Irregular functional data in which densely sampled curves are observed over different ranges pose a challenge for modeling and inference, and sensitivity to outlier curves is a concern in applications. Motivated by applications in quantitative ultrasound signal analysis, this paper investigates a class of robust M-estimators for partially observed functional data including functional location and quantile estimators. Consistency of the estimators is established under general conditions on the partial observation process. Under smoothness conditions on the class of M-estimators, asymptotic Gaussian process approximations are established and used for large sample inference. The large sample approximations justify a bootstrap approximation for robust inferences about the functional response process. The performance is demonstrated in simulations and in the analysis of irregular functional data from quantitative ultrasound analysis.
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 applie…
We consider continuous-time diffusion models driven by fractional Brownian motion. Observations are assumed to possess a non-trivial likelihood given the latent path. Due to the non-Markovianity and high-dimensionality of the latent paths, estimating posterior expectations is a computationally challenging undertaking. We present a reparameterization framework based on the Davies and Harte method for sampling stationary Gaussian processes and use this framework to construct a Markov chain Monte Carlo algorithm that allows computationally efficient Bayesian inference. The Markov chain Monte Carl…
Typical Bayesian inference requires parameter identification via likelihood parameterization, which has invited criticism for being less flexible than the Frequentist framework and subject to misspecification. Though misspecification may be avoided by functional parameter inference under a nonparametric model space, there does not exist a flexible Bayesian semiparametric model that would allow full control over the marginal prior over any general functional parameter. We present the technique of $θ$-augmentation which helps us manipulate nonparametric models into semiparametric ones that direc…
In this paper we consider Bayesian parameter inference for partially observed fractional Brownian motion (fBM) models. The approach we follow is to time-discretize the hidden process and then to design Markov chain Monte Carlo (MCMC) algorithms to sample from the posterior density on the parameters given data. We rely on a novel representation of the time discretization, which seeks to sample from an approximation of the posterior and then corrects via importance sampling; the approximation reduces the time (in terms of total observation time T) by O(T). This method is extended by using a mult…
In this article, we develop a semiparametric Bayesian estimation and model selection approach for partially linear additive models in conditional quantile regression. The asymmetric Laplace distribution provides a mechanism for Bayesian inferences of quantile regression models based on the check loss. The advantage of this new method is that nonlinear, linear and zero function components can be separated automatically and simultaneously during model fitting without the need of pre-specification or parameter tuning. This is achieved by spike-and-slab priors using two sets of indicator variables…
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 sequ…
Stochastic kinetic models are often used to describe complex biological processes. Typically these models are analytically intractable and have unknown parameters which need to be estimated from observed data. Ideally we would have measurements on all interacting chemical species in the process, observed continuously in time. However, in practice, measurements are taken only at a relatively few time-points. In some situations, only very limited observation of the process is available, such as when experimenters can only observe noisy observations on the proportion of cells that are alive. This…
Models of stochastic processes are widely used in almost all fields of science. Theory validation, parameter estimation, and prediction all require model calibration and statistical inference using data. However, data are almost always incomplete observations of reality. This leads to a great challenge for statistical inference because the likelihood function will be intractable for almost all partially observed stochastic processes. This renders many statistical methods, especially within a Bayesian framework, impossible to implement. Therefore, computationally expensive likelihood-free appro…
We provide a comprehensive semi-parametric study of Bayesian partially identified econometric models. While the existing literature on Bayesian partial identification has mostly focused on the structural parameter, our primary focus is on Bayesian credible sets (BCS's) of the unknown identified set and the posterior distribution of its support function. We construct a (two-sided) BCS based on the support function of the identified set. We prove the Bernstein-von Mises theorem for the posterior distribution of the support function. This powerful result in turn infers that, while the BCS and the…
Bayesian nonparametric (BNP) models provide elegant methods for discovering underlying latent features within a data set, but inference in such models can be slow. We exploit the fact that completely random measures, which commonly used models like the Dirichlet process and the beta-Bernoulli process can be expressed as, are decomposable into independent sub-measures. We use this decomposition to partition the latent measure into a finite measure containing only instantiated components, and an infinite measure containing all other components. We then select different inference algorithms for t…
Amortised inference enables scalable learning of sequential latent-variable models (LVMs) with the evidence lower bound (ELBO). In this setting, variational posteriors are often only partially conditioned. While the true posteriors depend, e.g., on the entire sequence of observations, approximate posteriors are only informed by past observations. This mimics the Bayesian filter -- a mixture of smoothing posteriors. Yet, we show that the ELBO objective forces partially-conditioned amortised posteriors to approximate products of smoothing posteriors instead. Consequently, the learned generative …
In the functional linear regression model, many methods have been proposed and studied to estimate the slope function while the functional predictor was observed in the entire domain. However, works on functional linear regression models with partially observed trajectories have received less attention. In this paper, to fill the literature gap we consider the scenario where individual functional predictor may be observed only on part of the domain. Depending on whether measurement error is presented in functional predictors, two methods are developed, one is based on linear functionals of the…
This paper is concerned with model averaging estimation for partially linear functional score models. These models predict a scalar response using both parametric effect of scalar predictors and non-parametric effect of a functional predictor. Within this context, we develop a Mallows-type criterion for choosing weights. The resulting model averaging estimator is proved to be asymptotically optimal under certain regularity conditions in terms of achieving the smallest possible squared error loss. Simulation studies demonstrate its superiority or comparability to information criterion score-bas…
In some multivariate problems with missing data, pairs of variables exist that are never observed together. For example, some modern biological tools can produce data of this form. As a result of this structure, the covariance matrix is only partially identifiable, and point estimation requires that identifying assumptions be made. These assumptions can introduce an unknown and potentially large bias into the inference. This paper presents a method based on semidefinite programming for automatically quantifying this potential bias by computing the range of possible equal-likelihood inferred va…
This article deals with the problem of functional classification for L2-valued random covariates when some of the covariates may have missing or unobservable fragments. Here, it is allowed for both the training sample as well as the new unclassified observation to have missing fragments in their functional covariates. Furthermore, unlike most previous results in the literature, where covariate fragments are typically assumed to be missing completely at random, we do not impose any such assumptions here. Given the observed segments of the curves, we construct a kernel-type classifier which is q…
New estimators for the mean and the covariance function for partially observed functional data are proposed using a detour via the fundamental theorem of calculus. The new estimators allow for a consistent estimation of the mean and covariance function under specific violations of the missing-completely-at-random assumption. The requirements of the estimation procedure can be tested using a sequential multiple hypothesis test procedure. An extensive simulation study compares the new estimators with the classical estimators from the literature in different missing data scenarios. The proposed m…
In causal estimation problems, the parameter of interest is often only partially identified, implying that the parameter cannot be recovered exactly, even with infinite data. Here, we study Bayesian inference for partially identified treatment effects in multi-treatment causal inference problems with unobserved confounding. In principle, inferring the partially identified treatment effects is natural under the Bayesian paradigm, but the results can be highly sensitive to parameterization and prior specification, often in surprising ways. It is thus essential to understand which aspects of the …
Hematopoiesis is the process of blood cell formation, through which progenitor stem cells differentiate into mature forms, such as white and red blood cells or mature platelets. While the precursors of the mature forms share many regulatory pathways involving common cellular nuclear factors, specific networks of regulation shape their fate towards one lineage or another. In this study, we aim to analyse the complex regulatory network that drives the formation of mature red blood cells and platelets from their common precursor. To this aim, we develop a dedicated graphical model which we infer …
Functional data analysis has been extensively conducted. In this study, we consider a partially functional model, under which some covariates are scalars and have linear effects, while some other variables are functional and have unspecified nonlinear effects. Significantly advancing from the existing literature, we consider a model with interactions between the functional and scalar covariates. To accommodate long-tailed error distributions which are not uncommon in data analysis, we adopt the quantile technique for estimation. To achieve more interpretable estimation, and to accommodate many…
Partially observed Markov process (POMP) models, also known as hidden Markov models or state space models, are ubiquitous tools for time series analysis. The R package pomp provides a very flexible framework for Monte Carlo statistical investigations using nonlinear, non-Gaussian POMP models. A range of modern statistical methods for POMP models have been implemented in this framework including sequential Monte Carlo, iterated filtering, particle Markov chain Monte Carlo, approximate Bayesian computation, maximum synthetic likelihood estimation, nonlinear forecasting, and trajectory matching. …
The Generalized Additive Model (GAM) is a powerful tool and has been well studied. This model class helps to identify additive regression structure. Via available test procedures one may identify the regression structure even sharper if some component functions have parametric form. The Generalized Additive Partially Linear Models (GAPLM) enjoy the simplicity of the GLM and the flexibility of the GAM because they combine both parametric and nonparametric components. We use the hybrid spline-backfitted kernel estimation method, which combines the best features of both spline and kernel methods …
In this paper, a competing risks model is analyzed based on improved adaptive type-II progressive censored sample (IAT-II PCS). Two independent competing causes of failures are considered. It is assumed that lifetimes of the competing causes of failure follow exponential distributions with different means. Maximum likelihood estimators (MLEs) for the unknown model parameters are obtained. Using asymptotic normality property of MLE, the asymptotic confidence intervals are constructed. Existence and uniqueness properties of the MLEs are studied. Further, bootstrap confidence intervals are comput…
We construct a generalization of the Ornstein-Uhlenbeck processes on the cone of covariance matrices endowed with the Log-Euclidean and the Affine-Invariant metrics. Our development exploits the Riemannian geometric structure of symmetric positive definite matrices viewed as a differential manifold. We then provide Bayesian inference for discretely observed diffusion processes of covariance matrices based on an MCMC algorithm built with the help of a novel diffusion bridge sampler accounting for the geometric structure. Our proposed algorithm is illustrated with a real data financial applicati…
We consider the problem of static Bayesian inference for partially observed Levy-process models. We develop a methodology which allows one to infer static parameters and some states of the process, without a bias from the time-discretization of the afore-mentioned Levy process. The unbiased method is exceptionally amenable to parallel implementation and can be computationally efficient relative to competing approaches. We implement the method on S & P 500 log-return daily data and compare it to some Markov chain Monte Carlo (MCMC) algorithm.
This paper considers inference in a partially identified moment (in)equality model with many moment inequalities. We propose a novel two-step inference procedure that combines the methods proposed by Chernozhukov, Chetverikov and Kato (2018a) (CCK18, hereafter) with a first step moment inequality selection based on the Lasso. Our method controls asymptotic size uniformly, both in underlying parameter and data distribution. Also, the power of our method compares favorably with that of the corresponding two-step method in CCK18 for large parts of the parameter space, both in theory and in simula…
A novel generalized additive scalar-on-function regression model for partially observed multidimensional functional data: An application to air quality classification
We develop a stochastic epidemic model progressing over dynamic networks, where infection rates are heterogeneous and may vary with individual-level covariates. The joint dynamics are modeled as a continuous-time Markov chain such that disease transmission is constrained by the contact network structure, and network evolution is in turn influenced by individual disease statuses. To accommodate partial epidemic observations commonly seen in real-world data, we propose a likelihood-based inference method based on the stochastic EM algorithm, introducing key innovations that include efficient con…
A new statistical procedure, based on a modified spline basis, is proposed to identify the linear components in the panel data model with fixed effects. Under some mild assumptions, the proposed procedure is shown to consistently estimate the underlying regression function, correctly select the linear components, and effectively conduct the statistical inference. When compared to existing methods for detection of linearity in the panel model, our approach is demonstrated to be theoretically justified as well as practically convenient. We provide a computational algorithm that implements the pr…
Topic models, and more specifically the class of Latent Dirichlet Allocation (LDA), are widely used for probabilistic modeling of text. MCMC sampling from the posterior distribution is typically performed using a collapsed Gibbs sampler. We propose a parallel sparse partially collapsed Gibbs sampler and compare its speed and efficiency to state-of-the-art samplers for topic models on five well-known text corpora of differing sizes and properties. In particular, we propose and compare two different strategies for sampling the parameter block with latent topic indicators. The experiments show th…
In this paper, we apply empirical likelihood method to inference for the regression parameters in the partial functional linear regression models based on B spline. We prove that the empirical log likelihood ratio for the regression parameters converges in law to a weighted sum of independent chi square distributions and run simulations to assess the finite sample performance of our method.
We propose a generative model and an inference scheme for epidemic processes on dynamic, adaptive contact networks. Network evolution is formulated as a link-Markovian process, which is then coupled to an individual-level stochastic SIR model, in order to describe the interplay between epidemic dynamics on a network and network link changes. A Markov chain Monte Carlo framework is developed for likelihood-based inference from partial epidemic observations, with a novel data augmentation algorithm specifically designed to deal with missing individual recovery times under the dynamic network set…
We consider inference for the mean and covariance functions of covariate adjusted functional data using Local Linear Kernel (LLK) estimators. By means of a double asymptotic, we differentiate between sparse and dense covariate adjusted functional data - depending on the relative order of m (the discretization points per function) and n (the number of functions). Our simulation results demonstrate that the existing asymptotic normality results can lead to severely misleading inferences in finite samples. We explain this phenomenon based on our theoretical results and propose finite-sample corre…
In the near future, millions of load curves measuring the electricity consumption of French households in small time grids (probably half hours) will be available. All these collected load curves represent a huge amount of information which could be exploited using survey sampling techniques. In particular, the total consumption of a specific cus- tomer group (for example all the customers of an electricity supplier) could be estimated using unequal probability random sampling methods. Unfortunately, data collection may undergo technical problems resulting in missing values. In this paper we s…
We propose simple inferential approaches for the fixed effects in complex functional mixed effects models. We estimate the fixed effects under the independence of functional residuals assumption and then bootstrap independent units (e.g. subjects) to estimate the variability of and conduct inference in the form of hypothesis testing on the fixed effects parameters. Simulations show excellent coverage probability of the confidence intervals and size of tests. Methods are motivated by and applied to the Baltimore Longitudinal Study of Aging (BLSA), though they are applicable to other studies tha…
We introduce flexible robust functional regression models, using various heavy-tailed processes, including a Student $t$-process. We propose efficient algorithms in estimating parameters for the marginal mean inferences and in predicting conditional means as well interpolation and extrapolation for the subject-specific inferences. We develop bootstrap prediction intervals for conditional mean curves. Numerical studies show that the proposed model provides robust analysis against data contamination or distribution misspecification, and the proposed prediction intervals maintain the nominal conf…
