (FCM). The proposed method has been developed in this research in order to construct hybrid method between (HMRF) and threshold. These methods have been applied on 4 different patient data sets. The result of comparison among these methods shows that the proposed method gives good results for brain tissue detection, and is more robust and effective compared with (FCM) techniques
Directory of Open Access Journals (Sweden)
Yisu Lu
2014-01-01
Full Text Available Brain-tumor segmentation is an important clinical requirement for brain-tumor diagnosis and radiotherapy planning. It is well-known that the number of clusters is one of the most important parameters for automatic segmentation. However, it is difficult to define owing to the high diversity in appearance of tumor tissue among different patients and the ambiguous boundaries of lesions. In this study, a nonparametric mixture of Dirichlet process (MDP model is applied to segment the tumor images, and the MDP segmentation can be performed without the initialization of the number of clusters. Because the classical MDP segmentation cannot be applied for real-time diagnosis, a new nonparametric segmentation algorithm combined with anisotropic diffusion and a Markov random field (MRF smooth constraint is proposed in this study. Besides the segmentation of single modal brain-tumor images, we developed the algorithm to segment multimodal brain-tumor images by the magnetic resonance (MR multimodal features and obtain the active tumor and edema in the same time. The proposed algorithm is evaluated using 32 multimodal MR glioma image sequences, and the segmentation results are compared with other approaches. The accuracy and computation time of our algorithm demonstrates very impressive performance and has a great potential for practical real-time clinical use.
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Abdulbaqi, Hayder Saad [School of Physics, Universiti Sains Malaysia, 11700, Penang (Malaysia); Department of Physics, College of Education, University of Al-Qadisiya, Al-Qadisiya (Iraq); Jafri, Mohd Zubir Mat; Omar, Ahmad Fairuz; Mustafa, Iskandar Shahrim Bin [School of Physics, Universiti Sains Malaysia, 11700, Penang (Malaysia); Abood, Loay Kadom [Department of Computer Science, College of Science, University of Baghdad, Baghdad (Iraq)
2015-04-24
Brain tumors, are an abnormal growth of tissues in the brain. They may arise in people of any age. They must be detected early, diagnosed accurately, monitored carefully, and treated effectively in order to optimize patient outcomes regarding both survival and quality of life. Manual segmentation of brain tumors from CT scan images is a challenging and time consuming task. Size and location accurate detection of brain tumor plays a vital role in the successful diagnosis and treatment of tumors. Brain tumor detection is considered a challenging mission in medical image processing. The aim of this paper is to introduce a scheme for tumor detection in CT scan images using two different techniques Hidden Markov Random Fields (HMRF) and Fuzzy C-means (FCM). The proposed method has been developed in this research in order to construct hybrid method between (HMRF) and threshold. These methods have been applied on 4 different patient data sets. The result of comparison among these methods shows that the proposed method gives good results for brain tissue detection, and is more robust and effective compared with (FCM) techniques.
Osman Nuri UÇAN; SAĞIROĞLU, Mahmut Şamil
2002-01-01
This paper describes a Markov Random Field model for coupled range and confidence signals. Beamforming is a method used to bring a range image from backscattered echos of acoustic signals. Another information is confidence of signal which associated point by point with this range data. In the proposed algorithm, the range and confidence images are modeled as Markov Random Fields whose probability distributions are specified by a single energy function. The optimization of this model gives rec...
Directory of Open Access Journals (Sweden)
Enrique Gracia
2014-01-01
Full Text Available This paper uses spatial data of cases of intimate partner violence against women (IPVAW to examine neighborhood-level influences on small-area variations in IPVAW risk in a police district of the city of Valencia (Spain. To analyze area variations in IPVAW risk and its association with neighborhood-level explanatory variables we use a Bayesian spatial random-effects modeling approach, as well as disease mapping methods to represent risk probabilities in each area. Analyses show that IPVAW cases are more likely in areas of high immigrant concentration, high public disorder and crime, and high physical disorder. Results also show a spatial component indicating remaining variability attributable to spatially structured random effects. Bayesian spatial modeling offers a new perspective to identify IPVAW high and low risk areas, and provides a new avenue for the design of better-informed prevention and intervention strategies.
Rubin, Yoram; Chen, Xingyuan; Murakami, Haruko; Hahn, Melanie
2010-10-01
This paper addresses the inverse problem in spatially variable fields such as hydraulic conductivity in groundwater aquifers or rainfall intensity in hydrology. Common to all these problems is the existence of a complex pattern of spatial variability of the target variables and observations, the multiple sources of data available for characterizing the fields, the complex relations between the observed and target variables and the multiple scales and frequencies of the observations. The method of anchored distributions (MAD) that we propose here is a general Bayesian method of inverse modeling of spatial random fields that addresses this complexity. The central elements of MAD are a modular classification of all relevant data and a new concept called "anchors." Data types are classified by the way they relate to the target variable, as either local or nonlocal and as either direct or indirect. Anchors are devices for localization of data: they are used to convert nonlocal, indirect data into local distributions of the target variables. The target of the inversion is the derivation of the joint distribution of the anchors and structural parameters, conditional to all measurements, regardless of scale or frequency of measurement. The structural parameters describe large-scale trends of the target variable fields, whereas the anchors capture local inhomogeneities. Following inversion, the joint distribution of anchors and structural parameters is used for generating random fields of the target variable(s) that are conditioned on the nonlocal, indirect data through their anchor representation. We demonstrate MAD through a detailed case study that assimilates point measurements of the conductivity with head measurements from natural gradient flow. The resulting statistical distributions of the parameters are non-Gaussian. Similarly, the moments of the estimates of the hydraulic head are non-Gaussian. We provide an extended discussion of MAD vis à vis other inversion
Dwyer, Michael G; Bergsland, Niels; Zivadinov, Robert
2014-04-15
SIENA and similar techniques have demonstrated the utility of performing "direct" measurements as opposed to post-hoc comparison of cross-sectional data for the measurement of whole brain (WB) atrophy over time. However, gray matter (GM) and white matter (WM) atrophy are now widely recognized as important components of neurological disease progression, and are being actively evaluated as secondary endpoints in clinical trials. Direct measures of GM/WM change with advantages similar to SIENA have been lacking. We created a robust and easily-implemented method for direct longitudinal analysis of GM/WM atrophy, SIENAX multi-time-point (SIENAX-MTP). We built on the basic halfway-registration and mask composition components of SIENA to improve the raw output of FMRIB's FAST tissue segmentation tool. In addition, we created LFAST, a modified version of FAST incorporating a 4th dimension in its hidden Markov random field model in order to directly represent time. The method was validated by scan-rescan, simulation, comparison with SIENA, and two clinical effect size comparisons. All validation approaches demonstrated improved longitudinal precision with the proposed SIENAX-MTP method compared to SIENAX. For GM, simulation showed better correlation with experimental volume changes (r=0.992 vs. 0.941), scan-rescan showed lower standard deviations (3.8% vs. 8.4%), correlation with SIENA was more robust (r=0.70 vs. 0.53), and effect sizes were improved by up to 68%. Statistical power estimates indicated a potential drop of 55% in the number of subjects required to detect the same treatment effect with SIENAX-MTP vs. SIENAX. The proposed direct GM/WM method significantly improves on the standard SIENAX technique by trading a small amount of bias for a large reduction in variance, and may provide more precise data and additional statistical power in longitudinal studies. PMID:24333394
DEFF Research Database (Denmark)
Hartelius, Karsten; Carstensen, Jens Michael
2003-01-01
A method for locating distorted grid structures in images is presented. The method is based on the theories of template matching and Bayesian image restoration. The grid is modeled as a deformable template. Prior knowledge of the grid is described through a Markov random field (MRF) model which...... represents the spatial coordinates of the grid nodes. Knowledge of how grid nodes are depicted in the observed image is described through the observation model. The prior consists of a node prior and an arc (edge) prior, both modeled as Gaussian MRFs. The node prior models variations in the positions of grid...... nodes and the arc prior models variations in row and column spacing across the grid. Grid matching is done by placing an initial rough grid over the image and applying an ensemble annealing scheme to maximize the posterior distribution of the grid. The method can be applied to noisy images with missing...
El Yazid Boudaren, Mohamed; Monfrini, Emmanuel; Pieczynski, Wojciech; Aïssani, Amar
2014-11-01
Hidden Markov chains have been shown to be inadequate for data modeling under some complex conditions. In this work, we address the problem of statistical modeling of phenomena involving two heterogeneous system states. Such phenomena may arise in biology or communications, among other fields. Namely, we consider that a sequence of meaningful words is to be searched within a whole observation that also contains arbitrary one-by-one symbols. Moreover, a word may be interrupted at some site to be carried on later. Applying plain hidden Markov chains to such data, while ignoring their specificity, yields unsatisfactory results. The Phasic triplet Markov chain, proposed in this paper, overcomes this difficulty by means of an auxiliary underlying process in accordance with the triplet Markov chains theory. Related Bayesian restoration techniques and parameters estimation procedures according to the new model are then described. Finally, to assess the performance of the proposed model against the conventional hidden Markov chain model, experiments are conducted on synthetic and real data. PMID:26353069
Bayesian statistics an introduction
Lee, Peter M
2012-01-01
Bayesian Statistics is the school of thought that combines prior beliefs with the likelihood of a hypothesis to arrive at posterior beliefs. The first edition of Peter Lee’s book appeared in 1989, but the subject has moved ever onwards, with increasing emphasis on Monte Carlo based techniques. This new fourth edition looks at recent techniques such as variational methods, Bayesian importance sampling, approximate Bayesian computation and Reversible Jump Markov Chain Monte Carlo (RJMCMC), providing a concise account of the way in which the Bayesian approach to statistics develops as wel
Directory of Open Access Journals (Sweden)
Guillaume Marrelec
Full Text Available The use of mutual information as a similarity measure in agglomerative hierarchical clustering (AHC raises an important issue: some correction needs to be applied for the dimensionality of variables. In this work, we formulate the decision of merging dependent multivariate normal variables in an AHC procedure as a Bayesian model comparison. We found that the Bayesian formulation naturally shrinks the empirical covariance matrix towards a matrix set a priori (e.g., the identity, provides an automated stopping rule, and corrects for dimensionality using a term that scales up the measure as a function of the dimensionality of the variables. Also, the resulting log Bayes factor is asymptotically proportional to the plug-in estimate of mutual information, with an additive correction for dimensionality in agreement with the Bayesian information criterion. We investigated the behavior of these Bayesian alternatives (in exact and asymptotic forms to mutual information on simulated and real data. An encouraging result was first derived on simulations: the hierarchical clustering based on the log Bayes factor outperformed off-the-shelf clustering techniques as well as raw and normalized mutual information in terms of classification accuracy. On a toy example, we found that the Bayesian approaches led to results that were similar to those of mutual information clustering techniques, with the advantage of an automated thresholding. On real functional magnetic resonance imaging (fMRI datasets measuring brain activity, it identified clusters consistent with the established outcome of standard procedures. On this application, normalized mutual information had a highly atypical behavior, in the sense that it systematically favored very large clusters. These initial experiments suggest that the proposed Bayesian alternatives to mutual information are a useful new tool for hierarchical clustering.
Theoretical evaluation of the detectability of random lesions in bayesian emission reconstruction
International Nuclear Information System (INIS)
Detecting cancerous lesion is an important task in positron emission tomography (PET). Bayesian methods based on the maximum a posteriori principle (also called penalized maximum likelihood methods) have been developed to deal with the low signal to noise ratio in the emission data. Similar to the filter cut-off frequency in the filtered backprojection method, the prior parameters in Bayesian reconstruction control the resolution and noise trade-off and hence affect detectability of lesions in reconstructed images. Bayesian reconstructions are difficult to analyze because the resolution and noise properties are nonlinear and object-dependent. Most research has been based on Monte Carlo simulations, which are very time consuming. Building on the recent progress on the theoretical analysis of image properties of statistical reconstructions and the development of numerical observers, here we develop a theoretical approach for fast computation of lesion detectability in Bayesian reconstruction. The results can be used to choose the optimum hyperparameter for the maximum lesion detectability. New in this work is the use of theoretical expressions that explicitly model the statistical variation of the lesion and background without assuming that the object variation is (locally) stationary. The theoretical results are validated using Monte Carlo simulations. The comparisons show good agreement between the theoretical predications and the Monte Carlo results
Multivariate longitudinal data analysis with mixed effects hidden Markov models.
Raffa, Jesse D; Dubin, Joel A
2015-09-01
Multiple longitudinal responses are often collected as a means to capture relevant features of the true outcome of interest, which is often hidden and not directly measurable. We outline an approach which models these multivariate longitudinal responses as generated from a hidden disease process. We propose a class of models which uses a hidden Markov model with separate but correlated random effects between multiple longitudinal responses. This approach was motivated by a smoking cessation clinical trial, where a bivariate longitudinal response involving both a continuous and a binomial response was collected for each participant to monitor smoking behavior. A Bayesian method using Markov chain Monte Carlo is used. Comparison of separate univariate response models to the bivariate response models was undertaken. Our methods are demonstrated on the smoking cessation clinical trial dataset, and properties of our approach are examined through extensive simulation studies. PMID:25761965
Energy Technology Data Exchange (ETDEWEB)
Fudym, O [RAPSODEE UMR 2392 CNRS, Mines Albi, Campus Jarlard, Albi (France); Orlande, H R B [PEM/COPPE, Federal University of Rio de Janeiro (Brazil); Bamford, M; Batsale, J C [TREFLE-ENSAM, UMR 8508 CNRS, Talence (France)], E-mail: fudym@enstimac.fr
2008-11-01
This paper aims at the identification of spatially-dependent thermophysical properties and is focused on the mapping of thermal diffusivity. A one-dimensional heat conduction problem is used for the comparison of ordinary least-squares, maximum a posteriori and Markov Chain Monte Carlo methods. Simulated temperature measurements are used in the inverse analysis, which is based on a nodal strategy that results on a linear estimation problem. The nodal strategy relies on the availability of temperature measurements with fine spatial resolution and high frequency, typical of nowadays infrared cameras.
An examination of disparities in cancer incidence in Texas using Bayesian random coefficient models
Sparks, Corey
2015-01-01
Disparities in cancer risk exist between ethnic groups in the United States. These disparities often result from differential access to healthcare, differences in socioeconomic status and differential exposure to carcinogens. This study uses cancer incidence data from the population based Texas Cancer Registry to investigate the disparities in digestive and respiratory cancers from 2000 to 2008. A Bayesian hierarchical regression approach is used. All models are fit using the INLA method of B...
Nonparametric Bayesian Classification
Coram, M A
2002-01-01
A Bayesian approach to the classification problem is proposed in which random partitions play a central role. It is argued that the partitioning approach has the capacity to take advantage of a variety of large-scale spatial structures, if they are present in the unknown regression function $f_0$. An idealized one-dimensional problem is considered in detail. The proposed nonparametric prior uses random split points to partition the unit interval into a random number of pieces. This prior is found to provide a consistent estimate of the regression function in the $\\L^p$ topology, for any $1 \\leq p < \\infty$, and for arbitrary measurable $f_0:[0,1] \\rightarrow [0,1]$. A Markov chain Monte Carlo (MCMC) implementation is outlined and analyzed. Simulation experiments are conducted to show that the proposed estimate compares favorably with a variety of conventional estimators. A striking resemblance between the posterior mean estimate and the bagged CART estimate is noted and discussed. For higher dimensions, a ...
Markov Chain Order estimation with Conditional Mutual Information
Papapetrou, Maria; 10.1016/j.physa.2012.12.017.
2013-01-01
We introduce the Conditional Mutual Information (CMI) for the estimation of the Markov chain order. For a Markov chain of $K$ symbols, we define CMI of order $m$, $I_c(m)$, as the mutual information of two variables in the chain being $m$ time steps apart, conditioning on the intermediate variables of the chain. We find approximate analytic significance limits based on the estimation bias of CMI and develop a randomization significance test of $I_c(m)$, where the randomized symbol sequences are formed by random permutation of the components of the original symbol sequence. The significance test is applied for increasing $m$ and the Markov chain order is estimated by the last order for which the null hypothesis is rejected. We present the appropriateness of CMI-testing on Monte Carlo simulations and compare it to the Akaike and Bayesian information criteria, the maximal fluctuation method (Peres-Shields estimator) and a likelihood ratio test for increasing orders using $\\phi$-divergence. The order criterion of...
A hidden Markov Model for image fusion and their joint segmentation in medical image computing
Féron, O; Feron, Olivier; Mohammad-Djafari, Ali
2004-01-01
In this work we propose a Bayesian framework for fully automated image fusion and their joint segmentation. More specifically, we consider the case where we have observed images of the same object through different image processes or through different spectral bands. The objective of this work is then to propose a coherent approach to combine these data sets and obtain a segmented image which can be considered as the fusion result of these observations. The proposed approach is based on a Hidden Markov Modeling (HMM) of the images with common segmentation, or equivalently, with common hidden classification label variables which are modeled by the Potts Markov Random Field. We propose an appropriate Markov Chain Monte Carlo (MCMC) algorithm to implement the method and show some simulation results and applications.
Phan, Kevin; Xie, Ashleigh; Kumar, Narendra; Wong, Sophia; Medi, Caroline; La Meir, Mark; Yan, Tristan D
2015-08-01
Simplified maze procedures involving radiofrequency, cryoenergy and microwave energy sources have been increasingly utilized for surgical treatment of atrial fibrillation as an alternative to the traditional cut-and-sew approach. In the absence of direct comparisons, a Bayesian network meta-analysis is another alternative to assess the relative effect of different treatments, using indirect evidence. A Bayesian meta-analysis of indirect evidence was performed using 16 published randomized trials identified from 6 databases. Rank probability analysis was used to rank each intervention in terms of their probability of having the best outcome. Sinus rhythm prevalence beyond the 12-month follow-up was similar between the cut-and-sew, microwave and radiofrequency approaches, which were all ranked better than cryoablation (respectively, 39, 36, and 25 vs 1%). The cut-and-sew maze was ranked worst in terms of mortality outcomes compared with microwave, radiofrequency and cryoenergy (2 vs 19, 34, and 24%, respectively). The cut-and-sew maze procedure was associated with significantly lower stroke rates compared with microwave ablation [odds ratio <0.01; 95% confidence interval 0.00, 0.82], and ranked the best in terms of pacemaker requirements compared with microwave, radiofrequency and cryoenergy (81 vs 14, and 1, <0.01% respectively). Bayesian rank probability analysis shows that the cut-and-sew approach is associated with the best outcomes in terms of sinus rhythm prevalence and stroke outcomes, and remains the gold standard approach for AF treatment. Given the limitations of indirect comparison analysis, these results should be viewed with caution and not over-interpreted. PMID:25391388
Elvira, Clément; Dobigeon, Nicolas
2015-01-01
Sparse representations have proven their efficiency in solving a wide class of inverse problems encountered in signal and image processing. Conversely, enforcing the information to be spread uniformly over representation coefficients exhibits relevant properties in various applications such as digital communications. Anti-sparse regularization can be naturally expressed through an $\\ell_{\\infty}$-norm penalty. This paper derives a probabilistic formulation of such representations. A new probability distribution, referred to as the democratic prior, is first introduced. Its main properties as well as three random variate generators for this distribution are derived. Then this probability distribution is used as a prior to promote anti-sparsity in a Gaussian linear inverse problem, yielding a fully Bayesian formulation of anti-sparse coding. Two Markov chain Monte Carlo (MCMC) algorithms are proposed to generate samples according to the posterior distribution. The first one is a standard Gibbs sampler. The seco...
The Entropy of Conditional Markov Trajectories
Kafsi, Mohamed; Grossglauser, Matthias; Thiran, Patrick
2012-01-01
To quantify the randomness of Markov trajectories with fixed initial and final states, Ekroot and Cover proposed a closed-form expression for the entropy of trajectories of an irreducible finite state Markov chain. Numerous applications, including the study of random walks on graphs, require the computation of the entropy of Markov trajectories conditioned on a set of intermediate states. However, the expression of Ekroot and Cover does not allow for computing this quantity. In this paper, we...
International Nuclear Information System (INIS)
The Laser Interferometer Space Antenna (LISA) defines new demands on data analysis efforts in its all-sky gravitational wave survey, recording simultaneously thousands of galactic compact object binary foreground sources and tens to hundreds of background sources like binary black hole mergers and extreme-mass ratio inspirals. We approach this problem with an adaptive and fully automatic Reversible Jump Markov Chain Monte Carlo sampler, able to sample from the joint posterior density function (as established by Bayes theorem) for a given mixture of signals ''out of the box'', handling the total number of signals as an additional unknown parameter beside the unknown parameters of each individual source and the noise floor. We show in examples from the LISA Mock Data Challenge implementing the full response of LISA in its TDI description that this sampler is able to extract monochromatic Double White Dwarf signals out of colored instrumental noise and additional foreground and background noise successfully in a global fitting approach. We introduce 2 examples with fixed number of signals (MCMC sampling), and 1 example with unknown number of signals (RJ-MCMC), the latter further promoting the idea behind an experimental adaptation of the model indicator proposal densities in the main sampling stage. We note that the experienced runtimes and degeneracies in parameter extraction limit the shown examples to the extraction of a low but realistic number of signals.
MAGIC: Exact Bayesian Covariance Estimation and Signal Reconstruction for Gaussian Random Fields
Wandelt, Benjamin D.
2004-01-01
In this talk I describe MAGIC, an efficient approach to covariance estimation and signal reconstruction for Gaussian random fields (MAGIC Allows Global Inference of Covariance). It solves a long-standing problem in the field of cosmic microwave background (CMB) data analysis but is in fact a general technique that can be applied to noisy, contaminated and incomplete or censored measurements of either spatial or temporal Gaussian random fields. In this talk I will phrase the method in a way th...
Markov chains and decision processes for engineers and managers
Sheskin, Theodore J
2010-01-01
Markov Chain Structure and ModelsHistorical NoteStates and TransitionsModel of the WeatherRandom WalksEstimating Transition ProbabilitiesMultiple-Step Transition ProbabilitiesState Probabilities after Multiple StepsClassification of StatesMarkov Chain StructureMarkov Chain ModelsProblemsReferencesRegular Markov ChainsSteady State ProbabilitiesFirst Passage to a Target StateProblemsReferencesReducible Markov ChainsCanonical Form of the Transition MatrixTh
Energy Technology Data Exchange (ETDEWEB)
Huang, Maoyi; Ray, Jaideep; Hou, Zhangshuan; Ren, Huiying; Liu, Ying; Swiler, Laura P.
2016-07-04
The Community Land Model (CLM) has been widely used in climate and Earth system modeling. Accurate estimation of model parameters is needed for reliable model simulations and predictions under current and future conditions, respectively. In our previous work, a subset of hydrological parameters has been identified to have significant impact on surface energy fluxes at selected flux tower sites based on parameter screening and sensitivity analysis, which indicate that the parameters could potentially be estimated from surface flux observations at the towers. To date, such estimates do not exist. In this paper, we assess the feasibility of applying a Bayesian model calibration technique to estimate CLM parameters at selected flux tower sites under various site conditions. The parameters are estimated as a joint probability density function (PDF) that provides estimates of uncertainty of the parameters being inverted, conditional on climatologically-average latent heat fluxes derived from observations. We find that the simulated mean latent heat fluxes from CLM using the calibrated parameters are generally improved at all sites when compared to those obtained with CLM simulations using default parameter sets. Further, our calibration method also results in credibility bounds around the simulated mean fluxes which bracket the measured data. The modes (or maximum a posteriori values) and 95% credibility intervals of the site-specific posterior PDFs are tabulated as suggested parameter values for each site. Analysis of relationships between the posterior PDFs and site conditions suggests that the parameter values are likely correlated with the plant functional type, which needs to be confirmed in future studies by extending the approach to more sites.
Bayesian Analysis of Multivariate Probit Models
Siddhartha Chib; Edward Greenberg
1996-01-01
This paper provides a unified simulation-based Bayesian and non-Bayesian analysis of correlated binary data using the multivariate probit model. The posterior distribution is simulated by Markov chain Monte Carlo methods, and maximum likelihood estimates are obtained by a Markov chain Monte Carlo version of the E-M algorithm. Computation of Bayes factors from the simulation output is also considered. The methods are applied to a bivariate data set, to a 534-subject, four-year longitudinal dat...
Hidden Markov model using Dirichlet process for de-identification.
Chen, Tao; Cullen, Richard M; Godwin, Marshall
2015-12-01
For the 2014 i2b2/UTHealth de-identification challenge, we introduced a new non-parametric Bayesian hidden Markov model using a Dirichlet process (HMM-DP). The model intends to reduce task-specific feature engineering and to generalize well to new data. In the challenge we developed a variational method to learn the model and an efficient approximation algorithm for prediction. To accommodate out-of-vocabulary words, we designed a number of feature functions to model such words. The results show the model is capable of understanding local context cues to make correct predictions without manual feature engineering and performs as accurately as state-of-the-art conditional random field models in a number of categories. To incorporate long-range and cross-document context cues, we developed a skip-chain conditional random field model to align the results produced by HMM-DP, which further improved the performance. PMID:26407642
Chen, Yu-Pei; Guo, Rui; Liu, Na; Liu, Xu; Mao, Yan-Ping; Tang, Ling-Long; Zhou, Guan-qun; Lin, Ai-Hua; Sun, Ying; Ma, Jun
2015-01-01
Background: Due to the lack of studies, it remains unclear whether the additional neoadjuvant chemotherapy (NACT) to concurrent chemoradiotherapy (CCRT) is superior to CCRT alone for locoregionally advanced nasopharyngeal carcinoma (NPC). The main objective of this Bayesian network meta-analysis was to determine the efficacy of NACT+CCRT as compared with CCRT alone. Methods: We comprehensively searched databases and extracted data from randomized controlled trials involving NPC patients who r...
Entropy: The Markov Ordering Approach
Gorban, A N; Judge, G
2010-01-01
The focus of this article is on entropy and Markov processes. We study the properties of functionals which are invariant with respect to monotonic transformations and analyze two invariant "additivity" properties: (i) existence of a monotonic transformation which makes the functional additive with respect to the joining of independent systems and (ii) existence of a monotonic transformation which makes the functional additive with respect to the partitioning of the space of states. All Lyapunov functionals for Markov chains which have properties (i) and (ii) are derived. We describe the most general ordering of the distribution space, with respect to which all continuous-time Markov processes are monotonic (the {\\em Markov order}). The solution differs significantly from the ordering given by the inequality of entropy growth. For inference, this approach results in a convex compact set of conditionally "most random" distributions.
Raberto, Marco; Scalas, Enrico
2011-01-01
In this paper, we outline a model of graph (or network) dynamics based on two ingredients. The first ingredient is a Markov chain on the space of possible graphs. The second ingredient is a semi-Markov counting process of renewal type. The model consists in subordinating the Markov chain to the semi-Markov counting process. In simple words, this means that the chain transitions occur at random time instants called epochs. The model is quite rich and its possible connections with algebraic geometry are briefly discussed. Moreover, for the sake of simplicity, we focus on the space of undirected graphs with a fixed number of nodes. However, in an example, we present an interbank market model where it is meaningful to use directed graphs or even weighted graphs.
Graphs: Associated Markov Chains
Murthy, Garimella Rama
2012-01-01
In this research paper, weighted / unweighted, directed / undirected graphs are associated with interesting Discrete Time Markov Chains (DTMCs) as well as Continuous Time Markov Chains (CTMCs). The equilibrium / transient behaviour of such Markov chains is studied. Also entropy dynamics (Shannon entropy) of certain structured Markov chains is investigated. Finally certain structured graphs and the associated Markov chains are studied.
Energy Technology Data Exchange (ETDEWEB)
Frank, T.D. [Center for the Ecological Study of Perception and Action, Department of Psychology, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269 (United States)], E-mail: till.frank@uconn.edu
2008-06-16
Some elementary properties and examples of Markov processes are reviewed. It is shown that the definition of the Markov property naturally leads to a classification of Markov processes into linear and nonlinear ones.
International Nuclear Information System (INIS)
Some elementary properties and examples of Markov processes are reviewed. It is shown that the definition of the Markov property naturally leads to a classification of Markov processes into linear and nonlinear ones
A Bayesian nonlinear mixed-effects disease progression model
Kim, Seongho; Jang, Hyejeong; Wu, Dongfeng; Abrams, Judith
2016-01-01
A nonlinear mixed-effects approach is developed for disease progression models that incorporate variation in age in a Bayesian framework. We further generalize the probability model for sensitivity to depend on age at diagnosis, time spent in the preclinical state and sojourn time. The developed models are then applied to the Johns Hopkins Lung Project data and the Health Insurance Plan for Greater New York data using Bayesian Markov chain Monte Carlo and are compared with the estimation method that does not consider random-effects from age. Using the developed models, we obtain not only age-specific individual-level distributions, but also population-level distributions of sensitivity, sojourn time and transition probability. PMID:26798562
Energy Technology Data Exchange (ETDEWEB)
Saldanha Filho, Paulo Carlos
1998-02-01
Stochastic simulation has been employed in petroleum reservoir characterization as a modeling tool able to reconcile information from several different sources. It has the ability to preserve the variability of the modeled phenomena and permits transference of geological knowledge to numerical models of flux, whose predictions on reservoir constitute the main basis for reservoir management decisions. Several stochastic models have been used and/or suggested, depending on the nature of the phenomena to be described. Markov Random Fields (MRFs) appear as an alternative for the modeling of discrete variables, mainly reservoirs with mosaic architecture of facies. In this dissertation, the reader is introduced to the stochastic modeling by MRFs in a generic sense. The main aspects of the technique are reviewed. MRF Conceptual Background is described: its characterization through the Markovian property and the equivalence to Gibbs distributions. The framework for generic modeling of MRFs is described. The classical models of Ising and Potts-Strauss are specific in this context and are related to models of Ising and Potts-Strauss are specific in this context and are related to models used in petroleum reservoir characterization. The problem of parameter estimation is discussed. The maximum pseudolikelihood estimators for some models are presented. Estimators for two models useful for reservoir characterization are developed, and represent a new contribution to the subject. Five algorithms for the Conditional Simulation of MRFs are described: the Metropolis algorithm, the algorithm of German and German (Gibbs sampler), the algorithm of Swendsen-Wang, the algorithm of Wolff, and the algorithm of Flinn. Finally, examples of simulation for some of the models discussed are presented, along with their implications on the modelling of petroleum reservoirs. (author)
Bayesian modeling using WinBUGS
Ntzoufras, Ioannis
2009-01-01
A hands-on introduction to the principles of Bayesian modeling using WinBUGS Bayesian Modeling Using WinBUGS provides an easily accessible introduction to the use of WinBUGS programming techniques in a variety of Bayesian modeling settings. The author provides an accessible treatment of the topic, offering readers a smooth introduction to the principles of Bayesian modeling with detailed guidance on the practical implementation of key principles. The book begins with a basic introduction to Bayesian inference and the WinBUGS software and goes on to cover key topics, including: Markov Chain Monte Carlo algorithms in Bayesian inference Generalized linear models Bayesian hierarchical models Predictive distribution and model checking Bayesian model and variable evaluation Computational notes and screen captures illustrate the use of both WinBUGS as well as R software to apply the discussed techniques. Exercises at the end of each chapter allow readers to test their understanding of the presented concepts and all ...
Markov processes and controlled Markov chains
Filar, Jerzy; Chen, Anyue
2002-01-01
The general theory of stochastic processes and the more specialized theory of Markov processes evolved enormously in the second half of the last century. In parallel, the theory of controlled Markov chains (or Markov decision processes) was being pioneered by control engineers and operations researchers. Researchers in Markov processes and controlled Markov chains have been, for a long time, aware of the synergies between these two subject areas. However, this may be the first volume dedicated to highlighting these synergies and, almost certainly, it is the first volume that emphasizes the contributions of the vibrant and growing Chinese school of probability. The chapters that appear in this book reflect both the maturity and the vitality of modern day Markov processes and controlled Markov chains. They also will provide an opportunity to trace the connections that have emerged between the work done by members of the Chinese school of probability and the work done by the European, US, Central and South Ameri...
Entropy Computation in Partially Observed Markov Chains
Desbouvries, François
2006-11-01
Let X = {Xn}n∈N be a hidden process and Y = {Yn}n∈N be an observed process. We assume that (X,Y) is a (pairwise) Markov Chain (PMC). PMC are more general than Hidden Markov Chains (HMC) and yet enable the development of efficient parameter estimation and Bayesian restoration algorithms. In this paper we propose a fast (i.e., O(N)) algorithm for computing the entropy of {Xn}n=0N given an observation sequence {yn}n=0N.
Directory of Open Access Journals (Sweden)
R.J. Boys
2002-01-01
Full Text Available This paper describes a Bayesian approach to determining the order of a finite state Markov chain whose transition probabilities are themselves governed by a homogeneous finite state Markov chain. It extends previous work on homogeneous Markov chains to more general and applicable hidden Markov models. The method we describe uses a Markov chain Monte Carlo algorithm to obtain samples from the (posterior distribution for both the order of Markov dependence in the observed sequence and the other governing model parameters. These samples allow coherent inferences to be made straightforwardly in contrast to those which use information criteria. The methods are illustrated by their application to both simulated and real data sets.
Discrete Quantum Markov Chains
Faigle, Ulrich
2010-01-01
A framework for finite-dimensional quantum Markov chains on Hilbert spaces is introduced. Quantum Markov chains generalize both classical Markov chains with possibly hidden states and existing models of quantum walks on finite graphs. Quantum Markov chains are based on Markov operations that may be applied to quantum systems and include quantum measurements, for example. It is proved that quantum Markov chains are asymptotically stationary and hence possess ergodic and entropic properties. With a quantum Markov chain one may associate a quantum Markov process, which is a stochastic process in the classical sense. Generalized Markov chains allow a representation with respect to a generalized Markov source model with definite (but possibly hidden) states relative to which observables give rise to classical stochastic processes. It is demonstrated that this model allows for observables to violate Bell's inequality.
Microstructure Image Simulation of Minced Pork Based on Markov Random Field%基于Markov随机场的猪肉糜微结构图像模拟
Institute of Scientific and Technical Information of China (English)
李华北; 赵杰文
2001-01-01
A stochastic simulation model of minced pork microstructure image was derived with the help of Markov random field theory and Gibbs distribution. The minced pork images of various microstructure were simulated iteratively, and the obtained images were compared with their original ones. The analysis and simulation for the microstructure images of minced food material are key processes in quantitatively studying the influence of microstructure pattern on rheological behavior. By getting the geometry features of minced food material microstructure from the known rheological behavior, the dynamic mechanism and process of the microstructure can be investigated and studied further, therefore the relationship between the rheological behavior and the microstructure was founded. So the conditions quantitatively describing rheological behavior of the minced food material were provided.%利用Markov随机场和Gibbs分布理论，建立了猪肉糜微结构图像的随机场模型，然后通过迭代方法，对不同微结构的猪肉糜图像进行了随机模拟，同时对随机模拟图像和原始图像作了对比分析。 糜状食品物料微观结构图像的分析和模拟是定量研究其微结构模式形态对流变特性影响的关键问题。通过从已知流变特性反演糜状食品物料微结构的几何形态，可以更深入地探讨、研究微结构形成的动力学机制和过程，进而沟通流变特性和微结构形态之间的联系，从而为定量描述糜状食品物料的流变特性提供了条件。
Institute of Scientific and Technical Information of China (English)
崔静
2012-01-01
On the basic of the general theory of Markov Chains,relations between characteristic number and taboo probability of Markov chains in random enviroments are discussed and the decomposition of characteristic number of strong recurrence is given.The property of distribrution moments is obtained by means of the general decomposition formula of Taboo probability,which has enriched the correspanding result of Markov Chairs in randon envirionments described in literatures.%利用马氏链的一般理论讨论了随机环境中马氏链的特征数和禁止概率的关系,给出了强常返状态特征数的分解公式,利用禁止概率的一般分解公式研究了分布矩的性质,丰富了现有文献中的随机环境中马氏链的相关结果。
Bayesian network learning for natural hazard assessments
Vogel, Kristin
2016-04-01
Even though quite different in occurrence and consequences, from a modelling perspective many natural hazards share similar properties and challenges. Their complex nature as well as lacking knowledge about their driving forces and potential effects make their analysis demanding. On top of the uncertainty about the modelling framework, inaccurate or incomplete event observations and the intrinsic randomness of the natural phenomenon add up to different interacting layers of uncertainty, which require a careful handling. Thus, for reliable natural hazard assessments it is crucial not only to capture and quantify involved uncertainties, but also to express and communicate uncertainties in an intuitive way. Decision-makers, who often find it difficult to deal with uncertainties, might otherwise return to familiar (mostly deterministic) proceedings. In the scope of the DFG research training group „NatRiskChange" we apply the probabilistic framework of Bayesian networks for diverse natural hazard and vulnerability studies. The great potential of Bayesian networks was already shown in previous natural hazard assessments. Treating each model component as random variable, Bayesian networks aim at capturing the joint distribution of all considered variables. Hence, each conditional distribution of interest (e.g. the effect of precautionary measures on damage reduction) can be inferred. The (in-)dependencies between the considered variables can be learned purely data driven or be given by experts. Even a combination of both is possible. By translating the (in-)dependences into a graph structure, Bayesian networks provide direct insights into the workings of the system and allow to learn about the underlying processes. Besides numerous studies on the topic, learning Bayesian networks from real-world data remains challenging. In previous studies, e.g. on earthquake induced ground motion and flood damage assessments, we tackled the problems arising with continuous variables
Robust Tracking of Small Displacements With a Bayesian Estimator.
Dumont, Douglas M; Byram, Brett C
2016-01-01
Radiation-force-based elasticity imaging describes a group of techniques that use acoustic radiation force (ARF) to displace tissue to obtain qualitative or quantitative measurements of tissue properties. Because ARF-induced displacements are on the order of micrometers, tracking these displacements in vivo can be challenging. Previously, it has been shown that Bayesian-based estimation can overcome some of the limitations of a traditional displacement estimator such as normalized cross-correlation (NCC). In this work, we describe a Bayesian framework that combines a generalized Gaussian-Markov random field (GGMRF) prior with an automated method for selecting the prior's width. We then evaluate its performance in the context of tracking the micrometer-order displacements encountered in an ARF-based method such as ARF impulse (ARFI) imaging. The results show that bias, variance, and mean-square error (MSE) performance vary with prior shape and width, and that an almost one order-of-magnitude reduction in MSE can be achieved by the estimator at the automatically selected prior width. Lesion simulations show that the proposed estimator has a higher contrast-to-noise ratio but lower contrast than NCC, median-filtered NCC, and the previous Bayesian estimator, with a non-Gaussian prior shape having better lesion-edge resolution than a Gaussian prior. In vivo results from a cardiac, radio-frequency ablation ARFI imaging dataset show quantitative improvements in lesion contrast-to-noise ratio over NCC as well as the previous Bayesian estimator. PMID:26529761
Bayesian Estimation and Inference Using Stochastic Electronics.
Thakur, Chetan Singh; Afshar, Saeed; Wang, Runchun M; Hamilton, Tara J; Tapson, Jonathan; van Schaik, André
2016-01-01
In this paper, we present the implementation of two types of Bayesian inference problems to demonstrate the potential of building probabilistic algorithms in hardware using single set of building blocks with the ability to perform these computations in real time. The first implementation, referred to as the BEAST (Bayesian Estimation and Stochastic Tracker), demonstrates a simple problem where an observer uses an underlying Hidden Markov Model (HMM) to track a target in one dimension. In this implementation, sensors make noisy observations of the target position at discrete time steps. The tracker learns the transition model for target movement, and the observation model for the noisy sensors, and uses these to estimate the target position by solving the Bayesian recursive equation online. We show the tracking performance of the system and demonstrate how it can learn the observation model, the transition model, and the external distractor (noise) probability interfering with the observations. In the second implementation, referred to as the Bayesian INference in DAG (BIND), we show how inference can be performed in a Directed Acyclic Graph (DAG) using stochastic circuits. We show how these building blocks can be easily implemented using simple digital logic gates. An advantage of the stochastic electronic implementation is that it is robust to certain types of noise, which may become an issue in integrated circuit (IC) technology with feature sizes in the order of tens of nanometers due to their low noise margin, the effect of high-energy cosmic rays and the low supply voltage. In our framework, the flipping of random individual bits would not affect the system performance because information is encoded in a bit stream. PMID:27047326
Dynamic risk management with Markov decision processes
Mundt, André Philipp
2008-01-01
An important tool in risk management is the implementation of risk measures. We study dynamic models where risk measures and dynamic risk measures can be applied. In particular, we solve various portfolio optimization problems and introduce a class of dynamic risk measures via the notion of Markov decision processes. Using Bayesian control theory we furthermore derive an extension of the latter setting when we face model uncertainty.
Grey-Markov Model for Road Accidents Forecasting
Institute of Scientific and Technical Information of China (English)
李相勇; 严余松; 蒋葛夫
2003-01-01
In order to improve the forecasting precision of road accidents, by introducing Markov chains forecasting method, a grey-Markov model for forecasting road accidents is established based on grey forecasting method. The model combines the advantages of both grey forecasting method and Markov chains forecasting method, overcomes the influence of random fluctuation data on forecasting precision and widens the application scope of the grey forecasting. An application example is conducted to evaluate the grey-Markov model, which shows that the precision of the grey-Markov model is better than that of grey model in forecasting road accidents.
Bayesian Modelling of fMRI Time Series
DEFF Research Database (Denmark)
Højen-Sørensen, Pedro; Hansen, Lars Kai; Rasmussen, Carl Edward
2000-01-01
We present a Hidden Markov Model (HMM) for inferring the hidden psychological state (or neural activity) during single trial fMRI activation experiments with blocked task paradigms. Inference is based on Bayesian methodology, using a combination of analytical and a variety of Markov Chain Monte...
Bayesian Modelling of fMRI Time Series
DEFF Research Database (Denmark)
Højen-Sørensen, Pedro; Hansen, Lars Kai; Rasmussen, Carl Edward
We present a Hidden Markov Model (HMM) for inferring the hidden psychological state (or neural activity) during single trial fMRI activation experiments with blocked task paradigms. Inference is based on Bayesian methodology, using a combination of analytical and a variety of Markov Chain Monte...
Nonuniform Markov Geometric Measures
Neunhäuserer, J.
2015-01-01
We generalize results of Fan and Zhang [6] on absolute continuity and singularity of the golden Markov geometric series to nonuniform stochastic series given by arbitrary Markov process. In addition we describe an application of these results in fractal geometry.
A Bayesian test for periodic signals in red noise
Vaughan, S
2009-01-01
Many astrophysical sources, especially compact accreting sources, show strong, random brightness fluctuations with broad power spectra in addition to periodic or quasi-periodic oscillations (QPOs) that have narrower spectra. The random nature of the dominant source of variance greatly complicates the process of searching for possible weak periodic signals. We have addressed this problem using the tools of Bayesian statistics; in particular using Markov chain Monte Carlo techniques to approximate the posterior distribution of model parameters, and posterior predictive model checking to assess model fits and search for periodogram outliers that may represent periodic signals. The methods developed are applied to two example datasets, both long XMM-Newton observations of highly variable Seyfert 1 galaxies: RE J1034+396 and Mrk 766. In both cases a bend (or break) in the power spectrum is evident. In the case of RE J1034+396 the previously reported QPO is found but with somewhat weaker statistical significance th...
Quantum Markov fields on graphs
Accardi, Luigi; Ohno, Hiromichi; Mukhamedov, Farrukh
2009-01-01
We introduce generalized quantum Markov states and generalized d-Markov chains which extend the notion quantum Markov chains on spin systems to that on $C^*$-algebras defined by general graphs. As examples of generalized d-Markov chains, we construct the entangled Markov fields on tree graphs. The concrete examples of generalized d-Markov chains on Cayley trees are also investigated.
Markov processes for stochastic modeling
Ibe, Oliver
2008-01-01
Markov processes are used to model systems with limited memory. They are used in many areas including communications systems, transportation networks, image segmentation and analysis, biological systems and DNA sequence analysis, random atomic motion and diffusion in physics, social mobility, population studies, epidemiology, animal and insect migration, queueing systems, resource management, dams, financial engineering, actuarial science, and decision systems. This book, which is written for upper level undergraduate and graduate students, and researchers, presents a unified presentat
A unified Bayesian hierarchical model for MRI tissue classification.
Feng, Dai; Liang, Dong; Tierney, Luke
2014-04-15
Various works have used magnetic resonance imaging (MRI) tissue classification extensively to study a number of neurological and psychiatric disorders. Various noise characteristics and other artifacts make this classification a challenging task. Instead of splitting the procedure into different steps, we extend a previous work to develop a unified Bayesian hierarchical model, which addresses both the partial volume effect and intensity non-uniformity, the two major acquisition artifacts, simultaneously. We adopted a normal mixture model with the means and variances depending on the tissue types of voxels to model the observed intensity values. We modeled the relationship among the components of the index vector of tissue types by a hidden Markov model, which captures the spatial similarity of voxels. Furthermore, we addressed the partial volume effect by construction of a higher resolution image in which each voxel is divided into subvoxels. Finally, We achieved the bias field correction by using a Gaussian Markov random field model with a band precision matrix designed in light of image filtering. Sparse matrix methods and parallel computations based on conditional independence are exploited to improve the speed of the Markov chain Monte Carlo simulation. The unified model provides more accurate tissue classification results for both simulated and real data sets. PMID:24738112
Bayesian target tracking based on particle filter
Institute of Scientific and Technical Information of China (English)
无
2005-01-01
For being able to deal with the nonlinear or non-Gaussian problems, particle filters have been studied by many researchers. Based on particle filter, the extended Kalman filter (EKF) proposal function is applied to Bayesian target tracking. Markov chain Monte Carlo (MCMC) method, the resampling step, etc novel techniques are also introduced into Bayesian target tracking. And the simulation results confirm the improved particle filter with these techniques outperforms the basic one.
Bayesian approach to rough set
Marwala, Tshilidzi
2007-01-01
This paper proposes an approach to training rough set models using Bayesian framework trained using Markov Chain Monte Carlo (MCMC) method. The prior probabilities are constructed from the prior knowledge that good rough set models have fewer rules. Markov Chain Monte Carlo sampling is conducted through sampling in the rough set granule space and Metropolis algorithm is used as an acceptance criteria. The proposed method is tested to estimate the risk of HIV given demographic data. The results obtained shows that the proposed approach is able to achieve an average accuracy of 58% with the accuracy varying up to 66%. In addition the Bayesian rough set give the probabilities of the estimated HIV status as well as the linguistic rules describing how the demographic parameters drive the risk of HIV.
Bayesian regularisation methods in a hybrid MLP-HMM system.
Renals, Steve; MacKay, David
1993-01-01
We have applied Bayesian regularisation methods to multi-layer percepuon (MLP) training in the context of a hybrid MLP-HMM (hidden Markov model) continuous speech recognition system. The Bayesian framework adopted here allows an objective setting of the regularisation parameters, according to the training data. Experiments have been carried out on the ARPA Resource Management database.
Chain ladder method: Bayesian bootstrap versus classical bootstrap
Peters, Gareth W.; Mario V. W\\"uthrich; Shevchenko, Pavel V.
2010-01-01
The intention of this paper is to estimate a Bayesian distribution-free chain ladder (DFCL) model using approximate Bayesian computation (ABC) methodology. We demonstrate how to estimate quantities of interest in claims reserving and compare the estimates to those obtained from classical and credibility approaches. In this context, a novel numerical procedure utilising Markov chain Monte Carlo (MCMC), ABC and a Bayesian bootstrap procedure was developed in a truly distribution-free setting. T...
Institute of Scientific and Technical Information of China (English)
林达; 徐新; 潘雪峰; 张海涛
2014-01-01
提出了一种新的MSTAR SAR图像分割方法.该方法首先根据地物的散射机制进行属性散射中心(attributed scattering centers,ASC)特征提取,构造属性散射中心特征向量;然后使用马尔科夫随机场(Markov random field,MRF)结合属性散射中心特征对MSTAR SAR图像进行空间邻城关系描述;最后运用标号代价能量优化算法得到最终的分割结果.MSTAR SAR数据上的实验结果证明了其有效性.
Markov Model Applied to Gene Evolution
Institute of Scientific and Technical Information of China (English)
季星来; 孙之荣
2001-01-01
The study of nucleotide substitution is very important both to our understanding of gene evolution and to reliable estimation of phylogenetic relationships. In this paper nucleotide substitution is assumed to be random and the Markov model is applied to the study of the evolution of genes. Then a non-linear optimization approach is proposed for estimating substitution in real sequences. This substitution is called the "Nucleotide State Transfer Matrix". One of the most important conclusions from this work is that gene sequence evolution conforms to the Markov process. Also, some theoretical evidences for random evolution are given from energy analysis of DNA replication.
Bayesian theory and applications
Dellaportas, Petros; Polson, Nicholas G; Stephens, David A
2013-01-01
The development of hierarchical models and Markov chain Monte Carlo (MCMC) techniques forms one of the most profound advances in Bayesian analysis since the 1970s and provides the basis for advances in virtually all areas of applied and theoretical Bayesian statistics. This volume guides the reader along a statistical journey that begins with the basic structure of Bayesian theory, and then provides details on most of the past and present advances in this field. The book has a unique format. There is an explanatory chapter devoted to each conceptual advance followed by journal-style chapters that provide applications or further advances on the concept. Thus, the volume is both a textbook and a compendium of papers covering a vast range of topics. It is appropriate for a well-informed novice interested in understanding the basic approach, methods and recent applications. Because of its advanced chapters and recent work, it is also appropriate for a more mature reader interested in recent applications and devel...
FIRAT, Mehmet Ziya
2001-01-01
The main environmental effects in a mixed model are comparison or contemporary group effects or more precisely herd-year-month of calving subclass effects. The controversial subject of much discussion about the choice between treating contemporary group effects as fixed or as random has not still been settled in dairy cow evaluation. However, these effects are usually treated as fixed since nonrandom associations between sires and herds may lead to biased predictions if herd-year-month effect...
Time series segmentation with shifting means hidden markov models
Directory of Open Access Journals (Sweden)
Ath. Kehagias
2006-01-01
Full Text Available We present a new family of hidden Markov models and apply these to the segmentation of hydrological and environmental time series. The proposed hidden Markov models have a discrete state space and their structure is inspired from the shifting means models introduced by Chernoff and Zacks and by Salas and Boes. An estimation method inspired from the EM algorithm is proposed, and we show that it can accurately identify multiple change-points in a time series. We also show that the solution obtained using this algorithm can serve as a starting point for a Monte-Carlo Markov chain Bayesian estimation method, thus reducing the computing time needed for the Markov chain to converge to a stationary distribution.
Time series segmentation with shifting means hidden markov models
Kehagias, Ath.; Fortin, V.
2006-08-01
We present a new family of hidden Markov models and apply these to the segmentation of hydrological and environmental time series. The proposed hidden Markov models have a discrete state space and their structure is inspired from the shifting means models introduced by Chernoff and Zacks and by Salas and Boes. An estimation method inspired from the EM algorithm is proposed, and we show that it can accurately identify multiple change-points in a time series. We also show that the solution obtained using this algorithm can serve as a starting point for a Monte-Carlo Markov chain Bayesian estimation method, thus reducing the computing time needed for the Markov chain to converge to a stationary distribution.
DEFF Research Database (Denmark)
Justesen, Jørn
2005-01-01
A simple construction of two-dimensional (2-D) fields is presented. Rows and columns are outcomes of the same Markov chain. The entropy can be calculated explicitly.......A simple construction of two-dimensional (2-D) fields is presented. Rows and columns are outcomes of the same Markov chain. The entropy can be calculated explicitly....
Bayesian Approach to Neuro-Rough Models for Modelling HIV
Marwala, Tshilidzi
2007-01-01
This paper proposes a new neuro-rough model for modelling the risk of HIV from demographic data. The model is formulated using Bayesian framework and trained using Markov Chain Monte Carlo method and Metropolis criterion. When the model was tested to estimate the risk of HIV infection given the demographic data it was found to give the accuracy of 62% as opposed to 58% obtained from a Bayesian formulated rough set model trained using Markov chain Monte Carlo method and 62% obtained from a Bayesian formulated multi-layered perceptron (MLP) model trained using hybrid Monte. The proposed model is able to combine the accuracy of the Bayesian MLP model and the transparency of Bayesian rough set model.
Directory of Open Access Journals (Sweden)
Megas Françoise
2010-03-01
Full Text Available Abstract Background Antibodies directed against haemagglutinin, measured by the haemagglutination inhibition (HI assay are essential to protective immunity against influenza infection. An HI titre of 1:40 is generally accepted to correspond to a 50% reduction in the risk of contracting influenza in a susceptible population, but limited attempts have been made to further quantify the association between HI titre and protective efficacy. Methods We present a model, using a meta-analytical approach, that estimates the level of clinical protection against influenza at any HI titre level. Source data were derived from a systematic literature review that identified 15 studies, representing a total of 5899 adult subjects and 1304 influenza cases with interval-censored information on HI titre. The parameters of the relationship between HI titre and clinical protection were estimated using Bayesian inference with a consideration of random effects and censorship in the available information. Results A significant and positive relationship between HI titre and clinical protection against influenza was observed in all tested models. This relationship was found to be similar irrespective of the type of viral strain (A or B and the vaccination status of the individuals. Conclusion Although limitations in the data used should not be overlooked, the relationship derived in this analysis provides a means to predict the efficacy of inactivated influenza vaccines when only immunogenicity data are available. This relationship can also be useful for comparing the efficacy of different influenza vaccines based on their immunological profile.
Node Augmentation Technique in Bayesian Network Evidence Analysis and Marshaling
Energy Technology Data Exchange (ETDEWEB)
Keselman, Dmitry [Los Alamos National Laboratory; Tompkins, George H [Los Alamos National Laboratory; Leishman, Deborah A [Los Alamos National Laboratory
2010-01-01
Given a Bayesian network, sensitivity analysis is an important activity. This paper begins by describing a network augmentation technique which can simplifY the analysis. Next, we present two techniques which allow the user to determination the probability distribution of a hypothesis node under conditions of uncertain evidence; i.e. the state of an evidence node or nodes is described by a user specified probability distribution. Finally, we conclude with a discussion of three criteria for ranking evidence nodes based on their influence on a hypothesis node. All of these techniques have been used in conjunction with a commercial software package. A Bayesian network based on a directed acyclic graph (DAG) G is a graphical representation of a system of random variables that satisfies the following Markov property: any node (random variable) is independent of its non-descendants given the state of all its parents (Neapolitan, 2004). For simplicities sake, we consider only discrete variables with a finite number of states, though most of the conclusions may be generalized.
Markov Process of Muscle Motors
Kondratiev, Yu; Pirogov, S
2007-01-01
We study a Markov random process describing a muscle molecular motor behavior. Every motor is either bound up with a thin filament or unbound. In the bound state the motor creates a force proportional to its displacement from the neutral position. In both states the motor spend an exponential time depending on the state. The thin filament moves at its velocity proportional to average of all displacements of all motors. We assume that the time which a motor stays at the bound state does not depend on its displacement. Then one can find an exact solution of a non-linear equation appearing in the limit of infinite number of the motors.
Piecewise deterministic Markov processes : an analytic approach
Alkurdi, Taleb Salameh Odeh
2013-01-01
The subject of this thesis, piecewise deterministic Markov processes, an analytic approach, is on the border between analysis and probability theory. Such processes can either be viewed as random perturbations of deterministic dynamical systems in an impulsive fashion, or as a particular kind of sto
Shape-Driven Nested Markov Tessellations
Schreiber, Tomasz
2011-01-01
A new and rather broad class of stationary (i.e. stochastically translation invariant) random tessellations of the $d$-dimensional Euclidean space is introduced, which are called shape-driven nested Markov tessellations. Locally, these tessellations are constructed by means of a spatio-temporal random recursive split dynamics governed by a family of Markovian split kernel, generalizing thereby the -- by now classical -- construction of iteration stable random tessellations. By providing an explicit global construction of the tessellations, it is shown that under suitable assumptions on the split kernels (shape-driven), there exists a unique time-consistent whole-space tessellation-valued Markov process of stationary random tessellations compatible with the given split kernels. Beside the existence and uniqueness result, the typical cell and some aspects of the first-order geometry of these tessellations are in the focus of our discussion.
Optimal Filter Approximations in Conditionally Gaussian Pairwise Markov Switching Models
Abbassi, N; Benboudjema, D; Derrode, Stéphane; Pieczynski, W
2015-01-01
—We consider a general triplet Markov Gaussian linear system (X, R, Y), where X is an hidden continuous random sequence, R is an hidden discrete Markov chain, Y is an observed continuous random sequence. When the triplet (X, R, Y) is a classical " Conditionally Gaussian Linear State-Space Model " (CGLSSM), the mean square error optimal filter is not workable with a reasonable complexity and different approximate methods, e.g. based on particle filters, are used. We propose two contributions. ...
Markov chain Monte Carlo test of toric homogeneous Markov chains
Takemura, Akimichi; Hara, Hisayuki
2010-01-01
Markov chain models are used in various fields, such behavioral sciences or econometrics. Although the goodness of fit of the model is usually assessed by large sample approximation, it is desirable to use conditional tests if the sample size is not large. We study Markov bases for performing conditional tests of the toric homogeneous Markov chain model, which is the envelope exponential family for the usual homogeneous Markov chain model. We give a complete description of a Markov basis for ...
On approximation of Markov binomial distributions
Xia, Aihua; Zhang, Mei
2009-01-01
For a Markov chain $\\mathbf{X}=\\{X_i,i=1,2,...,n\\}$ with the state space $\\{0,1\\}$, the random variable $S:=\\sum_{i=1}^nX_i$ is said to follow a Markov binomial distribution. The exact distribution of $S$, denoted $\\mathcal{L}S$, is very computationally intensive for large $n$ (see Gabriel [Biometrika 46 (1959) 454--460] and Bhat and Lal [Adv. in Appl. Probab. 20 (1988) 677--680]) and this paper concerns suitable approximate distributions for $\\mathcal{L}S$ when $\\mathbf{X}$ is stationary. We...
Windisch, Tobias
2015-01-01
The mixing behaviour of Markov chains on lattice points of polytopes using Markov bases is examined. It is shown that, in fixed dimension, these Markov chains do not mix rapidly. As a way out, a method of how to adapt Markov bases in order to achieve the fastest mixing behaviour is introduced.
Fuzzy Markov chains: uncertain probabilities
James J. Buckley; Eslami, Esfandiar
2002-01-01
We consider finite Markov chains where there are uncertainties in some of the transition probabilities. These uncertainties are modeled by fuzzy numbers. Using a restricted fuzzy matrix multiplication we investigate the properties of regular, and absorbing, fuzzy Markov chains and show that the basic properties of these classical Markov chains generalize to fuzzy Markov chains.
Lesaffre, Emmanuel
2012-01-01
The growth of biostatistics has been phenomenal in recent years and has been marked by considerable technical innovation in both methodology and computational practicality. One area that has experienced significant growth is Bayesian methods. The growing use of Bayesian methodology has taken place partly due to an increasing number of practitioners valuing the Bayesian paradigm as matching that of scientific discovery. In addition, computational advances have allowed for more complex models to be fitted routinely to realistic data sets. Through examples, exercises and a combination of introd
Massey, J. L.
1975-01-01
A regular Markov source is defined as the output of a deterministic, but noisy, channel driven by the state sequence of a regular finite-state Markov chain. The rate of such a source is the per letter uncertainty of its digits. The well-known result that the rate of a unifilar regular Markov source is easily calculable is demonstrated, where unifilarity means that the present state of the Markov chain and the next output of the deterministic channel uniquely determine the next state. At present, there is no known method to calculate the rate of a nonunifilar source. Two tentative approaches to this unsolved problem are given, namely source identical twins and the master-slave source, which appear to shed some light on the question of rate calculation for a nonunifilar source.
Bielecki, Tomasz R.; Jakubowski, Jacek; Niewęgłowski, Mariusz
2011-01-01
This article continues our study of Markovian consistency and Markov copulae. In particular, we characterize the weak Markovian consistency for finite Markov chains. We discuss some aspects of dependence between the components of a multivariate Markov chain in the context of weak Markovian consistency and strong Markovian consistency. In this connection, we also introduce and discuss the concept of weak Markov copulae.
Draper, D.
2001-01-01
© 2012 Springer Science+Business Media, LLC. All rights reserved. Article Outline: Glossary Definition of the Subject and Introduction The Bayesian Statistical Paradigm Three Examples Comparison with the Frequentist Statistical Paradigm Future Directions Bibliography
Large deviations for Markov processes with resetting.
Meylahn, Janusz M; Sabhapandit, Sanjib; Touchette, Hugo
2015-12-01
Markov processes restarted or reset at random times to a fixed state or region in space have been actively studied recently in connection with random searches, foraging, and population dynamics. Here we study the large deviations of time-additive functions or observables of Markov processes with resetting. By deriving a renewal formula linking generating functions with and without resetting, we are able to obtain the rate function of such observables, characterizing the likelihood of their fluctuations in the long-time limit. We consider as an illustration the large deviations of the area of the Ornstein-Uhlenbeck process with resetting. Other applications involving diffusions, random walks, and jump processes with resetting or catastrophes are discussed. PMID:26764673
Bayesian analysis toolkit - BAT
International Nuclear Information System (INIS)
Statistical treatment of data is an essential part of any data analysis and interpretation. Different statistical methods and approaches can be used, however the implementation of these approaches is complicated and at times inefficient. The Bayesian analysis toolkit (BAT) is a software package developed in C++ framework that facilitates the statistical analysis of the data using Bayesian theorem. The tool evaluates the posterior probability distributions for models and their parameters using Markov Chain Monte Carlo which in turn provide straightforward parameter estimation, limit setting and uncertainty propagation. Additional algorithms, such as simulated annealing, allow extraction of the global mode of the posterior. BAT sets a well-tested environment for flexible model definition and also includes a set of predefined models for standard statistical problems. The package is interfaced to other software packages commonly used in high energy physics, such as ROOT, Minuit, RooStats and CUBA. We present a general overview of BAT and its algorithms. A few physics examples are shown to introduce the spectrum of its applications. In addition, new developments and features are summarized.
Bayesian inference for Hawkes processes
DEFF Research Database (Denmark)
Rasmussen, Jakob Gulddahl
The Hawkes process is a practically and theoretically important class of point processes, but parameter-estimation for such a process can pose various problems. In this paper we explore and compare two approaches to Bayesian inference. The first approach is based on the so-called conditional...... intensity function, while the second approach is based on an underlying clustering and branching structure in the Hawkes process. For practical use, MCMC (Markov chain Monte Carlo) methods are employed. The two approaches are compared numerically using three examples of the Hawkes process....
Bayesian inference for Hawkes processes
DEFF Research Database (Denmark)
Rasmussen, Jakob Gulddahl
2013-01-01
The Hawkes process is a practically and theoretically important class of point processes, but parameter-estimation for such a process can pose various problems. In this paper we explore and compare two approaches to Bayesian inference. The first approach is based on the so-called conditional...... intensity function, while the second approach is based on an underlying clustering and branching structure in the Hawkes process. For practical use, MCMC (Markov chain Monte Carlo) methods are employed. The two approaches are compared numerically using three examples of the Hawkes process....
Elsheikh, Ahmed H.
2014-02-01
An efficient Bayesian calibration method based on the nested sampling (NS) algorithm and non-intrusive polynomial chaos method is presented. Nested sampling is a Bayesian sampling algorithm that builds a discrete representation of the posterior distributions by iteratively re-focusing a set of samples to high likelihood regions. NS allows representing the posterior probability density function (PDF) with a smaller number of samples and reduces the curse of dimensionality effects. The main difficulty of the NS algorithm is in the constrained sampling step which is commonly performed using a random walk Markov Chain Monte-Carlo (MCMC) algorithm. In this work, we perform a two-stage sampling using a polynomial chaos response surface to filter out rejected samples in the Markov Chain Monte-Carlo method. The combined use of nested sampling and the two-stage MCMC based on approximate response surfaces provides significant computational gains in terms of the number of simulation runs. The proposed algorithm is applied for calibration and model selection of subsurface flow models. © 2013.
Validi, AbdoulAhad
2013-01-01
This study introduces a non-intrusive approach in the context of low-rank separated representation to construct a surrogate of high-dimensional stochastic functions, e.g., PDEs/ODEs, in order to decrease the computational cost of Markov Chain Monte Carlo simulations in Bayesian inference. The surrogate model is constructed via a regularized alternative least-square regression with Tikhonov regularization using a roughening matrix computing the gradient of the solution, in conjunction with a perturbation-based error indicator to detect optimal model complexities. The model approximates a vector of a continuous solution at discrete values of a physical variable. The required number of random realizations to achieve a successful approximation linearly depends on the function dimensionality. The computational cost of the model construction is quadratic in the number of random inputs, which potentially tackles the curse of dimensionality in high-dimensional stochastic functions. Furthermore, this vector valued sep...
Fast sampling from a Hidden Markov Model posterior for large data
DEFF Research Database (Denmark)
Bonnevie, Rasmus; Hansen, Lars Kai
2014-01-01
Hidden Markov Models are of interest in a broad set of applications including modern data driven systems involving very large data sets. However, approximate inference methods based on Bayesian averaging are precluded in such applications as each sampling step requires a full sweep over the data...... sets offering fast access to approximate posterior samples. In a specific example we see that the new scheme is a hundred times faster than conventional Markov Chain Monte Carlo sampling using the Forward-backward method....
Dynamic temperature selection for parallel-tempering in Markov chain Monte Carlo simulations
Vousden, Will; Farr, Will M.; Mandel, Ilya
2015-01-01
Modern problems in astronomical Bayesian inference require efficient methods for sampling from complex, high-dimensional, often multi-modal probability distributions. Most popular methods, such as Markov chain Monte Carlo sampling, perform poorly on strongly multi-modal probability distributions, rarely jumping between modes or settling on just one mode without finding others. Parallel tempering addresses this problem by sampling simultaneously with separate Markov chains from tempered versio...
International Nuclear Information System (INIS)
Bayesian algorithms are developed to solve inverse problems in gamma imaging and photofission tomography. The first part of this work is devoted to the modeling of our measurement systems. Two models have been found for both applications: the first one is a simple conventional model and the second one is a cascaded point process model. EM and MCMC Bayesian algorithms for image restoration and image reconstruction have been developed for these models and compared. The cascaded point process model does not improve significantly the results previously obtained by the classical model. To original approaches have been proposed, which increase the results previously obtained. The first approach uses an inhomogeneous Markov Random Field as a prior law, and makes the regularization parameter spatially vary. However, the problem of the estimation of hyper-parameters has not been solved. In the case of the deconvolution of point sources, a second approach has been proposed, which introduces a high level prior model. The picture is modeled as a list of objects, whose parameters and number are unknown. The results obtained with this method are more accurate than those obtained with the conventional Markov Random Field prior model and require less computational costs. (author)
Bayesian auxiliary variable models for binary and multinomial regression
Holmes, C C; HELD, L.
2006-01-01
In this paper we discuss auxiliary variable approaches to Bayesian binary and multinomial regression. These approaches are ideally suited to automated Markov chain Monte Carlo simulation. In the first part we describe a simple technique using joint updating that improves the performance of the conventional probit regression algorithm. In the second part we discuss auxiliary variable methods for inference in Bayesian logistic regression, including covariate set uncertainty. Fina...
Bayesian estimation of parameters in a regional hydrological model
Engeland, K.; Gottschalk, L.
2002-01-01
This study evaluates the applicability of the distributed, process-oriented Ecomag model for prediction of daily streamflow in ungauged basins. The Ecomag model is applied as a regional model to nine catchments in the NOPEX area, using Bayesian statistics to estimate the posterior distribution of the model parameters conditioned on the observed streamflow. The distribution is calculated by Markov Chain Monte Carlo (MCMC) analysis. The Bayesian method requires formulation of a likelihood funct...
Bayesian estimation of parameters in a regional hydrological model
Engeland, K.; Gottschalk, L.
2002-01-01
This study evaluates the applicability of the distributed, process-oriented Ecomag model for prediction of daily streamflow in ungauged basins. The Ecomag model is applied as a regional model to nine catchments in the NOPEX area, using Bayesian statistics to estimate the posterior distribution of the model parameters conditioned on the observed streamflow. The distribution is calculated by Markov Chain Monte Carlo (MCMC) analysis. The Bayesian method requires formulation of ...
Bayesian Analysis of Dynamic Multivariate Models with Multiple Structural Breaks
Sugita, Katsuhiro
2006-01-01
This paper considers a vector autoregressive model or a vector error correction model with multiple structural breaks in any subset of parameters, using a Bayesian approach with Markov chain Monte Carlo simulation technique. The number of structural breaks is determined as a sort of model selection by the posterior odds. For a cointegrated model, cointegrating rank is also allowed to change with breaks. Bayesian approach by Strachan (Journal of Business and Economic Statistics 21 (2003) 185) ...
A survey of current Bayesian gene mapping method
Molitor John; Marjoram Paul; Conti David; Thomas Duncan
2004-01-01
Abstract Recently, there has been much interest in the use of Bayesian statistical methods for performing genetic analyses. Many of the computational difficulties previously associated with Bayesian analysis, such as multidimensional integration, can now be easily overcome using modern high-speed computers and Markov chain Monte Carlo (MCMC) methods. Much of this new technology has been used to perform gene mapping, especially through the use of multi-locus linkage disequilibrium techniques. ...
A Non-Parametric Bayesian Method for Inferring Hidden Causes
Wood, Frank; Griffiths, Thomas; Ghahramani, Zoubin
2012-01-01
We present a non-parametric Bayesian approach to structure learning with hidden causes. Previous Bayesian treatments of this problem define a prior over the number of hidden causes and use algorithms such as reversible jump Markov chain Monte Carlo to move between solutions. In contrast, we assume that the number of hidden causes is unbounded, but only a finite number influence observable variables. This makes it possible to use a Gibbs sampler to approximate the distribution over causal stru...
Bayesian Inference and Optimal Design in the Sparse Linear Model
Seeger, Matthias; Steinke, Florian; Tsuda, Koji
2007-01-01
The sparse linear model has seen many successful applications in Statistics, Machine Learning, and Computational Biology, such as identification of gene regulatory networks from micro-array expression data. Prior work has either approximated Bayesian inference by expensive Markov chain Monte Carlo, or replaced it by point estimation. We show how to obtain a good approximation to Bayesian analysis efficiently, using the Expectation Propagation method. We also address the problems of optimal de...
Bayesian Variable Selection for Detecting Adaptive Genomic Differences Among Populations
Riebler, Andrea; Held, Leonhard; Stephan, Wolfgang
2008-01-01
We extend an Fst-based Bayesian hierarchical model, implemented via Markov chain Monte Carlo, for the detection of loci that might be subject to positive selection. This model divides the Fst-influencing factors into locus-specific effects, population-specific effects, and effects that are specific for the locus in combination with the population. We introduce a Bayesian auxiliary variable for each locus effect to automatically select nonneutral locus effects. As a by-product, the efficiency ...
Putting Markov Chains Back into Markov Chain Monte Carlo
Barker, Richard J.; Schofield, Matthew R.
2007-01-01
Markov chain theory plays an important role in statistical inference both in the formulation of models for data and in the construction of efficient algorithms for inference. The use of Markov chains in modeling data has a long history, however the use of Markov chain theory in developing algorithms for statistical inference has only become popular recently. Using mark-recapture models as an illustration, we show how Markov chains can be used for developing demographic models and also ...
Hidden hybrid Markov/semi-Markov chains.
GUÉDON, YANN
2005-01-01
http://www.sciencedirect.com/science?ₒb=IssueURL&_tockey=%23TOC%235880%232005%23999509996%23596026%23FLA%23&ₐuth=y&view=c&ₐcct=C000056834&_version=1&_urlVersion=0&_userid=2292769&md5=87e7f8be94f92a8574da566c600ce631 International audience Models that combine Markovian states with implicit geometric state occupancy distributions and semi-Markovian states with explicit state occupancy distributions, are investigated. This type of model retains the flexibility of hidden semi-Markov chains ...
Quantile pyramids for Bayesian nonparametrics
2009-01-01
P\\'{o}lya trees fix partitions and use random probabilities in order to construct random probability measures. With quantile pyramids we instead fix probabilities and use random partitions. For nonparametric Bayesian inference we use a prior which supports piecewise linear quantile functions, based on the need to work with a finite set of partitions, yet we show that the limiting version of the prior exists. We also discuss and investigate an alternative model based on the so-called substitut...
Song, Guo-Min; Tian, Xu; Zhang, Lei; Ou, Yang-Xiang; Yi, Li-Juan; Shuai, Ting; Zhou, Jian-Guo; Zeng, Zi; Yang, Hong-Ling
2015-07-01
Enteral immunonutrition (EIN) has been established to be as a significantly important modality to prevent the postoperative infectious and noninfectious complications, enhance the immunity of host, and eventually improve the prognosis of gastrointestinal (GI) cancer patients undergoing surgery. However, different support routes, which are the optimum option, remain unclear. To evaluate the effects of different EIN support regimes for patients who underwent selective surgery for resectable GI malignancy, a Bayesian network meta-analysis (NMA) of randomized controlled trials (RCTs) was conducted. A search of PubMed, EMBASE, and the Cochrane Central Register of Controlled Trials (CENTRAL) was electronically searched until the end of December 2014. Moreover, we manually checked reference lists of eligible trials and review and retrieval unpublished literature. RCTs which investigated the comparative effects of EIN versus standard enteral nutrition (EN) or different EIN regimes were included if the clinical outcomes information can be extracted from it. A total of 27 RCTs were incorporated into this study. Pair-wise meta-analyses suggested that preoperative (relative risk [RR], 0.58; 95% confidence interval [CI], 0.43-0.78), postoperative (RR, 0.63; 95% CI, 0.52-0.76), and perioperative EIN methods (RR, 0.46; 95% CI, 0.34-0.62) reduced incidence of postoperative infectious complications compared with standard EN. Moreover, perioperative EIN (RR, 0.65; 95% CI, 0.44-0.95) reduced the incidence of postoperative noninfectious complications, and the postoperative (mean difference [MD], -2.38; 95% CI, -3.4 to -1.31) and perioperative EIN (MD, -2.64; 95% CI, -3.28 to -1.99) also shortened the length of postoperative hospitalization compared with standard EN. NMA found that EIN support effectively improved the clinical outcomes of patients who underwent selective surgery for GI cancer compared with standard EN. Our results suggest EIN support is promising alternative for
A clustering approach for estimating parameters of a profile hidden Markov model.
Aghdam, Rosa; Pezeshk, Hamid; Malekpour, Seyed Amir; Shemehsavar, Soudabeh; Eslahchi, Changiz
2013-01-01
A Profile Hidden Markov Model (PHMM) is a standard form of a Hidden Markov Models used for modeling protein and DNA sequence families based on multiple alignment. In this paper, we implement Baum-Welch algorithm and the Bayesian Monte Carlo Markov Chain (BMCMC) method for estimating parameters of small artificial PHMM. In order to improve the prediction accuracy of the estimation of the parameters of the PHMM, we classify the training data using the weighted values of sequences in the PHMM then apply an algorithm for estimating parameters of the PHMM. The results show that the BMCMC method performs better than the Maximum Likelihood estimation. PMID:23865165
Markov Processes: Linguistics and Zipf's Law
Kanter, I.; Kessler, D. A.
1995-05-01
It is shown that a 2-parameter random Markov process constructed with N states and biased random transitions gives rise to a stationary distribution where the probabilities of occurrence of the states, P\\(k\\), k = 1,...,N, exhibit the following three universal behaviors which characterize biological sequences and texts in natural languages: (a) the rank-ordered frequencies of occurrence of words are given by Zipf's law P\\(k\\)~1/kρ, where ρ\\(k\\) is slowly increasing for small k; (b) the frequencies of occurrence of letters are given by P\\(k\\) = A-Dln\\(k\\); and (c) long-range correlations are observed over long but finite intervals, as a result of the quasiergodicity of the Markov process.
Sensitivity of hidden Markov models
Mitrophanov, Alexander Yu.; Lomsadze, Alexandre; Borodovsky, Mark
2005-01-01
We derive a tight perturbation bound for hidden Markov models. Using this bound, we show that, in many cases, the distribution of a hidden Markov model is considerably more sensitive to perturbations in the emission probabilities than to perturbations in the transition probability matrix and the initial distribution of the underlying Markov chain. Our approach can also be used to assess the sensitivity of other stochastic models, such as mixture processes and semi-Markov ...
A new Markov Binomial distribution.
Omey, Edward; Minkova, Leda D.
2011-01-01
In this paper, we introduce a two state homogeneous Markov chain and define a geometric distribution related to this Markov chain. We define also the negative binomial distribution similar to the classical case and call it NB related to interrupted Markov chain. The new binomial distribution is related to the interrupted Markov chain. Some characterization properties of the Geometric distributions are given. Recursion formulas and probability mass functions for the NB distribution and the new...
On Markov Chains and Filtrations
Spreij, Peter
1997-01-01
In this paper we rederive some well known results for continuous time Markov processes that live on a finite state space.Martingale techniques are used throughout the paper. Special attention is paid to the construction of a continuous timeMarkov process, when we start from a discrete time Markov chain. The Markov property here holds with respect tofiltrations that need not be minimal.
Sequential Markov coalescent algorithms for population models with demographic structure
A. Eriksson; Mahjani, B.; Mehlig, B.
2009-01-01
We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an approximation to the coalescent suggested by McVean and Cardin, and Marjoram and Wall. Within this algorithm we compute, for two individuals randomly sampled from the population, the correlation between times to the most recent common ancestor and the linkag...
Risk-Averse Control of Undiscounted Transient Markov Models
Cavus, Ozlem
2012-01-01
We use Markov risk measures to formulate a risk-averse version of the undiscounted total cost problem for a transient controlled Markov process. We derive risk-averse dynamic programming equations and we show that a randomized policy may be strictly better than deterministic policies, when risk measures are employed. We illustrate the results on an optimal stopping problem and an organ transplant problem.
Piecewise deterministic Markov processes: an analytic approach
Alkurdi, Taleb Salameh Odeh
2013-01-01
The subject of this thesis, piecewise deterministic Markov processes, an analytic approach, is on the border between analysis and probability theory. Such processes can either be viewed as random perturbations of deterministic dynamical systems in an impulsive fashion, or as a particular kind of stochastic process in continuous time in which parts of the sample trajectories are deterministic. Accordingly, questions concerning theses processes may be approached starting from either side. The a...
On adaptive Markov chain Monte Carlo algorithms
Atchadé, Yves F.; Rosenthal, Jeffrey S.
2005-01-01
We look at adaptive Markov chain Monte Carlo algorithms that generate stochastic processes based on sequences of transition kernels, where each transition kernel is allowed to depend on the history of the process. We show under certain conditions that the stochastic process generated is ergodic, with appropriate stationary distribution. We use this result to analyse an adaptive version of the random walk Metropolis algorithm where the scale parameter σ is sequentially adapted using a Robbins-...
A Nonparametric Bayesian Approach For Emission Tomography Reconstruction
International Nuclear Information System (INIS)
We introduce a PET reconstruction algorithm following a nonparametric Bayesian (NPB) approach. In contrast with Expectation Maximization (EM), the proposed technique does not rely on any space discretization. Namely, the activity distribution--normalized emission intensity of the spatial poisson process--is considered as a spatial probability density and observations are the projections of random emissions whose distribution has to be estimated. This approach is nonparametric in the sense that the quantity of interest belongs to the set of probability measures on Rk (for reconstruction in k-dimensions) and it is Bayesian in the sense that we define a prior directly on this spatial measure. In this context, we propose to model the nonparametric probability density as an infinite mixture of multivariate normal distributions. As a prior for this mixture we consider a Dirichlet Process Mixture (DPM) with a Normal-Inverse Wishart (NIW) model as base distribution of the Dirichlet Process. As in EM-family reconstruction, we use a data augmentation scheme where the set of hidden variables are the emission locations for each observed line of response in the continuous object space. Thanks to the data augmentation, we propose a Markov Chain Monte Carlo (MCMC) algorithm (Gibbs sampler) which is able to generate draws from the posterior distribution of the spatial intensity. A difference with EM is that one step of the Gibbs sampler corresponds to the generation of emission locations while only the expected number of emissions per pixel/voxel is used in EM. Another key difference is that the estimated spatial intensity is a continuous function such that there is no need to compute a projection matrix. Finally, draws from the intensity posterior distribution allow the estimation of posterior functionnals like the variance or confidence intervals. Results are presented for simulated data based on a 2D brain phantom and compared to Bayesian MAP-EM
A Nonparametric Bayesian Approach For Emission Tomography Reconstruction
Barat, Éric; Dautremer, Thomas
2007-11-01
We introduce a PET reconstruction algorithm following a nonparametric Bayesian (NPB) approach. In contrast with Expectation Maximization (EM), the proposed technique does not rely on any space discretization. Namely, the activity distribution—normalized emission intensity of the spatial poisson process—is considered as a spatial probability density and observations are the projections of random emissions whose distribution has to be estimated. This approach is nonparametric in the sense that the quantity of interest belongs to the set of probability measures on Rk (for reconstruction in k-dimensions) and it is Bayesian in the sense that we define a prior directly on this spatial measure. In this context, we propose to model the nonparametric probability density as an infinite mixture of multivariate normal distributions. As a prior for this mixture we consider a Dirichlet Process Mixture (DPM) with a Normal-Inverse Wishart (NIW) model as base distribution of the Dirichlet Process. As in EM-family reconstruction, we use a data augmentation scheme where the set of hidden variables are the emission locations for each observed line of response in the continuous object space. Thanks to the data augmentation, we propose a Markov Chain Monte Carlo (MCMC) algorithm (Gibbs sampler) which is able to generate draws from the posterior distribution of the spatial intensity. A difference with EM is that one step of the Gibbs sampler corresponds to the generation of emission locations while only the expected number of emissions per pixel/voxel is used in EM. Another key difference is that the estimated spatial intensity is a continuous function such that there is no need to compute a projection matrix. Finally, draws from the intensity posterior distribution allow the estimation of posterior functionnals like the variance or confidence intervals. Results are presented for simulated data based on a 2D brain phantom and compared to Bayesian MAP-EM.
Partially Hidden Markov Models
DEFF Research Database (Denmark)
Forchhammer, Søren Otto; Rissanen, Jorma
1996-01-01
Partially Hidden Markov Models (PHMM) are introduced. They differ from the ordinary HMM's in that both the transition probabilities of the hidden states and the output probabilities are conditioned on past observations. As an illustration they are applied to black and white image compression where...
Partially Hidden Markov Models
DEFF Research Database (Denmark)
Forchhammer, Søren Otto; Rissanen, Jorma
1996-01-01
Partially Hidden Markov Models (PHMM) are introduced. They differ from the ordinary HMM's in that both the transition probabilities of the hidden states and the output probabilities are conditioned on past observations. As an illustration they are applied to black and white image compression wher...
DEFF Research Database (Denmark)
Kohlenbach, Ulrich Wilhelm
We show that the so-called weak Markov's principle (WMP) which states that every pseudo-positive real number is positive is underivable in E-HA + AC. Since allows one to formalize (atl eastl arge parts of) Bishop's constructive mathematics, this makes it unlikely that WMP can be proved within the...
Smith, R. M.
1991-01-01
Numerous applications in the area of computer system analysis can be effectively studied with Markov reward models. These models describe the behavior of the system with a continuous-time Markov chain, where a reward rate is associated with each state. In a reliability/availability model, upstates may have reward rate 1 and down states may have reward rate zero associated with them. In a queueing model, the number of jobs of certain type in a given state may be the reward rate attached to that state. In a combined model of performance and reliability, the reward rate of a state may be the computational capacity, or a related performance measure. Expected steady-state reward rate and expected instantaneous reward rate are clearly useful measures of the Markov reward model. More generally, the distribution of accumulated reward or time-averaged reward over a finite time interval may be determined from the solution of the Markov reward model. This information is of great practical significance in situations where the workload can be well characterized (deterministically, or by continuous functions e.g., distributions). The design process in the development of a computer system is an expensive and long term endeavor. For aerospace applications the reliability of the computer system is essential, as is the ability to complete critical workloads in a well defined real time interval. Consequently, effective modeling of such systems must take into account both performance and reliability. This fact motivates our use of Markov reward models to aid in the development and evaluation of fault tolerant computer systems.
Frequentism and Bayesianism: A Python-driven Primer
VanderPlas, Jake
2014-01-01
This paper presents a brief, semi-technical comparison of the essential features of the frequentist and Bayesian approaches to statistical inference, with several illustrative examples implemented in Python. The differences between frequentism and Bayesianism fundamentally stem from differing definitions of probability, a philosophical divide which leads to distinct approaches to the solution of statistical problems as well as contrasting ways of asking and answering questions about unknown parameters. After an example-driven discussion of these differences, we briefly compare several leading Python statistical packages which implement frequentist inference using classical methods and Bayesian inference using Markov Chain Monte Carlo.
Single channel signal component separation using Bayesian estimation
Institute of Scientific and Technical Information of China (English)
Cai Quanwei; Wei Ping; Xiao Xianci
2007-01-01
A Bayesian estimation method to separate multicomponent signals with single channel observation is presented in this paper. By using the basis function projection, the component separation becomes a problem of limited parameter estimation. Then, a Bayesian model for estimating parameters is set up. The reversible jump MCMC (Monte Carlo Markov Chain) algorithmis adopted to perform the Bayesian computation. The method can jointly estimate the parameters of each component and the component number. Simulation results demonstrate that the method has low SNR threshold and better performance.
Cohomological dimension of Markov compacta
Dranishnikov, Alexander
2006-01-01
We rephrase Gromov's definition of Markov compacta, introduce a subclass of Markov compacta defined by one building block and study cohomological dimensions of these compacta. We show that for a Markov compactum $X$, $\\dim_{\\Z_{(p)}}X=\\dim_{\\Q}X$ for all but finitely many primes $p$ where $\\Z_{(p)}$ is the localization of $\\Z$ at $p$. We construct Markov compacta of arbitrarily large dimension having $\\dim_{\\Q}X=1$ as well as Markov compacta of arbitrary large rational dimension with $\\dim_{\\...
Bayesian Fusion of Multi-Band Images
Wei, Qi; Tourneret, Jean-Yves
2013-01-01
In this paper, a Bayesian fusion technique for remotely sensed multi-band images is presented. The observed images are related to the high spectral and high spatial resolution image to be recovered through physical degradations, e.g., spatial and spectral blurring and/or subsampling defined by the sensor characteristics. The fusion problem is formulated within a Bayesian estimation framework. An appropriate prior distribution exploiting geometrical consideration is introduced. To compute the Bayesian estimator of the scene of interest from its posterior distribution, a Markov chain Monte Carlo algorithm is designed to generate samples asymptotically distributed according to the target distribution. To efficiently sample from this high-dimension distribution, a Hamiltonian Monte Carlo step is introduced in the Gibbs sampling strategy. The efficiency of the proposed fusion method is evaluated with respect to several state-of-the-art fusion techniques. In particular, low spatial resolution hyperspectral and mult...
Estimation and uncertainty of reversible Markov models
Trendelkamp-Schroer, Benjamin; Paul, Fabian; Noé, Frank
2015-01-01
Reversibility is a key concept in the theory of Markov models, simplified kinetic models for the conforma- tion dynamics of molecules. The analysis and interpretation of the transition matrix encoding the kinetic properties of the model relies heavily on the reversibility property. The estimation of a reversible transition matrix from simulation data is therefore crucial to the successful application of the previously developed theory. In this work we discuss methods for the maximum likelihood estimation of transition matrices from finite simulation data and present a new algorithm for the estimation if reversibility with respect to a given stationary vector is desired. We also develop new methods for the Bayesian posterior inference of reversible transition matrices with and without given stationary vector taking into account the need for a suitable prior distribution preserving the meta-stable features of the observed process during posterior inference.
Bayesian image restoration, using configurations
DEFF Research Database (Denmark)
Thorarinsdottir, Thordis Linda
2006-01-01
configurations are expressed in terms of the mean normal measure of the random set. These probabilities are used as prior probabilities in a Bayesian image restoration approach. Estimation of the remaining parameters in the model is outlined for the salt and pepper noise. The inference in the model is discussed...
Bayesian image restoration, using configurations
DEFF Research Database (Denmark)
Thorarinsdottir, Thordis
configurations are expressed in terms of the mean normal measure of the random set. These probabilities are used as prior probabilities in a Bayesian image restoration approach. Estimation of the remaining parameters in the model is outlined for salt and pepper noise. The inference in the model is discussed in...
Kirstein, Roland
2005-01-01
This paper presents a modification of the inspection game: The ?Bayesian Monitoring? model rests on the assumption that judges are interested in enforcing compliant behavior and making correct decisions. They may base their judgements on an informative but imperfect signal which can be generated costlessly. In the original inspection game, monitoring is costly and generates a perfectly informative signal. While the inspection game has only one mixed strategy equilibrium, three Perfect Bayesia...
Kim, Jee-Seon; Bolt, Daniel M.
2007-01-01
The purpose of this ITEMS module is to provide an introduction to Markov chain Monte Carlo (MCMC) estimation for item response models. A brief description of Bayesian inference is followed by an overview of the various facets of MCMC algorithms, including discussion of prior specification, sampling procedures, and methods for evaluating chain…
Teaching Markov Chain Monte Carlo: Revealing the Basic Ideas behind the Algorithm
Stewart, Wayne; Stewart, Sepideh
2014-01-01
For many scientists, researchers and students Markov chain Monte Carlo (MCMC) simulation is an important and necessary tool to perform Bayesian analyses. The simulation is often presented as a mathematical algorithm and then translated into an appropriate computer program. However, this can result in overlooking the fundamental and deeper…
Herschtal, A.; Foroudi, F.; Greer, P. B.; Eade, T. N.; Hindson, B. R.; Kron, T.
2012-05-01
Early approaches to characterizing errors in target displacement during a fractionated course of radiotherapy assumed that the underlying fraction-to-fraction variability in target displacement, known as the ‘treatment error’ or ‘random error’, could be regarded as constant across patients. More recent approaches have modelled target displacement allowing for differences in random error between patients. However, until recently it has not been feasible to compare the goodness of fit of alternate models of random error rigorously. This is because the large volumes of real patient data necessary to distinguish between alternative models have only very recently become available. This work uses real-world displacement data collected from 365 patients undergoing radical radiotherapy for prostate cancer to compare five candidate models for target displacement. The simplest model assumes constant random errors across patients, while other models allow for random errors that vary according to one of several candidate distributions. Bayesian statistics and Markov Chain Monte Carlo simulation of the model parameters are used to compare model goodness of fit. We conclude that modelling the random error as inverse gamma distributed provides a clearly superior fit over all alternatives considered. This finding can facilitate more accurate margin recipes and correction strategies.
A Bayesian method for inferring transmission chains in a partially observed epidemic.
Energy Technology Data Exchange (ETDEWEB)
Marzouk, Youssef M.; Ray, Jaideep
2008-10-01
We present a Bayesian approach for estimating transmission chains and rates in the Abakaliki smallpox epidemic of 1967. The epidemic affected 30 individuals in a community of 74; only the dates of appearance of symptoms were recorded. Our model assumes stochastic transmission of the infections over a social network. Distinct binomial random graphs model intra- and inter-compound social connections, while disease transmission over each link is treated as a Poisson process. Link probabilities and rate parameters are objects of inference. Dates of infection and recovery comprise the remaining unknowns. Distributions for smallpox incubation and recovery periods are obtained from historical data. Using Markov chain Monte Carlo, we explore the joint posterior distribution of the scalar parameters and provide an expected connectivity pattern for the social graph and infection pathway.
Predicting Complex Word Emotions and Topics through a Hierarchical Bayesian Network
Institute of Scientific and Technical Information of China (English)
2012-01-01
In this paper, we provide a Word Emotion Topic （WET） model to predict the complex word e- motion information from text, and discover the dis- trbution of emotions among different topics. A complex emotion is defined as the combination of one or more singular emotions from following 8 basic emotion categories： joy, love, expectation, sur- prise, anxiety, sorrow, anger and hate. We use a hi- erarchical Bayesian network to model the emotions and topics in the text. Both the complex emotions and topics are drawn from raw texts, without con- sidering any complicated language features. Our ex- periment shows promising results of word emotion prediction, which outperforms the traditional parsing methods such as the Hidden Markov Model and the Conditional Random Fields（CRFs） on raw text. We also explore the topic distribution by examining the emotion topic variation in an emotion topic diagram.
Bayesian anomaly detection in heterogeneous media with applications to geophysical tomography
Simon, Martin
2014-11-01
In this paper, we consider the problem of detecting a parameterized anomaly in an isotropic, stationary and ergodic conductivity random field via electrical impedance tomography. A homogenization result for a stochastic forward problem built on the complete electrode model is derived, which serves as the basis for a two-stage numerical method in the framework of Bayesian inverse problems. The novelty of this method lies in the introduction of an enhanced error model accounting for the approximation errors that result from reducing the full forward model to a homogenized one. In the first stage, a MAP estimate for the reduced forward model equipped with the enhanced error model is computed. Then, in the second stage, a bootstrap prior based on the first stage results is defined and the resulting posterior distribution is sampled via Markov chain Monte Carlo. We provide the theoretical foundation of the proposed method, discuss different aspects of a numerical implementation and present numerical experiments to support our findings.
Bayesian Reliability Analysis of Non-Stationarity in Multi-agent Systems
Directory of Open Access Journals (Sweden)
TONT Gabriela
2013-05-01
Full Text Available The Bayesian methods provide information about the meaningful parameters in a statistical analysis obtained by combining the prior and sampling distributions to form the posterior distribution of theparameters. The desired inferences are obtained from this joint posterior. An estimation strategy for hierarchical models, where the resulting joint distribution of the associated model parameters cannotbe evaluated analytically, is to use sampling algorithms, known as Markov Chain Monte Carlo (MCMC methods, from which approximate solutions can be obtained. Both serial and parallel configurations of subcomponents are permitted. The capability of time-dependent method to describe a multi-state system is based on a case study, assessingthe operatial situation of studied system. The rationality and validity of the presented model are demonstrated via a case of study. The effect of randomness of the structural parameters is alsoexamined.
Variance bounding Markov chains
Roberts, Gareth O.; Jeffrey S. Rosenthal
2008-01-01
We introduce a new property of Markov chains, called variance bounding. We prove that, for reversible chains at least, variance bounding is weaker than, but closely related to, geometric ergodicity. Furthermore, variance bounding is equivalent to the existence of usual central limit theorems for all L2 functionals. Also, variance bounding (unlike geometric ergodicity) is preserved under the Peskun order. We close with some applications to Metropolis–Hastings algorithms.
Analysis of Gumbel Model for Software Reliability Using Bayesian Paradigm
Directory of Open Access Journals (Sweden)
Raj Kumar
2012-12-01
Full Text Available In this paper, we have illustrated the suitability of Gumbel Model for software reliability data. The model parameters are estimated using likelihood based inferential procedure: classical as well as Bayesian. The quasi Newton-Raphson algorithm is applied to obtain the maximum likelihood estimates and associated probability intervals. The Bayesian estimates of the parameters of Gumbel model are obtained using Markov Chain Monte Carlo(MCMC simulation method in OpenBUGS(established software for Bayesian analysis using Markov Chain Monte Carlo methods. The R functions are developed to study the statistical properties, model validation and comparison tools of the model and the output analysis of MCMC samples generated from OpenBUGS. Details of applying MCMC to parameter estimation for the Gumbel model are elaborated and a real software reliability data set is considered to illustrate the methods of inference discussed in this paper.
Bayesian Network--Response Regression
WANG, LU; Durante, Daniele; Dunson, David B.
2016-01-01
There is an increasing interest in learning how human brain networks vary with continuous traits (e.g., personality, cognitive abilities, neurological disorders), but flexible procedures to accomplish this goal are limited. We develop a Bayesian semiparametric model, which combines low-rank factorizations and Gaussian process priors to allow flexible shifts of the conditional expectation for a network-valued random variable across the feature space, while including subject-specific random eff...
A Bayesian test for periodic signals in red noise
Vaughan, S.
2010-02-01
Many astrophysical sources, especially compact accreting sources, show strong, random brightness fluctuations with broad power spectra in addition to periodic or quasi-periodic oscillations (QPOs) that have narrower spectra. The random nature of the dominant source of variance greatly complicates the process of searching for possible weak periodic signals. We have addressed this problem using the tools of Bayesian statistics; in particular, using Markov Chain Monte Carlo techniques to approximate the posterior distribution of model parameters, and posterior predictive model checking to assess model fits and search for periodogram outliers that may represent periodic signals. The methods developed are applied to two example data sets, both long XMM-Newton observations of highly variable Seyfert 1 galaxies: RE J1034 + 396 and Mrk 766. In both cases, a bend (or break) in the power spectrum is evident. In the case of RE J1034 + 396, the previously reported QPO is found but with somewhat weaker statistical significance than reported in previous analyses. The difference is due partly to the improved continuum modelling, better treatment of nuisance parameters and partly to different data selection methods.
Assessing fit in Bayesian models for spatial processes
Jun, M.
2014-09-16
© 2014 John Wiley & Sons, Ltd. Gaussian random fields are frequently used to model spatial and spatial-temporal data, particularly in geostatistical settings. As much of the attention of the statistics community has been focused on defining and estimating the mean and covariance functions of these processes, little effort has been devoted to developing goodness-of-fit tests to allow users to assess the models\\' adequacy. We describe a general goodness-of-fit test and related graphical diagnostics for assessing the fit of Bayesian Gaussian process models using pivotal discrepancy measures. Our method is applicable for both regularly and irregularly spaced observation locations on planar and spherical domains. The essential idea behind our method is to evaluate pivotal quantities defined for a realization of a Gaussian random field at parameter values drawn from the posterior distribution. Because the nominal distribution of the resulting pivotal discrepancy measures is known, it is possible to quantitatively assess model fit directly from the output of Markov chain Monte Carlo algorithms used to sample from the posterior distribution on the parameter space. We illustrate our method in a simulation study and in two applications.
Markov or not Markov - this should be a question
Bickenbach, Frank; Bode, Eckhardt
2002-01-01
Although it is well known that Markov process theory, frequently applied in the literature on income convergence, imposes some very restrictive assumptions upon the data generating process, these assumptions have generally been taken for granted so far. The present paper proposes, resp. recalls chi-square tests of the Markov property, of spatial independence, and of homogeneity across time and space to assess the reliability of estimated Markov transition matrices. As an illustration we show ...
Generator estimation of Markov jump processes
Metzner, P.; Dittmer, E.; Jahnke, T.; Schütte, Ch.
2007-11-01
Estimating the generator of a continuous-time Markov jump process based on incomplete data is a problem which arises in various applications ranging from machine learning to molecular dynamics. Several methods have been devised for this purpose: a quadratic programming approach (cf. [D.T. Crommelin, E. Vanden-Eijnden, Fitting timeseries by continuous-time Markov chains: a quadratic programming approach, J. Comp. Phys. 217 (2006) 782-805]), a resolvent method (cf. [T. Müller, Modellierung von Proteinevolution, PhD thesis, Heidelberg, 2001]), and various implementations of an expectation-maximization algorithm ([S. Asmussen, O. Nerman, M. Olsson, Fitting phase-type distributions via the EM algorithm, Scand. J. Stat. 23 (1996) 419-441; I. Holmes, G.M. Rubin, An expectation maximization algorithm for training hidden substitution models, J. Mol. Biol. 317 (2002) 753-764; U. Nodelman, C.R. Shelton, D. Koller, Expectation maximization and complex duration distributions for continuous time Bayesian networks, in: Proceedings of the twenty-first conference on uncertainty in AI (UAI), 2005, pp. 421-430; M. Bladt, M. Sørensen, Statistical inference for discretely observed Markov jump processes, J.R. Statist. Soc. B 67 (2005) 395-410]). Some of these methods, however, seem to be known only in a particular research community, and have later been reinvented in a different context. The purpose of this paper is to compile a catalogue of existing approaches, to compare the strengths and weaknesses, and to test their performance in a series of numerical examples. These examples include carefully chosen model problems and an application to a time series from molecular dynamics.
Grinfeld, Michael; Knight, Philip A.; Wade, Andrew R.
2012-01-01
We study a class of Markovian systems of N elements taking values in [0,1] that evolve in discrete time t via randomized replacement rules based on the ranks of the elements. These rank-driven processes are inspired by variants of the Bak-Sneppen model of evolution, in which the system represents an evolutionary `fitness landscape' and which is famous as a simple model displaying self-organized criticality. Our main results are concerned with long-time large- N asymptotics for the general model in which, at each time step, K randomly chosen elements are discarded and replaced by independent U[0,1] variables, where the ranks of the elements to be replaced are chosen, independently at each time step, according to a distribution κ N on {1,2,…, N} K . Our main results are that, under appropriate conditions on κ N , the system exhibits threshold behavior at s ∗∈[0,1], where s ∗ is a function of κ N , and the marginal distribution of a randomly selected element converges to U[ s ∗,1] as t→∞ and N→∞. Of this class of models, results in the literature have previously been given for special cases only, namely the `mean-field' or `random neighbor' Bak-Sneppen model. Our proofs avoid the heuristic arguments of some of the previous work and use Foster-Lyapunov ideas. Our results extend existing results and establish their natural, more general context. We derive some more specialized results for the particular case where K=2. One of our technical tools is a result on convergence of stationary distributions for families of uniformly ergodic Markov chains on increasing state-spaces, which may be of independent interest.
BAT - Bayesian Analysis Toolkit
International Nuclear Information System (INIS)
One of the most vital steps in any data analysis is the statistical analysis and comparison with the prediction of a theoretical model. The many uncertainties associated with the theoretical model and the observed data require a robust statistical analysis tool. The Bayesian Analysis Toolkit (BAT) is a powerful statistical analysis software package based on Bayes' Theorem, developed to evaluate the posterior probability distribution for models and their parameters. It implements Markov Chain Monte Carlo to get the full posterior probability distribution that in turn provides a straightforward parameter estimation, limit setting and uncertainty propagation. Additional algorithms, such as Simulated Annealing, allow to evaluate the global mode of the posterior. BAT is developed in C++ and allows for a flexible definition of models. A set of predefined models covering standard statistical cases are also included in BAT. It has been interfaced to other commonly used software packages such as ROOT, Minuit, RooStats and CUBA. An overview of the software and its algorithms is provided along with several physics examples to cover a range of applications of this statistical tool. Future plans, new features and recent developments are briefly discussed.
On approximation of Markov binomial distributions
Xia, Aihua; 10.3150/09-BEJ194
2010-01-01
For a Markov chain $\\mathbf{X}=\\{X_i,i=1,2,...,n\\}$ with the state space $\\{0,1\\}$, the random variable $S:=\\sum_{i=1}^nX_i$ is said to follow a Markov binomial distribution. The exact distribution of $S$, denoted $\\mathcal{L}S$, is very computationally intensive for large $n$ (see Gabriel [Biometrika 46 (1959) 454--460] and Bhat and Lal [Adv. in Appl. Probab. 20 (1988) 677--680]) and this paper concerns suitable approximate distributions for $\\mathcal{L}S$ when $\\mathbf{X}$ is stationary. We conclude that the negative binomial and binomial distributions are appropriate approximations for $\\mathcal{L}S$ when $\\operatorname {Var}S$ is greater than and less than $\\mathbb{E}S$, respectively. Also, due to the unique structure of the distribution, we are able to derive explicit error estimates for these approximations.
Nuclear security assessment with Markov model approach
International Nuclear Information System (INIS)
Nuclear security risk assessment with the Markov model based on random event is performed to explore evaluation methodology for physical protection in nuclear facilities. Because the security incidences are initiated by malicious and intentional acts, expert judgment and Bayes updating are used to estimate scenario and initiation likelihood, and it is assumed that the Markov model derived from stochastic process can be applied to incidence sequence. Both an unauthorized intrusion as Design Based Threat (DBT) and a stand-off attack as beyond-DBT are assumed to hypothetical facilities, and performance of physical protection and mitigation and minimization of consequence are investigated to develop the assessment methodology in a semi-quantitative manner. It is shown that cooperation between facility operator and security authority is important to respond to the beyond-DBT incidence. (author)
Modeling Multisource-heterogeneous Information Based on Random Set and Fuzzy Set Theory
Institute of Scientific and Technical Information of China (English)
WEN Cheng-lin; XU Xiao-bin
2006-01-01
This paper presents a new idea, named as modeling multisensor-heterogeneous information, to incorporate the fuzzy logic methodologies with mulitsensor-multitarget system under the framework of random set theory. Firstly, based on strong random set and weak random set, the unified form to describe both data (unambiguous information) and fuzzy evidence (uncertain information) is introduced. Secondly, according to signatures of fuzzy evidence, two Bayesian-markov nonlinear measurement models are proposed to fuse effectively data and fuzzy evidence. Thirdly, by use of "the models-based signature-matching scheme", the operation of the statistics of fuzzy evidence defined as random set can be translated into that of the membership functions of relative point state variables. These works are the basis to construct qualitative measurement models and to fuse data and fuzzy evidence.
Markov chain analysis of single spin flip Ising simulations
International Nuclear Information System (INIS)
The Markov processes defined by random and loop-based schemes for single spin flip attempts in Monte Carlo simulations of the 2D Ising model are investigated, by explicitly constructing their transition matrices. Their analysis reveals that loops over all lattice sites using a Metropolis-type single spin flip probability often do not define ergodic Markov chains, and have distorted dynamical properties even if they are ergodic. The transition matrices also enable a comparison of the dynamics of random versus loop spin selection and Glauber versus Metropolis probabilities
Institute of Scientific and Technical Information of China (English)
Xiaoyun MO; Jieming ZHOU; Hui OU; Xiangqun YANG
2013-01-01
Given a new Double-Markov risk model DM =(μ,Q,v,H; Y,Z) and Double-Markov risk process U ={U(t),t ≥ 0}.The ruin or survival problem is addressed.Equations which the survival probability satisfied and the formulas of calculating survival probability are obtained.Recursion formulas of calculating the survival probability and analytic expression of recursion items are obtained.The conclusions are expressed by Q matrix for a Markov chain and transition probabilities for another Markov Chain.
Bessiere, Pierre; Ahuactzin, Juan Manuel; Mekhnacha, Kamel
2013-01-01
Probability as an Alternative to Boolean LogicWhile logic is the mathematical foundation of rational reasoning and the fundamental principle of computing, it is restricted to problems where information is both complete and certain. However, many real-world problems, from financial investments to email filtering, are incomplete or uncertain in nature. Probability theory and Bayesian computing together provide an alternative framework to deal with incomplete and uncertain data. Decision-Making Tools and Methods for Incomplete and Uncertain DataEmphasizing probability as an alternative to Boolean
A Duration Hidden Markov Model for the Identification of Regimes in Stock Market Returns
DEFF Research Database (Denmark)
Ntantamis, Christos
This paper introduces a Duration Hidden Markov Model to model bull and bear market regime switches in the stock market; the duration of each state of the Markov Chain is a random variable that depends on a set of exogenous variables. The model not only allows the endogenous determination...
Bayesian kinematic earthquake source models
Minson, S. E.; Simons, M.; Beck, J. L.; Genrich, J. F.; Galetzka, J. E.; Chowdhury, F.; Owen, S. E.; Webb, F.; Comte, D.; Glass, B.; Leiva, C.; Ortega, F. H.
2009-12-01
Most coseismic, postseismic, and interseismic slip models are based on highly regularized optimizations which yield one solution which satisfies the data given a particular set of regularizing constraints. This regularization hampers our ability to answer basic questions such as whether seismic and aseismic slip overlap or instead rupture separate portions of the fault zone. We present a Bayesian methodology for generating kinematic earthquake source models with a focus on large subduction zone earthquakes. Unlike classical optimization approaches, Bayesian techniques sample the ensemble of all acceptable models presented as an a posteriori probability density function (PDF), and thus we can explore the entire solution space to determine, for example, which model parameters are well determined and which are not, or what is the likelihood that two slip distributions overlap in space. Bayesian sampling also has the advantage that all a priori knowledge of the source process can be used to mold the a posteriori ensemble of models. Although very powerful, Bayesian methods have up to now been of limited use in geophysical modeling because they are only computationally feasible for problems with a small number of free parameters due to what is called the "curse of dimensionality." However, our methodology can successfully sample solution spaces of many hundreds of parameters, which is sufficient to produce finite fault kinematic earthquake models. Our algorithm is a modification of the tempered Markov chain Monte Carlo (tempered MCMC or TMCMC) method. In our algorithm, we sample a "tempered" a posteriori PDF using many MCMC simulations running in parallel and evolutionary computation in which models which fit the data poorly are preferentially eliminated in favor of models which better predict the data. We present results for both synthetic test problems as well as for the 2007 Mw 7.8 Tocopilla, Chile earthquake, the latter of which is constrained by InSAR, local high
BAYESIAN IMAGE RESTORATION, USING CONFIGURATIONS
Directory of Open Access Journals (Sweden)
Thordis Linda Thorarinsdottir
2011-05-01
Full Text Available In this paper, we develop a Bayesian procedure for removing noise from images that can be viewed as noisy realisations of random sets in the plane. The procedure utilises recent advances in configuration theory for noise free random sets, where the probabilities of observing the different boundary configurations are expressed in terms of the mean normal measure of the random set. These probabilities are used as prior probabilities in a Bayesian image restoration approach. Estimation of the remaining parameters in the model is outlined for salt and pepper noise. The inference in the model is discussed in detail for 3 X 3 and 5 X 5 configurations and examples of the performance of the procedure are given.
Computationally efficient Bayesian inference for inverse problems.
Energy Technology Data Exchange (ETDEWEB)
Marzouk, Youssef M.; Najm, Habib N.; Rahn, Larry A.
2007-10-01
Bayesian statistics provides a foundation for inference from noisy and incomplete data, a natural mechanism for regularization in the form of prior information, and a quantitative assessment of uncertainty in the inferred results. Inverse problems - representing indirect estimation of model parameters, inputs, or structural components - can be fruitfully cast in this framework. Complex and computationally intensive forward models arising in physical applications, however, can render a Bayesian approach prohibitive. This difficulty is compounded by high-dimensional model spaces, as when the unknown is a spatiotemporal field. We present new algorithmic developments for Bayesian inference in this context, showing strong connections with the forward propagation of uncertainty. In particular, we introduce a stochastic spectral formulation that dramatically accelerates the Bayesian solution of inverse problems via rapid evaluation of a surrogate posterior. We also explore dimensionality reduction for the inference of spatiotemporal fields, using truncated spectral representations of Gaussian process priors. These new approaches are demonstrated on scalar transport problems arising in contaminant source inversion and in the inference of inhomogeneous material or transport properties. We also present a Bayesian framework for parameter estimation in stochastic models, where intrinsic stochasticity may be intermingled with observational noise. Evaluation of a likelihood function may not be analytically tractable in these cases, and thus several alternative Markov chain Monte Carlo (MCMC) schemes, operating on the product space of the observations and the parameters, are introduced.
Evaluating impacts using a BACI design, ratios, and a Bayesian approach with a focus on restoration.
Conner, Mary M; Saunders, W Carl; Bouwes, Nicolaas; Jordan, Chris
2015-10-01
Before-after-control-impact (BACI) designs are an effective method to evaluate natural and human-induced perturbations on ecological variables when treatment sites cannot be randomly chosen. While effect sizes of interest can be tested with frequentist methods, using Bayesian Markov chain Monte Carlo (MCMC) sampling methods, probabilities of effect sizes, such as a ≥20 % increase in density after restoration, can be directly estimated. Although BACI and Bayesian methods are used widely for assessing natural and human-induced impacts for field experiments, the application of hierarchal Bayesian modeling with MCMC sampling to BACI designs is less common. Here, we combine these approaches and extend the typical presentation of results with an easy to interpret ratio, which provides an answer to the main study question-"How much impact did a management action or natural perturbation have?" As an example of this approach, we evaluate the impact of a restoration project, which implemented beaver dam analogs, on survival and density of juvenile steelhead. Results indicated the probabilities of a ≥30 % increase were high for survival and density after the dams were installed, 0.88 and 0.99, respectively, while probabilities for a higher increase of ≥50 % were variable, 0.17 and 0.82, respectively. This approach demonstrates a useful extension of Bayesian methods that can easily be generalized to other study designs from simple (e.g., single factor ANOVA, paired t test) to more complicated block designs (e.g., crossover, split-plot). This approach is valuable for estimating the probabilities of restoration impacts or other management actions. PMID:27613291
Bayesian networks in educational assessment
Almond, Russell G; Steinberg, Linda S; Yan, Duanli; Williamson, David M
2015-01-01
Bayesian inference networks, a synthesis of statistics and expert systems, have advanced reasoning under uncertainty in medicine, business, and social sciences. This innovative volume is the first comprehensive treatment exploring how they can be applied to design and analyze innovative educational assessments. Part I develops Bayes nets’ foundations in assessment, statistics, and graph theory, and works through the real-time updating algorithm. Part II addresses parametric forms for use with assessment, model-checking techniques, and estimation with the EM algorithm and Markov chain Monte Carlo (MCMC). A unique feature is the volume’s grounding in Evidence-Centered Design (ECD) framework for assessment design. This “design forward” approach enables designers to take full advantage of Bayes nets’ modularity and ability to model complex evidentiary relationships that arise from performance in interactive, technology-rich assessments such as simulations. Part III describes ECD, situates Bayes nets as ...
MCMC joint separation and segmentation of hidden Markov fields
Snoussi, H; Snoussi, Hichem; Mohammad-Djafari, Ali
2002-01-01
In this contribution, we consider the problem of the blind separation of noisy instantaneously mixed images. The images are modelized by hidden Markov fields with unknown parameters. Given the observed images, we give a Bayesian formulation and we propose to solve the resulting data augmentation problem by implementing a Monte Carlo Markov Chain (MCMC) procedure. We separate the unknown variables into two categories: 1. The parameters of interest which are the mixing matrix, the noise covariance and the parameters of the sources distributions. 2. The hidden variables which are the unobserved sources and the unobserved pixels classification labels. The proposed algorithm provides in the stationary regime samples drawn from the posterior distributions of all the variables involved in the problem leading to a flexibility in the cost function choice. We discuss and characterize some problems of non identifiability and degeneracies of the parameters likelihood and the behavior of the MCMC algorithm in this case. F...
Application of Markov Chains to Stock Trends
Directory of Open Access Journals (Sweden)
Kevin J. Doubleday
2011-01-01
Full Text Available Problem statement: Modeling of the Dow Jones Industrial Average is frequently attempted in order to determine trading strategies with maximum payoff. Changes in the DJIA are important since movements may affect both individuals and corporations profoundly. Previous work showed that modeling a market as a random walk was valid and that a market may be viewed as having the Markov property. Approach: The aim of this research was to determine the relationship between a diverse portfolio of stocks and the market as a whole. To that end, the DJIA was analyzed using a discrete time stochastic model, namely a Markov Chain. Two models were highlighted, where the DJIA was considered as being in a state of (1 gain or loss and (2 small, moderate, or large gain or loss. A portfolio of five stocks was then considered and two models of the portfolio much the same as those for the DJIA. These models were used to obtain transitional probabilities and steady state probabilities. Results: Our results indicated that the portfolio behaved similarly to the entire DJIA, both in the simple model and the partitioned model. Conclusion: When treated as a Markov process, the entire market was useful in gauging how a diverse portfolio of stocks might behave. Future work may include different classifications of states to refine the transition matrices.
Nonlinear Markov processes: Deterministic case
Energy Technology Data Exchange (ETDEWEB)
Frank, T.D. [Center for the Ecological Study of Perception and Action, Department of Psychology, University of Connecticut, 406 Babbidge Road, Storrs, CT 06269 (United States)], E-mail: till.frank@uconn.edu
2008-10-06
Deterministic Markov processes that exhibit nonlinear transition mechanisms for probability densities are studied. In this context, the following issues are addressed: Markov property, conditional probability densities, propagation of probability densities, multistability in terms of multiple stationary distributions, stability analysis of stationary distributions, and basin of attraction of stationary distribution.
Nonlinear Markov processes: Deterministic case
International Nuclear Information System (INIS)
Deterministic Markov processes that exhibit nonlinear transition mechanisms for probability densities are studied. In this context, the following issues are addressed: Markov property, conditional probability densities, propagation of probability densities, multistability in terms of multiple stationary distributions, stability analysis of stationary distributions, and basin of attraction of stationary distribution
Tutorial on Exact Belief Propagation in Bayesian Networks: from Messages to Algorithms
Nuel, G
2012-01-01
In Bayesian networks, exact belief propagation is achieved through message passing algorithms. These algorithms (ex: inward and outward) provide only a recursive definition of the corresponding messages. In contrast, when working on hidden Markov models and variants, one classically first defines explicitly these messages (forward and backward quantities), and then derive all results and algorithms. In this paper, we generalize the hidden Markov model approach by introducing an explicit definition of the messages in Bayesian networks, from which we derive all the relevant properties and results including the recursive algorithms that allow to compute these messages. Two didactic examples (the precipitation hidden Markov model and the pedigree Bayesian network) are considered along the paper to illustrate the new formalism and standalone R source code is provided in the appendix.
Bayesian tomographic reconstruction of microsystems
Salem, Sofia Fekih; Vabre, Alexandre; Mohammad-Djafari, Ali
2007-11-01
The microtomography by X ray transmission plays an increasingly dominating role in the study and the understanding of microsystems. Within this framework, an experimental setup of high resolution X ray microtomography was developed at CEA-List to quantify the physical parameters related to the fluids flow in microsystems. Several difficulties rise from the nature of experimental data collected on this setup: enhanced error measurements due to various physical phenomena occurring during the image formation (diffusion, beam hardening), and specificities of the setup (limited angle, partial view of the object, weak contrast). To reconstruct the object we must solve an inverse problem. This inverse problem is known to be ill-posed. It therefore needs to be regularized by introducing prior information. The main prior information we account for is that the object is composed of a finite known number of different materials distributed in compact regions. This a priori information is introduced via a Gauss-Markov field for the contrast distributions with a hidden Potts-Markov field for the class materials in the Bayesian estimation framework. The computations are done by using an appropriate Markov Chain Monte Carlo (MCMC) technique. In this paper, we present first the basic steps of the proposed algorithms. Then we focus on one of the main steps in any iterative reconstruction method which is the computation of forward and adjoint operators (projection and backprojection). A fast implementation of these two operators is crucial for the real application of the method. We give some details on the fast computation of these steps and show some preliminary results of simulations.
A Bayesian spatio-temporal geostatistical model with an auxiliary lattice for large datasets
Xu, Ganggang
2015-01-01
When spatio-temporal datasets are large, the computational burden can lead to failures in the implementation of traditional geostatistical tools. In this paper, we propose a computationally efficient Bayesian hierarchical spatio-temporal model in which the spatial dependence is approximated by a Gaussian Markov random field (GMRF) while the temporal correlation is described using a vector autoregressive model. By introducing an auxiliary lattice on the spatial region of interest, the proposed method is not only able to handle irregularly spaced observations in the spatial domain, but it is also able to bypass the missing data problem in a spatio-temporal process. Because the computational complexity of the proposed Markov chain Monte Carlo algorithm is of the order O(n) with n the total number of observations in space and time, our method can be used to handle very large spatio-temporal datasets with reasonable CPU times. The performance of the proposed model is illustrated using simulation studies and a dataset of precipitation data from the coterminous United States.
Non-Markov property of certain eigenvalue processes analogous to Dyson's model
Fukushima, Ryoki; Yano, Kouji
2009-01-01
It is proven that the eigenvalue process of Dyson's random matrix process of size two becomes non-Markov if the common coefficient $1/\\sqrt{2}$ in the non-diagonal entries is replaced by a different positive number.
A comparison of strategies for Markov chain Monte Carlo computation in quantitative genetics
DEFF Research Database (Denmark)
Waagepetersen, Rasmus; Ibanez-Escriche, Noelia; Sorensen, Daniel
2008-01-01
In quantitative genetics, Markov chain Monte Carlo (MCMC) methods are indispensable for statistical inference in non-standard models like generalized linear models with genetic random effects or models with genetically structured variance heterogeneity. A particular challenge for MCMC applications...
Bayesian seismic AVO inversion
Energy Technology Data Exchange (ETDEWEB)
Buland, Arild
2002-07-01
A new linearized AVO inversion technique is developed in a Bayesian framework. The objective is to obtain posterior distributions for P-wave velocity, S-wave velocity and density. Distributions for other elastic parameters can also be assessed, for example acoustic impedance, shear impedance and P-wave to S-wave velocity ratio. The inversion algorithm is based on the convolutional model and a linearized weak contrast approximation of the Zoeppritz equation. The solution is represented by a Gaussian posterior distribution with explicit expressions for the posterior expectation and covariance, hence exact prediction intervals for the inverted parameters can be computed under the specified model. The explicit analytical form of the posterior distribution provides a computationally fast inversion method. Tests on synthetic data show that all inverted parameters were almost perfectly retrieved when the noise approached zero. With realistic noise levels, acoustic impedance was the best determined parameter, while the inversion provided practically no information about the density. The inversion algorithm has also been tested on a real 3-D dataset from the Sleipner Field. The results show good agreement with well logs but the uncertainty is high. The stochastic model includes uncertainties of both the elastic parameters, the wavelet and the seismic and well log data. The posterior distribution is explored by Markov chain Monte Carlo simulation using the Gibbs sampler algorithm. The inversion algorithm has been tested on a seismic line from the Heidrun Field with two wells located on the line. The uncertainty of the estimated wavelet is low. In the Heidrun examples the effect of including uncertainty of the wavelet and the noise level was marginal with respect to the AVO inversion results. We have developed a 3-D linearized AVO inversion method with spatially coupled model parameters where the objective is to obtain posterior distributions for P-wave velocity, S
Flexible Bayesian Nonparametric Priors and Bayesian Computational Methods
Zhu, Weixuan
2016-01-01
The definition of vectors of dependent random probability measures is a topic of interest in Bayesian nonparametrics. They represent dependent nonparametric prior distributions that are useful for modelling observables for which specific covariate values are known. Our first contribution is the introduction of novel multivariate vectors of two-parameter Poisson-Dirichlet process. The dependence is induced by applying a L´evy copula to the marginal L´evy intensities. Our attenti...
Directory of Open Access Journals (Sweden)
M. Bagnara
2014-10-01
Full Text Available Forest models are being increasingly used to study ecosystem functioning, through the reproduction of carbon fluxes and productivity in very different forests all over the world. Over the last two decades, the need for simple and "easy to use" models for practical applications, characterized by few parameters and equations, has become clear, and some have been developed for this purpose. These models aim to represent the main drivers underlying forest ecosystem processes while being applicable to the widest possible range of forest ecosystems. Recently, it has also become clear that model performance should not be assessed only in terms of accuracy of estimations and predictions, but also in terms of estimates of model uncertainties. Therefore, the Bayesian approach has increasingly been applied to calibrate forest models, with the aim of estimating the uncertainty of their results, and of comparing their performances. Some forest models, considered to be user-friendly, rely on a multiplicative or quasi-multiplicative mathematical structure, which is known to cause problems during the calibration process, mainly due to high correlations between parameters. In a Bayesian framework using a Markov Chain Monte Carlo sampling this is likely to impair the reaching of a proper convergence of the chains and the sampling from the correct posterior distribution. Here we show two methods to reach proper convergence when using a forest model with a multiplicative structure, applying different algorithms with different number of iterations during the Markov Chain Monte Carlo or a two-steps calibration. The results showed that recently proposed algorithms for adaptive calibration do not confer a clear advantage over the Metropolis–Hastings Random Walk algorithm for the forest model used here. Moreover, the calibration remains time consuming and mathematically difficult, so advantages of using a fast and user-friendly model can be lost due to the calibration
Bayesian statistical ionospheric tomography improved by incorporating ionosonde measurements
Norberg, Johannes; Virtanen, Ilkka I.; Roininen, Lassi; Vierinen, Juha; Orispää, Mikko; Kauristie, Kirsti; Lehtinen, Markku S.
2016-04-01
We validate two-dimensional ionospheric tomography reconstructions against EISCAT incoherent scatter radar measurements. Our tomography method is based on Bayesian statistical inversion with prior distribution given by its mean and covariance. We employ ionosonde measurements for the choice of the prior mean and covariance parameters and use the Gaussian Markov random fields as a sparse matrix approximation for the numerical computations. This results in a computationally efficient tomographic inversion algorithm with clear probabilistic interpretation. We demonstrate how this method works with simultaneous beacon satellite and ionosonde measurements obtained in northern Scandinavia. The performance is compared with results obtained with a zero-mean prior and with the prior mean taken from the International Reference Ionosphere 2007 model. In validating the results, we use EISCAT ultra-high-frequency incoherent scatter radar measurements as the ground truth for the ionization profile shape. We find that in comparison to the alternative prior information sources, ionosonde measurements improve the reconstruction by adding accurate information about the absolute value and the altitude distribution of electron density. With an ionosonde at continuous disposal, the presented method enhances stand-alone near-real-time ionospheric tomography for the given conditions significantly.
Effect of Markov and Non-Markov Classical Noise on Entanglement Dynamics
Bordone, Paolo; Benedetti, Claudia
2012-01-01
We analyze the effect of a classical noise into the entanglement dynamics between two particles, initially entangled, subject to continuous time quantum walks in a one-dimensional lattice. The noise is modeled by randomizing the transition amplitudes from one site to another. Both Markovian and non-Markovian environments are considered. For the Markov regime an exponential decay of the initial quantum correlation is found, while the loss of coherence of the quantum state increases monotonically with time up to a saturation value depending upon the degrees of freedom of the system. For the non-Markov regime the presence or absence of entanglement revival and entanglement sudden death phenomena is found or deduced depending on the peculiar characteristics of the noise. Our results indicate that the entanglement dynamics in the non-Markovian regime is affected by the persistence of the memory effects of the environment and by its intrinsic features.
Markov chains theory and applications
Sericola, Bruno
2013-01-01
Markov chains are a fundamental class of stochastic processes. They are widely used to solve problems in a large number of domains such as operational research, computer science, communication networks and manufacturing systems. The success of Markov chains is mainly due to their simplicity of use, the large number of available theoretical results and the quality of algorithms developed for the numerical evaluation of many metrics of interest.The author presents the theory of both discrete-time and continuous-time homogeneous Markov chains. He carefully examines the explosion phenomenon, the
Quadratic Variation by Markov Chains
DEFF Research Database (Denmark)
Hansen, Peter Reinhard; Horel, Guillaume
We introduce a novel estimator of the quadratic variation that is based on the the- ory of Markov chains. The estimator is motivated by some general results concerning filtering contaminated semimartingales. Specifically, we show that filtering can in prin- ciple remove the effects of market...... microstructure noise in a general framework where little is assumed about the noise. For the practical implementation, we adopt the dis- crete Markov chain model that is well suited for the analysis of financial high-frequency prices. The Markov chain framework facilitates simple expressions and elegant analyti...
Bayesian Magnetohydrodynamic Seismology of Coronal Loops
Arregui, Inigo
2011-01-01
We perform a Bayesian parameter inference in the context of resonantly damped transverse coronal loop oscillations. The forward problem is solved in terms of parametric results for kink waves in one-dimensional flux tubes in the thin tube and thin boundary approximations. For the inverse problem, we adopt a Bayesian approach to infer the most probable values of the relevant parameters, for given observed periods and damping times, and to extract their confidence levels. The posterior probability distribution functions are obtained by means of Markov Chain Monte Carlo simulations, incorporating observed uncertainties in a consistent manner. We find well localized solutions in the posterior probability distribution functions for two of the three parameters of interest, namely the Alfven travel time and the transverse inhomogeneity length-scale. The obtained estimates for the Alfven travel time are consistent with previous inversion results, but the method enables us to additionally constrain the transverse inho...
Markov Logic An Interface Layer for Artificial Intelligence
Domingos, Pedro
2009-01-01
Most subfields of computer science have an interface layer via which applications communicate with the infrastructure, and this is key to their success (e.g., the Internet in networking, the relational model in databases, etc.). So far this interface layer has been missing in AI. First-order logic and probabilistic graphical models each have some of the necessary features, but a viable interface layer requires combining both. Markov logic is a powerful new language that accomplishes this by attaching weights to first-order formulas and treating them as templates for features of Markov random f
Harmonic Oscillator Model for Radin's Markov-Chain Experiments
International Nuclear Information System (INIS)
The conscious observer stands as a central figure in the measurement problem of quantum mechanics. Recent experiments by Radin involving linear Markov chains driven by random number generators illuminate the role and temporal dynamics of observers interacting with quantum mechanically labile systems. In this paper a Lagrangian interpretation of these experiments indicates that the evolution of Markov chain probabilities can be modeled as damped harmonic oscillators. The results are best interpreted in terms of symmetric equicausal determinism rather than strict retrocausation, as posited by Radin. Based on the present analysis, suggestions are made for more advanced experiments
Estimation in autoregressive models with Markov regime
Ríos, Ricardo; Rodríguez, Luis
2005-01-01
In this paper we derive the consistency of the penalized likelihood method for the number state of the hidden Markov chain in autoregressive models with Markov regimen. Using a SAEM type algorithm to estimate the models parameters. We test the null hypothesis of hidden Markov Model against an autoregressive process with Markov regime.
Compressing redundant information in Markov chains
Aletti, Giacomo
2006-01-01
Given a strongly stationary Markov chain and a finite set of stopping rules, we prove the existence of a polynomial algorithm which projects the Markov chain onto a minimal Markov chain without redundant information. Markov complexity is hence defined and tested on some classical problems.
A Bayesian Nonparametric IRT Model
Karabatsos, George
2015-01-01
This paper introduces a flexible Bayesian nonparametric Item Response Theory (IRT) model, which applies to dichotomous or polytomous item responses, and which can apply to either unidimensional or multidimensional scaling. This is an infinite-mixture IRT model, with person ability and item difficulty parameters, and with a random intercept parameter that is assigned a mixing distribution, with mixing weights a probit function of other person and item parameters. As a result of its flexibility...
Bayesian Optimization for Adaptive MCMC
Mahendran, Nimalan; Wang, Ziyu; Hamze, Firas; De Freitas, Nando
2011-01-01
This paper proposes a new randomized strategy for adaptive MCMC using Bayesian optimization. This approach applies to non-differentiable objective functions and trades off exploration and exploitation to reduce the number of potentially costly objective function evaluations. We demonstrate the strategy in the complex setting of sampling from constrained, discrete and densely connected probabilistic graphical models where, for each variation of the problem, one needs to adjust the parameters o...
Bayesian phylogeography finds its roots.
Directory of Open Access Journals (Sweden)
Philippe Lemey
2009-09-01
Full Text Available As a key factor in endemic and epidemic dynamics, the geographical distribution of viruses has been frequently interpreted in the light of their genetic histories. Unfortunately, inference of historical dispersal or migration patterns of viruses has mainly been restricted to model-free heuristic approaches that provide little insight into the temporal setting of the spatial dynamics. The introduction of probabilistic models of evolution, however, offers unique opportunities to engage in this statistical endeavor. Here we introduce a Bayesian framework for inference, visualization and hypothesis testing of phylogeographic history. By implementing character mapping in a Bayesian software that samples time-scaled phylogenies, we enable the reconstruction of timed viral dispersal patterns while accommodating phylogenetic uncertainty. Standard Markov model inference is extended with a stochastic search variable selection procedure that identifies the parsimonious descriptions of the diffusion process. In addition, we propose priors that can incorporate geographical sampling distributions or characterize alternative hypotheses about the spatial dynamics. To visualize the spatial and temporal information, we summarize inferences using virtual globe software. We describe how Bayesian phylogeography compares with previous parsimony analysis in the investigation of the influenza A H5N1 origin and H5N1 epidemiological linkage among sampling localities. Analysis of rabies in West African dog populations reveals how virus diffusion may enable endemic maintenance through continuous epidemic cycles. From these analyses, we conclude that our phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms.
A Bayesian framework to estimate diversification rates and their variation through time and space
Directory of Open Access Journals (Sweden)
Silvestro Daniele
2011-10-01
Full Text Available Abstract Background Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification. Results We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinidae and Lupinus (Fabaceae. In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in diversification. Conclusions Our approach provides a flexible framework for the estimation of diversification parameters and hypothesis testing while simultaneously accounting for uncertainties in the divergence times and incomplete taxon sampling.
Texture-preserving Bayesian image reconstruction for low-dose CT
Zhang, Hao; Han, Hao; Hu, Yifan; Liu, Yan; Ma, Jianhua; Li, Lihong; Moore, William; Liang, Zhengrong
2016-03-01
Markov random field (MRF) model has been widely used in Bayesian image reconstruction to reconstruct piecewise smooth images in the presence of noise, such as in low-dose X-ray computed tomography (LdCT). While it can preserve edge sharpness via edge-preserving potential function, its regional smoothing may sacrifice tissue image textures, which have been recognized as useful imaging biomarkers, and thus it compromises clinical tasks such as differentiating malignant vs. benign lesions, e.g., lung nodule or colon polyp. This study aims to shift the edge preserving regional noise smoothing paradigm to texture-preserving framework for LdCT image reconstruction while retaining the advantage of MRF's neighborhood system on edge preservation. Specifically, we adapted the MRF model to incorporate the image textures of lung, bone, fat, muscle, etc. from previous full-dose CT scan as a priori knowledge for texture-preserving Bayesian reconstruction of current LdCT images. To show the feasibility of proposed reconstruction framework, experiments using clinical patient scans (with lung nodule or colon polyp) were conducted. The experimental outcomes showed noticeable gain by the a priori knowledge for LdCT image reconstruction with the well-known Haralick texture measures. Thus, it is conjectured that texture-preserving LdCT reconstruction has advantages over edge-preserving regional smoothing paradigm for texture-specific clinical applications.
A Bayesian approach to estimating the prehepatic insulin secretion rate
DEFF Research Database (Denmark)
Andersen, Kim Emil; Højbjerre, Malene
the time courses of insulin and C-peptide subsequently are used as known forcing functions. In this work we adopt a Bayesian graphical model to describe the unied model simultaneously. We develop a model that also accounts for both measurement error and process variability. The parameters are estimated...... by a Bayesian approach where efficient posterior sampling is made available through the use of Markov chain Monte Carlo methods. Hereby the ill-posed estimation problem inherited in the coupled differential equation model is regularized by the use of prior knowledge. The method is demonstrated on experimental...
Energy Technology Data Exchange (ETDEWEB)
Stawinski, G
1998-10-26
Bayesian algorithms are developed to solve inverse problems in gamma imaging and photofission tomography. The first part of this work is devoted to the modeling of our measurement systems. Two models have been found for both applications: the first one is a simple conventional model and the second one is a cascaded point process model. EM and MCMC Bayesian algorithms for image restoration and image reconstruction have been developed for these models and compared. The cascaded point process model does not improve significantly the results previously obtained by the classical model. To original approaches have been proposed, which increase the results previously obtained. The first approach uses an inhomogeneous Markov Random Field as a prior law, and makes the regularization parameter spatially vary. However, the problem of the estimation of hyper-parameters has not been solved. In the case of the deconvolution of point sources, a second approach has been proposed, which introduces a high level prior model. The picture is modeled as a list of objects, whose parameters and number are unknown. The results obtained with this method are more accurate than those obtained with the conventional Markov Random Field prior model and require less computational costs. (author)
Assessing confidence in phylogenetic trees : bootstrap versus Markov chain Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Burr, Tom; Doak, J. E. (Justin E.); Gattiker, J. R. (James R.); Stanbro, W. D. (William D.)
2002-01-01
Recent implementations of Bayesian approaches are one of the largest advances in phylogenetic tree estimation in the last 10 years. Markov chain Monte Carlo (MCMC) is used in these new approaches to estimate the Bayesian posterior probability for each tree topology of interest. Our goal is to assess the confidence in the estimated tree (particularly in whether prespecified groups are monophyletic) using MCMC and to compare the Bayesian estimate of confidence to a bootstrap-based estimate of confidence. We compare the Bayesian posterior probability to the bootstrap probability for specified groups in two real sets of influenza sequences and two sets of simulated sequences for our comparison. We conclude that the bootstrap estimate is adequate compared to the MCMC estimate except perhaps if the number of DNA sites is small.
Bayesian artificial intelligence
Korb, Kevin B
2010-01-01
Updated and expanded, Bayesian Artificial Intelligence, Second Edition provides a practical and accessible introduction to the main concepts, foundation, and applications of Bayesian networks. It focuses on both the causal discovery of networks and Bayesian inference procedures. Adopting a causal interpretation of Bayesian networks, the authors discuss the use of Bayesian networks for causal modeling. They also draw on their own applied research to illustrate various applications of the technology.New to the Second EditionNew chapter on Bayesian network classifiersNew section on object-oriente
DEFF Research Database (Denmark)
Jensen, Finn Verner; Nielsen, Thomas Dyhre
2016-01-01
Mathematically, a Bayesian graphical model is a compact representation of the joint probability distribution for a set of variables. The most frequently used type of Bayesian graphical models are Bayesian networks. The structural part of a Bayesian graphical model is a graph consisting of nodes and...... largely due to the availability of efficient inference algorithms for answering probabilistic queries about the states of the variables in the network. Furthermore, to support the construction of Bayesian network models, learning algorithms are also available. We give an overview of the Bayesian network...
Stability of Markov regenerative switched linear systems
Ogura, Masaki; Preciado, Victor M.
2015-01-01
In this paper, we give a necessary and sufficient condition for mean stability of switched linear systems having a Markov regenerative process as its switching signal. This class of switched linear systems, which we call Markov regenerative switched linear systems, contains Markov jump linear systems and semi-Markov jump linear systems as special cases. We show that a Markov regenerative switched linear system is $m$th mean stable if and only if a particular matrix is Schur stable, under the ...
Bibliometric Application of Markov Chains.
Pao, Miranda Lee; McCreery, Laurie
1986-01-01
A rudimentary description of Markov Chains is presented in order to introduce its use to describe and to predict authors' movements among subareas of the discipline of ethnomusicology. Other possible applications are suggested. (Author)
Reviving Markov processes and applications
International Nuclear Information System (INIS)
In this dissertation we study a procedure which restarts a Markov process when the process is killed by some arbitrary multiplicative functional. The regenerative nature of this revival procedure is characterized through a Markov renewal equation. An interesting duality between the revival procedure and the classical killing operation is found. Under the condition that the multiplicative functional possesses an intensity, the generators of the revival process can be written down explicitly. An intimate connection is also found between the perturbation of the sample path of a Markov process and the perturbation of a generator (in Kato's sense). The applications of the theory include the study of the processes like piecewise-deterministic Markov process, virtual waiting time process and the first entrance decomposition (taboo probability)
VIGoR: Variational Bayesian Inference for Genome-Wide Regression
Onogi, Akio; Iwata, Hiroyoshi
2016-01-01
Genome-wide regression using a number of genome-wide markers as predictors is now widely used for genome-wide association mapping and genomic prediction. We developed novel software for genome-wide regression which we named VIGoR (variational Bayesian inference for genome-wide regression). Variational Bayesian inference is computationally much faster than widely used Markov chain Monte Carlo algorithms. VIGoR implements seven regression methods, and is provided as a command line program packa...
Evaluating The Markov Assumption For Web Usage Mining
DEFF Research Database (Denmark)
Jespersen, S.; Pedersen, Torben Bach; Thorhauge, J.
2003-01-01
Web usage mining concerns the discovery of common browsing patterns, i.e., pages requested in sequence, from web logs. To cope with the enormous amounts of data, several aggregated structures based on statistical models of web surfing have appeared, e.g., the Hypertext Probabilistic Grammar (HPG...... knowledge there has been no systematic study of the validity of the Markov assumption wrt.\\ web usage mining and the resulting quality of the mined browsing patterns. In this paper we systematically investigate the quality of browsing patterns mined from structures based on the Markov assumption. Formal......, that long rules are generally more distorted than shorter rules and that the model yield knowledge of a higher quality when applied to more random usage patterns. Thus we conclude that Markov-based structures for web usage mining are best suited for tasks demanding less accuracy such as pre...
Kieftenbeld, Vincent; Natesan, Prathiba
2012-01-01
Markov chain Monte Carlo (MCMC) methods enable a fully Bayesian approach to parameter estimation of item response models. In this simulation study, the authors compared the recovery of graded response model parameters using marginal maximum likelihood (MML) and Gibbs sampling (MCMC) under various latent trait distributions, test lengths, and…
Methods for Bayesian power spectrum inference with galaxy surveys
Jasche, Jens
2013-01-01
We derive and implement a full Bayesian large scale structure inference method aiming at precision recovery of the cosmological power spectrum from galaxy redshift surveys. Our approach improves over previous Bayesian methods by performing a joint inference of the three dimensional density field, the cosmological power spectrum, luminosity dependent galaxy biases and corresponding normalizations. We account for all joint and correlated uncertainties between all inferred quantities. Classes of galaxies with different biases are treated as separate sub samples. The method therefore also allows the combined analysis of more than one galaxy survey. In particular, it solves the problem of inferring the power spectrum from galaxy surveys with non-trivial survey geometries by exploring the joint posterior distribution with efficient implementations of multiple block Markov chain and Hybrid Monte Carlo methods. Our Markov sampler achieves high statistical efficiency in low signal to noise regimes by using a determini...
Bayesian Model Averaging in the Instrumental Variable Regression Model
Gary Koop; Robert Leon Gonzalez; Rodney Strachan
2011-01-01
This paper considers the instrumental variable regression model when there is uncertainly about the set of instruments, exogeneity restrictions, the validity of identifying restrictions and the set of exogenous regressors. This uncertainly can result in a huge number of models. To avoid statistical problems associated with standard model selection procedures, we develop a reversible jump Markov chain Monte Carlo algorithm that allows us to do Bayesian model averaging. The algorithm is very fl...
Bayesian Methods for Neural Networks and Related Models
Titterington, D.M.
2004-01-01
Models such as feed-forward neural networks and certain other structures investigated in the computer science literature are not amenable to closed-form Bayesian analysis. The paper reviews the various approaches taken to overcome this difficulty, involving the use of Gaussian approximations, Markov chain Monte Carlo simulation routines and a class of non-Gaussian but “deterministic” approximations called variational approximations.
Random construction of interpolating sets for high dimensional integration
Huber, Mark
2011-01-01
Many high dimensional integrals can be reduced to the problem of finding the relative measures of two sets. Often one set will be exponentially larger than the other, making it difficult to compare the sizes. A standard method of dealing with this problem is to interpolate between the sets with a sequence of nested sets where neighboring sets have relative measures bounded above by a constant. Choosing such a well balanced sequence can be very difficult in practice. Here a new approach that automatically creates such sets is presented. These well balanced sets allow for faster approximation algorithms for integrals and sums, and better tempering and annealing Markov chains for generating random samples. Applications such as finding the partition function of the Ising model and normalizing constants for posterior distributions in Bayesian methods are discussed.
Yuan, Ying; MacKinnon, David P.
2009-01-01
This article proposes Bayesian analysis of mediation effects. Compared to conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian mediation analysis, inference is straightforward and exact, which makes it appealing for studies with small samples. Third, the Bayesian approach is conceptua...
Infinite Factorial Unbounded-State Hidden Markov Model.
Valera, Isabel; Ruiz, Francisco J R; Perez-Cruz, Fernando
2016-09-01
There are many scenarios in artificial intelligence, signal processing or medicine, in which a temporal sequence consists of several unknown overlapping independent causes, and we are interested in accurately recovering those canonical causes. Factorial hidden Markov models (FHMMs) present the versatility to provide a good fit to these scenarios. However, in some scenarios, the number of causes or the number of states of the FHMM cannot be known or limited a priori. In this paper, we propose an infinite factorial unbounded-state hidden Markov model (IFUHMM), in which the number of parallel hidden Markovmodels (HMMs) and states in each HMM are potentially unbounded. We rely on a Bayesian nonparametric (BNP) prior over integer-valued matrices, in which the columns represent the Markov chains, the rows the time indexes, and the integers the state for each chain and time instant. First, we extend the existent infinite factorial binary-state HMM to allow for any number of states. Then, we modify this model to allow for an unbounded number of states and derive an MCMC-based inference algorithm that properly deals with the trade-off between the unbounded number of states and chains. We illustrate the performance of our proposed models in the power disaggregation problem. PMID:26571511
Bayesian Games with Intentions
Bjorndahl, Adam; Halpern, Joseph Y.; Pass, Rafael
2016-01-01
We show that standard Bayesian games cannot represent the full spectrum of belief-dependent preferences. However, by introducing a fundamental distinction between intended and actual strategies, we remove this limitation. We define Bayesian games with intentions, generalizing both Bayesian games and psychological games, and prove that Nash equilibria in psychological games correspond to a special class of equilibria as defined in our setting.
The impact of spatial scales and spatial smoothing on the outcome of bayesian spatial model.
Directory of Open Access Journals (Sweden)
Su Yun Kang
Full Text Available Discretization of a geographical region is quite common in spatial analysis. There have been few studies into the impact of different geographical scales on the outcome of spatial models for different spatial patterns. This study aims to investigate the impact of spatial scales and spatial smoothing on the outcomes of modelling spatial point-based data. Given a spatial point-based dataset (such as occurrence of a disease, we study the geographical variation of residual disease risk using regular grid cells. The individual disease risk is modelled using a logistic model with the inclusion of spatially unstructured and/or spatially structured random effects. Three spatial smoothness priors for the spatially structured component are employed in modelling, namely an intrinsic Gaussian Markov random field, a second-order random walk on a lattice, and a Gaussian field with Matérn correlation function. We investigate how changes in grid cell size affect model outcomes under different spatial structures and different smoothness priors for the spatial component. A realistic example (the Humberside data is analyzed and a simulation study is described. Bayesian computation is carried out using an integrated nested Laplace approximation. The results suggest that the performance and predictive capacity of the spatial models improve as the grid cell size decreases for certain spatial structures. It also appears that different spatial smoothness priors should be applied for different patterns of point data.
How Much Can We Learn from a Single Chromatographic Experiment? A Bayesian Perspective.
Wiczling, Paweł; Kaliszan, Roman
2016-01-01
In this work, we proposed and investigated a Bayesian inference procedure to find the desired chromatographic conditions based on known analyte properties (lipophilicity, pKa, and polar surface area) using one preliminary experiment. A previously developed nonlinear mixed effect model was used to specify the prior information about a new analyte with known physicochemical properties. Further, the prior (no preliminary data) and posterior predictive distribution (prior + one experiment) were determined sequentially to search towards the desired separation. The following isocratic high-performance reversed-phase liquid chromatographic conditions were sought: (1) retention time of a single analyte within the range of 4-6 min and (2) baseline separation of two analytes with retention times within the range of 4-10 min. The empirical posterior Bayesian distribution of parameters was estimated using the "slice sampling" Markov Chain Monte Carlo (MCMC) algorithm implemented in Matlab. The simulations with artificial analytes and experimental data of ketoprofen and papaverine were used to test the proposed methodology. The simulation experiment showed that for a single and two randomly selected analytes, there is 97% and 74% probability of obtaining a successful chromatogram using none or one preliminary experiment. The desired separation for ketoprofen and papaverine was established based on a single experiment. It was confirmed that the search for a desired separation rarely requires a large number of chromatographic analyses at least for a simple optimization problem. The proposed Bayesian-based optimization scheme is a powerful method of finding a desired chromatographic separation based on a small number of preliminary experiments. PMID:26607659
International Nuclear Information System (INIS)
Complete text of publication follows. This paper employs Bayesian inference theory to study parameterization, parameter uncertainty estimation, and nonlinearity for the one-dimensional magnetotelluric (MT) inverse problem. In the Bayesian formulation, the complex impedance data and the model parameters (conductivities and/or layer thicknesses) are all considered as random variables. The multi-dimensional posterior probability density (PPD), combining data and prior information, is interpreted in terms of parameter estimates, uncertainties, and interrelationships which require optimizing and integrating the PPD. In the nonlinear formulation, optimization is carried out using an adaptive-hybrid algorithm that combines very-fast simulated annealing and the downhill simplex method. Integration applies Markov-chain Monte Carlo sampling, rotated to a principal-component parameter space for efficient sampling of correlated parameters. Since appropriate model parameterizations are generally not known a priori, both over- and under-parameterized approaches are considered. For over-parameterization, prior information is included which favours simple structure in a manner similar to regularized (Occam's) inversion. The data error variance and tradeoff parameter regulating data and prior information are included as nuisance parameters in the PPD sampling. For under-parameterization, the maximum a posteriori (MAP) solution is determined for a sequence of problems with an increasing number of layers, and the appropriate parameterization is chosen using the Bayesian information criterion for model selection. The nonlinear inversion results in terms of one- and two-dimensional marginal probability distributions and marginal probability profiles are compared to linearized inversion results for both the under- and over-parameterized approaches. Although generally similar, some significant differences in recovered parameter uncertainties between the nonlinear and (approximate
Adiabatic condition and the quantum hitting time of Markov chains
International Nuclear Information System (INIS)
We present an adiabatic quantum algorithm for the abstract problem of searching marked vertices in a graph, or spatial search. Given a random walk (or Markov chain) P on a graph with a set of unknown marked vertices, one can define a related absorbing walk P' where outgoing transitions from marked vertices are replaced by self-loops. We build a Hamiltonian H(s) from the interpolated Markov chain P(s)=(1-s)P+sP' and use it in an adiabatic quantum algorithm to drive an initial superposition over all vertices to a superposition over marked vertices. The adiabatic condition implies that, for any reversible Markov chain and any set of marked vertices, the running time of the adiabatic algorithm is given by the square root of the classical hitting time. This algorithm therefore demonstrates a novel connection between the adiabatic condition and the classical notion of hitting time of a random walk. It also significantly extends the scope of previous quantum algorithms for this problem, which could only obtain a full quadratic speedup for state-transitive reversible Markov chains with a unique marked vertex.
On Markov parameters in system identification
Phan, Minh; Juang, Jer-Nan; Longman, Richard W.
1991-01-01
A detailed discussion of Markov parameters in system identification is given. Different forms of input-output representation of linear discrete-time systems are reviewed and discussed. Interpretation of sampled response data as Markov parameters is presented. Relations between the state-space model and particular linear difference models via the Markov parameters are formulated. A generalization of Markov parameters to observer and Kalman filter Markov parameters for system identification is explained. These extended Markov parameters play an important role in providing not only a state-space realization, but also an observer/Kalman filter for the system of interest.
Laser-based detection and tracking moving objects using data-driven Markov chain Monte Carlo
Vu, Trung-Dung; Aycard, Olivier
2009-01-01
We present a method of simultaneous detection and tracking moving objects from a moving vehicle equipped with a single layer laser scanner. A model-based approach is introduced to interpret the laser measurement sequence by hypotheses of moving object trajectories over a sliding window of time. Knowledge of various aspects including object model, measurement model, motion model are integrated in one theoretically sound Bayesian framework. The data-driven Markov chain Monte Carlo (DDMCMC) tech...
Farr, W. M.; Stevens, D; Mandel, Ilya
2015-01-01
Selection among alternative theoretical models given an observed dataset is an important challenge in many areas of physics and astronomy. Reversible-jump Markov chain Monte Carlo (RJMCMC) is an extremely powerful technique for performing Bayesian model selection, but it suffers from a fundamental difficulty and it requires jumps between model parameter spaces, but cannot efficiently explore both parameter spaces at once. Thus, a naive jump between parameter spaces is unlikely to be accepted ...
Recursive estimation of high-order Markov chains: Approximation by finite mixtures
Czech Academy of Sciences Publication Activity Database
Kárný, Miroslav
2016-01-01
Roč. 326, č. 1 (2016), s. 188-201. ISSN 0020-0255 R&D Projects: GA ČR GA13-13502S Institutional support: RVO:67985556 Keywords : Markov chain * Approximate parameter estimation * Bayesian recursive estimation * Adaptive systems * Kullback–Leibler divergence * Forgetting Subject RIV: BC - Control Systems Theory Impact factor: 4.038, year: 2014 http://library.utia.cas.cz/separaty/2015/AS/karny-0447119.pdf
Doing bayesian data analysis a tutorial with R and BUGS
Kruschke, John K
2011-01-01
There is an explosion of interest in Bayesian statistics, primarily because recently created computational methods have finally made Bayesian analysis obtainable to a wide audience. Doing Bayesian Data Analysis, A Tutorial Introduction with R and BUGS provides an accessible approach to Bayesian data analysis, as material is explained clearly with concrete examples. The book begins with the basics, including essential concepts of probability and random sampling, and gradually progresses to advanced hierarchical modeling methods for realistic data. The text delivers comprehensive coverage of all
Markov Property of the Solution of the Stochastic Generalized Equations
Directory of Open Access Journals (Sweden)
Khaldi Khaled
2007-01-01
Full Text Available Some models of probabilities are described by generalized stochastic equations. These models (like that prediction lead to the resolution of boundary problems for random distributions (generalized equations. We are interested in the equation in Lx = f in S ⊂ IRd where L is a linear operator, f is a random distribution and to the class of boundary conditions on the frontier Γ = ∂S in order to define for the corresponding boundary conditions. The resolutions of boundary problems for random distributions lead to the Markov property for the solution of these equations.
ESTIMATE OF THE HYPSOMETRIC RELATIONSHIP WITH NONLINEAR MODELS FITTED BY EMPIRICAL BAYESIAN METHODS
Directory of Open Access Journals (Sweden)
Monica Fabiana Bento Moreira
2015-09-01
Full Text Available In this paper we propose a Bayesian approach to solve the inference problem with restriction on parameters, regarding to nonlinear models used to represent the hypsometric relationship in clones of Eucalyptus sp. The Bayesian estimates are calculated using Monte Carlo Markov Chain (MCMC method. The proposed method was applied to different groups of actual data from which two were selected to show the results. These results were compared to the results achieved by the minimum square method, highlighting the superiority of the Bayesian approach, since this approach always generate the biologically consistent results for hipsometric relationship.
Asymptotic evolution of quantum Markov chains
International Nuclear Information System (INIS)
The iterated quantum operations, so called quantum Markov chains, play an important role in various branches of physics. They constitute basis for many discrete models capable to explore fundamental physical problems, such as the approach to thermal equilibrium, or the asymptotic dynamics of macroscopic physical systems far from thermal equilibrium. On the other hand, in the more applied area of quantum technology they also describe general characteristic properties of quantum networks or they can describe different quantum protocols in the presence of decoherence. A particularly, an interesting aspect of these quantum Markov chains is their asymptotic dynamics and its characteristic features. We demonstrate there is always a vector subspace (typically low-dimensional) of so-called attractors on which the resulting superoperator governing the iterative time evolution of quantum states can be diagonalized and in which the asymptotic quantum dynamics takes place. As the main result interesting algebraic relations are presented for this set of attractors which allow to specify their dual basis and to determine them in a convenient way. Based on this general theory we show some generalizations concerning the theory of fixed points or asymptotic evolution of random quantum operations.
DEFF Research Database (Denmark)
Dalgaard, Jens; Pena, Jose; Kocka, Tomas
2004-01-01
We propose a method to assist the user in the interpretation of the best Bayesian network model indu- ced from data. The method consists in extracting relevant features from the model (e.g. edges, directed paths and Markov blankets) and, then, assessing the con¯dence in them by studying multiple...
Bayesian interpolation in a dynamic sinusoidal model with application to packet-loss concealment
DEFF Research Database (Denmark)
Nielsen, Jesper Kjær; Christensen, Mads Græsbøll; Cemgil, Ali Taylan;
2010-01-01
a Bayesian inference scheme for the missing observations, hidden states and model parameters of the dynamic model. The inference scheme is based on a Markov chain Monte Carlo method known as Gibbs sampler. We illustrate the performance of the inference scheme to the application of packet-loss concealment...
Bayesian prediction of spatial count data using generalized linear mixed models
DEFF Research Database (Denmark)
Christensen, Ole Fredslund; Waagepetersen, Rasmus Plenge
2002-01-01
Spatial weed count data are modeled and predicted using a generalized linear mixed model combined with a Bayesian approach and Markov chain Monte Carlo. Informative priors for a data set with sparse sampling are elicited using a previously collected data set with extensive sampling. Furthermore, ...
A simulated annealing-based method for learning Bayesian networks from statistical data
Czech Academy of Sciences Publication Activity Database
Janžura, Martin; Nielsen, Jan
2006-01-01
Roč. 21, č. 3 (2006), s. 335-348. ISSN 0884-8173 R&D Projects: GA ČR GA201/03/0478 Institutional research plan: CEZ:AV0Z10750506 Keywords : Bayesian network * simulated annealing * Markov Chain Monte Carlo Subject RIV: BA - General Mathematics Impact factor: 0.429, year: 2006
A General and Flexible Approach to Estimating the Social Relations Model Using Bayesian Methods
Ludtke, Oliver; Robitzsch, Alexander; Kenny, David A.; Trautwein, Ulrich
2013-01-01
The social relations model (SRM) is a conceptual, methodological, and analytical approach that is widely used to examine dyadic behaviors and interpersonal perception within groups. This article introduces a general and flexible approach to estimating the parameters of the SRM that is based on Bayesian methods using Markov chain Monte Carlo…
Recurrence and Transience for Branching Random Walks in an iid Random Environment
Müller, Sebastian
2006-01-01
We give three different criteria for transience of a Branching Markov Chain. These conditions enable us to give a classification of Branching Random Walks in Random Environment (BRWRE) on Cayley Graphs in recurrence and transience. This classification is stated explicitly for BRWRE on $\\Z^d.$ Furthermore, we emphasize the interplay between Branching Markov Chains and the spectral radius. We prove properties of the spectral radius of the Random Walk in Random Environment with the help of appro...
A tutorial on Bayesian Normal linear regression
Klauenberg, Katy; Wübbeler, Gerd; Mickan, Bodo; Harris, Peter; Elster, Clemens
2015-12-01
Regression is a common task in metrology and often applied to calibrate instruments, evaluate inter-laboratory comparisons or determine fundamental constants, for example. Yet, a regression model cannot be uniquely formulated as a measurement function, and consequently the Guide to the Expression of Uncertainty in Measurement (GUM) and its supplements are not applicable directly. Bayesian inference, however, is well suited to regression tasks, and has the advantage of accounting for additional a priori information, which typically robustifies analyses. Furthermore, it is anticipated that future revisions of the GUM shall also embrace the Bayesian view. Guidance on Bayesian inference for regression tasks is largely lacking in metrology. For linear regression models with Gaussian measurement errors this tutorial gives explicit guidance. Divided into three steps, the tutorial first illustrates how a priori knowledge, which is available from previous experiments, can be translated into prior distributions from a specific class. These prior distributions have the advantage of yielding analytical, closed form results, thus avoiding the need to apply numerical methods such as Markov Chain Monte Carlo. Secondly, formulas for the posterior results are given, explained and illustrated, and software implementations are provided. In the third step, Bayesian tools are used to assess the assumptions behind the suggested approach. These three steps (prior elicitation, posterior calculation, and robustness to prior uncertainty and model adequacy) are critical to Bayesian inference. The general guidance given here for Normal linear regression tasks is accompanied by a simple, but real-world, metrological example. The calibration of a flow device serves as a running example and illustrates the three steps. It is shown that prior knowledge from previous calibrations of the same sonic nozzle enables robust predictions even for extrapolations.
Markov Networks in Evolutionary Computation
Shakya, Siddhartha
2012-01-01
Markov networks and other probabilistic graphical modes have recently received an upsurge in attention from Evolutionary computation community, particularly in the area of Estimation of distribution algorithms (EDAs). EDAs have arisen as one of the most successful experiences in the application of machine learning methods in optimization, mainly due to their efficiency to solve complex real-world optimization problems and their suitability for theoretical analysis. This book focuses on the different steps involved in the conception, implementation and application of EDAs that use Markov networks, and undirected models in general. It can serve as a general introduction to EDAs but covers also an important current void in the study of these algorithms by explaining the specificities and benefits of modeling optimization problems by means of undirected probabilistic models. All major developments to date in the progressive introduction of Markov networks based EDAs are reviewed in the book. Hot current researc...
Learning Bayesian Networks from Correlated Data
Bae, Harold; Monti, Stefano; Montano, Monty; Steinberg, Martin H.; Perls, Thomas T.; Sebastiani, Paola
2016-05-01
Bayesian networks are probabilistic models that represent complex distributions in a modular way and have become very popular in many fields. There are many methods to build Bayesian networks from a random sample of independent and identically distributed observations. However, many observational studies are designed using some form of clustered sampling that introduces correlations between observations within the same cluster and ignoring this correlation typically inflates the rate of false positive associations. We describe a novel parameterization of Bayesian networks that uses random effects to model the correlation within sample units and can be used for structure and parameter learning from correlated data without inflating the Type I error rate. We compare different learning metrics using simulations and illustrate the method in two real examples: an analysis of genetic and non-genetic factors associated with human longevity from a family-based study, and an example of risk factors for complications of sickle cell anemia from a longitudinal study with repeated measures.
Markov Models for Handwriting Recognition
Plotz, Thomas
2011-01-01
Since their first inception, automatic reading systems have evolved substantially, yet the recognition of handwriting remains an open research problem due to its substantial variation in appearance. With the introduction of Markovian models to the field, a promising modeling and recognition paradigm was established for automatic handwriting recognition. However, no standard procedures for building Markov model-based recognizers have yet been established. This text provides a comprehensive overview of the application of Markov models in the field of handwriting recognition, covering both hidden
A Markov-binomial distribution
Santos, J.; S. Van Gulck; OMEY, E.
2007-01-01
Let ${X_{i},igeq 1}$ denote a sequence of $left{ 0,1 ight} $%-variables and suppose that the sequence forms a {sc Markov} Chain. In the paperwe study the number of successes $S_{n}=X_{1}+X_{2}+cdots+X_{n}$ and we studythe number of experiments $Y(r)$ up to the $r$-$th$ success. In the i.i.d.case $S_{n}$ has a binomial distribution and $Y(r)$ has a negative binomialdistribution and the asymptotic behaviour is well known. In the more general{sc Markov} chain case, we prove a central limit theor...
Examples in Markov decision processes
Piunovskiy, A B
2012-01-01
This invaluable book provides approximately eighty examples illustrating the theory of controlled discrete-time Markov processes. Except for applications of the theory to real-life problems like stock exchange, queues, gambling, optimal search etc, the main attention is paid to counter-intuitive, unexpected properties of optimization problems. Such examples illustrate the importance of conditions imposed in the theorems on Markov Decision Processes. Many of the examples are based upon examples published earlier in journal articles or textbooks while several other examples are new. The aim was
Adaptive Partially Hidden Markov Models
DEFF Research Database (Denmark)
Forchhammer, Søren Otto; Rasmussen, Tage
1996-01-01
Partially Hidden Markov Models (PHMM) have recently been introduced. The transition and emission probabilities are conditioned on the past. In this report, the PHMM is extended with a multiple token version. The different versions of the PHMM are applied to bi-level image coding.......Partially Hidden Markov Models (PHMM) have recently been introduced. The transition and emission probabilities are conditioned on the past. In this report, the PHMM is extended with a multiple token version. The different versions of the PHMM are applied to bi-level image coding....
Graph-Based Lossless Markov Lumpings
Geiger, Bernhard C.; Hofer-Temmel, Christoph
2015-01-01
We use results from zero-error information theory to determine the set of non-injective functions through which a Markov chain can be projected without losing information. These lumping functions can be found by clique partitioning of a graph related to the Markov chain. Lossless lumping is made possible by exploiting the (sufficiently sparse) temporal structure of the Markov chain. Eliminating edges in the transition graph of the Markov chain trades the required output alphabet size versus i...
Generating Semi-Markov Models Automatically
Johnson, Sally C.
1990-01-01
Abstract Semi-Markov Specification Interface to SURE Tool (ASSIST) program developed to generate semi-Markov model automatically from description in abstract, high-level language. ASSIST reads input file describing failure behavior of system in abstract language and generates Markov models in format needed for input to Semi-Markov Unreliability Range Evaluator (SURE) program (COSMIC program LAR-13789). Facilitates analysis of behavior of fault-tolerant computer. Written in PASCAL.
A canonical representation for aggregated Markov processes
Larget, Bret
1998-01-01
A deterministic function of a Markov process is called an aggregated Markov process. We give necessary and sufficient conditions for the equivalence of continuous-time aggregated Markov processes. For both discrete- and continuous-time, we show that any aggregated Markov process which satisfies mild regularity conditions can be directly converted to a canonical representation which is unique for each class of equivalent models, and furthermore, is a minimal parameterization ...
Zhang, Linlin; Guindani, Michele; Versace, Francesco; Vannucci, Marina
2014-07-15
In this paper we present a novel wavelet-based Bayesian nonparametric regression model for the analysis of functional magnetic resonance imaging (fMRI) data. Our goal is to provide a joint analytical framework that allows to detect regions of the brain which exhibit neuronal activity in response to a stimulus and, simultaneously, infer the association, or clustering, of spatially remote voxels that exhibit fMRI time series with similar characteristics. We start by modeling the data with a hemodynamic response function (HRF) with a voxel-dependent shape parameter. We detect regions of the brain activated in response to a given stimulus by using mixture priors with a spike at zero on the coefficients of the regression model. We account for the complex spatial correlation structure of the brain by using a Markov random field (MRF) prior on the parameters guiding the selection of the activated voxels, therefore capturing correlation among nearby voxels. In order to infer association of the voxel time courses, we assume correlated errors, in particular long memory, and exploit the whitening properties of discrete wavelet transforms. Furthermore, we achieve clustering of the voxels by imposing a Dirichlet process (DP) prior on the parameters of the long memory process. For inference, we use Markov Chain Monte Carlo (MCMC) sampling techniques that combine Metropolis-Hastings schemes employed in Bayesian variable selection with sampling algorithms for nonparametric DP models. We explore the performance of the proposed model on simulated data, with both block- and event-related design, and on real fMRI data. PMID:24650600
Binary hidden Markov models and varieties
Critch, Andrew J
2012-01-01
The technological applications of hidden Markov models have been extremely diverse and successful, including natural language processing, gesture recognition, gene sequencing, and Kalman filtering of physical measurements. HMMs are highly non-linear statistical models, and just as linear models are amenable to linear algebraic techniques, non-linear models are amenable to commutative algebra and algebraic geometry. This paper examines closely those HMMs in which all the random variables, called nodes, are binary. Its main contributions are (1) minimal defining equations for the 4-node model, comprising 21 quadrics and 29 cubics, which were computed using Gr\\"obner bases in the cumulant coordinates of Sturmfels and Zwiernik, and (2) a birational parametrization for every binary HMM, with an explicit inverse for recovering the hidden parameters in terms of observables. The new model parameters in (2) are hence rationally identifiable in the sense of Sullivant, Garcia-Puente, and Spielvogel, and each model's Zar...
Neuroevolution Mechanism for Hidden Markov Model
Directory of Open Access Journals (Sweden)
Nabil M. Hewahi
2011-12-01
Full Text Available Hidden Markov Model (HMM is a statistical model based on probabilities. HMM is becoming one of the major models involved in many applications such as natural language
processing, handwritten recognition, image processing, prediction systems and many more. In this research we are concerned with finding out the best HMM for a certain application domain. We propose a neuroevolution process that is based first on converting the HMM to a neural network, then generating many neural networks at random where each represents a HMM. We proceed by
applying genetic operators to obtain new set of neural networks where each represents HMMs, and updating the population. Finally select the best neural network based on a fitness function.
Annotations of two examples about Markov process
TANG, RONG
2013-01-01
In this paper, we discuss an incorrect example that a Markov process does not satisfy strong Markov property, and analyzes the reason of mistake. In the end, we point out it is not reasonable to define strong Markov property by using transition probability functions since transition probability functions might not be one and only.
On a Result for Finite Markov Chains
Kulathinal, Sangita; Ghosh, Lagnojita
2006-01-01
In an undergraduate course on stochastic processes, Markov chains are discussed in great detail. Textbooks on stochastic processes provide interesting properties of finite Markov chains. This note discusses one such property regarding the number of steps in which a state is reachable or accessible from another state in a finite Markov chain with M…
State Information in Bayesian Games
Cuff, Paul
2009-01-01
Two-player zero-sum repeated games are well understood. Computing the value of such a game is straightforward. Additionally, if the payoffs are dependent on a random state of the game known to one, both, or neither of the players, the resulting value of the game has been analyzed under the framework of Bayesian games. This investigation considers the optimal performance in a game when a helper is transmitting state information to one of the players. Encoding information for an adversarial setting (game) requires a different result than rate-distortion theory provides. Game theory has accentuated the importance of randomization (mixed strategy), which does not find a significant role in most communication modems and source coding codecs. Higher rates of communication, used in the right way, allow the message to include the necessary random component useful in games.
Inference in Hidden Markov Models with Explicit State Duration Distributions
Dewar, Michael; Wiggins, Chris; Wood, Frank
2012-01-01
In this letter we borrow from the inference techniques developed for unbounded state-cardinality (nonparametric) variants of the HMM and use them to develop a tuning-parameter free, black-box inference procedure for Explicit-state-duration hidden Markov models (EDHMM). EDHMMs are HMMs that have latent states consisting of both discrete state-indicator and discrete state-duration random variables. In contrast to the implicit geometric state duration distribution possessed by the standard HMM, ...
Bayesian Inference of a Multivariate Regression Model
Directory of Open Access Journals (Sweden)
Marick S. Sinay
2014-01-01
Full Text Available We explore Bayesian inference of a multivariate linear regression model with use of a flexible prior for the covariance structure. The commonly adopted Bayesian setup involves the conjugate prior, multivariate normal distribution for the regression coefficients and inverse Wishart specification for the covariance matrix. Here we depart from this approach and propose a novel Bayesian estimator for the covariance. A multivariate normal prior for the unique elements of the matrix logarithm of the covariance matrix is considered. Such structure allows for a richer class of prior distributions for the covariance, with respect to strength of beliefs in prior location hyperparameters, as well as the added ability, to model potential correlation amongst the covariance structure. The posterior moments of all relevant parameters of interest are calculated based upon numerical results via a Markov chain Monte Carlo procedure. The Metropolis-Hastings-within-Gibbs algorithm is invoked to account for the construction of a proposal density that closely matches the shape of the target posterior distribution. As an application of the proposed technique, we investigate a multiple regression based upon the 1980 High School and Beyond Survey.
An assessment of linkage disequilibrium in Holstein cattle using a Bayesian network.
Morota, G; Valente, B D; Rosa, G J M; Weigel, K A; Gianola, D
2012-12-01
Linkage disequilibrium (LD) is defined as a non-random association of the distributions of alleles at different loci within a population. This association between loci is valuable in prediction of quantitative traits in animals and plants and in genome-wide association studies. A question that arises is whether standard metrics such as D' and r(2) reflect complex associations in a genetic system properly. It seems reasonable to take the view that loci associate and interact together as a system or network, as opposed to in a simple pairwise manner. We used a Bayesian network (BN) as a representation of choice for an LD network. A BN is a graphical depiction of a probability distribution and can represent sets of conditional independencies. Moreover, it provides a visual display of the joint distribution of the set of random variables in question. The usefulness of BN for linkage disequilibrium was explored and illustrated using genetic marker loci found to have the strongest effects on milk protein in Holstein cattle based on three strategies for ranking marker effect estimates: posterior means, standardized posterior means and additive genetic variance. Two different algorithms, Tabu search (a local score-based algorithm) and incremental association Markov blanket (a constraint-based algorithm), coupled with the chi-square test, were used for learning the structure of the BN and were compared with the reference r(2) metric represented as an LD heat map. The BN captured several genetic markers associated as clusters, implying that markers are inter-related in a complicated manner. Further, the BN detected conditionally dependent markers. The results confirm that LD relationships are of a multivariate nature and that r(2) gives an incomplete description and understanding of LD. Use of an LD Bayesian network enables inferring associations between loci in a systems framework and provides a more accurate picture of LD than that resulting from the use of pairwise
Maximizing entropy over Markov processes
DEFF Research Database (Denmark)
Biondi, Fabrizio; Legay, Axel; Nielsen, Bo Friis; Wasowski, Andrzej
The channel capacity of a deterministic system with confidential data is an upper bound on the amount of bits of data an attacker can learn from the system. We encode all possible attacks to a system using a probabilistic specification, an Interval Markov Chain. Then the channel capacity computat...
Markov Monitoring with Unknown States
Smyth, Padhraic
1993-01-01
Pattern recognition methods and hidden Markov models can be effective tools for online health monitoring of communications systems. Previous work has assumed that the states in the system model are exhaustive. This can be a significant drawback in real-world fault monitoring applications where it is difficult if not impossible to model all the possible fault states of the system in advance.
Maximizing Entropy over Markov Processes
DEFF Research Database (Denmark)
Biondi, Fabrizio; Legay, Axel; Nielsen, Bo Friis; Wąsowski, Andrzej
The channel capacity of a deterministic system with confidential data is an upper bound on the amount of bits of data an attacker can learn from the system. We encode all possible attacks to a system using a probabilistic specification, an Interval Markov Chain. Then the channel capacity computat......The channel capacity of a deterministic system with confidential data is an upper bound on the amount of bits of data an attacker can learn from the system. We encode all possible attacks to a system using a probabilistic specification, an Interval Markov Chain. Then the channel capacity...... a reward function, a polynomial algorithm to verify the existence of an system maximizing entropy among those respecting a specification, a procedure for the maximization of reward functions over Interval Markov Chains and its application to synthesize an implementation maximizing entropy. We show...... how to use Interval Markov Chains to model abstractions of deterministic systems with confidential data, and use the above results to compute their channel capacity. These results are a foundation for ongoing work on computing channel capacity for abstractions of programs derived from code....
Large deviations on Markov towers
International Nuclear Information System (INIS)
We give a sufficient condition to hold a full large deviation principle for Markov tower maps induced from return time functions. As an application of this result we show the large deviation principle of level 2 for some class of smooth dynamical systems with nonuniform hyperbolicity
Inferring animal densities from tracking data using Markov chains.
Directory of Open Access Journals (Sweden)
Hal Whitehead
Full Text Available The distributions and relative densities of species are keys to ecology. Large amounts of tracking data are being collected on a wide variety of animal species using several methods, especially electronic tags that record location. These tracking data are effectively used for many purposes, but generally provide biased measures of distribution, because the starts of the tracks are not randomly distributed among the locations used by the animals. We introduce a simple Markov-chain method that produces unbiased measures of relative density from tracking data. The density estimates can be over a geographical grid, and/or relative to environmental measures. The method assumes that the tracked animals are a random subset of the population in respect to how they move through the habitat cells, and that the movements of the animals among the habitat cells form a time-homogenous Markov chain. We illustrate the method using simulated data as well as real data on the movements of sperm whales. The simulations illustrate the bias introduced when the initial tracking locations are not randomly distributed, as well as the lack of bias when the Markov method is used. We believe that this method will be important in giving unbiased estimates of density from the growing corpus of animal tracking data.
Rubin, Donald B.
1981-01-01
The Bayesian bootstrap is the Bayesian analogue of the bootstrap. Instead of simulating the sampling distribution of a statistic estimating a parameter, the Bayesian bootstrap simulates the posterior distribution of the parameter; operationally and inferentially the methods are quite similar. Because both methods of drawing inferences are based on somewhat peculiar model assumptions and the resulting inferences are generally sensitive to these assumptions, neither method should be applied wit...
International Nuclear Information System (INIS)
This study introduces a non-intrusive approach in the context of low-rank separated representation to construct a surrogate of high-dimensional stochastic functions, e.g., PDEs/ODEs, in order to decrease the computational cost of Markov Chain Monte Carlo simulations in Bayesian inference. The surrogate model is constructed via a regularized alternative least-square regression with Tikhonov regularization using a roughening matrix computing the gradient of the solution, in conjunction with a perturbation-based error indicator to detect optimal model complexities. The model approximates a vector of a continuous solution at discrete values of a physical variable. The required number of random realizations to achieve a successful approximation linearly depends on the function dimensionality. The computational cost of the model construction is quadratic in the number of random inputs, which potentially tackles the curse of dimensionality in high-dimensional stochastic functions. Furthermore, this vector-valued separated representation-based model, in comparison to the available scalar-valued case, leads to a significant reduction in the cost of approximation by an order of magnitude equal to the vector size. The performance of the method is studied through its application to three numerical examples including a 41-dimensional elliptic PDE and a 21-dimensional cavity flow
Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity
DEFF Research Database (Denmark)
Gammelmark, S.; Molmer, K.; Alt, W.;
2014-01-01
We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian...... manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory......, the atomic state is determined in a Bayesian manner from the measurement data, and we present an iterative protocol, which determines both the atomic state and the model parameters. As a new element in the treatment of observed quantum systems, we employ a Bayesian approach that conditions the atomic...
Markov chain aggregation for agent-based models
Banisch, Sven
2016-01-01
This self-contained text develops a Markov chain approach that makes the rigorous analysis of a class of microscopic models that specify the dynamics of complex systems at the individual level possible. It presents a general framework of aggregation in agent-based and related computational models, one which makes use of lumpability and information theory in order to link the micro and macro levels of observation. The starting point is a microscopic Markov chain description of the dynamical process in complete correspondence with the dynamical behavior of the agent-based model (ABM), which is obtained by considering the set of all possible agent configurations as the state space of a huge Markov chain. An explicit formal representation of a resulting “micro-chain” including microscopic transition rates is derived for a class of models by using the random mapping representation of a Markov process. The type of probability distribution used to implement the stochastic part of the model, which defines the upd...
Energy Technology Data Exchange (ETDEWEB)
Menke, Jan [University Medical Center Goettingen, Institute for Diagnostic and Interventional Radiology, Goettingen (Germany); Kowalski, Joerg [Dr. Lauterbach-Klinik, Department of Cardiology, Bad Liebenstein (Germany)
2016-02-15
To meta-analyze diagnostic accuracy, test yield and utility of coronary computed tomography angiography (CCTA) in coronary artery disease (CAD) by an intention-to-diagnose approach with inclusion of unevaluable results. Four databases were searched from 1/2005 to 3/2013 for prospective studies that used 16-320-row or dual-source CTs and provided 3 x 2 patient-level data of CCTA (positive, negative, or unevaluable) versus catheter angiography (positive or negative) for diagnosing ≥50 % coronary stenoses. A Bayesian multivariate 3 x 2 random-effects meta-analysis considered unevaluable CCTAs. Thirty studies (3422 patients) were included. Compared to 16-40 row CT, test yield and accuracy of CCTA has significantly increased with ≥64-row CT (P < 0.05). In ≥64-row CT, about 2.5 % (95 %-CI, 0.9-4.8 %) of diseased patients and 7.5 % (4.5-11.2 %) of non-diseased patients had unevaluable CCTAs. A positive likelihood ratio of 8.9 (6.1-13.5) indicated moderate suitability for identifying CAD. A negative likelihood ratio of 0.022 (0.01-0.04) indicated excellent suitability for excluding CAD. Unevaluable CCTAs had an equivocal likelihood ratio of 0.42 (0.22-0.71). In the utility analysis, CCTA was useful at intermediate pre-test probabilities (16-70 %). CCTA is useful at intermediate CAD pre-test probabilities. Positive CCTAs require verification to confirm CAD, unevaluable CCTAs require alternative diagnostics, and negative CCTAs exclude obstructive CAD with high certainty. (orig.)
International Nuclear Information System (INIS)
To meta-analyze diagnostic accuracy, test yield and utility of coronary computed tomography angiography (CCTA) in coronary artery disease (CAD) by an intention-to-diagnose approach with inclusion of unevaluable results. Four databases were searched from 1/2005 to 3/2013 for prospective studies that used 16-320-row or dual-source CTs and provided 3 x 2 patient-level data of CCTA (positive, negative, or unevaluable) versus catheter angiography (positive or negative) for diagnosing ≥50 % coronary stenoses. A Bayesian multivariate 3 x 2 random-effects meta-analysis considered unevaluable CCTAs. Thirty studies (3422 patients) were included. Compared to 16-40 row CT, test yield and accuracy of CCTA has significantly increased with ≥64-row CT (P < 0.05). In ≥64-row CT, about 2.5 % (95 %-CI, 0.9-4.8 %) of diseased patients and 7.5 % (4.5-11.2 %) of non-diseased patients had unevaluable CCTAs. A positive likelihood ratio of 8.9 (6.1-13.5) indicated moderate suitability for identifying CAD. A negative likelihood ratio of 0.022 (0.01-0.04) indicated excellent suitability for excluding CAD. Unevaluable CCTAs had an equivocal likelihood ratio of 0.42 (0.22-0.71). In the utility analysis, CCTA was useful at intermediate pre-test probabilities (16-70 %). CCTA is useful at intermediate CAD pre-test probabilities. Positive CCTAs require verification to confirm CAD, unevaluable CCTAs require alternative diagnostics, and negative CCTAs exclude obstructive CAD with high certainty. (orig.)
Understanding Computational Bayesian Statistics
Bolstad, William M
2011-01-01
A hands-on introduction to computational statistics from a Bayesian point of view Providing a solid grounding in statistics while uniquely covering the topics from a Bayesian perspective, Understanding Computational Bayesian Statistics successfully guides readers through this new, cutting-edge approach. With its hands-on treatment of the topic, the book shows how samples can be drawn from the posterior distribution when the formula giving its shape is all that is known, and how Bayesian inferences can be based on these samples from the posterior. These ideas are illustrated on common statistic
International Nuclear Information System (INIS)
Bayesian analysis of Laser Interferometer Space Antenna (LISA) data sets based on Markov chain Monte Carlo methods has been shown to be a challenging problem, in part due to the complicated structure of the likelihood function consisting of several isolated local maxima that dramatically reduces the efficiency of the sampling techniques. Here we introduce a new fully Markovian algorithm, a delayed rejection Metropolis-Hastings Markov chain Monte Carlo method, to efficiently explore these kind of structures and we demonstrate its performance on selected LISA data sets containing a known number of stellar-mass binary signals embedded in Gaussian stationary noise.
Musenge, Eustasius; Chirwa, Tobias Freeman; Kahn, Kathleen; Vounatsou, Penelope
2013-06-01
Longitudinal mortality data with few deaths usually have problems of zero-inflation. This paper presents and applies two Bayesian models which cater for zero-inflation, spatial and temporal random effects. To reduce the computational burden experienced when a large number of geo-locations are treated as a Gaussian field (GF) we transformed the field to a Gaussian Markov Random Fields (GMRF) by triangulation. We then modelled the spatial random effects using the Stochastic Partial Differential Equations (SPDEs). Inference was done using a computationally efficient alternative to Markov chain Monte Carlo (MCMC) called Integrated Nested Laplace Approximation (INLA) suited for GMRF. The models were applied to data from 71,057 children aged 0 to under 10 years from rural north-east South Africa living in 15,703 households over the years 1992-2010. We found protective effects on HIV/TB mortality due to greater birth weight, older age and more antenatal clinic visits during pregnancy (adjusted RR (95% CI)): 0.73(0.53;0.99), 0.18(0.14;0.22) and 0.96(0.94;0.97) respectively. Therefore childhood HIV/TB mortality could be reduced if mothers are better catered for during pregnancy as this can reduce mother-to-child transmissions and contribute to improved birth weights. The INLA and SPDE approaches are computationally good alternatives in modelling large multilevel spatiotemporal GMRF data structures.
Apples and oranges: avoiding different priors in Bayesian DNA sequence analysis
Directory of Open Access Journals (Sweden)
Posch Stefan
2010-03-01
Full Text Available Abstract Background One of the challenges of bioinformatics remains the recognition of short signal sequences in genomic DNA such as donor or acceptor splice sites, splicing enhancers or silencers, translation initiation sites, transcription start sites, transcription factor binding sites, nucleosome binding sites, miRNA binding sites, or insulator binding sites. During the last decade, a wealth of algorithms for the recognition of such DNA sequences has been developed and compared with the goal of improving their performance and to deepen our understanding of the underlying cellular processes. Most of these algorithms are based on statistical models belonging to the family of Markov random fields such as position weight matrix models, weight array matrix models, Markov models of higher order, or moral Bayesian networks. While in many comparative studies different learning principles or different statistical models have been compared, the influence of choosing different prior distributions for the model parameters when using different learning principles has been overlooked, and possibly lead to questionable conclusions. Results With the goal of allowing direct comparisons of different learning principles for models from the family of Markov random fields based on the same a-priori information, we derive a generalization of the commonly-used product-Dirichlet prior. We find that the derived prior behaves like a Gaussian prior close to the maximum and like a Laplace prior in the far tails. In two case studies, we illustrate the utility of the derived prior for a direct comparison of different learning principles with different models for the recognition of binding sites of the transcription factor Sp1 and human donor splice sites. Conclusions We find that comparisons of different learning principles using the same a-priori information can lead to conclusions different from those of previous studies in which the effect resulting from different
Policy Recognition in the Abstract Hidden Markov Model
Bui, H H; West, G; 10.1613/jair.839
2011-01-01
In this paper, we present a method for recognising an agent's behaviour in dynamic, noisy, uncertain domains, and across multiple levels of abstraction. We term this problem on-line plan recognition under uncertainty and view it generally as probabilistic inference on the stochastic process representing the execution of the agent's plan. Our contributions in this paper are twofold. In terms of probabilistic inference, we introduce the Abstract Hidden Markov Model (AHMM), a novel type of stochastic processes, provide its dynamic Bayesian network (DBN) structure and analyse the properties of this network. We then describe an application of the Rao-Blackwellised Particle Filter to the AHMM which allows us to construct an efficient, hybrid inference method for this model. In terms of plan recognition, we propose a novel plan recognition framework based on the AHMM as the plan execution model. The Rao-Blackwellised hybrid inference for AHMM can take advantage of the independence properties inherent in a model of p...
Markov Equivalences for Subclasses of Loopless Mixed Graphs
Sadeghi, Kayvan
2011-01-01
In this paper we discuss four problems regarding Markov equivalences for subclasses of loopless mixed graphs. We classify these four problems as finding conditions for internal Markov equivalence, which is Markov equivalence within a subclass, for external Markov equivalence, which is Markov equivalence between subclasses, for representational Markov equivalence, which is the possibility of a graph from a subclass being Markov equivalent to a graph from another subclass, and finding algorithm...
Frühwirth-Schnatter, Sylvia
1990-01-01
In the paper at hand we apply it to Bayesian statistics to obtain "Fuzzy Bayesian Inference". In the subsequent sections we will discuss a fuzzy valued likelihood function, Bayes' theorem for both fuzzy data and fuzzy priors, a fuzzy Bayes' estimator, fuzzy predictive densities and distributions, and fuzzy H.P.D .-Regions. (author's abstract)
Yuan, Ying; MacKinnon, David P.
2009-01-01
In this article, we propose Bayesian analysis of mediation effects. Compared with conventional frequentist mediation analysis, the Bayesian approach has several advantages. First, it allows researchers to incorporate prior information into the mediation analysis, thus potentially improving the efficiency of estimates. Second, under the Bayesian…
The Equivalence Forms of Random Kolmogorov Forward (Backward) Equations
Institute of Scientific and Technical Information of China (English)
HU Di-he; HU Xiao-yu
2005-01-01
The concepts of Markov process in random environment, q-matrix in random environment and q-process in random environment are introduced. Three forms of random Kolmoogrov farward (or backward) equations are introduced and the equivalence of these three forms are also proved. Moreover any conservative q-process in random environment satisfies random Kolmogrov backward equation.
THE ANALYTICAL PROPERTIES FOR HOMOGENEOUS RANDOM TRANSITION FUNCTIONS
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
The concepts of Markov process in random environment and homogeneous random transition functions are introduced. The necessary and sufficient conditions for homogeneous random transition function are given. The main results in this article are the analytical properties, such as continuity, differentiability, random Kolmogorov backward equation and random Kolmogorov forward equation of homogeneous random transition functions.
Markov Tracking for Agent Coordination
Washington, Richard; Lau, Sonie (Technical Monitor)
1998-01-01
Partially observable Markov decision processes (POMDPs) axe an attractive representation for representing agent behavior, since they capture uncertainty in both the agent's state and its actions. However, finding an optimal policy for POMDPs in general is computationally difficult. In this paper we present Markov Tracking, a restricted problem of coordinating actions with an agent or process represented as a POMDP Because the actions coordinate with the agent rather than influence its behavior, the optimal solution to this problem can be computed locally and quickly. We also demonstrate the use of the technique on sequential POMDPs, which can be used to model a behavior that follows a linear, acyclic trajectory through a series of states. By imposing a "windowing" restriction that restricts the number of possible alternatives considered at any moment to a fixed size, a coordinating action can be calculated in constant time, making this amenable to coordination with complex agents.
Isotropic Markov semigroups on ultra-metric spaces
International Nuclear Information System (INIS)
Let (X,d) be a separable ultra-metric space with compact balls. Given a reference measure μ on X and a distance distribution function σ on [0,∞), a symmetric Markov semigroup {Pt}t⩾0 acting in L2(X,μ) is constructed. Let {Xt} be the corresponding Markov process. The authors obtain upper and lower bounds for its transition density and its Green function, give a transience criterion, estimate its moments, and describe the Markov generator L and its spectrum, which is pure point. In the particular case when X=Qpn, where Qp is the field of p-adic numbers, the construction recovers the Taibleson Laplacian (spectral multiplier), and one can also apply the theory to the study of the Vladimirov Laplacian. Even in this well-established setting, several of the results are new. The paper also describes the relation between the processes involved and Kigami's jump processes on the boundary of a tree which are induced by a random walk. In conclusion, examples illustrating the interplay between the fractional derivatives and random walks are provided. Bibliography: 66 titles
Lee, Lee-Min; Jean, Fu-Rong
2016-08-01
The hidden Markov models have been widely applied to systems with sequential data. However, the conditional independence of the state outputs will limit the output of a hidden Markov model to be a piecewise constant random sequence, which is not a good approximation for many real processes. In this paper, a high-order hidden Markov model for piecewise linear processes is proposed to better approximate the behavior of a real process. A parameter estimation method based on the expectation-maximization algorithm was derived for the proposed model. Experiments on speech recognition of noisy Mandarin digits were conducted to examine the effectiveness of the proposed method. Experimental results show that the proposed method can reduce the recognition error rate compared to a baseline hidden Markov model. PMID:27586781
Applying Markov Chains for NDVI Time Series Forecasting of Latvian Regions
Directory of Open Access Journals (Sweden)
Stepchenko Arthur
2015-12-01
Full Text Available Time series of earth observation based estimates of vegetation inform about variations in vegetation at the scale of Latvia. A vegetation index is an indicator that describes the amount of chlorophyll (the green mass and shows the relative density and health of vegetation. NDVI index is an important variable for vegetation forecasting and management of various problems, such as climate change monitoring, energy usage monitoring, managing the consumption of natural resources, agricultural productivity monitoring, drought monitoring and forest fire detection. In this paper, we make a one-step-ahead prediction of 7-daily time series of NDVI index using Markov chains. The choice of a Markov chain is due to the fact that a Markov chain is a sequence of random variables where each variable is located in some state. And a Markov chain contains probabilities of moving from one state to other.
Weighted multirate q-Markov Cover identification using PRBS – an application to engine systems
Directory of Open Access Journals (Sweden)
Zhu G. George
2000-01-01
Full Text Available The q-Markov COVariance Equivalent Realization (q-Markov Cover method for identification uses either pulse, white noise or PRBS (Pseudo-Random Binary Signal as test excitation. This paper extended the q-Markov Cover using PRBS to the weighted multirate case, that is, the sample rate of the PRBS signal is different from the system output one. Then, the multirate PRBS q-Markov Cover is applied to identify a diesel engine model from the fuel command input to the engine speed output. The identified engine model has order of two and approximates the pure fuel system time delay using a first-order transfer function with a non-minimum phase numerator. Finally, the identified engine model was successfully used for designing engine idle speed governor and obtained satisfactory performance in the first try.
Nablus2014 CIMPA Summer School : Analysis of Random Structures
Nicodeme, Pierre; Pouyanne, Nicolas; Chauvin, Brigitte; Lumbroso, Jeremie; Morcrette, Basile; Mailler, Cécile
2015-01-01
List of the courses:- A Gentle Introduction to Analytic Combinatorics- Markov Chains and Martingales applied to the analysis of random structures- Polya Urn Models - analytic and probabilistic approaches- Random Trees and Probabilities - Automata and Motif Statistics
Complexity analysis of accelerated MCMC methods for Bayesian inversion
Hoang, Viet Ha; Schwab, Christoph; Stuart, Andrew M.
2013-08-01
The Bayesian approach to inverse problems, in which the posterior probability distribution on an unknown field is sampled for the purposes of computing posterior expectations of quantities of interest, is starting to become computationally feasible for partial differential equation (PDE) inverse problems. Balancing the sources of error arising from finite-dimensional approximation of the unknown field, the PDE forward solution map and the sampling of the probability space under the posterior distribution are essential for the design of efficient computational Bayesian methods for PDE inverse problems. We study Bayesian inversion for a model elliptic PDE with an unknown diffusion coefficient. We provide complexity analyses of several Markov chain Monte Carlo (MCMC) methods for the efficient numerical evaluation of expectations under the Bayesian posterior distribution, given data δ. Particular attention is given to bounds on the overall work required to achieve a prescribed error level ε. Specifically, we first bound the computational complexity of ‘plain’ MCMC, based on combining MCMC sampling with linear complexity multi-level solvers for elliptic PDE. Our (new) work versus accuracy bounds show that the complexity of this approach can be quite prohibitive. Two strategies for reducing the computational complexity are then proposed and analyzed: first, a sparse, parametric and deterministic generalized polynomial chaos (gpc) ‘surrogate’ representation of the forward response map of the PDE over the entire parameter space, and, second, a novel multi-level Markov chain Monte Carlo strategy which utilizes sampling from a multi-level discretization of the posterior and the forward PDE. For both of these strategies, we derive asymptotic bounds on work versus accuracy, and hence asymptotic bounds on the computational complexity of the algorithms. In particular, we provide sufficient conditions on the regularity of the unknown coefficients of the PDE and on the
Markov processes characterization and convergence
Ethier, Stewart N
2009-01-01
The Wiley-Interscience Paperback Series consists of selected books that have been made more accessible to consumers in an effort to increase global appeal and general circulation. With these new unabridged softcover volumes, Wiley hopes to extend the lives of these works by making them available to future generations of statisticians, mathematicians, and scientists."[A]nyone who works with Markov processes whose state space is uncountably infinite will need this most impressive book as a guide and reference."-American Scientist"There is no question but that space should immediately be reserved for [this] book on the library shelf. Those who aspire to mastery of the contents should also reserve a large number of long winter evenings."-Zentralblatt f?r Mathematik und ihre Grenzgebiete/Mathematics Abstracts"Ethier and Kurtz have produced an excellent treatment of the modern theory of Markov processes that [is] useful both as a reference work and as a graduate textbook."-Journal of Statistical PhysicsMarkov Proce...
Bayesian modeling of ChIP-chip data using latent variables.
Wu, Mingqi
2009-10-26
BACKGROUND: The ChIP-chip technology has been used in a wide range of biomedical studies, such as identification of human transcription factor binding sites, investigation of DNA methylation, and investigation of histone modifications in animals and plants. Various methods have been proposed in the literature for analyzing the ChIP-chip data, such as the sliding window methods, the hidden Markov model-based methods, and Bayesian methods. Although, due to the integrated consideration of uncertainty of the models and model parameters, Bayesian methods can potentially work better than the other two classes of methods, the existing Bayesian methods do not perform satisfactorily. They usually require multiple replicates or some extra experimental information to parametrize the model, and long CPU time due to involving of MCMC simulations. RESULTS: In this paper, we propose a Bayesian latent model for the ChIP-chip data. The new model mainly differs from the existing Bayesian models, such as the joint deconvolution model, the hierarchical gamma mixture model, and the Bayesian hierarchical model, in two respects. Firstly, it works on the difference between the averaged treatment and control samples. This enables the use of a simple model for the data, which avoids the probe-specific effect and the sample (control/treatment) effect. As a consequence, this enables an efficient MCMC simulation of the posterior distribution of the model, and also makes the model more robust to the outliers. Secondly, it models the neighboring dependence of probes by introducing a latent indicator vector. A truncated Poisson prior distribution is assumed for the latent indicator variable, with the rationale being justified at length. CONCLUSION: The Bayesian latent method is successfully applied to real and ten simulated datasets, with comparisons with some of the existing Bayesian methods, hidden Markov model methods, and sliding window methods. The numerical results indicate that the
Bayesian modeling of ChIP-chip data using latent variables
Directory of Open Access Journals (Sweden)
Tian Yanan
2009-10-01
Full Text Available Abstract Background The ChIP-chip technology has been used in a wide range of biomedical studies, such as identification of human transcription factor binding sites, investigation of DNA methylation, and investigation of histone modifications in animals and plants. Various methods have been proposed in the literature for analyzing the ChIP-chip data, such as the sliding window methods, the hidden Markov model-based methods, and Bayesian methods. Although, due to the integrated consideration of uncertainty of the models and model parameters, Bayesian methods can potentially work better than the other two classes of methods, the existing Bayesian methods do not perform satisfactorily. They usually require multiple replicates or some extra experimental information to parametrize the model, and long CPU time due to involving of MCMC simulations. Results In this paper, we propose a Bayesian latent model for the ChIP-chip data. The new model mainly differs from the existing Bayesian models, such as the joint deconvolution model, the hierarchical gamma mixture model, and the Bayesian hierarchical model, in two respects. Firstly, it works on the difference between the averaged treatment and control samples. This enables the use of a simple model for the data, which avoids the probe-specific effect and the sample (control/treatment effect. As a consequence, this enables an efficient MCMC simulation of the posterior distribution of the model, and also makes the model more robust to the outliers. Secondly, it models the neighboring dependence of probes by introducing a latent indicator vector. A truncated Poisson prior distribution is assumed for the latent indicator variable, with the rationale being justified at length. Conclusion The Bayesian latent method is successfully applied to real and ten simulated datasets, with comparisons with some of the existing Bayesian methods, hidden Markov model methods, and sliding window methods. The numerical results
Energy Technology Data Exchange (ETDEWEB)
Zhang, Guannan [ORNL; Webster, Clayton G [ORNL; Gunzburger, Max D [ORNL
2012-09-01
Although Bayesian analysis has become vital to the quantification of prediction uncertainty in groundwater modeling, its application has been hindered due to the computational cost associated with numerous model executions needed for exploring the posterior probability density function (PPDF) of model parameters. This is particularly the case when the PPDF is estimated using Markov Chain Monte Carlo (MCMC) sampling. In this study, we develop a new approach that improves computational efficiency of Bayesian inference by constructing a surrogate system based on an adaptive sparse-grid high-order stochastic collocation (aSG-hSC) method. Unlike previous works using first-order hierarchical basis, we utilize a compactly supported higher-order hierar- chical basis to construct the surrogate system, resulting in a significant reduction in the number of computational simulations required. In addition, we use hierarchical surplus as an error indi- cator to determine adaptive sparse grids. This allows local refinement in the uncertain domain and/or anisotropic detection with respect to the random model parameters, which further improves computational efficiency. Finally, we incorporate a global optimization technique and propose an iterative algorithm for building the surrogate system for the PPDF with multiple significant modes. Once the surrogate system is determined, the PPDF can be evaluated by sampling the surrogate system directly with very little computational cost. The developed method is evaluated first using a simple analytical density function with multiple modes and then using two synthetic groundwater reactive transport models. The groundwater models represent different levels of complexity; the first example involves coupled linear reactions and the second example simulates nonlinear ura- nium surface complexation. The results show that the aSG-hSC is an effective and efficient tool for Bayesian inference in groundwater modeling in comparison with conventional
Directory of Open Access Journals (Sweden)
Gerstein Mark B
2010-10-01
Full Text Available Abstract Background Copy number variants (CNVs have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comparative genomic hybridization (array-CGH and newly developed read-depth approach through ultrahigh throughput genomic sequencing both provide rapid, robust, and comprehensive methods to identify CNVs on a whole-genome scale. Results We developed a Bayesian statistical analysis algorithm for the detection of CNVs from both types of genomic data. The algorithm can analyze such data obtained from PCR-based bacterial artificial chromosome arrays, high-density oligonucleotide arrays, and more recently developed high-throughput DNA sequencing. Treating parameters--e.g., the number of CNVs, the position of each CNV, and the data noise level--that define the underlying data generating process as random variables, our approach derives the posterior distribution of the genomic CNV structure given the observed data. Sampling from the posterior distribution using a Markov chain Monte Carlo method, we get not only best estimates for these unknown parameters but also Bayesian credible intervals for the estimates. We illustrate the characteristics of our algorithm by applying it to both synthetic and experimental data sets in comparison to other segmentation algorithms. Conclusions In particular, the synthetic data comparison shows that our method is more sensitive than other approaches at low false positive rates. Furthermore, given its Bayesian origin, our method can also be seen as a technique to refine CNVs identified by fast point-estimate methods and also as a framework to integrate array-CGH and sequencing data with other CNV-related biological knowledge, all through informative priors.
BAT-The Bayesian Analysis Toolkit
International Nuclear Information System (INIS)
The main goals of data analysis are to infer the free parameters of models from data, to draw conclusions on the models' validity, and to compare their predictions allowing to select the most appropriate model. The Bayesian Analysis Toolkit, BAT, is a tool developed to evaluate the posterior probability distribution for models and their parameters. It is centered around Bayes' Theorem and is realized with the use of Markov Chain Monte Carlo giving access to the full posterior probability distribution. This enables straightforward parameter estimation, limit setting and uncertainty propagation. Additional algorithms, such as Simulated Annealing, allow to evaluate the global mode of the posterior. BAT is implemented in C++ and allows for a flexible definition of models. It is interfaced to software packages commonly used in high-energy physics: ROOT, Minuit, RooStats and CUBA. A set of predefined models exists to cover standard statistical problems.
Non symmetric random walk on infinite graph
Marcin J. Zygmunt
2011-01-01
We investigate properties of a non symmetric Markov's chain on an infinite graph. We show the connection with matrix valued random walk polynomials which satisfy the orthogonality formula with respect to non a symmetric matrix valued measure.
Non symmetric random walk on infinite graph
Directory of Open Access Journals (Sweden)
Marcin J. Zygmunt
2011-01-01
Full Text Available We investigate properties of a non symmetric Markov's chain on an infinite graph. We show the connection with matrix valued random walk polynomials which satisfy the orthogonality formula with respect to non a symmetric matrix valued measure.
Bayesian estimation of parameters in a regional hydrological model
Directory of Open Access Journals (Sweden)
K. Engeland
2002-01-01
Full Text Available This study evaluates the applicability of the distributed, process-oriented Ecomag model for prediction of daily streamflow in ungauged basins. The Ecomag model is applied as a regional model to nine catchments in the NOPEX area, using Bayesian statistics to estimate the posterior distribution of the model parameters conditioned on the observed streamflow. The distribution is calculated by Markov Chain Monte Carlo (MCMC analysis. The Bayesian method requires formulation of a likelihood function for the parameters and three alternative formulations are used. The first is a subjectively chosen objective function that describes the goodness of fit between the simulated and observed streamflow, as defined in the GLUE framework. The second and third formulations are more statistically correct likelihood models that describe the simulation errors. The full statistical likelihood model describes the simulation errors as an AR(1 process, whereas the simple model excludes the auto-regressive part. The statistical parameters depend on the catchments and the hydrological processes and the statistical and the hydrological parameters are estimated simultaneously. The results show that the simple likelihood model gives the most robust parameter estimates. The simulation error may be explained to a large extent by the catchment characteristics and climatic conditions, so it is possible to transfer knowledge about them to ungauged catchments. The statistical models for the simulation errors indicate that structural errors in the model are more important than parameter uncertainties. Keywords: regional hydrological model, model uncertainty, Bayesian analysis, Markov Chain Monte Carlo analysis
Constructing 1/ωα noise from reversible Markov chains
Erland, Sveinung; Greenwood, Priscilla E.
2007-09-01
This paper gives sufficient conditions for the output of 1/ωα noise from reversible Markov chains on finite state spaces. We construct several examples exhibiting this behavior in a specified range of frequencies. We apply simple representations of the covariance function and the spectral density in terms of the eigendecomposition of the probability transition matrix. The results extend to hidden Markov chains. We generalize the results for aggregations of AR1-processes of C. W. J. Granger [J. Econometrics 14, 227 (1980)]. Given the eigenvalue function, there is a variety of ways to assign values to the states such that the 1/ωα condition is satisfied. We show that a random walk on a certain state space is complementary to the point process model of 1/ω noise of B. Kaulakys and T. Meskauskas [Phys. Rev. E 58, 7013 (1998)]. Passing to a continuous state space, we construct 1/ωα noise which also has a long memory.
Smail, Linda
2016-06-01
The basic task of any probabilistic inference system in Bayesian networks is computing the posterior probability distribution for a subset or subsets of random variables, given values or evidence for some other variables from the same Bayesian network. Many methods and algorithms have been developed to exact and approximate inference in Bayesian networks. This work compares two exact inference methods in Bayesian networks-Lauritzen-Spiegelhalter and the successive restrictions algorithm-from the perspective of computational efficiency. The two methods were applied for comparison to a Chest Clinic Bayesian Network. Results indicate that the successive restrictions algorithm shows more computational efficiency than the Lauritzen-Spiegelhalter algorithm.
Criterion of Semi-Markov Dependent Risk Model
Institute of Scientific and Technical Information of China (English)
Xiao Yun MO; Xiang Qun YANG
2014-01-01
A rigorous definition of semi-Markov dependent risk model is given. This model is a generalization of the Markov dependent risk model. A criterion and necessary conditions of semi-Markov dependent risk model are obtained. The results clarify relations between elements among semi-Markov dependent risk model more clear and are applicable for Markov dependent risk model.
A Hidden Markov Approach to Modeling Interevent Earthquake Times
Chambers, D.; Ebel, J. E.; Kafka, A. L.; Baglivo, J.
2003-12-01
A hidden Markov process, in which the interevent time distribution is a mixture of exponential distributions with different rates, is explored as a model for seismicity that does not follow a Poisson process. In a general hidden Markov model, one assumes that a system can be in any of a finite number k of states and there is a random variable of interest whose distribution depends on the state in which the system resides. The system moves probabilistically among the states according to a Markov chain; that is, given the history of visited states up to the present, the conditional probability that the next state is a specified one depends only on the present state. Thus the transition probabilities are specified by a k by k stochastic matrix. Furthermore, it is assumed that the actual states are unobserved (hidden) and that only the values of the random variable are seen. From these values, one wishes to estimate the sequence of states, the transition probability matrix, and any parameters used in the state-specific distributions. The hidden Markov process was applied to a data set of 110 interevent times for earthquakes in New England from 1975 to 2000. Using the Baum-Welch method (Baum et al., Ann. Math. Statist. 41, 164-171), we estimate the transition probabilities, find the most likely sequence of states, and estimate the k means of the exponential distributions. Using k=2 states, we found the data were fit well by a mixture of two exponential distributions, with means of approximately 5 days and 95 days. The steady state model indicates that after approximately one fourth of the earthquakes, the waiting time until the next event had the first exponential distribution and three fourths of the time it had the second. Three and four state models were also fit to the data; the data were inconsistent with a three state model but were well fit by a four state model.
On Russian Roulette Estimates for Bayesian Inference with Doubly-Intractable Likelihoods
Lyne, Anne-Marie; Girolami, Mark; Atchadé, Yves; Strathmann, Heiko; Simpson, Daniel
2013-01-01
A large number of statistical models are “doubly-intractable”: the likelihood normalising term, which is a function of the model parameters, is intractable, as well as the marginal likelihood (model evidence). This means that standard inference techniques to sample from the posterior, such as Markov chain Monte Carlo (MCMC), cannot be used. Examples include, but are not confined to, massive Gaussian Markov random fields, autologistic models and Exponential random graph models. A number of app...
Nested Markov Compliance Class Model in the Presence of Time-Varying Noncompliance
LIN, Julia Y.; Ten Have, Thomas R.; Elliott, Michael R.
2009-01-01
We consider a Markov structure for partially unobserved time-varying compliance classes in the Imbens-Rubin (1997) compliance model framework. The context is a longitudinal randomized intervention study where subjects are randomized once at baseline, outcomes and patient adherence are measured at multiple follow-ups, and patient adherence to their randomized treatment could vary over time. We propose a nested latent compliance class model where we use time-invariant subject-specific complianc...
Spectral methods for quantum Markov chains
International Nuclear Information System (INIS)
The aim of this project is to contribute to our understanding of quantum time evolutions, whereby we focus on quantum Markov chains. The latter constitute a natural generalization of the ubiquitous concept of a classical Markov chain to describe evolutions of quantum mechanical systems. We contribute to the theory of such processes by introducing novel methods that allow us to relate the eigenvalue spectrum of the transition map to convergence as well as stability properties of the Markov chain.
Continuously monitored barrier options under Markov processes
Aleksandar Mijatovic; Martijn Pistorius
2009-01-01
In this paper we present an algorithm for pricing barrier options in one-dimensional Markov models. The approach rests on the construction of an approximating continuous-time Markov chain that closely follows the dynamics of the given Markov model. We illustrate the method by implementing it for a range of models, including a local Levy process and a local volatility jump-diffusion. We also provide a convergence proof and error estimates for this algorithm.
Capturing changes in flood risk with Bayesian approaches for flood damage assessment
Vogel, Kristin; Schröter, Kai; Kreibich, Heidi; Thieken, Annegret; Müller, Meike; Sieg, Tobias; Laudan, Jonas; Kienzler, Sarah; Weise, Laura; Merz, Bruno; Scherbaum, Frank
2016-04-01
Flood risk is a function of hazard as well as of exposure and vulnerability. All three components are under change over space and time and have to be considered for reliable damage estimations and risk analyses, since this is the basis for an efficient, adaptable risk management. Hitherto, models for estimating flood damage are comparatively simple and cannot sufficiently account for changing conditions. The Bayesian network approach allows for a multivariate modeling of complex systems without relying on expert knowledge about physical constraints. In a Bayesian network each model component is considered to be a random variable. The way of interactions between those variables can be learned from observations or be defined by expert knowledge. Even a combination of both is possible. Moreover, the probabilistic framework captures uncertainties related to the prediction and provides a probability distribution for the damage instead of a point estimate. The graphical representation of Bayesian networks helps to study the change of probabilities for changing circumstances and may thus simplify the communication between scientists and public authorities. In the framework of the DFG-Research Training Group "NatRiskChange" we aim to develop Bayesian networks for flood damage and vulnerability assessments of residential buildings and companies under changing conditions. A Bayesian network learned from data, collected over the last 15 years in flooded regions in the Elbe and Danube catchments (Germany), reveals the impact of many variables like building characteristics, precaution and warning situation on flood damage to residential buildings. While the handling of incomplete and hybrid (discrete mixed with continuous) data are the most challenging issues in the study on residential buildings, a similar study, that focuses on the vulnerability of small to medium sized companies, bears new challenges. Relying on a much smaller data set for the determination of the model
Likelihood free inference for Markov processes: a comparison.
Owen, Jamie; Wilkinson, Darren J; Gillespie, Colin S
2015-04-01
Approaches to Bayesian inference for problems with intractable likelihoods have become increasingly important in recent years. Approximate Bayesian computation (ABC) and "likelihood free" Markov chain Monte Carlo techniques are popular methods for tackling inference in these scenarios but such techniques are computationally expensive. In this paper we compare the two approaches to inference, with a particular focus on parameter inference for stochastic kinetic models, widely used in systems biology. Discrete time transition kernels for models of this type are intractable for all but the most trivial systems yet forward simulation is usually straightforward. We discuss the relative merits and drawbacks of each approach whilst considering the computational cost implications and efficiency of these techniques. In order to explore the properties of each approach we examine a range of observation regimes using two example models. We use a Lotka-Volterra predator-prey model to explore the impact of full or partial species observations using various time course observations under the assumption of known and unknown measurement error. Further investigation into the impact of observation error is then made using a Schlögl system, a test case which exhibits bi-modal state stability in some regions of parameter space. PMID:25720092
Markov chain Monte Carlo methods: an introductory example
Klauenberg, Katy; Elster, Clemens
2016-02-01
When the Guide to the Expression of Uncertainty in Measurement (GUM) and methods from its supplements are not applicable, the Bayesian approach may be a valid and welcome alternative. Evaluating the posterior distribution, estimates or uncertainties involved in Bayesian inferences often requires numerical methods to avoid high-dimensional integrations. Markov chain Monte Carlo (MCMC) sampling is such a method—powerful, flexible and widely applied. Here, a concise introduction is given, illustrated by a simple, typical example from metrology. The Metropolis-Hastings algorithm is the most basic and yet flexible MCMC method. Its underlying concepts are explained and the algorithm is given step by step. The few lines of software code required for its implementation invite interested readers to get started. Diagnostics to evaluate the performance and common algorithmic choices are illustrated to calibrate the Metropolis-Hastings algorithm for efficiency. Routine application of MCMC algorithms may be hindered currently by the difficulty to assess the convergence of MCMC output and thus to assure the validity of results. An example points to the importance of convergence and initiates discussion about advantages as well as areas of research. Available software tools are mentioned throughout.
Almost but not quite 2D, Non-linear Bayesian Inversion of CSEM Data
Ray, A.; Key, K.; Bodin, T.
2013-12-01
The geophysical inverse problem can be elegantly stated in a Bayesian framework where a probability distribution can be viewed as a statement of information regarding a random variable. After all, the goal of geophysical inversion is to provide information on the random variables of interest - physical properties of the earth's subsurface. However, though it may be simple to postulate, a practical difficulty of fully non-linear Bayesian inversion is the computer time required to adequately sample the model space and extract the information we seek. As a consequence, in geophysical problems where evaluation of a full 2D/3D forward model is computationally expensive, such as marine controlled source electromagnetic (CSEM) mapping of the resistivity of seafloor oil and gas reservoirs, Bayesian studies have largely been conducted with 1D forward models. While the 1D approximation is indeed appropriate for exploration targets with planar geometry and geological stratification, it only provides a limited, site-specific idea of uncertainty in resistivity with depth. In this work, we extend our fully non-linear 1D Bayesian inversion to a 2D model framework, without requiring the usual regularization of model resistivities in the horizontal or vertical directions used to stabilize quasi-2D inversions. In our approach, we use the reversible jump Markov-chain Monte-Carlo (RJ-MCMC) or trans-dimensional method and parameterize the subsurface in a 2D plane with Voronoi cells. The method is trans-dimensional in that the number of cells required to parameterize the subsurface is variable, and the cells dynamically move around and multiply or combine as demanded by the data being inverted. This approach allows us to expand our uncertainty analysis of resistivity at depth to more than a single site location, allowing for interactions between model resistivities at different horizontal locations along a traverse over an exploration target. While the model is parameterized in 2D, we
Markov process functionals in finance and insurance
Institute of Scientific and Technical Information of China (English)
GENG Xian-min; LI Liang
2009-01-01
The Maxkov property of Maxkov process functionals which axe frequently used in economy, finance, engineering and statistic analysis is studied. The conditions to judge Maxkov property of some important Markov process functionals axe presented, the following conclusions are obtained: the multidimensional process with independent increments is a multidimensional Markov process; the functional in the form of path integral of process with independent incre-ments is a Markov process; the surplus process with the doubly stochastic Poisson process is a vector Markov process. The conditions for linear transformation of vector Maxkov process being still a Maxkov process are given.
Barbu, Vlad
2008-01-01
Semi-Markov processes are much more general and better adapted to applications than the Markov ones because sojourn times in any state can be arbitrarily distributed, as opposed to the geometrically distributed sojourn time in the Markov case. This book concerns with the estimation of discrete-time semi-Markov and hidden semi-Markov processes
Variational data assimilation using targetted random walks
Cotter, S. L.
2011-02-15
The variational approach to data assimilation is a widely used methodology for both online prediction and for reanalysis. In either of these scenarios, it can be important to assess uncertainties in the assimilated state. Ideally, it is desirable to have complete information concerning the Bayesian posterior distribution for unknown state given data. We show that complete computational probing of this posterior distribution is now within the reach in the offline situation. We introduce a Markov chain-Monte Carlo (MCMC) method which enables us to directly sample from the Bayesian posterior distribution on the unknown functions of interest given observations. Since we are aware that these methods are currently too computationally expensive to consider using in an online filtering scenario, we frame this in the context of offline reanalysis. Using a simple random walk-type MCMC method, we are able to characterize the posterior distribution using only evaluations of the forward model of the problem, and of the model and data mismatch. No adjoint model is required for the method we use; however, more sophisticated MCMC methods are available which exploit derivative information. For simplicity of exposition, we consider the problem of assimilating data, either Eulerian or Lagrangian, into a low Reynolds number flow in a two-dimensional periodic geometry. We will show that in many cases it is possible to recover the initial condition and model error (which we describe as unknown forcing to the model) from data, and that with increasing amounts of informative data, the uncertainty in our estimations reduces. © 2011 John Wiley & Sons, Ltd.
Directory of Open Access Journals (Sweden)
Gao Shouguo
2011-08-01
Full Text Available Abstract Background Bayesian Network (BN is a powerful approach to reconstructing genetic regulatory networks from gene expression data. However, expression data by itself suffers from high noise and lack of power. Incorporating prior biological knowledge can improve the performance. As each type of prior knowledge on its own may be incomplete or limited by quality issues, integrating multiple sources of prior knowledge to utilize their consensus is desirable. Results We introduce a new method to incorporate the quantitative information from multiple sources of prior knowledge. It first uses the Naïve Bayesian classifier to assess the likelihood of functional linkage between gene pairs based on prior knowledge. In this study we included cocitation in PubMed and schematic similarity in Gene Ontology annotation. A candidate network edge reservoir is then created in which the copy number of each edge is proportional to the estimated likelihood of linkage between the two corresponding genes. In network simulation the Markov Chain Monte Carlo sampling algorithm is adopted, and samples from this reservoir at each iteration to generate new candidate networks. We evaluated the new algorithm using both simulated and real gene expression data including that from a yeast cell cycle and a mouse pancreas development/growth study. Incorporating prior knowledge led to a ~2 fold increase in the number of known transcription regulations recovered, without significant change in false positive rate. In contrast, without the prior knowledge BN modeling is not always better than a random selection, demonstrating the necessity in network modeling to supplement the gene expression data with additional information. Conclusion our new development provides a statistical means to utilize the quantitative information in prior biological knowledge in the BN modeling of gene expression data, which significantly improves the performance.
Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
Neuwald, Andrew F; Altschul, Stephen F
2016-05-01
We describe a Bayesian Markov chain Monte Carlo (MCMC) sampler for protein multiple sequence alignment (MSA) that, as implemented in the program GISMO and applied to large numbers of diverse sequences, is more accurate than the popular MSA programs MUSCLE, MAFFT, Clustal-Ω and Kalign. Features of GISMO central to its performance are: (i) It employs a "top-down" strategy with a favorable asymptotic time complexity that first identifies regions generally shared by all the input sequences, and then realigns closely related subgroups in tandem. (ii) It infers position-specific gap penalties that favor insertions or deletions (indels) within each sequence at alignment positions in which indels are invoked in other sequences. This favors the placement of insertions between conserved blocks, which can be understood as making up the proteins' structural core. (iii) It uses a Bayesian statistical measure of alignment quality based on the minimum description length principle and on Dirichlet mixture priors. Consequently, GISMO aligns sequence regions only when statistically justified. This is unlike methods based on the ad hoc, but widely used, sum-of-the-pairs scoring system, which will align random sequences. (iv) It defines a system for exploring alignment space that provides natural avenues for further experimentation through the development of new sampling strategies for more efficiently escaping from suboptimal traps. GISMO's superior performance is illustrated using 408 protein sets containing, on average, 235 sequences. These sets correspond to NCBI Conserved Domain Database alignments, which have been manually curated in the light of available crystal structures, and thus provide a means to assess alignment accuracy. GISMO fills a different niche than other MSA programs, namely identifying and aligning a conserved domain present within a large, diverse set of full length sequences. The GISMO program is available at http://gismo.igs.umaryland.edu/. PMID:27192614
Dinamika Pada Rantai Markov Dengan Dua Komponen (Dinamika On Two Compotent Markov Chains)
Yakub, Riki
2010-01-01
Dinamika pada rantai Markov dengan dua komponen dipengaruhi oleh nilai eigen dari matriks probabilitas transisinya serta keadaan awal yang diberikan. Berdasarkan nilai λ2 yang diperoleh, dinamika pada rantai Markov dengan dua komponen dapat dikelompokkan menjadi 3 bagian utama. Yaitu: a. Dinamika pada rantai Markov dengan dua komponen jika nilai 0
Fast MCMC sampling for hidden markov models to determine copy number variations
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Mahmud Md Pavel
2011-11-01
Full Text Available Abstract Background Hidden Markov Models (HMM are often used for analyzing Comparative Genomic Hybridization (CGH data to identify chromosomal aberrations or copy number variations by segmenting observation sequences. For efficiency reasons the parameters of a HMM are often estimated with maximum likelihood and a segmentation is obtained with the Viterbi algorithm. This introduces considerable uncertainty in the segmentation, which can be avoided with Bayesian approaches integrating out parameters using Markov Chain Monte Carlo (MCMC sampling. While the advantages of Bayesian approaches have been clearly demonstrated, the likelihood based approaches are still preferred in practice for their lower running times; datasets coming from high-density arrays and next generation sequencing amplify these problems. Results We propose an approximate sampling technique, inspired by compression of discrete sequences in HMM computations and by kd-trees to leverage spatial relations between data points in typical data sets, to speed up the MCMC sampling. Conclusions We test our approximate sampling method on simulated and biological ArrayCGH datasets and high-density SNP arrays, and demonstrate a speed-up of 10 to 60 respectively 90 while achieving competitive results with the state-of-the art Bayesian approaches. Availability: An implementation of our method will be made available as part of the open source GHMM library from http://ghmm.org.
Granade, Christopher; Cory, D G
2015-01-01
In recent years, Bayesian methods have been proposed as a solution to a wide range of issues in quantum state and process tomography. State-of- the-art Bayesian tomography solutions suffer from three problems: numerical intractability, a lack of informative prior distributions, and an inability to track time-dependent processes. Here, we solve all three problems. First, we use modern statistical methods, as pioneered by Husz\\'ar and Houlsby and by Ferrie, to make Bayesian tomography numerically tractable. Our approach allows for practical computation of Bayesian point and region estimators for quantum states and channels. Second, we propose the first informative priors on quantum states and channels. Finally, we develop a method that allows online tracking of time-dependent states and estimates the drift and diffusion processes affecting a state. We provide source code and animated visual examples for our methods.
Entropy Rate for Hidden Markov Chains with rare transitions
Peres, Yuval; Quas, Anthony
2010-01-01
We consider Hidden Markov Chains obtained by passing a Markov Chain with rare transitions through a noisy memoryless channel. We obtain asymptotic estimates for the entropy of the resulting Hidden Markov Chain as the transition rate is reduced to zero.
Bayesian exploratory factor analysis
Gabriella Conti; Sylvia Frühwirth-Schnatter; James Heckman; Rémi Piatek
2014-01-01
This paper develops and applies a Bayesian approach to Exploratory Factor Analysis that improves on ad hoc classical approaches. Our framework relies on dedicated factor models and simultaneously determines the number of factors, the allocation of each measurement to a unique factor, and the corresponding factor loadings. Classical identifi cation criteria are applied and integrated into our Bayesian procedure to generate models that are stable and clearly interpretable. A Monte Carlo study c...
Bayesian Exploratory Factor Analysis
Conti, Gabriella; Frühwirth-Schnatter, Sylvia; Heckman, James J.; Piatek, Rémi
2014-01-01
This paper develops and applies a Bayesian approach to Exploratory Factor Analysis that improves on ad hoc classical approaches. Our framework relies on dedicated factor models and simultaneously determines the number of factors, the allocation of each measurement to a unique factor, and the corresponding factor loadings. Classical identification criteria are applied and integrated into our Bayesian procedure to generate models that are stable and clearly interpretable. A Monte Carlo study co...
Bayesian Exploratory Factor Analysis
Gabriella Conti; Sylvia Fruehwirth-Schnatter; Heckman, James J.; Remi Piatek
2014-01-01
This paper develops and applies a Bayesian approach to Exploratory Factor Analysis that improves on \\emph{ad hoc} classical approaches. Our framework relies on dedicated factor models and simultaneously determines the number of factors, the allocation of each measurement to a unique factor, and the corresponding factor loadings. Classical identification criteria are applied and integrated into our Bayesian procedure to generate models that are stable and clearly interpretable. A Monte Carlo s...
Bayesian exploratory factor analysis
Conti, Gabriella; Frühwirth-Schnatter, Sylvia; Heckman, James J.; Piatek, Rémi
2014-01-01
This paper develops and applies a Bayesian approach to Exploratory Factor Analysis that improves on ad hoc classical approaches. Our framework relies on dedicated factor models and simultaneously determines the number of factors, the allocation of each measurement to a unique factor, and the corresponding factor loadings. Classical identification criteria are applied and integrated into our Bayesian procedure to generate models that are stable and clearly interpretable. A Monte Carlo st...
Bayesian exploratory factor analysis
Conti, Gabriella; Frühwirth-Schnatter, Sylvia; Heckman, James; Piatek, Rémi
2014-01-01
This paper develops and applies a Bayesian approach to Exploratory Factor Analysis that improves on ad hoc classical approaches. Our framework relies on dedicated factor models and simultaneously determines the number of factors, the allocation of each measurement to a unique factor, and the corresponding factor loadings. Classical identification criteria are applied and integrated into our Bayesian procedure to generate models that are stable and clearly interpretable. A Monte Carlo study co...
Carbonetto, Peter; Kisynski, Jacek; De Freitas, Nando; Poole, David L
2012-01-01
The Bayesian Logic (BLOG) language was recently developed for defining first-order probability models over worlds with unknown numbers of objects. It handles important problems in AI, including data association and population estimation. This paper extends BLOG by adopting generative processes over function spaces - known as nonparametrics in the Bayesian literature. We introduce syntax for reasoning about arbitrary collections of objects, and their properties, in an intuitive manner. By expl...
Bayesian default probability models
Andrlíková, Petra
2014-01-01
This paper proposes a methodology for default probability estimation for low default portfolios, where the statistical inference may become troublesome. The author suggests using logistic regression models with the Bayesian estimation of parameters. The piecewise logistic regression model and Box-Cox transformation of credit risk score is used to derive the estimates of probability of default, which extends the work by Neagu et al. (2009). The paper shows that the Bayesian models are more acc...
Schmidt games and Markov partitions
International Nuclear Information System (INIS)
Let T be a C2-expanding self-map of a compact, connected, C∞, Riemannian manifold M. We correct a minor gap in the proof of a theorem from the literature: the set of points whose forward orbits are nondense has full Hausdorff dimension. Our correction allows us to strengthen the theorem. Combining the correction with Schmidt games, we generalize the theorem in dimension one: given a point x0 in M, the set of points whose forward orbit closures miss x0 is a winning set. Finally, our key lemma, the no matching lemma, may be of independent interest in the theory of symbolic dynamics or the theory of Markov partitions
Markov constant and quantum instabilities
Pelantová, Edita; Starosta, Štěpán; Znojil, Miloslav
2016-04-01
For a qualitative analysis of spectra of certain two-dimensional rectangular-well quantum systems several rigorous methods of number theory are shown productive and useful. These methods (and, in particular, a generalization of the concept of Markov constant known in Diophantine approximation theory) are shown to provide a new mathematical insight in the phenomenologically relevant occurrence of anomalies in the spectra. Our results may inspire methodical innovations ranging from the description of the stability properties of metamaterials and of certain hiddenly unitary quantum evolution models up to the clarification of the mechanisms of occurrence of ghosts in quantum cosmology.
Directory of Open Access Journals (Sweden)
J. Norberg
2015-09-01
Full Text Available We validate two-dimensional ionospheric tomography reconstructions against EISCAT incoherent scatter radar measurements. Our tomography method is based on Bayesian statistical inversion with prior distribution given by its mean and covariance. We employ ionosonde measurements for the choice of the prior mean and covariance parameters, and use the Gaussian Markov random fields as a sparse matrix approximation for the numerical computations. This results in a computationally efficient and statistically clear inversion algorithm for tomography. We demonstrate how this method works with simultaneous beacon satellite and ionosonde measurements obtained in northern Scandinavia. The performance is compared with results obtained with a zero mean prior and with the prior mean taken from the International Reference Ionosphere 2007 model. In validating the results, we use EISCAT UHF incoherent scatter radar measurements as the ground truth for the ionization profile shape. We find that ionosonde measurements improve the reconstruction by adding accurate information about the absolute value and the height distribution of electron density, and outperforms the alternative prior information sources. With an ionosonde at continuous disposal, the presented method enhances stand-alone near real-time ionospheric tomography for the given conditions significantly.
Zhou, Haiming; Hanson, Timothy; Knapp, Roland
2015-12-01
The global emergence of Batrachochytrium dendrobatidis (Bd) has caused the extinction of hundreds of amphibian species worldwide. It has become increasingly important to be able to precisely predict time to Bd arrival in a population. The data analyzed herein present a unique challenge in terms of modeling because there is a strong spatial component to Bd arrival time and the traditional proportional hazards assumption is grossly violated. To address these concerns, we develop a novel marginal Bayesian nonparametric survival model for spatially correlated right-censored data. This class of models assumes that the logarithm of survival times marginally follow a mixture of normal densities with a linear-dependent Dirichlet process prior as the random mixing measure, and their joint distribution is induced by a Gaussian copula model with a spatial correlation structure. To invert high-dimensional spatial correlation matrices, we adopt a full-scale approximation that can capture both large- and small-scale spatial dependence. An efficient Markov chain Monte Carlo algorithm with delayed rejection is proposed for posterior computation, and an R package spBayesSurv is provided to fit the model. This approach is first evaluated through simulations, then applied to threatened frog populations in Sequoia-Kings Canyon National Park. PMID:26148536
A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation.
Redelings, Benjamin D; Kumagai, Seiji; Tatarenkov, Andrey; Wang, Liuyang; Sakai, Ann K; Weller, Stephen G; Culley, Theresa M; Avise, John C; Uyenoyama, Marcy K
2015-11-01
We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about reproduction under pure hermaphroditism, gynodioecy, and a model developed to describe the self-fertilizing killifish Kryptolebias marmoratus. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens sampling formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet process prior model. Our sampler is designed to accommodate additional information, including observations pertaining to the sex ratio, the intensity of inbreeding depression, and other aspects of reproduction. It can provide joint posterior distributions for the population-wide proportion of uniparental individuals, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual. Further, estimation of all basic parameters of a given model permits estimation of functions of those parameters, including the proportion of the gene pool contributed by each sex and relative effective numbers. PMID:26374460
Norberg, J.; Virtanen, I. I.; Roininen, L.; Vierinen, J.; Orispää, M.; Kauristie, K.; Lehtinen, M. S.
2015-09-01
We validate two-dimensional ionospheric tomography reconstructions against EISCAT incoherent scatter radar measurements. Our tomography method is based on Bayesian statistical inversion with prior distribution given by its mean and covariance. We employ ionosonde measurements for the choice of the prior mean and covariance parameters, and use the Gaussian Markov random fields as a sparse matrix approximation for the numerical computations. This results in a computationally efficient and statistically clear inversion algorithm for tomography. We demonstrate how this method works with simultaneous beacon satellite and ionosonde measurements obtained in northern Scandinavia. The performance is compared with results obtained with a zero mean prior and with the prior mean taken from the International Reference Ionosphere 2007 model. In validating the results, we use EISCAT UHF incoherent scatter radar measurements as the ground truth for the ionization profile shape. We find that ionosonde measurements improve the reconstruction by adding accurate information about the absolute value and the height distribution of electron density, and outperforms the alternative prior information sources. With an ionosonde at continuous disposal, the presented method enhances stand-alone near real-time ionospheric tomography for the given conditions significantly.
A Bayesian approach to modeling and predicting pitting flaws in steam generator tubes
International Nuclear Information System (INIS)
Steam generators in nuclear power plants have experienced varying degrees of under-deposit pitting corrosion. A probabilistic model to accurately predict pitting damage is necessary for effective life-cycle management of steam generators. This paper presents an advanced probabilistic model of pitting corrosion characterizing the inherent randomness of the pitting process and measurement uncertainties of the in-service inspection (ISI) data obtained from eddy current (EC) inspections. A Markov chain Monte Carlo simulation-based Bayesian method, enhanced by a data augmentation technique, is developed for estimating the model parameters. The proposed model is able to predict the actual pit number, the actual pit depth as well as the maximum pit depth, which is the main interest of the pitting corrosion model. The study also reveals the significance of inspection uncertainties in the modeling of pitting flaws using the ISI data: Without considering the probability-of-detection issues and measurement errors, the leakage risk resulted from the pitting corrosion would be under-estimated, despite the fact that the actual pit depth would usually be over-estimated.
A Bayesian analysis of extrasolar planet data for HD 208487
Gregory, P. C.
2005-01-01
Precision radial velocity data for HD 208487 has been re-analyzed using a new Bayesian multi-planet Kepler periodogram. The periodgram employs a parallel tempering Markov chain Monte Carlo algorithm with a novel statistical control system. We confirm the previously reported orbit (Tinney et al. 2005) of 130 days. In addition, we conclude there is strong evidence for a second planet with a period of 998 -62 +57 days, an eccentricity of 0.19 -0.18 +0.05, and an M sin i = 0.46 -0.13 +0.05 of Jup...
Spatial correlation in Bayesian logistic regression with misclassification
DEFF Research Database (Denmark)
Bihrmann, Kristine; Toft, Nils; Nielsen, Søren Saxmose;
2014-01-01
Standard logistic regression assumes that the outcome is measured perfectly. In practice, this is often not the case, which could lead to biased estimates if not accounted for. This study presents Bayesian logistic regression with adjustment for misclassification of the outcome applied to data with....... Parameters were estimated by Markov Chain Monte Carlo methods, using slice sampling to improve convergence. The results demonstrated that adjustment for misclassification must be included to produce unbiased regression estimates. With strong correlation the ICAR model performed best. With weak or moderate...
Properly quantized history-dependent Parrondo games, Markov processes, and multiplexing circuits
International Nuclear Information System (INIS)
Highlights: → History-dependent Parrondo games are viewed as Markov processes. → Quantum mechanical analogues of these Markov processes are constructed. → These quantum analogues restrict to the original process on measurement. → Relationship between these analogues and a quantum circuits is exhibited. - Abstract: In the context of quantum information theory, 'quantization' of various mathematical and computational constructions is said to occur upon the replacement, at various points in the construction, of the classical randomization notion of probability distribution with higher order randomization notions from quantum mechanics such as quantum superposition with measurement. For this to be done 'properly', a faithful copy of the original construction is required to exist within the new quantum one, just as is required when a function is extended to a larger domain. Here procedures for extending history-dependent Parrondo games, Markov processes and multiplexing circuits to their quantum versions are analyzed from a game theoretic viewpoint, and from this viewpoint, proper quantizations developed.
Estimating hidden semi-Markov chains from discrete sequences.
Guédon, Yann
2003-01-01
International audience This article addresses the estimation of hidden semi-Markov chains from nonstationary discrete sequences. Hidden semi-Markov chains are particularly useful to model the succession of homogeneous zones or segments along sequences. A discrete hidden semi-Markov chain is composed of a nonobservable state process, which is a semi-Markov chain, and a discrete output process. Hidden semi-Markov chains generalize hidden Markov chains and enable the modeling of various durat...
An increment type set-indexed Markov property
Balança, Paul
2012-01-01
In this article is introduced and studied a set-indexed Markov property named C-Markov. This new definition fulfils one important expectation for a Markov property: there exists a natural set-indexed generalization of the concept of transition operator which leads to characterization and construction theorems for C-Markov processes. Several other usual Markovian notions, including Feller and strong Markov properties, can also be developed in this framework. Actually, the C-Markov property tur...
Conditional Markov Chains Part II: Consistency and Copulae
Bielecki, Tomasz R.; Jakubowski, Jacek; Niewęgłowski, Mariusz
2015-01-01
In this paper we continue the study of conditional Markov chains (CMCs) with finite state spaces, that we initiated in Bielecki, Jakubowski and Niew\\k{e}g\\l owski (2015). Here, we turn our attention to the study of Markov consistency and Markov copulae with regard to CMCs, and thus we follow up on the study of Markov consistency and Markov copulae for ordinary Markov chains that we presented in Bielecki, Jakubowski and Niew\\k{e}g\\l owski (2013).
SISTEMUL DE AŞTEPTARE [SM / M /∞] CU FLUX SEMI-MARKOV. CRITERIUL DE MEDIERE
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Iulia DAMIAN
2015-12-01
Full Text Available În articol sunt analizate reţelele semimarkoviene de servire şi este studiată convergenţa slabă în procesele de aşteptare în schema de mediere. De asemenea, este studiat criteriul de mediere a sistemului de aşteptare semi-Markov [SM / M /∞] prin evoluţia aleatoare şi folosind operatorul de compensaţie a procesului extins Markov de reînnoire.QUEUING SYSTEM WITH SEMI-MARKOV FLOW [SM / M /∞]. AVERAGE SCHEME In this article study the queuing system where the input flow is described by a semi-Markov process, the service time is exponentially distributed. This article is about of the weak convergence in average scheme. It is study average scheme for semi-Markov queuing systems [SM / M /∞] by a random evolution approach and using compensating operator of the corresponding extended Markov process.
Dynamic temperature selection for parallel-tempering in Markov chain Monte Carlo simulations
Vousden, Will; Mandel, Ilya
2015-01-01
Modern problems in astronomical Bayesian inference require efficient methods for sampling from complex, high-dimensional, often multi-modal probability distributions. Most popular methods, such as Markov chain Monte Carlo sampling, perform poorly on strongly multi-modal probability distributions, rarely jumping between modes or settling on just one mode without finding others. Parallel tempering addresses this problem by sampling simultaneously with separate Markov chains from tempered versions of the target distribution with reduced contrast levels. Gaps between modes can be traversed at higher temperatures, while individual modes can be efficiently explored at lower temperatures. In this paper, we investigate how one might choose the ladder of temperatures to achieve lower autocorrelation time for the sampler (and therefore more efficient sampling). In particular, we present a simple, easily-implemented algorithm for dynamically adapting the temperature configuration of a sampler while sampling in order to ...