Miracle-dz/UniFAR-FTUs huggingface dataset:
Recycling Intermediate Steps to Improve Hamiltonian Monte Carlo

Hamiltonian Monte Carlo (HMC) and related algorithms have become routinely used in Bayesian computation. In this article, we present a simple and provably accurate method to improve the efficiency of HMC and related algorithms with essentially no extra computational cost. This is achieved by {recycling the intermediate states along simulated trajectories of Hamiltonian dynamics. Standard algorithms use only the end points of trajectories, wastefully discarding all the intermediate states. Compared to the alternative methods for utilizing the intermediate states, our algorithm is simpler to apply in practice and requires little programming effort beyond the usual implementations of HMC and related algorithms. Our algorithm applies straightforwardly to the no-U-turn sampler, arguably the most popular variant of HMC. Through a variety of experiments, we demonstrate that our recycling algorithm yields substantial computational efficiency gains.
Consistent community detection in multi-relational data through restricted multi-layer stochastic blockmodel

In recent years there has been an increased interest in statistical analysis of data with multiple types of relations among a set of entities. Such multi-relational data can be represented as multi-layer graphs where the set of vertices represents the entities and multiple types of edges represent the different relations among them. For community detection in multi-layer graphs, we consider two random graph models, the multi-layer stochastic blockmodel (MLSBM) and a model with a restricted parameter space, the restricted multi-layer stochastic blockmodel (RMLSBM). We derive consistency results for community assignments of the maximum likelihood estimators (MLEs) in both models where MLSBM is assumed to be the true model, and either the number of nodes or the number of types of edges or both grow. We compare MLEs in the two models with other baseline approaches, such as separate modeling of layers, aggregating the layers and majority voting. RMLSBM is shown to have advantage over MLSBM when either the growth rate of the number of communities is high or the growth rate of the average degree of the component graphs in the multi-graph is low. We also derive minimax rates of error and sharp thresholds for achieving consistency of community detection in both models, which are then used to compare the multi-layer models with a baseline model, the aggregate stochastic block model. The simulation studies and real data applications confirm the superior performance of the multi-layer approaches in comparison to the baseline procedures.
Bayesian Computing with INLA: A Review

The key operation in Bayesian inference is to compute high-dimensional integrals. An old approximate technique is the Laplace method or approximation, which dates back to Pierre-Simon Laplace (1774). This simple idea approximates the integrand with a second-order Taylor expansion around the mode and computes the integral analytically. By developing a nested version of this classical idea, combined with modern numerical techniques for sparse matrices, we obtain the approach of integrated nested Laplace approximations (INLA) to do approximate Bayesian inference for latent Gaussian models (LGMs). LGMs represent an important model abstraction for Bayesian inference and include a large proportion of the statistical models used today. In this review, we discuss the reasons for the success of the INLA approach, the R-INLA package, why it is so accurate, why the approximations are very quick to compute, and why LGMs make such a useful concept for Bayesian computing.
Quantile Processes for Semi and Nonparametric Regression

A collection of quantile curves provides a complete picture of conditional distributions. Properly centered and scaled versions of estimated curves at various quantile levels give rise to the so-called quantile regression process (QRP). In this paper, we establish weak convergence of QRP in a general series approximation framework, which includes linear models with increasing dimension, nonparametric models and partial linear models. An interesting consequence is obtained in the last class of models, where parametric and non-parametric estimators are shown to be asymptotically independent. Applications of our general process convergence results include the construction of non-crossing quantile curves and the estimation of conditional distribution functions. As a result of independent interest, we obtain a series of Bahadur representations with exponential bounds for tail probabilities of all remainder terms. Bounds of this kind are potentially useful in analyzing statistical inference procedures under divide-and-conquer setup.
Handling Missing Data in Within-Trial Cost-Effectiveness Analysis: a Review with Future Guidelines

Cost-Effectiveness Analyses (CEAs) alongside randomised controlled trials (RCTs) are increasingly often designed to collect resource use and preference-based health status data for the purpose of healthcare technology assessment. However, because of the way these measures are collected, they are prone to missing data, which can ultimately affect the decision of whether an intervention is good value for money. We examine how missing cost and effect outcome data are handled in RCT-based CEAs, complementing a previous review (covering 2003-2009, 88 articles) with a new systematic review (2009-2015, 81 articles) focussing on two different perspectives. First, we review the description of the missing data, the statistical methods used to deal with them, and the quality of the judgement underpinning the choice of these methods. Second, we provide guidelines on how the information about missingness and related methods should be presented to improve the reporting and handling of missing data. Our review shows that missing data in within-RCT CEAs are still often inadequately handled and the overall level of information provided to support the chosen methods is rarely satisfactory.
Optimization for Gaussian Processes via Chaining

In this paper, we consider the problem of stochastic optimization under a bandit feedback model. We generalize the GP-UCB algorithm [Srinivas and al., 2012] to arbitrary kernels and search spaces. To do so, we use a notion of localized chaining to control the supremum of a Gaussian process, and provide a novel optimization scheme based on the computation of covering numbers. The theoretical bounds we obtain on the cumulative regret are more generic and present the same convergence rates as the GP-UCB algorithm. Finally, the algorithm is shown to be empirically more efficient than its natural competitors on simple and complex input spaces.
String Gaussian Process Kernels

We introduce a new class of nonstationary kernels, which we derive as covariance functions of a novel family of stochastic processes we refer to as string Gaussian processes (string GPs). We construct string GPs to allow for multiple types of local patterns in the data, while ensuring a mild global regularity condition. In this paper, we illustrate the efficacy of the approach using synthetic data and demonstrate that the model outperforms competing approaches on well studied, real-life datasets that exhibit nonstationary features.
Regularized Functional Canonical Correlation Analysis for Stochastic Processes

In this paper we derive the asymptotic distributions of two distinct regularized estimators for functional canonical correlation as well as their associated eigenvalues, eigenvectors and projection operators. The methods we developed utilize regularized estimators which approach the functional operators based in reproducing kernel Hilbert spaces (RKHS) as the regularization parameter approaches zero. In addition to providing some justification for the RKHS methods, we explore the asymptotics of regularized operators associated with both Tikhinov and truncated singular value decomposition (TSVD) type regularization. Together, these regularization methods represent two of the most commonly utilized forms of regularization.
Speeding up bootstrap computations: a vectorized implementation for statistics based on sample moments

In this note we propose a vectorized implementation of the non-parametric bootstrap for statistics based on sample moments. Basically, we adopt the multinomial sampling formulation of the non-parametric bootstrap, and compute bootstrap replications of sample moment statistics by simply weighting the observed data according to multinomial counts, instead of evaluating the statistic on a re-sampled version of the observed data. Using this formulation we can generate a matrix of bootstrap weights and compute the entire vector of bootstrap replications with a few matrix multiplications. Vectorization is particularly important for matrix-oriented programming languages such as R, where matrix/vector calculations tend to be faster than scalar operations implemented in a loop. We illustrate the gain in computational speed achieved by the vectorized implementation in real and simulated data sets, when bootstrapping Pearson's sample correlation coefficient.
Modeling the effect of temperature on ozone-related mortality

Climate change is expected to alter the distribution of ambient ozone levels and temperatures which, in turn, may impact public health. Much research has focused on the effect of short-term ozone exposures on mortality and morbidity while controlling for temperature as a confounder, but less is known about the joint effects of ozone and temperature. The extent of the health effects of changing ozone levels and temperatures will depend on whether these effects are additive or synergistic. In this paper we propose a spatial, semi-parametric model to estimate the joint ozone-temperature risk surfaces in 95 US urban areas. Our methodology restricts the ozone-temperature risk surfaces to be monotone in ozone and allows for both nonadditive and nonlinear effects of ozone and temperature. We use data from the National Mortality and Morbidity Air Pollution Study (NMMAPS) and show that the proposed model fits the data better than additive linear and nonlinear models. We then examine the synergistic effect of ozone and temperature both nationally and locally and find evidence of a nonlinear ozone effect and an ozone-temperature interaction at higher temperatures and ozone concentrations.
Achieving a Hyperlocal Housing Price Index: Overcoming Data Sparsity by Bayesian Dynamical Modeling of Multiple Data Streams

Understanding how housing values evolve over time is important to policy makers, consumers and real estate professionals. Existing methods for constructing housing indices are computed at a coarse spatial granularity, such as metropolitan regions, which can mask or distort price dynamics apparent in local markets, such as neighborhoods and census tracts. A challenge in moving to estimates at, for example, the census tract level is the sparsity of spatiotemporally localized house sales observations. Our work aims at addressing this challenge by leveraging observations from multiple census tracts discovered to have correlated valuation dynamics. Our proposed Bayesian nonparametric approach builds on the framework of latent factor models to enable a flexible, data-driven method for inferring the clustering of correlated census tracts. We explore methods for scalability and parallelizability of computations, yielding a housing valuation index at the level of census tract rather than zip code, and on a monthly basis rather than quarterly. Our analysis is provided on a large Seattle metropolitan housing dataset.
Gaussian Approximation of General Nonparametric Posterior Distributions

In a general class of Bayesian nonparametric models, we prove that the posterior distribution can be asymptotically approximated by a Gaussian process. Our results apply to nonparametric exponential family that contains both Gaussian and non-Gaussian regression, and also hold for both efficient (root-n) and inefficient (non root-n) estimation. Our general approximation theorem does not rely on posterior conjugacy, and can be verified in a class of Gaussian process priors that has a smoothing spline interpretation [59, 44]. In particular, the limiting posterior measure becomes prior-free under a Bayesian version of "under-smoothing" condition. Finally, we apply our approximation theorem to examine the asymptotic frequentist properties of Bayesian procedures such as credible regions and credible intervals.
Generalized Spectral Kernels

In this paper we propose a family of tractable kernels that is dense in the family of bounded positive semi-definite functions (i.e. can approximate any bounded kernel with arbitrary precision). We start by discussing the case of stationary kernels, and propose a family of spectral kernels that extends existing approaches such as spectral mixture kernels and sparse spectrum kernels. Our extension has two primary advantages. Firstly, unlike existing spectral approaches that yield infinite differentiability, the kernels we introduce allow learning the degree of differentiability of the latent function in Gaussian process (GP) models and functions in the reproducing kernel Hilbert space (RKHS) in other kernel methods. Secondly, we show that some of the kernels we propose require fewer parameters than existing spectral kernels for the same accuracy, thereby leading to faster and more robust inference. Finally, we generalize our approach and propose a flexible and tractable family of spectral kernels that we prove can approximate any continuous bounded nonstationary kernel.
Tensor Decomposition With Generalized Lasso Penalties

ABSTRACT We present an approach for penalized tensor decomposition (PTD) that estimates smoothly varying latent factors in multiway data. This generalizes existing work on sparse tensor decomposition and penalized matrix decompositions, in a manner parallel to the generalized lasso for regression and smoothing problems. Our approach presents many nontrivial challenges at the intersection of modeling and computation, which are studied in detail. An efficient coordinate-wise optimization algorithm for PTD is presented, and its convergence properties are characterized. The method is applied both to simulated data and real data on flu hospitalizations in Texas and motion-capture data from video cameras. These results show that our penalized tensor decomposition can offer major improvements on existing methods for analyzing multiway data that exhibit smooth spatial or temporal features.
A framework for statistical network modeling

Basic principles of statistical inference are commonly violated in network data analysis. Under the current approach, it is often impossible to identify a model that accommodates known empirical behaviors, possesses crucial inferential properties, and accurately models the data generating process. In the absence of one or more of these properties, sensible inference from network data cannot be assured. Our proposed framework decomposes every network model into a (relatively) exchangeable data generating process} and a sampling mechanism that relates observed data to the population network. This framework, which encompasses all models in current use as well as many new models, such as edge exchangeable and relationally exchangeable models, that lie outside the existing paradigm, offers a sound context within which to develop theory and methods for network analysis.
Degradation-based residual life prediction under different environments

Degradation modeling has traditionally relied on historical signals to estimate the behavior of the underlying degradation process. Many models assume that these historical signals are acquired under the same environmental conditions and can be observed along the entire lifespan of a component. In this paper, we relax these assumptions and present a more general statistical framework for modeling degradation signals that may have been collected under different types of environmental conditions. In addition, we consider applications where the historical signals are not necessarily observed continuously, that is, historical signals are sparse or fragmented. We consider the case where historical degradation signals are collected under known environmental states and another case where the environmental conditions are unknown during the acquisition of these historical data. For the first case, we use a classification algorithm to identify the environmental state of the units operating in the field. In the second case, a clustering step is required for clustering the historical degradation signals. The proposed model can provide accurate predictions of the lifetime or residual life distributions of engineering components that are still operated in the field. This is demonstrated by using simulated degradation signals as well as vibration-based degradation signals acquired from a rotating machinery setup.
An Overview of the Estimation of Large Covariance and Precision Matrices

Summary The estimation of large covariance and precision matrices is fundamental in modern multivariate analysis. However, problems arise from the statistical analysis of large panel economic and financial data. The covariance matrix reveals marginal correlations between variables, while the precision matrix encodes conditional correlations between pairs of variables given the remaining variables. In this paper, we provide a selective review of several recent developments on the estimation of large covariance and precision matrices. We focus on two general approaches: a rank-based method and a factor-model-based method. Theories and applications of both approaches are presented. These methods are expected to be widely applicable to the analysis of economic and financial data.
Quantifying Distributional Model Risk Via Optimal Transport

This paper deals with the problem of quantifying the impact of model misspecification when computing general expected values of interest. The methodology that we propose is applicable in great generality, in particular, we provide examples involving path dependent expectations of stochastic processes. Our approach consists in computing bounds for the expectation of interest regardless of the probability measure used, as long as the measure lies within a prescribed tolerance measured in terms of a flexible class of distances from a suitable baseline model. These distances, based on optimal transportation between probability measures, include Wasserstein's distances as particular cases. The proposed methodology is well-suited for risk analysis, as we demonstrate with a number of applications. We also discuss how to estimate the tolerance region non-parametrically using Skorokhod-type embeddings in some of these applications.
The Gibbs-plaid biclustering model

We propose and develop a Bayesian plaid model for biclustering that accounts for the prior dependency between genes (and/or conditions) through a stochastic relational graph. This work is motivated by the need for improved understanding of the molecular mechanisms of human diseases for which effective drugs are lacking, and based on the extensive raw data available through gene expression profiling. We model the prior dependency information from biological knowledge gathered from gene ontologies. Our model, the Gibbs-plaid model, assumes that the relational graph is governed by a Gibbs random field. To estimate the posterior distribution of the bicluster membership labels, we develop a stochastic algorithm that is partly based on the Wang-Landau flat-histogram algorithm. We apply our method to a gene expression database created from the study of retinal detachment, with the aim of confirming known or finding novel subnetworks of proteins associated with this disorder.
Non-stationary Spatial Modelling with Applications to Spatial Prediction of Precipitation

A non-stationary spatial Gaussian random field (GRF) is described as the solution of an inhomogeneous stochastic partial dierential equation (SPDE), where the covariance structure of the GRF is controlled by the coecients in the SPDE. This allows for a flexible way to vary the covariance structure, where intuition about the resulting structure can be gained from the local behaviour of the dierential equation. Additionally, computations can be done with computationally convenient Gaussian Markov random fields which approximate the true GRFs. The model is applied to a dataset of annual precipitation in the conterminous US. The non-stationary model performs better than a stationary model measured with both CRPS and the logarithmic scoring rule.
Efficient and adaptive linear regression in semi-supervised settings

We consider the linear regression problem under semi-supervised settings wherein the available data typically consists of: (i) a small or moderate sized 'labeled' data, and (ii) a much larger sized 'unlabeled' data. Such data arises naturally from settings where the outcome, unlike the covariates, is expensive to obtain, a frequent scenario in modern studies involving large databases like electronic medical records (EMR). Supervised estimators like the ordinary least squares (OLS) estimator utilize only the labeled data. It is often of interest to investigate if and when the unlabeled data can be exploited to improve estimation of the regression parameter in the adopted linear model. In this paper, we propose a class of 'Efficient and Adaptive Semi-Supervised Estimators' (EASE) to improve estimation efficiency. The EASE are two-step estimators adaptive to model mis-specification, leading to improved (optimal in some cases) efficiency under model mis-specification, and equal (optimal) efficiency under a linear model. This adaptive property, often unaddressed in the existing literature, is crucial for advocating 'safe' use of the unlabeled data. The construction of EASE primarily involves a flexible 'semi-non-parametric' imputation, including a smoothing step that works well even when the number of covariates is not small; and a follow up 'refitting' step along with a cross-validation (CV) strategy both of which have useful practical as well as theoretical implications towards addressing two important issues: under-smoothing and over-fitting. We establish asymptotic results including consistency, asymptotic normality and the adaptive properties of EASE. We also provide influence function expansions and a 'double' CV strategy for inference. The results are further validated through extensive simulations, followed by application to an EMR study on auto-immunity.
Some Considerations on the Back Door Theorem and Conditional Randomization

Abstract In this work, we propose a different “surgical modified model” for the construction of counterfactual variables under non-parametric structural equation models. This approach allows the simultaneous representation of counterfactual responses and observed treatment assignment, at least when the intervention is done in one node. Using the new proposal, the d-separation criterion is used to verify conditions related with ignorability or conditional ignorability, and a new proof of the back door theorem is provided under this framework