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Ajay Jasra

Publications and source records attributed to Ajay Jasra.

At least 127 records · Page 7Linked to original sources
arXiv2013

Computational Methods for a Class of Network Models

In the following article we provide an exposition of exact computational methods to perform parameter inference from partially observed network models. In particular, we consider the duplication attachment (DA) model which has a likelihood function that typically cannot be evaluated in any reasonable computational time. We consider a number of importance sampling (IS) and sequential Monte Carlo (SMC) methods for approximating the likelihood of the network model for a fixed parameter value. It is well-known that for IS, the relative variance of the likelihood estimate typically grows at an exponential rate in the time parameter (here this is associated to the size of the network): we prove that, under assumptions, the SMC method will have relative variance which can grow only polynomially. In order to perform parameter estimation, we develop particle Markov chain Monte Carlo (PMCMC) algorithms to perform Bayesian inference. Such algorithms use the afore-mentioned SMC algorithms within the transition dynamics. The approaches are illustrated numerically.

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arXiv2013

An Adaptive Sequential Monte Carlo Algorithm for Computing Permanents

We consider the computation of the permanent of a binary n by n matrix. It is well- known that the exact computation is a #P complete problem. A variety of Markov chain Monte Carlo (MCMC) computational algorithms have been introduced in the literature whose cost, in order to achieve a given level of accuracy, is O(n^7 log^4(n)). These algorithms use a particular collection of probability distributions, the `ideal' of which, (in some sense) are not known and need to be approximated. In this paper we propose an adaptive sequential Monte Carlo (SMC) algorithm that can both estimate the permanent and the ideal sequence of probabilities on the fly, with little user input. We provide theoretical results associated to the SMC estimate of the permanent, establishing its convergence and analyzing the relative variance of the estimate, in particular computating explicit bounds on the relative variance which depend upon n. Using this latter result, we provide a lower-bound on the computational cost, in order to achieve an arbitrarily small relative variance; we find that this cost is O(n^4 log^4(n)). Some numerical simulations are also given.

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arXiv2013

The Alive Particle Filter

In the following article we develop a particle filter for approximating Feynman-Kac models with indicator potentials. Examples of such models include approximate Bayesian computation (ABC) posteriors associated with hidden Markov models (HMMs) or rare-event problems. Such models require the use of advanced particle filter or Markov chain Monte Carlo (MCMC) algorithms e.g. Jasra et al. (2012), to perform estimation. One of the drawbacks of existing particle filters, is that they may 'collapse', in that the algorithm may terminate early, due to the indicator potentials. In this article, using a special case of the locally adaptive particle filter in Lee et al. (2013), which is closely related to Le Gland & Oudjane (2004), we use an algorithm which can deal with this latter problem, whilst introducing a random cost per-time step. This algorithm is investigated from a theoretical perspective and several results are given which help to validate the algorithms and to provide guidelines for their implementation. In addition, we show how this algorithm can be used within MCMC, using particle MCMC (Andrieu et al. 2010). Numerical examples are presented for ABC approximations of HMMs.

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arXiv2013

Approximate Inference for Observation Driven Time Series Models with Intractable Likelihoods

In the following article we consider approximate Bayesian parameter inference for observation driven time series models. Such statistical models appear in a wide variety of applications, including econometrics and applied mathematics. This article considers the scenario where the likelihood function cannot be evaluated point-wise; in such cases, one cannot perform exact statistical inference, including parameter estimation, which often requires advanced computational algorithms, such as Markov chain Monte Carlo (MCMC). We introduce a new approximation based upon approximate Bayesian computation (ABC). Under some conditions, we show that as $n\rightarrow\infty$, with $n$ the length of the time series, the ABC posterior has, almost surely, a maximum \emph{a posteriori} (MAP) estimator of the parameters which is different from the true parameter. However, a noisy ABC MAP, which perturbs the original data, asymptotically converges to the true parameter, almost surely. In order to draw statistical inference, for the ABC approximation adopted, standard MCMC algorithms can have acceptance probabilities that fall at an exponential rate in $n$ and slightly more advanced algorithms can mix poorly. We develop a new and improved MCMC kernel, which is based upon an exact approximation of a marginal algorithm, whose cost per-iteration is random but the expected cost, for good performance, is shown to be $\mathcal{O}(n^2)$ per-iteration.

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arXiv2013

The TimeMachine for Inference on Stochastic Trees

The simulation of genealogical trees backwards in time, from observations up to the most recent common ancestor (MRCA), is hindered by the fact that, while approaching the root of the tree, coalescent events become rarer, with a corresponding increase in computation time. The recently proposed "Time Machine" tackles this issue by stopping the simulation of the tree before reaching the MRCA and correcting for the induced bias. We present a computationally efficient implementation of this approach that exploits multithreading.

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arXiv2013

A sequential algorithm for fast fitting of Dirichlet process mixture models

In this article we propose an improvement on the sequential updating and greedy search (SUGS) algorithm Wang and Dunson for fast fitting of Dirichlet process mixture models. The SUGS algorithm provides a means for very fast approximate Bayesian inference for mixture data which is particularly of use when data sets are so large that many standard Markov chain Monte Carlo (MCMC) algorithms cannot be applied efficiently, or take a prohibitively long time to converge. In particular, these ideas are used to initially interrogate the data, and to refine models such that one can potentially apply exact data analysis later on. SUGS relies upon sequentially allocating data to clusters and proceeding with an update of the posterior on the subsequent allocations and parameters which assumes this allocation is correct. Our modification softens this approach, by providing a probability distribution over allocations, with a similar computational cost; this approach has an interpretation as a variational Bayes procedure and hence we term it variational SUGS (VSUGS). It is shown in simulated examples that VSUGS can out-perform, in terms of density estimation and classification, the original SUGS algorithm in many scenarios. In addition, we present a data analysis for flow cytometry data, and SNP data via a three-class dirichlet process mixture model illustrating the apparent improvement over SUGS.

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arXiv2012

Static Parameter Estimation for ABC Approximations of Hidden Markov Models

In this article we focus on Maximum Likelihood estimation (MLE) for the static parameters of hidden Markov models (HMMs). We will consider the case where one cannot or does not want to compute the conditional likelihood density of the observation given the hidden state because of increased computational complexity or analytical intractability. Instead we will assume that one may obtain samples from this conditional likelihood and hence use approximate Bayesian computation (ABC) approximations of the original HMM. ABC approximations are biased, but the bias can be controlled to arbitrary precision via a parameter ε>0; the bias typically goes to zero as ε\searrow 0. We first establish that the bias in the log-likelihood and gradient of the log-likelihood of the ABC approximation, for a fixed batch of data, is no worse than \mathcal{O}(nε), n being the number of data; hence, for computational reasons, one might expect reasonable parameter estimates using such an ABC approximation. Turning to the computational problem of estimating $θ$, we propose, using the ABC-sequential Monte Carlo (SMC) algorithm in Jasra et al. (2012), an approach based upon simultaneous perturbation stochastic approximation (SPSA). Our method is investigated on two numerical examples

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arXiv2012

Marginal Likelihood Computation for Hidden Markov Models via Generalized Two-Filter Smoothing

In this note we introduce an estimate for the marginal likelihood associated to hidden Markov models (HMMs) using sequential Monte Carlo (SMC) approximations of the generalized two-filter smoothing decomposition (Briers, 2010). This estimate is shown to be unbiased and a central limit theorem (CLT) is established. This latter CLT also allows one to prove a CLT associated to estimates of expectations w.r.t. a marginal of the joint smoothing distribution; these form some of the first theoretical results associated to the SMC approximation of the generalized two-filter smoothing decomposition. The new estimate and its application is investigated from a numerical perspective.

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arXiv2012

Approximate Bayesian Computation for Smoothing

We consider a method for approximate inference in hidden Markov models (HMMs). The method circumvents the need to evaluate conditional densities of observations given the hidden states. It may be considered an instance of Approximate Bayesian Computation (ABC) and it involves the introduction of auxiliary variables valued in the same space as the observations. The quality of the approximation may be controlled to arbitrary precision through a parameter ε>0 . We provide theoretical results which quantify, in terms of ε, the ABC error in approximation of expectations of additive functionals with respect to the smoothing distributions. Under regularity assumptions, this error is O(nε), where n is the number of time steps over which smoothing is performed. For numerical implementation we adopt the forward-only sequential Monte Carlo (SMC) scheme of [16] and quantify the combined error from the ABC and SMC approximations. This forms some of the first quantitative results for ABC methods which jointly treat the ABC and simulation errors, with a finite number of data and simulated samples. When the HMM has unknown static parameters, we consider particle Markov chain Monte Carlo [2] (PMCMC) methods for batch statistical inference.

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arXiv2012

A Bayesian Mixture of Lasso Regressions with t-Errors

Motivated by a challenging problem in financial trading we are presented with a mixture of regressions with variable selection problem. In this regard, one is faced with data which possess outliers, skewness and, simultaneously, due to the nature of financial trading, one would like to be able to construct clusters with specific predictors that are fairly sparse. We develop a Bayesian mixture of lasso regressions with $t-$errors to reflect these specific demands. The resulting model is necessarily complex and to fit the model to real data, we develop a state-of-the-art Particle Markov chain Monte Carlo (PMCMC) algorithm based upon sequential Monte Carlo (SMC) methods. The model and algorithm are investigated on both simulated and real data.

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arXiv2012

On the Stability of Sequential Monte Carlo Methods in High Dimensions

We investigate the stability of a Sequential Monte Carlo (SMC) method applied to the problem of sampling from a target distribution on $\mathbb{R}^d$ for large $d$. It is well known that using a single importance sampling step one produces an approximation for the target that deteriorates as the dimension $d$ increases, unless the number of Monte Carlo samples $N$ increases at an exponential rate in $d$. We show that this degeneracy can be avoided by introducing a sequence of artificial targets, starting from a `simple' density and moving to the one of interest, using an SMC method to sample from the sequence. Using this class of SMC methods with a fixed number of samples, one can produce an approximation for which the effective sample size (ESS) converges to a random variable $\varepsilon_N$ as $d\rightarrow\infty$ with $1<\varepsilon_{N}<N$. The convergence is achieved with a computational cost proportional to $Nd^2$. If $\varepsilon_N\ll N$, we can raise its value by introducing a number of resampling steps, say $m$ (where $m$ is independent of $d$). In this case, ESS converges to a random variable $\varepsilon_{N,m}$ as $d\rightarrow\infty$ and $\lim_{m\to\infty}\varepsilon_{N,m}=N$. Also, we show that the Monte Carlo error for estimating a fixed dimensional marginal expectation is of order $\frac{1}{\sqrt{N}}$ uniformly in $d$. The results imply that, in high dimensions, SMC algorithms can efficiently control the variability of the importance sampling weights and estimate fixed dimensional marginals at a cost which is less than exponential in $d$ and indicate that, in high dimensions, resampling leads to a reduction in the Monte Carlo error and increase in the ESS.

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arXiv2012

On adaptive resampling strategies for sequential Monte Carlo methods

Sequential Monte Carlo (SMC) methods are a class of techniques to sample approximately from any sequence of probability distributions using a combination of importance sampling and resampling steps. This paper is concerned with the convergence analysis of a class of SMC methods where the times at which resampling occurs are computed online using criteria such as the effective sample size. This is a popular approach amongst practitioners but there are very few convergence results available for these methods. By combining semigroup techniques with an original coupling argument, we obtain functional central limit theorems and uniform exponential concentration estimates for these algorithms.

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arXiv2012

Linear Variance Bounds for Particle Approximations of Time-Homogeneous Feynman-Kac Formulae

This article establishes sufficient conditions for a linear-in-time bound on the non-asymptotic variance of particle approximations of time-homogeneous Feynman-Kac formulae. These formulae appear in a wide variety of applications including option pricing in finance and risk sensitive control in engineering. In direct Monte Carlo approximation of these formulae, the non-asymptotic variance typically increases at an exponential rate in the time parameter. It is shown that a linear bound holds when a non-negative kernel, defined by the logarithmic potential function and Markov kernel which specify the Feynman-Kac model, satisfies a type of multiplicative drift condition and other regularity assumptions. Examples illustrate that these conditions are general and flexible enough to accommodate two rather extreme cases, which can occur in the context of a non-compact state space: 1) when the potential function is bounded above, not bounded below and the Markov kernel is not ergodic; and 2) when the potential function is not bounded above, but the Markov kernel itself satisfies a multiplicative drift condition.

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arXiv2012

Robust model-based clustering with gene ranking

Cluster analysis of biological samples using gene expression measurements is a common task which aids the discovery of heterogeneous biological sub-populations having distinct mRNA profiles. Several model-based clustering algorithms have been proposed in which the distribution of gene expression values within each sub-group is assumed to be Gaussian. In the presence of noise and extreme observations, a mixture of Gaussian densities may over-fit and overestimate the true number of clusters. Moreover, commonly used model-based clustering algorithms do not generally provide a mechanism to quantify the relative contribution of each gene to the final partitioning of the data. We propose a penalised mixture of Student's t distributions for model-based clustering and gene ranking. Together with a bootstrap procedure, the proposed approach provides a means for ranking genes according to their contributions to the clustering process. Experimental results show that the algorithm performs well comparably to traditional Gaussian mixtures in the presence of outliers and longer tailed distributions. The algorithm also identifies the true informative genes with high sensitivity, and achieves improved model selection. An illustrative application to breast cancer data is also presented which confirms established tumor subclasses.

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arXiv2012

Inference for a Class of Partially Observed Point Process Models

This paper presents a simulation-based framework for sequential inference from partially and discretely observed point process (PP's) models with static parameters. Taking on a Bayesian perspective for the static parameters, we build upon sequential Monte Carlo (SMC) methods, investigating the problems of performing sequential filtering and smoothing in complex examples, where current methods often fail. We consider various approaches for approximating posterior distributions using SMC. Our approaches, with some theoretical discussion are illustrated on a doubly stochastic point process applied in the context of finance.

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arXiv2012

Bayesian Parameter Inference for Partially Observed Stopped Processes

In this article we consider Bayesian parameter inference associated to partially-observed stochastic processes that start from a set B0 and are stopped or killed at the first hitting time of a known set A. Such processes occur naturally within the context of a wide variety of applications. The associated posterior distributions are highly complex and posterior parameter inference requires the use of advanced Markov chain Monte Carlo (MCMC) techniques. Our approach uses a recently introduced simulation methodology, particle Markov chain Monte Carlo (PMCMC) (Andrieu et. al. 2010 [1]), where sequential Monte Carlo (SMC) approximations (see Doucet et. al. 2001 [18] and Liu 2001 [27]) are embedded within MCMC. However, when the parameter of interest is fixed, standard SMC algorithms are not always appropriate for many stopped processes. In Chen et. al. [11] and Del Moral 2004 [15] the authors introduce SMC approximations of multi-level Feynman-Kac formulae, which can lead to more efficient algorithms. This is achieved by devising a sequence of nested sets from B0 to A and then perform the resampling step only when the samples of the process reach intermediate level sets in the sequence. Naturally, the choice of the intermediate level sets is critical to the performance of such a scheme. In this paper, we demonstrate that multi-level SMC algorithms can be used as a proposal in PMCMC. In addition, we propose a flexible strategy that adapts the level sets for different parameter proposals. Our methodology is illustrated on the coalescent model with migration.

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arXiv2011

Error Bounds and Normalizing Constants for Sequential Monte Carlo in High Dimensions

In a recent paper Beskos et al (2011), the Sequential Monte Carlo (SMC) sampler introduced in Del Moral et al (2006), Neal (2001) has been shown to be asymptotically stable in the dimension of the state space d at a cost that is only polynomial in d, when N the number of Monte Carlo samples, is fixed. More precisely, it has been established that the effective sample size (ESS) of the ensuing (approximate) sample and the Monte Carlo error of fixed dimensional marginals will converge as $d$ grows, with a computational cost of $\mathcal{O}(Nd^2)$. In the present work, further results on SMC methods in high dimensions are provided as $d\to\infty$ and with $N$ fixed. We deduce an explicit bound on the Monte-Carlo error for estimates derived using the SMC sampler and the exact asymptotic relative $\mathbb{L}_2$-error of the estimate of the normalizing constant. We also establish marginal propagation of chaos properties of the algorithm. The accuracy in high-dimensions of some approximate SMC-based filtering schemes is also discussed.

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