Markov Chain Monte Carlo Algorithms for Gaussian Processes
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Scalable Nonparametric Bayesian Inference on Point Processes with Gaussian Processes
Scalable Nonparametric Bayesian Inference on Point Processes with Gaussian Processes Yves-Laurent Kom Samo [email protected] Stephen Roberts [email protected] Deparment of Engineering Science and Oxford-Man Institute, University of Oxford Abstract 2. Related Work In this paper we propose an efficient, scalable Non-parametric inference on point processes has been ex- non-parametric Gaussian process model for in- tensively studied in the literature. Rathbum & Cressie ference on Poisson point processes. Our model (1994) and Moeller et al. (1998) used a finite-dimensional does not resort to gridding the domain or to intro- piecewise constant log-Gaussian for the intensity function. ducing latent thinning points. Unlike competing Such approximations are limited in that the choice of the 3 models that scale as O(n ) over n data points, grid on which to represent the intensity function is arbitrary 2 our model has a complexity O(nk ) where k and one has to trade-off precision with computational com- n. We propose a MCMC sampler and show that plexity and numerical accuracy, with the complexity being the model obtained is faster, more accurate and cubic in the precision and exponential in the dimension of generates less correlated samples than competing the input space. Kottas (2006) and Kottas & Sanso (2007) approaches on both synthetic and real-life data. used a Dirichlet process mixture of Beta distributions as Finally, we show that our model easily handles prior for the normalised intensity function of a Poisson data sizes not considered thus far by alternate ap- process. Cunningham et al. -
Deep Neural Networks As Gaussian Processes
Published as a conference paper at ICLR 2018 DEEP NEURAL NETWORKS AS GAUSSIAN PROCESSES Jaehoon Lee∗y, Yasaman Bahri∗y, Roman Novak , Samuel S. Schoenholz, Jeffrey Pennington, Jascha Sohl-Dickstein Google Brain fjaehlee, yasamanb, romann, schsam, jpennin, [email protected] ABSTRACT It has long been known that a single-layer fully-connected neural network with an i.i.d. prior over its parameters is equivalent to a Gaussian process (GP), in the limit of infinite network width. This correspondence enables exact Bayesian inference for infinite width neural networks on regression tasks by means of evaluating the corresponding GP. Recently, kernel functions which mimic multi-layer random neural networks have been developed, but only outside of a Bayesian framework. As such, previous work has not identified that these kernels can be used as co- variance functions for GPs and allow fully Bayesian prediction with a deep neural network. In this work, we derive the exact equivalence between infinitely wide deep net- works and GPs. We further develop a computationally efficient pipeline to com- pute the covariance function for these GPs. We then use the resulting GPs to per- form Bayesian inference for wide deep neural networks on MNIST and CIFAR- 10. We observe that trained neural network accuracy approaches that of the corre- sponding GP with increasing layer width, and that the GP uncertainty is strongly correlated with trained network prediction error. We further find that test perfor- mance increases as finite-width trained networks are made wider and more similar to a GP, and thus that GP predictions typically outperform those of finite-width networks. -
Markov Chain Monte Carlo Convergence Diagnostics: a Comparative Review
Markov Chain Monte Carlo Convergence Diagnostics: A Comparative Review By Mary Kathryn Cowles and Bradley P. Carlin1 Abstract A critical issue for users of Markov Chain Monte Carlo (MCMC) methods in applications is how to determine when it is safe to stop sampling and use the samples to estimate characteristics of the distribu- tion of interest. Research into methods of computing theoretical convergence bounds holds promise for the future but currently has yielded relatively little that is of practical use in applied work. Consequently, most MCMC users address the convergence problem by applying diagnostic tools to the output produced by running their samplers. After giving a brief overview of the area, we provide an expository review of thirteen convergence diagnostics, describing the theoretical basis and practical implementation of each. We then compare their performance in two simple models and conclude that all the methods can fail to detect the sorts of convergence failure they were designed to identify. We thus recommend a combination of strategies aimed at evaluating and accelerating MCMC sampler convergence, including applying diagnostic procedures to a small number of parallel chains, monitoring autocorrelations and cross- correlations, and modifying parameterizations or sampling algorithms appropriately. We emphasize, however, that it is not possible to say with certainty that a finite sample from an MCMC algorithm is rep- resentative of an underlying stationary distribution. 1 Mary Kathryn Cowles is Assistant Professor of Biostatistics, Harvard School of Public Health, Boston, MA 02115. Bradley P. Carlin is Associate Professor, Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455. -
Meta-Learning MCMC Proposals
Meta-Learning MCMC Proposals Tongzhou Wang∗ Yi Wu Facebook AI Research University of California, Berkeley [email protected] [email protected] David A. Moorey Stuart J. Russell Google University of California, Berkeley [email protected] [email protected] Abstract Effective implementations of sampling-based probabilistic inference often require manually constructed, model-specific proposals. Inspired by recent progresses in meta-learning for training learning agents that can generalize to unseen environ- ments, we propose a meta-learning approach to building effective and generalizable MCMC proposals. We parametrize the proposal as a neural network to provide fast approximations to block Gibbs conditionals. The learned neural proposals generalize to occurrences of common structural motifs across different models, allowing for the construction of a library of learned inference primitives that can accelerate inference on unseen models with no model-specific training required. We explore several applications including open-universe Gaussian mixture models, in which our learned proposals outperform a hand-tuned sampler, and a real-world named entity recognition task, in which our sampler yields higher final F1 scores than classical single-site Gibbs sampling. 1 Introduction Model-based probabilistic inference is a highly successful paradigm for machine learning, with applications to tasks as diverse as movie recommendation [31], visual scene perception [17], music transcription [3], etc. People learn and plan using mental models, and indeed the entire enterprise of modern science can be viewed as constructing a sophisticated hierarchy of models of physical, mental, and social phenomena. Probabilistic programming provides a formal representation of models as sample-generating programs, promising the ability to explore a even richer range of models. -
Markov Chain Monte Carlo Edps 590BAY
Markov Chain Monte Carlo Edps 590BAY Carolyn J. Anderson Department of Educational Psychology c Board of Trustees, University of Illinois Fall 2019 Overivew Bayesian computing Markov Chains Metropolis Example Practice Assessment Metropolis 2 Practice Overview ◮ Introduction to Bayesian computing. ◮ Markov Chain ◮ Metropolis algorithm for mean of normal given fixed variance. ◮ Revisit anorexia data. ◮ Practice problem with SAT data. ◮ Some tools for assessing convergence ◮ Metropolis algorithm for mean and variance of normal. ◮ Anorexia data. ◮ Practice problem. ◮ Summary Depending on the book that you select for this course, read either Gelman et al. pp 2751-291 or Kruschke Chapters pp 143–218. I am relying more on Gelman et al. C.J. Anderson (Illinois) MCMC Fall 2019 2.2/ 45 Overivew Bayesian computing Markov Chains Metropolis Example Practice Assessment Metropolis 2 Practice Introduction to Bayesian Computing ◮ Our major goal is to approximate the posterior distributions of unknown parameters and use them to estimate parameters. ◮ The analytic computations are fine for simple problems, ◮ Beta-binomial for bounded counts ◮ Normal-normal for continuous variables ◮ Gamma-Poisson for (unbounded) counts ◮ Dirichelt-Multinomial for multicategory variables (i.e., a categorical variable) ◮ Models in the exponential family with small number of parameters ◮ For large number of parameters and more complex models ◮ Algebra of analytic solution becomes overwhelming ◮ Grid takes too much time. ◮ Too difficult for most applications. C.J. Anderson (Illinois) MCMC Fall 2019 3.3/ 45 Overivew Bayesian computing Markov Chains Metropolis Example Practice Assessment Metropolis 2 Practice Steps in Modeling Recall that the steps in an analysis: 1. Choose model for data (i.e., p(y θ)) and model for parameters | (i.e., p(θ) and p(θ y)). -
Gaussian Process Dynamical Models for Human Motion
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, VOL. 30, NO. 2, FEBRUARY 2008 283 Gaussian Process Dynamical Models for Human Motion Jack M. Wang, David J. Fleet, Senior Member, IEEE, and Aaron Hertzmann, Member, IEEE Abstract—We introduce Gaussian process dynamical models (GPDMs) for nonlinear time series analysis, with applications to learning models of human pose and motion from high-dimensional motion capture data. A GPDM is a latent variable model. It comprises a low- dimensional latent space with associated dynamics, as well as a map from the latent space to an observation space. We marginalize out the model parameters in closed form by using Gaussian process priors for both the dynamical and the observation mappings. This results in a nonparametric model for dynamical systems that accounts for uncertainty in the model. We demonstrate the approach and compare four learning algorithms on human motion capture data, in which each pose is 50-dimensional. Despite the use of small data sets, the GPDM learns an effective representation of the nonlinear dynamics in these spaces. Index Terms—Machine learning, motion, tracking, animation, stochastic processes, time series analysis. Ç 1INTRODUCTION OOD statistical models for human motion are important models such as hidden Markov model (HMM) and linear Gfor many applications in vision and graphics, notably dynamical systems (LDS) are efficient and easily learned visual tracking, activity recognition, and computer anima- but limited in their expressiveness for complex motions. tion. It is well known in computer vision that the estimation More expressive models such as switching linear dynamical of 3D human motion from a monocular video sequence is systems (SLDS) and nonlinear dynamical systems (NLDS), highly ambiguous. -
Modelling Multi-Object Activity by Gaussian Processes 1
LOY et al.: MODELLING MULTI-OBJECT ACTIVITY BY GAUSSIAN PROCESSES 1 Modelling Multi-object Activity by Gaussian Processes Chen Change Loy School of EECS [email protected] Queen Mary University of London Tao Xiang E1 4NS London, UK [email protected] Shaogang Gong [email protected] Abstract We present a new approach for activity modelling and anomaly detection based on non-parametric Gaussian Process (GP) models. Specifically, GP regression models are formulated to learn non-linear relationships between multi-object activity patterns ob- served from semantically decomposed regions in complex scenes. Predictive distribu- tions are inferred from the regression models to compare with the actual observations for real-time anomaly detection. The use of a flexible, non-parametric model alleviates the difficult problem of selecting appropriate model complexity encountered in parametric models such as Dynamic Bayesian Networks (DBNs). Crucially, our GP models need fewer parameters; they are thus less likely to overfit given sparse data. In addition, our approach is robust to the inevitable noise in activity representation as noise is modelled explicitly in the GP models. Experimental results on a public traffic scene show that our models outperform DBNs in terms of anomaly sensitivity, noise robustness, and flexibil- ity in modelling complex activity. 1 Introduction Activity modelling and automatic anomaly detection in video have received increasing at- tention due to the recent large-scale deployments of surveillance cameras. These tasks are non-trivial because complex activity patterns in a busy public space involve multiple objects interacting with each other over space and time, whilst anomalies are often rare, ambigu- ous and can be easily confused with noise caused by low image quality, unstable lighting condition and occlusion. -
Financial Time Series Volatility Analysis Using Gaussian Process State-Space Models
Financial Time Series Volatility Analysis Using Gaussian Process State-Space Models by Jianan Han Bachelor of Engineering, Hebei Normal University, China, 2010 A thesis presented to Ryerson University in partial fulfillment of the requirements for the degree of Master of Applied Science in the Program of Electrical and Computer Engineering Toronto, Ontario, Canada, 2015 c Jianan Han 2015 AUTHOR'S DECLARATION FOR ELECTRONIC SUBMISSION OF A THESIS I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I authorize Ryerson University to lend this thesis to other institutions or individuals for the purpose of scholarly research. I further authorize Ryerson University to reproduce this thesis by photocopying or by other means, in total or in part, at the request of other institutions or individuals for the purpose of scholarly research. I understand that my dissertation may be made electronically available to the public. ii Financial Time Series Volatility Analysis Using Gaussian Process State-Space Models Master of Applied Science 2015 Jianan Han Electrical and Computer Engineering Ryerson University Abstract In this thesis, we propose a novel nonparametric modeling framework for financial time series data analysis, and we apply the framework to the problem of time varying volatility modeling. Existing parametric models have a rigid transition function form and they often have over-fitting problems when model parameters are estimated using maximum likelihood methods. These drawbacks effect the models' forecast performance. To solve this problem, we take Bayesian nonparametric modeling approach. -
Gaussian-Random-Process.Pdf
The Gaussian Random Process Perhaps the most important continuous state-space random process in communications systems in the Gaussian random process, which, we shall see is very similar to, and shares many properties with the jointly Gaussian random variable that we studied previously (see lecture notes and chapter-4). X(t); t 2 T is a Gaussian r.p., if, for any positive integer n, any choice of coefficients ak; 1 k n; and any choice ≤ ≤ of sample time tk ; 1 k n; the random variable given by the following weighted sum of random variables is Gaussian:2 T ≤ ≤ X(t) = a1X(t1) + a2X(t2) + ::: + anX(tn) using vector notation we can express this as follows: X(t) = [X(t1);X(t2);:::;X(tn)] which, according to our study of jointly Gaussian r.v.s is an n-dimensional Gaussian r.v.. Hence, its pdf is known since we know the pdf of a jointly Gaussian random variable. For the random process, however, there is also the nasty little parameter t to worry about!! The best way to see the connection to the Gaussian random variable and understand the pdf of a random process is by example: Example: Determining the Distribution of a Gaussian Process Consider a continuous time random variable X(t); t with continuous state-space (in this case amplitude) defined by the following expression: 2 R X(t) = Y1 + tY2 where, Y1 and Y2 are independent Gaussian distributed random variables with zero mean and variance 2 2 σ : Y1;Y2 N(0; σ ). The problem is to find the one and two dimensional probability density functions of the random! process X(t): The one-dimensional distribution of a random process, also known as the univariate distribution is denoted by the notation FX;1(u; t) and defined as: P r X(t) u . -
Bayesian Phylogenetics and Markov Chain Monte Carlo Will Freyman
IB200, Spring 2016 University of California, Berkeley Lecture 12: Bayesian phylogenetics and Markov chain Monte Carlo Will Freyman 1 Basic Probability Theory Probability is a quantitative measurement of the likelihood of an outcome of some random process. The probability of an event, like flipping a coin and getting heads is notated P (heads). The probability of getting tails is then 1 − P (heads) = P (tails). • The joint probability of event A and event B both occuring is written as P (A; B). The joint probability of mutually exclusive events, like flipping a coin once and getting heads and tails, is 0. • The probability of A occuring given that B has already occurred is written P (AjB), which is read \the probability of A given B". This is a conditional probability. • The marginal probability of A is P (A), which is calculated by summing or integrating the joint probability over B. In other words, P (A) = P (A; B) + P (A; not B). • Joint, conditional, and marginal probabilities can be combined with the expression P (A; B) = P (A)P (BjA) = P (B)P (AjB). • The above expression can be rearranged into Bayes' theorem: P (BjA)P (A) P (AjB) = P (B) Bayes' theorem is a straightforward and uncontroversial way to calculate an inverse conditional probability. • If P (AjB) = P (A) and P (BjA) = P (B) then A and B are independent. Then the joint probability is calculated P (A; B) = P (A)P (B). 2 Interpretations of Probability What exactly is a probability? Does it really exist? There are two major interpretations of probability: • Frequentists believe that the probability of an event is its relative frequency over time. -
Gaussian Markov Processes
C. E. Rasmussen & C. K. I. Williams, Gaussian Processes for Machine Learning, the MIT Press, 2006, ISBN 026218253X. c 2006 Massachusetts Institute of Technology. www.GaussianProcess.org/gpml Appendix B Gaussian Markov Processes Particularly when the index set for a stochastic process is one-dimensional such as the real line or its discretization onto the integer lattice, it is very interesting to investigate the properties of Gaussian Markov processes (GMPs). In this Appendix we use X(t) to define a stochastic process with continuous time pa- rameter t. In the discrete time case the process is denoted ...,X−1,X0,X1,... etc. We assume that the process has zero mean and is, unless otherwise stated, stationary. A discrete-time autoregressive (AR) process of order p can be written as AR process p X Xt = akXt−k + b0Zt, (B.1) k=1 where Zt ∼ N (0, 1) and all Zt’s are i.i.d. Notice the order-p Markov property that given the history Xt−1,Xt−2,..., Xt depends only on the previous p X’s. This relationship can be conveniently expressed as a graphical model; part of an AR(2) process is illustrated in Figure B.1. The name autoregressive stems from the fact that Xt is predicted from the p previous X’s through a regression equation. If one stores the current X and the p − 1 previous values as a state vector, then the AR(p) scalar process can be written equivalently as a vector AR(1) process. Figure B.1: Graphical model illustrating an AR(2) process. -
FULLY BAYESIAN FIELD SLAM USING GAUSSIAN MARKOV RANDOM FIELDS Huan N
Asian Journal of Control, Vol. 18, No. 5, pp. 1–14, September 2016 Published online in Wiley Online Library (wileyonlinelibrary.com) DOI: 10.1002/asjc.1237 FULLY BAYESIAN FIELD SLAM USING GAUSSIAN MARKOV RANDOM FIELDS Huan N. Do, Mahdi Jadaliha, Mehmet Temel, and Jongeun Choi ABSTRACT This paper presents a fully Bayesian way to solve the simultaneous localization and spatial prediction problem using a Gaussian Markov random field (GMRF) model. The objective is to simultaneously localize robotic sensors and predict a spatial field of interest using sequentially collected noisy observations by robotic sensors. The set of observations consists of the observed noisy positions of robotic sensing vehicles and noisy measurements of a spatial field. To be flexible, the spatial field of interest is modeled by a GMRF with uncertain hyperparameters. We derive an approximate Bayesian solution to the problem of computing the predictive inferences of the GMRF and the localization, taking into account observations, uncertain hyperparameters, measurement noise, kinematics of robotic sensors, and uncertain localization. The effectiveness of the proposed algorithm is illustrated by simulation results as well as by experiment results. The experiment results successfully show the flexibility and adaptability of our fully Bayesian approach ina data-driven fashion. Key Words: Vision-based localization, spatial modeling, simultaneous localization and mapping (SLAM), Gaussian process regression, Gaussian Markov random field. I. INTRODUCTION However, there are a number of inapplicable situa- tions. For example, underwater autonomous gliders for Simultaneous localization and mapping (SLAM) ocean sampling cannot find usual geometrical models addresses the problem of a robot exploring an unknown from measurements of environmental variables such as environment under localization uncertainty [1].