Insights into complex, high-dimensional data can be obtained by discovering features of the data that match or do not match a model of interest. To formalize this task, we introduce the "data selection" problem: finding a lower-dimensional statistic - such as a subset of variables - that is well fit by a given parametric model of interest. A fully Bayesian approach to data selection would be to parametrically model the value of the statistic, nonparametrically model the remaining "background" components of the data, and perform standard Bayesian model selection for the choice of statistic. However, fitting a nonparametric model to high-dimensional data tends to be highly inefficient, statistically and computationally. We propose a novel score for performing both data selection and model selection, the "Stein volume criterion", that takes the form of a generalized marginal likelihood with a kernelized Stein discrepancy in place of the Kullback-Leibler divergence. The Stein volume criterion does not require one to fit or even specify a nonparametric background model, making it straightforward to compute - in many cases it is as simple as fitting the parametric model of interest with an alternative objective function. We prove that the Stein volume criterion is consistent for both data selection and model selection, and we establish consistency and asymptotic normality (Bernstein-von Mises) of the corresponding generalized posterior on parameters. We validate our method in simulation and apply it to the analysis of single-cell RNA sequencing datasets using probabilistic principal components analysis and a spin glass model of gene regulation.
Discrete data are abundant and often arise as counts or rounded data. However, even for linear regression models, conjugate priors and closed-form posteriors are typically unavailable, thereby necessitating approximations or Markov chain Monte Carlo for posterior inference. For a broad class of count and rounded data regression models, we introduce conjugate priors that enable closed-form posterior inference. Key posterior and predictive functionals are computable analytically or via direct Monte Carlo simulation. Crucially, the predictive distributions are discrete to match the support of the data and can be evaluated or simulated jointly across multiple covariate values. These tools are broadly useful for linear regression, nonlinear models via basis expansions, and model and variable selection. Multiple simulation studies demonstrate significant advantages in computing, predictive modeling, and selection relative to existing alternatives.
We consider Bayesian multiple hypothesis problem with independent and identically distributed observations. The classical, Sanov's theorem-based, analysis of the error probability allows one to characterize the best achievable error exponent. However, this analysis does not generalize to the case where the true distributions of the hypothesis are not exact or partially known via some nominal distributions. This problem has practical significance, because the nominal distributions may be quantized versions of the true distributions in a hardware implementation, or they may be estimates of the true distributions obtained from labeled training sequences as in statistical classification. In this paper, we develop a type-based analysis to investigate Bayesian multiple hypothesis testing problem. Our analysis allows one to explicitly calculate the error exponent of a given type and extends the classical analysis. As a generalization of the proposed method, we derive a robust test and obtain its error exponent for the case where the hypothesis distributions are not known but there exist nominal distribution that are close to true distributions in variational distance.
We consider online sequential decision problems where an agent must balance exploration and exploitation. We derive a set of Bayesian `optimistic' policies which, in the stochastic multi-armed bandit case, includes the Thompson sampling policy. We provide a new analysis showing that any algorithm producing policies in the optimistic set enjoys $\tilde O(\sqrt{AT})$ Bayesian regret for a problem with $A$ actions after $T$ rounds. We extend the regret analysis for optimistic policies to bilinear saddle-point problems which include zero-sum matrix games and constrained bandits as special cases. In this case we show that Thompson sampling can produce policies outside of the optimistic set and suffer linear regret in some instances. Finding a policy inside the optimistic set amounts to solving a convex optimization problem and we call the resulting algorithm `variational Bayesian optimistic sampling' (VBOS). The procedure works for any posteriors, \ie, it does not require the posterior to have any special properties, such as log-concavity, unimodality, or smoothness. The variational view of the problem has many useful properties, including the ability to tune the exploration-exploitation tradeoff, add regularization, incorporate constraints, and linearly parameterize the policy.
In this paper, we establish minimax optimal rates of convergence for prediction in a semi-functional linear model that consists of a functional component and a less smooth nonparametric component. Our results reveal that the smoother functional component can be learned with the minimax rate as if the nonparametric component were known. More specifically, a double-penalized least squares method is adopted to estimate both the functional and nonparametric components within the framework of reproducing kernel Hilbert spaces. By virtue of the representer theorem, an efficient algorithm that requires no iterations is proposed to solve the corresponding optimization problem, where the regularization parameters are selected by the generalized cross validation criterion. Numerical studies are provided to demonstrate the effectiveness of the method and to verify the theoretical analysis.
Population adjustment methods such as matching-adjusted indirect comparison (MAIC) are increasingly used to compare marginal treatment effects when there are cross-trial differences in effect modifiers and limited patient-level data. MAIC is sensitive to poor covariate overlap and cannot extrapolate beyond the observed covariate space. Current outcome regression-based alternatives can extrapolate but target a conditional treatment effect that is incompatible in the indirect comparison. When adjusting for covariates, one must integrate or average the conditional estimate over the population of interest to recover a compatible marginal treatment effect. We propose a marginalization method based on parametric G-computation that can be easily applied where the outcome regression is a generalized linear model or a Cox model. In addition, we introduce a novel general-purpose method based on multiple imputation, which we term multiple imputation marginalization (MIM) and is applicable to a wide range of models. Both methods can accommodate a Bayesian statistical framework, which naturally integrates the analysis into a probabilistic framework. A simulation study provides proof-of-principle for the methods and benchmarks their performance against MAIC and the conventional outcome regression. The marginalized outcome regression approaches achieve more precise and more accurate estimates than MAIC, particularly when covariate overlap is poor, and yield unbiased marginal treatment effect estimates under no failures of assumptions. Furthermore, the marginalized covariate-adjusted estimates provide greater precision and accuracy than the conditional estimates produced by the conventional outcome regression, which are systematically biased because the measure of effect is non-collapsible.
Partial observations of continuous time-series dynamics at arbitrary time stamps exist in many disciplines. Fitting this type of data using statistical models with continuous dynamics is not only promising at an intuitive level but also has practical benefits, including the ability to generate continuous trajectories and to perform inference on previously unseen time stamps. Despite exciting progress in this area, the existing models still face challenges in terms of their representational power and the quality of their variational approximations. We tackle these challenges with continuous latent process flows (CLPF), a principled architecture decoding continuous latent processes into continuous observable processes using a time-dependent normalizing flow driven by a stochastic differential equation. To optimize our model using maximum likelihood, we propose a novel piecewise construction of a variational posterior process and derive the corresponding variational lower bound using trajectory re-weighting. Our ablation studies demonstrate the effectiveness of our contributions in various inference tasks on irregular time grids. Comparisons to state-of-the-art baselines show our model's favourable performance on both synthetic and real-world time-series data.
A performance prediction method for massively parallel computation is proposed. The method is based on performance modeling and Bayesian inference to predict elapsed time T as a function of the number of used nodes P (T=T(P)). The focus is on extrapolation for larger values of P from the perspective of application researchers. The proposed method has several improvements over the method developed in a previous paper, and application to real-symmetric generalized eigenvalue problem shows promising prediction results. The method is generalizable and applicable to many other computations.
The semiparametric estimation approach, which includes inverse-probability-weighted and doubly robust estimation using propensity scores, is a standard tool for marginal structural models basically used in causal inference, and is rapidly being extended and generalized in various directions. On the other hand, although model selection is indispensable in statistical analysis, information criterion for selecting an appropriate marginal structure has just started to be developed. In this paper, based on the original idea of the information criterion, we derive an AIC-type criterion. We define a risk function based on the Kullback-Leibler divergence as the cornerstone of the information criterion, and treat a general causal inference model that is not necessarily of the type represented as a linear model. The causal effects to be estimated are those in the general population, such as the average treatment effect on the treated or the average treatment effect on the untreated. In light of the fact that doubly robust estimation, which allows either the model of the assignment variable or the model of the outcome variable to be wrong, is attached importance in this field, we will make the information criterion itself doubly robust, so that either one of the two can be wrong and still be a mathematically valid criterion.
In recent years, local differential privacy (LDP) has emerged as a technique of choice for privacy-preserving data collection in several scenarios when the aggregator is not trustworthy. LDP provides client-side privacy by adding noise at the user's end. Thus, clients need not rely on the trustworthiness of the aggregator. In this work, we provide a noise-aware probabilistic modeling framework, which allows Bayesian inference to take into account the noise added for privacy under LDP, conditioned on locally perturbed observations. Stronger privacy protection (compared to the central model) provided by LDP protocols comes at a much harsher privacy-utility trade-off. Our framework tackles several computational and statistical challenges posed by LDP for accurate uncertainty quantification under Bayesian settings. We demonstrate the efficacy of our framework in parameter estimation for univariate and multi-variate distributions as well as logistic and linear regression.
In this paper we introduce a covariance framework for the analysis of EEG and MEG data that takes into account observed temporal stationarity on small time scales and trial-to-trial variations. We formulate a model for the covariance matrix, which is a Kronecker product of three components that correspond to space, time and epochs/trials, and consider maximum likelihood estimation of the unknown parameter values. An iterative algorithm that finds approximations of the maximum likelihood estimates is proposed. We perform a simulation study to assess the performance of the estimator and investigate the influence of different assumptions about the covariance factors on the estimated covariance matrix and on its components. Apart from that, we illustrate our method on real EEG and MEG data sets. The proposed covariance model is applicable in a variety of cases where spontaneous EEG or MEG acts as source of noise and realistic noise covariance estimates are needed for accurate dipole localization, such as in evoked activity studies, or where the properties of spontaneous EEG or MEG are themselves the topic of interest, such as in combined EEG/fMRI experiments in which the correlation between EEG and fMRI signals is investigated.