Sampling Methods, Particle Filtering, and Markov-Chain Monte Carlo
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												  Lecture 15: Approximate Inference: Monte Carlo Methods10-708: Probabilistic Graphical Models 10-708, Spring 2017 Lecture 15: Approximate Inference: Monte Carlo methods Lecturer: Eric P. Xing Name: Yuan Liu(yuanl4), Yikang Li(yikangl) 1 Introduction We have already learned some exact inference methods in the previous lectures, such as the elimination algo- rithm, message-passing algorithm and the junction tree algorithms. However, there are many probabilistic models of practical interest for which exact inference is intractable. One important class of inference algo- rithms is based on deterministic approximation schemes and includes methods such as variational methods. This lecture will include an alternative very general and widely used framework for approximate inference based on stochastic simulation through sampling, also known as the Monte Carlo methods. The purpose of the Monte Carlo method is to find the expectation of some function f(x) with respect to a probability distribution p(x). Here, the components of x might comprise of discrete or continuous variables, or some combination of the two. Z hfi = f(x)p(x)dx The general idea behind sampling methods is to obtain a set of examples x(t)(where t = 1; :::; N) drawn from the distribution p(x). This allows the expectation (1) to be approximated by a finite sum N 1 X f^ = f(x(t)) N t=1 If the samples x(t) is i.i.d, it is clear that hf^i = hfi, and the variance of the estimator is h(f − hfi)2i=N. Monte Carlo methods work by drawing samples from the desired distribution, which can be accomplished even when it it not possible to write out the pdf.
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												  A Class of Measure-Valued Markov Chains and Bayesian NonparametricsBernoulli 18(3), 2012, 1002–1030 DOI: 10.3150/11-BEJ356 A class of measure-valued Markov chains and Bayesian nonparametrics STEFANO FAVARO1, ALESSANDRA GUGLIELMI2 and STEPHEN G. WALKER3 1Universit`adi Torino and Collegio Carlo Alberto, Dipartimento di Statistica e Matematica Ap- plicata, Corso Unione Sovietica 218/bis, 10134 Torino, Italy. E-mail: [email protected] 2Politecnico di Milano, Dipartimento di Matematica, P.zza Leonardo da Vinci 32, 20133 Milano, Italy. E-mail: [email protected] 3University of Kent, Institute of Mathematics, Statistics and Actuarial Science, Canterbury CT27NZ, UK. E-mail: [email protected] Measure-valued Markov chains have raised interest in Bayesian nonparametrics since the seminal paper by (Math. Proc. Cambridge Philos. Soc. 105 (1989) 579–585) where a Markov chain having the law of the Dirichlet process as unique invariant measure has been introduced. In the present paper, we propose and investigate a new class of measure-valued Markov chains defined via exchangeable sequences of random variables. Asymptotic properties for this new class are derived and applications related to Bayesian nonparametric mixture modeling, and to a generalization of the Markov chain proposed by (Math. Proc. Cambridge Philos. Soc. 105 (1989) 579–585), are discussed. These results and their applications highlight once again the interplay between Bayesian nonparametrics and the theory of measure-valued Markov chains. Keywords: Bayesian nonparametrics; Dirichlet process; exchangeable sequences; linear functionals
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												  Estimating Standard Errors for Importance Sampling Estimators with Multiple Markov ChainsEstimating standard errors for importance sampling estimators with multiple Markov chains Vivekananda Roy1, Aixin Tan2, and James M. Flegal3 1Department of Statistics, Iowa State University 2Department of Statistics and Actuarial Science, University of Iowa 3Department of Statistics, University of California, Riverside Aug 10, 2016 Abstract The naive importance sampling estimator, based on samples from a single importance density, can be numerically unstable. Instead, we consider generalized importance sampling estimators where samples from more than one probability distribution are combined. We study this problem in the Markov chain Monte Carlo context, where independent samples are replaced with Markov chain samples. If the chains converge to their respective target distributions at a polynomial rate, then under two finite moment conditions, we show a central limit theorem holds for the generalized estimators. Further, we develop an easy to implement method to calculate valid asymptotic standard errors based on batch means. We also provide a batch means estimator for calculating asymptotically valid standard errors of Geyer’s (1994) reverse logistic estimator. We illustrate the method via three examples. In particular, the generalized importance sampling estimator is used for Bayesian spatial modeling of binary data and to perform empirical Bayes variable selection where the batch means estimator enables standard error calculations in high-dimensional settings. arXiv:1509.06310v2 [math.ST] 11 Aug 2016 Key words and phrases: Bayes factors, Markov chain Monte Carlo, polynomial ergodicity, ratios of normalizing constants, reverse logistic estimator. 1 Introduction Let π(x) = ν(x)=m be a probability density function (pdf) on X with respect to a measure µ(·). R Suppose f : X ! R is a π integrable function and we want to estimate Eπf := X f(x)π(x)µ(dx).
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												  Markov Process DualityMarkov Process Duality Jan M. Swart Luminy, October 23 and 24, 2013 Jan M. Swart Markov Process Duality Markov Chains S finite set. RS space of functions f : S R. ! S For probability kernel P = (P(x; y))x;y2S and f R define left and right multiplication as 2 X X Pf (x) := P(x; y)f (y) and fP(x) := f (y)P(y; x): y y (I do not distinguish row and column vectors.) Def Chain X = (Xk )k≥0 of S-valued r.v.'s is Markov chain with transition kernel P and state space S if S E f (Xk+1) (X0;:::; Xk ) = Pf (Xk ) a:s: (f R ) 2 P (X0;:::; Xk ) = (x0;:::; xk ) , = P[X0 = x0]P(x0; x1) P(xk−1; xk ): ··· µ µ µ Write P ; E for process with initial law µ = P [X0 ]. x δx x 2 · P := P with δx (y) := 1fx=yg. E similar. Jan M. Swart Markov Process Duality Markov Chains Set k µ k x µk := µP (x) = P [Xk = x] and fk := P f (x) = E [f (Xk )]: Then the forward and backward equations read µk+1 = µk P and fk+1 = Pfk : In particular π invariant law iff πP = π. Function h harmonic iff Ph = h h(Xk ) martingale. , Jan M. Swart Markov Process Duality Random mapping representation (Zk )k≥1 i.i.d. with common law ν, take values in (E; ). φ : S E S measurable E × ! P(x; y) = P[φ(x; Z1) = y]: Random mapping representation (E; ; ν; φ) always exists, highly non-unique.
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												  Distilling Importance SamplingDistilling Importance Sampling Dennis Prangle1 1School of Mathematics, University of Bristol, United Kingdom Abstract in almost any setting, including in the presence of strong posterior dependence or discrete random variables. How- ever it only achieves a representative weighted sample at a Many complicated Bayesian posteriors are difficult feasible cost if the proposal is a reasonable approximation to approximate by either sampling or optimisation to the target distribution. methods. Therefore we propose a novel approach combining features of both. We use a flexible para- An alternative to Monte Carlo is to use optimisation to meterised family of densities, such as a normal- find the best approximation to the posterior from a family of ising flow. Given a density from this family approx- distributions. Typically this is done in the framework of vari- imating the posterior, we use importance sampling ational inference (VI). VI is computationally efficient but to produce a weighted sample from a more accur- has the drawback that it often produces poor approximations ate posterior approximation. This sample is then to the posterior distribution e.g. through over-concentration used in optimisation to update the parameters of [Turner et al., 2008, Yao et al., 2018]. the approximate density, which we view as dis- A recent improvement in VI is due to the development of tilling the importance sampling results. We iterate a range of flexible and computationally tractable distribu- these steps and gradually improve the quality of the tional families using normalising flows [Dinh et al., 2016, posterior approximation. We illustrate our method Papamakarios et al., 2019a]. These transform a simple base in two challenging examples: a queueing model random distribution to a complex distribution, using a se- and a stochastic differential equation model.
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												  1 Introduction Branching Mechanism in a Superprocess from a Branching数理解析研究所講究録 1157 巻 2000 年 1-16 1 An example of random snakes by Le Gall and its applications 渡辺信三 Shinzo Watanabe, Kyoto University 1 Introduction The notion of random snakes has been introduced by Le Gall ([Le 1], [Le 2]) to construct a class of measure-valued branching processes, called superprocesses or continuous state branching processes ([Da], [Dy]). A main idea is to produce the branching mechanism in a superprocess from a branching tree embedded in excur- sions at each different level of a Brownian sample path. There is no clear notion of particles in a superprocess; it is something like a cloud or mist. Nevertheless, a random snake could provide us with a clear picture of historical or genealogical developments of”particles” in a superprocess. ” : In this note, we give a sample pathwise construction of a random snake in the case when the underlying Markov process is a Markov chain on a tree. A simplest case has been discussed in [War 1] and [Wat 2]. The construction can be reduced to this case locally and we need to consider a recurrence family of stochastic differential equations for reflecting Brownian motions with sticky boundaries. A special case has been already discussed by J. Warren [War 2] with an application to a coalescing stochastic flow of piece-wise linear transformations in connection with a non-white or non-Gaussian predictable noise in the sense of B. Tsirelson. 2 Brownian snakes Throughout this section, let $\xi=\{\xi(t), P_{x}\}$ be a Hunt Markov process on a locally compact separable metric space $S$ endowed with a metric $d_{S}(\cdot, *)$ .
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												  Importance Sampling & Sequential Importance SamplingImportance Sampling & Sequential Importance Sampling Arnaud Doucet Departments of Statistics & Computer Science University of British Columbia A.D. () 1 / 40 Each distribution πn (dx1:n) = πn (x1:n) dx1:n is known up to a normalizing constant, i.e. γn (x1:n) πn (x1:n) = Zn We want to estimate expectations of test functions ϕ : En R n ! Eπn (ϕn) = ϕn (x1:n) πn (dx1:n) Z and/or the normalizing constants Zn. We want to do this sequentially; i.e. …rst π1 and/or Z1 at time 1 then π2 and/or Z2 at time 2 and so on. Generic Problem Consider a sequence of probability distributions πn n 1 de…ned on a f g sequence of (measurable) spaces (En, n) n 1 where E1 = E, f F g 1 = and En = En 1 E, n = n 1 . F F F F F A.D. () 2 / 40 We want to estimate expectations of test functions ϕ : En R n ! Eπn (ϕn) = ϕn (x1:n) πn (dx1:n) Z and/or the normalizing constants Zn. We want to do this sequentially; i.e. …rst π1 and/or Z1 at time 1 then π2 and/or Z2 at time 2 and so on. Generic Problem Consider a sequence of probability distributions πn n 1 de…ned on a f g sequence of (measurable) spaces (En, n) n 1 where E1 = E, f F g 1 = and En = En 1 E, n = n 1 . F F F F F Each distribution πn (dx1:n) = πn (x1:n) dx1:n is known up to a normalizing constant, i.e.
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												  1 Markov Chain Notation for a Continuous State SpaceThe Metropolis-Hastings Algorithm 1 Markov Chain Notation for a Continuous State Space A sequence of random variables X0;X1;X2;:::, is a Markov chain on a continuous state space if... ... where it goes depends on where is is but not where is was. I'd really just prefer that you have the “flavor" here. The previous Markov property equation that we had P (Xn+1 = jjXn = i; Xn−1 = in−1;:::;X0 = i0) = P (Xn+1 = jjXn = i) is uninteresting now since both of those probabilities are zero when the state space is con- tinuous. It would be better to say that, for any A ⊆ S, where S is the state space, we have P (Xn+1 2 AjXn = i; Xn−1 = in−1;:::;X0 = i0) = P (Xn+1 2 AjXn = i): Note that it is okay to have equalities on the right side of the conditional line. Once these continuous random variables have been observed, they are fixed and nailed down to discrete values. 1.1 Transition Densities The continuous state analog of the one-step transition probability pij is the one-step tran- sition density. We will denote this as p(x; y): This is not the probability that the chain makes a move from state x to state y. Instead, it is a probability density function in y which describes a curve under which area represents probability. x can be thought of as a parameter of this density. For example, given a Markov chain is currently in state x, the next value y might be drawn from a normal distribution centered at x.
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												  Simulation of Markov ChainsCopyright c 2007 by Karl Sigman 1 Simulating Markov chains Many stochastic processes used for the modeling of financial assets and other systems in engi- neering are Markovian, and this makes it relatively easy to simulate from them. Here we present a brief introduction to the simulation of Markov chains. Our emphasis is on discrete-state chains both in discrete and continuous time, but some examples with a general state space will be discussed too. 1.1 Definition of a Markov chain We shall assume that the state space S of our Markov chain is S = ZZ= f:::; −2; −1; 0; 1; 2;:::g, the integers, or a proper subset of the integers. Typical examples are S = IN = f0; 1; 2 :::g, the non-negative integers, or S = f0; 1; 2 : : : ; ag, or S = {−b; : : : ; 0; 1; 2 : : : ; ag for some integers a; b > 0, in which case the state space is finite. Definition 1.1 A stochastic process fXn : n ≥ 0g is called a Markov chain if for all times n ≥ 0 and all states i0; : : : ; i; j 2 S, P (Xn+1 = jjXn = i; Xn−1 = in−1;:::;X0 = i0) = P (Xn+1 = jjXn = i) (1) = Pij: Pij denotes the probability that the chain, whenever in state i, moves next (one unit of time later) into state j, and is referred to as a one-step transition probability. The square matrix P = (Pij); i; j 2 S; is called the one-step transition matrix, and since when leaving state i the chain must move to one of the states j 2 S, each row sums to one (e.g., forms a probability distribution): For each i X Pij = 1: j2S We are assuming that the transition probabilities do not depend on the time n, and so, in particular, using n = 0 in (1) yields Pij = P (X1 = jjX0 = i): (Formally we are considering only time homogenous MC's meaning that their transition prob- abilities are time-homogenous (time stationary).) The defining property (1) can be described in words as the future is independent of the past given the present state.
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												  Chapter 8: Markov Chains149 Chapter 8: Markov Chains 8.1 Introduction So far, we have examined several stochastic processes using transition diagrams and First-Step Analysis. The processes can be written as {X0, X1, X2,...}, where Xt is the state at time t. A.A.Markov On the transition diagram, Xt corresponds to 1856-1922 which box we are in at step t. In the Gambler’s Ruin (Section 2.7), Xt is the amount of money the gambler possesses after toss t. In the model for gene spread (Section 3.7), Xt is the number of animals possessing the harmful allele A in generation t. The processes that we have looked at via the transition diagram have a crucial property in common: Xt+1 depends only on Xt. It does not depend upon X0, X1,...,Xt−1. Processes like this are called Markov Chains. Example: Random Walk (see Chapter 4) none of these steps matter for time t+1 ? time t+1 time t ? In a Markov chain, the future depends only upon the present: NOT upon the past. 150 .. ...... .. .. ...... .. ....... ....... ....... ....... ... .... .... .... .. .. .. .. ... ... ... ... ....... ..... ..... ....... ........4................. ......7.................. The text-book image ...... ... ... ...... .... ... ... .... ... ... ... ... ... ... ... ... ... ... ... .... ... ... ... ... of a Markov chain has ... ... ... ... 1 ... .... ... ... ... ... ... ... ... .1.. 1... 1.. 3... ... ... ... ... ... ... ... ... 2 ... ... ... a flea hopping about at ... ..... ..... ... ...... ... ....... ...... ...... ....... ... ...... ......... ......... .. ........... ........ ......... ........... ........
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												  Markov Random Fields and Stochastic Image ModelsMarkov Random Fields and Stochastic Image Models Charles A. Bouman School of Electrical and Computer Engineering Purdue University Phone: (317) 494-0340 Fax: (317) 494-3358 email [email protected] Available from: http://dynamo.ecn.purdue.edu/»bouman/ Tutorial Presented at: 1995 IEEE International Conference on Image Processing 23-26 October 1995 Washington, D.C. Special thanks to: Ken Sauer Suhail Saquib Department of Electrical School of Electrical and Computer Engineering Engineering University of Notre Dame Purdue University 1 Overview of Topics 1. Introduction (b) Non-Gaussian MRF's 2. The Bayesian Approach i. Quadratic functions ii. Non-Convex functions 3. Discrete Models iii. Continuous MAP estimation (a) Markov Chains iv. Convex functions (b) Markov Random Fields (MRF) (c) Parameter Estimation (c) Simulation i. Estimation of σ (d) Parameter estimation ii. Estimation of T and p parameters 4. Application of MRF's to Segmentation 6. Application to Tomography (a) The Model (a) Tomographic system and data models (b) Bayesian Estimation (b) MAP Optimization (c) MAP Optimization (c) Parameter estimation (d) Parameter Estimation 7. Multiscale Stochastic Models (e) Other Approaches (a) Continuous models 5. Continuous Models (b) Discrete models (a) Gaussian Random Process Models 8. High Level Image Models i. Autoregressive (AR) models ii. Simultaneous AR (SAR) models iii. Gaussian MRF's iv. Generalization to 2-D 2 References in Statistical Image Modeling 1. Overview references [100, 89, 50, 54, 162, 4, 44] 4. Simulation and Stochastic Optimization Methods [118, 80, 129, 100, 68, 141, 61, 76, 62, 63] 2. Type of Random Field Model 5. Computational Methods used with MRF Models (a) Discrete Models i.
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												  Temporally-Reweighted Chinese Restaurant Process Mixtures for Clustering, Imputing, and Forecasting Multivariate Time SeriesTemporally-Reweighted Chinese Restaurant Process Mixtures for Clustering, Imputing, and Forecasting Multivariate Time Series Feras A. Saad Vikash K. Mansinghka Probabilistic Computing Project Probabilistic Computing Project Massachusetts Institute of Technology Massachusetts Institute of Technology Abstract there are tens or hundreds of time series. One chal- lenge in these settings is that the data may reflect un- derlying processes with widely varying, non-stationary This article proposes a Bayesian nonparamet- dynamics [13]. Another challenge is that standard ric method for forecasting, imputation, and parametric approaches such as state-space models and clustering in sparsely observed, multivariate vector autoregression often become statistically and time series data. The method is appropri- numerically unstable in high dimensions [20]. Models ate for jointly modeling hundreds of time se- from these families further require users to perform ries with widely varying, non-stationary dy- significant custom modeling on a per-dataset basis, or namics. Given a collection of N time se- to search over a large set of possible parameter set- ries, the Bayesian model first partitions them tings and model configurations. In econometrics and into independent clusters using a Chinese finance, there is an increasing need for multivariate restaurant process prior. Within a clus- methods that exploit sparsity, are computationally ef- ter, all time series are modeled jointly us- ficient, and can accurately model hundreds of time se- ing a novel \temporally-reweighted" exten- ries (see introduction of [15], and references therein). sion of the Chinese restaurant process mix- ture. Markov chain Monte Carlo techniques This paper presents a nonparametric Bayesian method are used to obtain samples from the poste- for multivariate time series that aims to address some rior distribution, which are then used to form of the above challenges.