Blackimportance Sampling and Its Optimality for Stochastic
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Lecture 15: Approximate Inference: Monte Carlo Methods
10-708: 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. -
Estimating Standard Errors for Importance Sampling Estimators with Multiple Markov Chains
Estimating 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). -
On Sampling from the Multivariate T Distribution by Marius Hofert
CONTRIBUTED RESEARCH ARTICLES 129 On Sampling from the Multivariate t Distribution by Marius Hofert Abstract The multivariate normal and the multivariate t distributions belong to the most widely used multivariate distributions in statistics, quantitative risk management, and insurance. In contrast to the multivariate normal distribution, the parameterization of the multivariate t distribution does not correspond to its moments. This, paired with a non-standard implementation in the R package mvtnorm, provides traps for working with the multivariate t distribution. In this paper, common traps are clarified and corresponding recent changes to mvtnorm are presented. Introduction A supposedly simple task in statistics courses and related applications is to generate random variates from a multivariate t distribution in R. When teaching such courses, we found several fallacies one might encounter when sampling multivariate t distributions with the well-known R package mvtnorm; see Genz et al.(2013). These fallacies have recently led to improvements of the package ( ≥ 0.9-9996) which we present in this paper1. To put them in the correct context, we first address the multivariate normal distribution. The multivariate normal distribution The multivariate normal distribution can be defined in various ways, one is with its stochastic represen- tation X = m + AZ, (1) where Z = (Z1, ... , Zk) is a k-dimensional random vector with Zi, i 2 f1, ... , kg, being independent standard normal random variables, A 2 Rd×k is an (d, k)-matrix, and m 2 Rd is the mean vector. The covariance matrix of X is S = AA> and the distribution of X (that is, the d-dimensional multivariate normal distribution) is determined solely by the mean vector m and the covariance matrix S; we can thus write X ∼ Nd(m, S). -
Distilling Importance Sampling
Distilling 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. -
EFFICIENT ESTIMATION and SIMULATION of the TRUNCATED MULTIVARIATE STUDENT-T DISTRIBUTION
Efficient estimation and simulation of the truncated multivariate student-t distribution Zdravko I. Botev, Pierre l’Ecuyer To cite this version: Zdravko I. Botev, Pierre l’Ecuyer. Efficient estimation and simulation of the truncated multivariate student-t distribution. 2015 Winter Simulation Conference, Dec 2015, Huntington Beach, United States. hal-01240154 HAL Id: hal-01240154 https://hal.inria.fr/hal-01240154 Submitted on 8 Dec 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Proceedings of the 2015 Winter Simulation Conference L. Yilmaz, W. K V. Chan, I. Moon, T. M. K. Roeder, C. Macal, and M. Rosetti, eds. EFFICIENT ESTIMATION AND SIMULATION OF THE TRUNCATED MULTIVARIATE STUDENT-t DISTRIBUTION Zdravko I. Botev Pierre L’Ecuyer School of Mathematics and Statistics DIRO, Universite´ de Montreal The University of New South Wales C.P. 6128, Succ. Centre-Ville Sydney, NSW 2052, AUSTRALIA Montreal´ (Quebec),´ H3C 3J7, CANADA ABSTRACT We propose an exponential tilting method for exact simulation from the truncated multivariate student-t distribution in high dimensions as an alternative to approximate Markov Chain Monte Carlo sampling. The method also allows us to accurately estimate the probability that a random vector with multivariate student-t distribution falls in a convex polytope. -
Importance Sampling & Sequential Importance Sampling
Importance 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. -
Stochastic Simulation APPM 7400
Stochastic Simulation APPM 7400 Lesson 1: Random Number Generators August 27, 2018 Lesson 1: Random Number Generators Stochastic Simulation August27,2018 1/29 Random Numbers What is a random number? Lesson 1: Random Number Generators Stochastic Simulation August27,2018 2/29 Random Numbers What is a random number? “You mean like... 5?” Lesson 1: Random Number Generators Stochastic Simulation August27,2018 2/29 Random Numbers What is a random number? “You mean like... 5?” Formal definition from probability: A random number is a number uniformly distributed between 0 and 1. Lesson 1: Random Number Generators Stochastic Simulation August27,2018 2/29 Random Numbers What is a random number? “You mean like... 5?” Formal definition from probability: A random number is a number uniformly distributed between 0 and 1. (It is a realization of a uniform(0,1) random variable.) Lesson 1: Random Number Generators Stochastic Simulation August27,2018 2/29 Random Numbers Here are some realizations: 0.8763857 0.2607807 0.7060687 0.0826960 Density 0.7569021 . 0 2 4 6 8 10 0.0 0.2 0.4 0.6 0.8 1.0 sample Lesson 1: Random Number Generators Stochastic Simulation August27,2018 3/29 Random Numbers Here are some realizations: 0.8763857 0.2607807 0.7060687 0.0826960 Density 0.7569021 . 0 2 4 6 8 10 0.0 0.2 0.4 0.6 0.8 1.0 sample Lesson 1: Random Number Generators Stochastic Simulation August27,2018 3/29 Random Numbers Here are some realizations: 0.8763857 0.2607807 0.7060687 0.0826960 Density 0.7569021 . -
Multivariate Stochastic Simulation with Subjective Multivariate Normal
MULTIVARIATE STOCHASTIC SIMULATION WITH SUBJECTIVE MULTIVARIATE NORMAL DISTRIBUTIONS1 Peter J. Ince2 and Joseph Buongiorno3 Abstract.-In many applications of Monte Carlo simulation in forestry or forest products, it may be known that some variables are correlated. However, for simplicity, in most simulations it has been assumed that random variables are independently distributed. This report describes an alternative Monte Carlo simulation technique for subjectivelyassessed multivariate normal distributions. The method requires subjective estimates of the 99-percent confidence interval for the expected value of each random variable and of the partial correlations among the variables. The technique can be used to generate pseudorandom data corresponding to the specified distribution. If the subjective parameters do not yield a positive definite covariance matrix, the technique determines minimal adjustments in variance assumptions needed to restore positive definiteness. The method is validated and then applied to a capital investment simulation for a new papermaking technology.In that example, with ten correlated random variables, no significant difference was detected between multivariate stochastic simulation results and results that ignored the correlation. In general, however, data correlation could affect results of stochastic simulation, as shown by the validation results. INTRODUCTION MONTE CARLO TECHNIQUE Generally, a mathematical model is used in stochastic The Monte Carlo simulation technique utilizes three simulation studies. In addition to randomness, correlation may essential elements: (1) a mathematical model to calculate a exist among the variables or parameters of such models.In the discrete numerical result or outcome as a function of one or case of forest ecosystems, for example, growth can be more discrete variables, (2) a sequence of random (or influenced by correlated variables, such as temperatures and pseudorandom) numbers to represent random probabilities, and precipitations. -
Stochastic Simulation
Agribusiness Analysis and Forecasting Stochastic Simulation Henry Bryant Texas A&M University Henry Bryant (Texas A&M University) Agribusiness Analysis and Forecasting 1 / 19 Stochastic Simulation In economics we use simulation because we can not experiment on live subjects, a business, or the economy without injury. In other fields they can create an experiment Health sciences they feed (or treat) lots of lab rats on different chemicals to see the results. Animal science researchers feed multiple pens of steers, chickens, cows, etc. on different rations. Engineers run a motor under different controlled situations (temp, RPMs, lubricants, fuel mixes). Vets treat different pens of animals with different meds. Agronomists set up randomized block treatments for a particular seed variety with different fertilizer levels. Henry Bryant (Texas A&M University) Agribusiness Analysis and Forecasting 2 / 19 Probability Distributions Parametric and Non-Parametric Distributions Parametric Dist. have known and well defined parameters that force their shapes to known patterns. Normal Distribution - Mean and Standard Deviation. Uniform - Minimum and Maximum Bernoulli - Probability of true Beta - Alpha, Beta, Minimum, Maximum Non-Parametric Distributions do not have pre-set shapes based on known parameters. The parameters are estimated each time to make the shape of the distribution fit the data. Empirical { Actual Observations and their Probabilities. Henry Bryant (Texas A&M University) Agribusiness Analysis and Forecasting 3 / 19 Typical Problem for Risk Analysis We have a stochastic variable that needs to be included in a business model. For example: Price forecast has residuals we could not explain and they are the stochastic component we need to simulate. -
Stochastic Vs. Deterministic Modeling of Intracellular Viral Kinetics R
J. theor. Biol. (2002) 218, 309–321 doi:10.1006/yjtbi.3078, available online at http://www.idealibrary.com on Stochastic vs. Deterministic Modeling of Intracellular Viral Kinetics R. Srivastavawz,L.Youw,J.Summersy and J.Yinnw wDepartment of Chemical Engineering, University of Wisconsin, 3633 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, U.S.A., zMcArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, WI 53706, U.S.A. and yDepartment of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, U.S.A. (Received on 5 February 2002, Accepted in revised form on 3 May 2002) Within its host cell, a complex coupling of transcription, translation, genome replication, assembly, and virus release processes determines the growth rate of a virus. Mathematical models that account for these processes can provide insights into the understanding as to how the overall growth cycle depends on its constituent reactions. Deterministic models based on ordinary differential equations can capture essential relationships among virus constituents. However, an infection may be initiated by a single virus particle that delivers its genome, a single molecule of DNA or RNA, to its host cell. Under such conditions, a stochastic model that allows for inherent fluctuations in the levels of viral constituents may yield qualitatively different behavior. To compare modeling approaches, we developed a simple model of the intracellular kinetics of a generic virus, which could be implemented deterministically or stochastically. The model accounted for reactions that synthesized and depleted viral nucleic acids and structural proteins. Linear stability analysis of the deterministic model showed the existence of two nodes, one stable and one unstable. -
Random Numbers and Stochastic Simulation
Stochastic Simulation and Randomness Random Number Generators Quasi-Random Sequences Scientific Computing: An Introductory Survey Chapter 13 – Random Numbers and Stochastic Simulation Prof. Michael T. Heath Department of Computer Science University of Illinois at Urbana-Champaign Copyright c 2002. Reproduction permitted for noncommercial, educational use only. Michael T. Heath Scientific Computing 1 / 17 Stochastic Simulation and Randomness Random Number Generators Quasi-Random Sequences Stochastic Simulation Stochastic simulation mimics or replicates behavior of system by exploiting randomness to obtain statistical sample of possible outcomes Because of randomness involved, simulation methods are also known as Monte Carlo methods Such methods are useful for studying Nondeterministic (stochastic) processes Deterministic systems that are too complicated to model analytically Deterministic problems whose high dimensionality makes standard discretizations infeasible (e.g., Monte Carlo integration) < interactive example > < interactive example > Michael T. Heath Scientific Computing 2 / 17 Stochastic Simulation and Randomness Random Number Generators Quasi-Random Sequences Stochastic Simulation, continued Two main requirements for using stochastic simulation methods are Knowledge of relevant probability distributions Supply of random numbers for making random choices Knowledge of relevant probability distributions depends on theoretical or empirical information about physical system being simulated By simulating large number of trials, probability -
Arxiv:2008.11456V2 [Physics.Optics]
Efficient stochastic simulation of rate equations and photon statistics of nanolasers Emil C. Andr´e,1 Jesper Mørk,1, 2 and Martijn Wubs1,2, ∗ 1Department of Photonics Engineering, Technical University of Denmark, Ørsteds Plads 345A, DK-2800 Kgs. Lyngby, Denmark 2NanoPhoton - Center for Nanophotonics, Technical University of Denmark, Ørsteds Plads 345A, DK-2800 Kgs. Lyngby, Denmark Based on a rate equation model for single-mode two-level lasers, two algorithms for stochastically simulating the dynamics and steady-state behaviour of micro- and nanolasers are described in detail. Both methods lead to steady-state photon numbers and statistics characteristic of lasers, but one of the algorithms is shown to be significantly more efficient. This algorithm, known as Gillespie’s First Reaction Method (FRM), gives up to a thousandfold reduction in computation time compared to earlier algorithms, while also circumventing numerical issues regarding time-increment size and ordering of events. The FRM is used to examine intra-cavity photon distributions, and it is found that the numerical results follow the analytics exactly. Finally, the FRM is applied to a set of slightly altered rate equations, and it is shown that both the analytical and numerical results exhibit features that are typically associated with the presence of strong inter-emitter correlations in nanolasers. I. INTRODUCTION transitions from thermal to coherent emission, and we will investigate the prospects of introducing effectively Optical cavities on the micro- and nanometer scale can altered rates of emission in the rate equations as a way reduce the number of available modes for light emission to qualitatively describe the effects of collective inter- and increase the coupling of spontaneously emitted light emitter correlations.