arXiv subjects

Pierre E. Jacob

Publications and source records attributed to Pierre E. Jacob.

36 records · Page 2Linked to original sources

arXiv2019

Clustering Time Series with Nonlinear Dynamics: A Bayesian Non-Parametric and Particle-Based Approach

We propose a general statistical framework for clustering multiple time series that exhibit nonlinear dynamics into an a-priori-unknown number of sub-groups. Our motivation comes from neuroscience, where an important problem is to identify, within a large assembly of neurons, subsets that respond similarly to a stimulus or contingency. Upon modeling the multiple time series as the output of a Dirichlet process mixture of nonlinear state-space models, we derive a Metropolis-within-Gibbs algorithm for full Bayesian inference that alternates between sampling cluster assignments and sampling parameter values that form the basis of the clustering. The Metropolis step employs recent innovations in particle-based methods. We apply the framework to clustering time series acquired from the prefrontal cortex of mice in an experiment designed to characterize the neural underpinnings of fear.

stat.ML↗

arXiv2019

Unbiased Smoothing using Particle Independent Metropolis-Hastings

We consider the approximation of expectations with respect to the distribution of a latent Markov process given noisy measurements. This is known as the smoothing problem and is often approached with particle and Markov chain Monte Carlo (MCMC) methods. These methods provide consistent but biased estimators when run for a finite time. We propose a simple way of coupling two MCMC chains built using Particle Independent Metropolis-Hastings (PIMH) to produce unbiased smoothing estimators. Unbiased estimators are appealing in the context of parallel computing, and facilitate the construction of confidence intervals. The proposed scheme only requires access to off-the-shelf Particle Filters (PF) and is thus easier to implement than recently proposed unbiased smoothers. The approach is demonstrated on a Lévy-driven stochastic volatility model and a stochastic kinetic model.

stat.CO↗

arXiv2018

Unbiased estimation of log normalizing constants with applications to Bayesian cross-validation

Posterior distributions often feature intractable normalizing constants, called marginal likelihoods or evidence, that are useful for model comparison via Bayes factors. This has motivated a number of methods for estimating ratios of normalizing constants in statistics. In computational physics the logarithm of these ratios correspond to free energy differences. Combining unbiased Markov chain Monte Carlo estimators with path sampling, also called thermodynamic integration, we propose new unbiased estimators of the logarithm of ratios of normalizing constants. As a by-product, we propose unbiased estimators of the Bayesian cross-validation criterion. The proposed estimators are consistent, asymptotically Normal and can easily benefit from parallel processing devices. Various examples are considered for illustration.

stat.CO↗

arXiv2018

Bayesian model comparison with the Hyvärinen score: computation and consistency

The Bayes factor is a widely used criterion in model comparison and its logarithm is a difference of out-of-sample predictive scores under the logarithmic scoring rule. However, when some of the candidate models involve vague priors on their parameters, the log-Bayes factor features an arbitrary additive constant that hinders its interpretation. As an alternative, we consider model comparison using the Hyvärinen score. We propose a method to consistently estimate this score for parametric models, using sequential Monte Carlo methods. We show that this score can be estimated for models with tractable likelihoods as well as nonlinear non-Gaussian state-space models with intractable likelihoods. We prove the asymptotic consistency of this new model selection criterion under strong regularity assumptions in the case of non-nested models, and we provide qualitative insights for the nested case. We also use existing characterizations of proper scoring rules on discrete spaces to extend the Hyvärinen score to discrete observations. Our numerical illustrations include Lévy-driven stochastic volatility models and diffusion models for population dynamics.

stat.ME↗

arXiv2018

Smoothing with Couplings of Conditional Particle Filters

In state space models, smoothing refers to the task of estimating a latent stochastic process given noisy measurements related to the process. We propose an unbiased estimator of smoothing expectations. The lack-of-bias property has methodological benefits: independent estimators can be generated in parallel, and confidence intervals can be constructed from the central limit theorem to quantify the approximation error. To design unbiased estimators, we combine a generic debiasing technique for Markov chains with a Markov chain Monte Carlo algorithm for smoothing. The resulting procedure is widely applicable and we show in numerical experiments that the removal of the bias comes at a manageable increase in variance. We establish the validity of the proposed estimators under mild assumptions. Numerical experiments are provided on toy models, including a setting of highly-informative observations, and a realistic Lotka-Volterra model with an intractable transition density.

stat.ME↗

arXiv2018

Unbiased Hamiltonian Monte Carlo with couplings

We propose a methodology to parallelize Hamiltonian Monte Carlo estimators. Our approach constructs a pair of Hamiltonian Monte Carlo chains that are coupled in such a way that they meet exactly after some random number of iterations. These chains can then be combined so that resulting estimators are unbiased. This allows us to produce independent replicates in parallel and average them to obtain estimators that are consistent in the limit of the number of replicates, instead of the usual limit of the number of Markov chain iterations. We investigate the scalability of our coupling in high dimensions on a toy example. The choice of algorithmic parameters and the efficiency of our proposed methodology are then illustrated on a logistic regression with 300 covariates, and a log-Gaussian Cox point processes model with low to fine grained discretizations.

stat.CO↗

arXiv2017

Better together? Statistical learning in models made of modules

In modern applications, statisticians are faced with integrating heterogeneous data modalities relevant for an inference, prediction, or decision problem. In such circumstances, it is convenient to use a graphical model to represent the statistical dependencies, via a set of connected "modules", each relating to a specific data modality, and drawing on specific domain expertise in their development. In principle, given data, the conventional statistical update then allows for coherent uncertainty quantification and information propagation through and across the modules. However, misspecification of any module can contaminate the estimate and update of others, often in unpredictable ways. In various settings, particularly when certain modules are trusted more than others, practitioners have preferred to avoid learning with the full model in favor of approaches that restrict the information propagation between modules, for example by restricting propagation to only particular directions along the edges of the graph. In this article, we investigate why these modular approaches might be preferable to the full model in misspecified settings. We propose principled criteria to choose between modular and full-model approaches. The question arises in many applied settings, including large stochastic dynamical systems, meta-analysis, epidemiological models, air pollution models, pharmacokinetics-pharmacodynamics, and causal inference with propensity scores.

stat.ME↗

arXiv2016

Coupling of Particle Filters

Particle filters provide Monte Carlo approximations of intractable quantities such as point-wise evaluations of the likelihood in state space models. In many scenarios, the interest lies in the comparison of these quantities as some parameter or input varies. To facilitate such comparisons, we introduce and study methods to couple two particle filters in such a way that the correlation between the two underlying particle systems is increased. The motivation stems from the classic variance reduction technique of positively correlating two estimators. The key challenge in constructing such a coupling stems from the discontinuity of the resampling step of the particle filter. As our first contribution, we consider coupled resampling algorithms. Within bootstrap particle filters, they improve the precision of finite-difference estimators of the score vector and boost the performance of particle marginal Metropolis--Hastings algorithms for parameter inference. The second contribution arises from the use of these coupled resampling schemes within conditional particle filters, allowing for unbiased estimators of smoothing functionals. The result is a new smoothing strategy that operates by averaging a number of independent and unbiased estimators, which allows for 1) straightforward parallelization and 2) the construction of accurate error estimates. Neither of the above is possible with existing particle smoothers.

stat.ME↗

arXiv2016

Bayesian inference in non-Markovian state-space models with applications to fractional order systems

Battery impedance spectroscopy models are given by fractional order (FO) differential equations. In the discrete-time domain, they give rise to state-space models where the latent process is not Markovian. Parameter estimation for these models is therefore challenging, especially for non-commensurate FO models. In this paper, we propose a Bayesian approach to identify the parameters of generic FO systems. The computational challenge is tackled with particle Markov chain Monte Carlo methods, with an implementation specifically designed for the non-Markovian setting. The approach is then applied to estimate the parameters of a battery non-commensurate FO equivalent circuit model. Extensive simulations are provided to study the practical identifiability of model parameters and their sensitivity to the choice of prior distributions, the number of observations, the magnitude of the input signal and the measurement noise.

math.OC↗

arXiv2015

Structural Identifiability Analysis of Fractional Order Models with Applications in Battery Systems

This paper presents a method for structural identifiability analysis of fractional order systems by using the coefficient mapping concept to determine whether the model parameters can uniquely be identified from input-output data. The proposed method is applicable to general non-commensurate fractional order models. Examples are chosen from battery fractional order equivalent circuit models (FO-ECMs). The battery FO-ECM consists of a series of parallel resistors and constant phase elements (CPEs) with fractional derivatives appearing in the CPEs. The FO-ECM is non-commensurate if more than one CPE is considered in the model. Currently, estimation of battery FO-ECMs is performed mainly by fitting in the frequency domain, requiring costly electrochemical impedance spectroscopy equipment. This paper aims to analyse the structural identifiability of battery FO-ECMs directly in the time domain. It is shown that FO-ECMs with finite numbers of CPEs are structurally identifiable. In particular, the FO-ECM with a single CPE is structurally globally identifiable.

math.OC↗

arXiv2015

Derivative-Free Estimation of the Score Vector and Observed Information Matrix with Application to State-Space Models

Ionides, King et al. (see e.g. Inference for nonlinear dynamical systems, PNAS 103) have recently introduced an original approach to perform maximum likelihood parameter estimation in state-space models which only requires being able to simulate the latent Markov model according to its prior distribution. Their methodology relies on an approximation of the score vector for general statistical models based upon an artificial posterior distribution and bypasses the calculation of any derivative. We show here that this score estimator can be derived from a simple application of Stein's lemma and how an additional application of this lemma provides an original derivative-free estimator of the observed information matrix. We establish that these estimators exhibit robustness properties compared to finite difference estimators while their bias and variance scale as well as finite difference type estimators, including simultaneous perturbations (see e.g. Spall, IEEE Trans. on Automatic Control 37), with respect to the dimension of the parameter. For state-space models where sequential Monte Carlo computation is required, these estimators can be further improved. In this specific context, we derive original derivative-free estimators of the score vector and observed information matrix which are computed using sequential Monte Carlo approximations of smoothed additive functionals associated with a modified version of the original state-space model.

stat.ME↗

arXiv2015

Parallel resampling in the particle filter

Modern parallel computing devices, such as the graphics processing unit (GPU), have gained significant traction in scientific and statistical computing. They are particularly well-suited to data-parallel algorithms such as the particle filter, or more generally Sequential Monte Carlo (SMC), which are increasingly used in statistical inference. SMC methods carry a set of weighted particles through repeated propagation, weighting and resampling steps. The propagation and weighting steps are straightforward to parallelise, as they require only independent operations on each particle. The resampling step is more difficult, as standard schemes require a collective operation, such as a sum, across particle weights. Focusing on this resampling step, we analyse two alternative schemes that do not involve a collective operation (Metropolis and rejection resamplers), and compare them to standard schemes (multinomial, stratified and systematic resamplers). We find that, in certain circumstances, the alternative resamplers can perform significantly faster on a GPU, and to a lesser extent on a CPU, than the standard approaches. Moreover, in single precision, the standard approaches are numerically biased for upwards of hundreds of thousands of particles, while the alternatives are not. This is particularly important given greater single- than double-precision throughput on modern devices, and the consequent temptation to use single precision with a greater number of particles. Finally, we provide auxiliary functions useful for implementation, such as for the permutation of ancestry vectors to enable in-place propagation.

stat.CO↗

arXiv2015

Sequential Bayesian inference for implicit hidden Markov models and current limitations

Hidden Markov models can describe time series arising in various fields of science, by treating the data as noisy measurements of an arbitrarily complex Markov process. Sequential Monte Carlo (SMC) methods have become standard tools to estimate the hidden Markov process given the observations and a fixed parameter value. We review some of the recent developments allowing the inclusion of parameter uncertainty as well as model uncertainty. The shortcomings of the currently available methodology are emphasised from an algorithmic complexity perspective. The statistical objects of interest for time series analysis are illustrated on a toy "Lotka-Volterra" model used in population ecology. Some open challenges are discussed regarding the scalability of the reviewed methodology to longer time series, higher-dimensional state spaces and more flexible models.

stat.ME↗

arXiv2015

On nonnegative unbiased estimators

We study the existence of algorithms generating almost surely nonnegative unbiased estimators. We show that given a nonconstant real-valued function $f$ and a sequence of unbiased estimators of $λ\in\mathbb{R}$, there is no algorithm yielding almost surely nonnegative unbiased estimators of $f(λ)\in\mathbb{R}^+$. The study is motivated by pseudo-marginal Monte Carlo algorithms that rely on such nonnegative unbiased estimators. These methods allow "exact inference" in intractable models, in the sense that integrals with respect to a target distribution can be estimated without any systematic error, even though the associated probability density function cannot be evaluated pointwise. We discuss the consequences of our results on the applicability of pseudo-marginal algorithms and thus on the possibility of exact inference in intractable models. We illustrate our study with particular choices of functions $f$ corresponding to known challenges in statistics, such as exact simulation of diffusions, inference in large datasets and doubly intractable distributions.

stat.ME↗

arXiv2014

Path storage in the particle filter

This article considers the problem of storing the paths generated by a particle filter and more generally by a sequential Monte Carlo algorithm. It provides a theoretical result bounding the expected memory cost by $T + C N \log N$ where $T$ is the time horizon, $N$ is the number of particles and $C$ is a constant, as well as an efficient algorithm to realise this. The theoretical result and the algorithm are illustrated with numerical experiments.

stat.CO↗

arXiv2014

The Wang-Landau algorithm reaches the flat histogram criterion in finite time

The Wang-Landau algorithm aims at sampling from a probability distribution, while penalizing some regions of the state space and favoring others. It is widely used, but its convergence properties are still unknown. We show that for some variations of the algorithm, the Wang-Landau algorithm reaches the so-called flat histogram criterion in finite time, and that this criterion can be never reached for other variations. The arguments are shown in a simple context - compact spaces, density functions bounded from both sides - for the sake of clarity, and could be extended to more general contexts.

math.ST↗

arXiv2012

Feynman-Kac particle integration with geometric interacting jumps

This article is concerned with the design and analysis of discrete time Feynman-Kac particle integration models with geometric interacting jump processes. We analyze two general types of model, corresponding to whether the reference process is in continuous or discrete time. For the former, we consider discrete generation particle models defined by arbitrarily fine time mesh approximations of the Feynman-Kac models with continuous time path integrals. For the latter, we assume that the discrete process is observed at integer times and we design new approximation models with geometric interacting jumps in terms of a sequence of intermediate time steps between the integers. In both situations, we provide non asymptotic bias and variance theorems w.r.t. the time step and the size of the system, yielding what appear to be the first results of this type for this class of Feynman-Kac particle integration models. We also discuss uniform convergence estimates w.r.t. the time horizon. Our approach is based on an original semigroup analysis with first order decompositions of the fluctuation errors.

math.PR↗

arXiv2012

SMC^2: an efficient algorithm for sequential analysis of state-space models

We consider the generic problem of performing sequential Bayesian inference in a state-space model with observation process y, state process x and fixed parameter theta. An idealized approach would be to apply the iterated batch importance sampling (IBIS) algorithm of Chopin (2002). This is a sequential Monte Carlo algorithm in the theta-dimension, that samples values of theta, reweights iteratively these values using the likelihood increments p(y_t|y_1:t-1, theta), and rejuvenates the theta-particles through a resampling step and a MCMC update step. In state-space models these likelihood increments are intractable in most cases, but they may be unbiasedly estimated by a particle filter in the x-dimension, for any fixed theta. This motivates the SMC^2 algorithm proposed in this article: a sequential Monte Carlo algorithm, defined in the theta-dimension, which propagates and resamples many particle filters in the x-dimension. The filters in the x-dimension are an example of the random weight particle filter as in Fearnhead et al. (2010). On the other hand, the particle Markov chain Monte Carlo (PMCMC) framework developed in Andrieu et al. (2010) allows us to design appropriate MCMC rejuvenation steps. Thus, the theta-particles target the correct posterior distribution at each iteration t, despite the intractability of the likelihood increments. We explore the applicability of our algorithm in both sequential and non-sequential applications and consider various degrees of freedom, as for example increasing dynamically the number of x-particles. We contrast our approach to various competing methods, both conceptually and empirically through a detailed simulation study, included here and in a supplement, and based on particularly challenging examples.

stat.CO↗