Restricted mean survival time (RMST) is an intuitive summary statistic for time-to-event random variables, and can be used for measuring treatment effects. Compared to hazard ratio, its estimation procedure is robust against the non-proportional hazards assumption. We propose nonparametric Bayeisan (BNP) estimators for RMST using a dependent stick-breaking process prior mixture model that adjusts for mixed-type covariates. The proposed Bayesian estimators can yield both group-level causal estimate and subject-level predictions. Besides, we propose a novel dependent stick-breaking process prior that on average results in narrower credible intervals while maintaining similar coverage probability compared to a dependent probit stick-breaking process prior. We conduct simulation studies to investigate the performance of the proposed BNP RMST estimators compared to existing frequentist approaches and under different Bayesian modeling choices. The proposed framework is applied to estimate the treatment effect of an immuno therapy among KRAS wild-type colorectal cancer patients.
Modeling longitudinal and survival data jointly offers many advantages such as addressing measurement error and missing data in the longitudinal processes, understanding and quantifying the association between the longitudinal markers and the survival events and predicting the risk of events based on the longitudinal markers. A joint model involves multiple submodels (one for each longitudinal/survival outcome) usually linked together through correlated or shared random effects. Their estimation is computationally expensive (particularly due to a multidimensional integration of the likelihood over the random effects distribution) so that inference methods become rapidly intractable, and restricts applications of joint models to a small number of longitudinal markers and/or random effects. We introduce a Bayesian approximation based on the Integrated Nested Laplace Approximation algorithm implemented in the R package R-INLA to alleviate the computational burden and allow the estimation of multivariate joint models with fewer restrictions. Our simulation studies show that R-INLA substantially reduces the computation time and the variability of the parameter estimates compared to alternative estimation strategies. We further apply the methodology to analyze 5 longitudinal markers (3 continuous, 1 count, 1 binary, and 16 random effects) and competing risks of death and transplantation in a clinical trial on primary biliary cholangitis. R-INLA provides a fast and reliable inference technique for applying joint models to the complex multivariate data encountered in health research.
We propose a general framework for obtaining probabilistic solutions to PDE-based inverse problems. Bayesian methods are attractive for uncertainty quantification but assume knowledge of the likelihood model or data generation process. This assumption is difficult to justify in many inverse problems, where the specification of the data generation process is not obvious. We adopt a Gibbs posterior framework that directly posits a regularized variational problem on the space of probability distributions of the parameter. We propose a novel model comparison framework that evaluates the optimality of a given loss based on its ''predictive performance''. We provide cross-validation procedures to calibrate the regularization parameter of the variational objective and compare multiple loss functions. Some novel theoretical properties of Gibbs posteriors are also presented. We illustrate the utility of our framework via a simulated example, motivated by dispersion-based wave models used to characterize arterial vessels in ultrasound vibrometry.
The target of dynamic prediction is to provide individualized risk predictions over time which can be updated as new data become available. Motivated by establishing a dynamic prediction model for the progressive eye disease, age-related macular degeneration (AMD), we proposed a time-dependent Cox model-based survival neural network (tdCoxSNN) to predict its progression on a continuous time scale using longitudinal fundus images. tdCoxSNN extends the time-dependent Cox model by utilizing a neural network to model the non-linear effect of the time-dependent covariates on the survival outcome. Additionally, by incorporating the convolutional neural network (CNN), tdCoxSNN can take the longitudinal raw images as input. We evaluate and compare our proposed method with joint modeling and landmarking approaches through comprehensive simulations using two time-dependent accuracy metrics, the Brier Score and dynamic AUC. We applied the proposed approach to two real datasets. One is a large AMD study, the Age-Related Eye Disease Study (AREDS), in which more than 50,000 fundus images were captured over a period of 12 years for more than 4,000 participants. Another is a public dataset of the primary biliary cirrhosis (PBC) disease, in which multiple lab tests were longitudinally collected to predict the time-to-liver transplant. Our approach achieves satisfactory prediction performance in both simulation studies and the two real data analyses. tdCoxSNN was implemented in PyTorch, Tensorflow, and R-Tensorflow.
Estimating the conditional mean function that relates predictive covariates to a response variable of interest is a fundamental task in statistics. In this paper, we propose some general nonparametric regression approaches that are widely applicable under very mild conditions. The method decomposes a function with a Lipschitz continuous $k$-th derivative into a sum of a $(k-1)$-monotone function and a parametric component. We implement well-established shape-restricted estimation procedures (such as isotonic regression) to handle the "nonparametric" components of the true regression function and combine them with a simple sample-splitting procedure to estimate the parametric components. The resulting estimators inherit several favorable properties from the shape-restricted regression estimators. Notably, it is (practically) tuning parameter-free, converges at the minimax rate, and exhibits a locally adaptive rate when the true regression function is "simple". Finally, a series of numerical studies are presented, confirming these theoretical properties.
High-dimensional spectral data -- routinely generated in dairy production -- are used to predict a range of traits in milk products. Partial least squares regression (PLSR) is ubiquitously used for these prediction tasks. However PLSR is not typically viewed as arising from statistical inference of a probabilistic model, and parameter uncertainty is rarely quantified. Additionally, PLSR does not easily lend itself to model-based modifications, coherent prediction intervals are not readily available, and the process of choosing the latent-space dimension, $\mathtt{Q}$, can be subjective and sensitive to data size. We introduce a Bayesian latent-variable model, emulating the desirable properties of PLSR while accounting for parameter uncertainty. The need to choose $\mathtt{Q}$ is eschewed through a nonparametric shrinkage prior. The flexibility of the proposed Bayesian partial least squares regression (BPLSR) framework is exemplified by considering sparsity modifications and allowing for multivariate response prediction. The BPLSR framework is used in two motivating settings: 1) trait prediction from mid-infrared spectral analyses of milk samples, and 2) milk pH prediction from surface-enhanced Raman spectral data. The prediction performance of BPLSR at least matches that of PLSR. Additionally, the provision of correctly calibrated prediction intervals objectively provides richer, more informative inference for stakeholders in dairy production.
In the present paper, we consider that $N$ diffusion processes $X^1,\dots,X^N$ are observed on $[0,T]$, where $T$ is fixed and $N$ grows to infinity. Contrary to most of the recent works, we no longer assume that the processes are independent. The dependency is modeled through correlations between the Brownian motions driving the diffusion processes. A nonparametric estimator of the drift function, which does not use the knowledge of the correlation matrix, is proposed and studied. Its integrated mean squared risk is bounded and an adaptive procedure is proposed. Few theoretical tools to handle this kind of dependency are available, and this makes our results new. Numerical experiments show that the procedure works in practice.
We investigate a generalized framework for estimating latent low-rank tensors in an online setting, encompassing both linear and generalized linear models. This framework offers a flexible approach for handling continuous or categorical variables. Additionally, we investigate two specific applications: online tensor completion and online binary tensor learning. To address these challenges, we propose the online Riemannian gradient descent algorithm, which demonstrates linear convergence and the ability to recover the low-rank component under appropriate conditions in all applications. Furthermore, we establish a precise entry-wise error bound for online tensor completion. Notably, our work represents the first attempt to incorporate noise in the online low-rank tensor recovery task. Intriguingly, we observe a surprising trade-off between computational and statistical aspects in the presence of noise. Increasing the step size accelerates convergence but leads to higher statistical error, whereas a smaller step size yields a statistically optimal estimator at the expense of slower convergence. Moreover, we conduct regret analysis for online tensor regression. Under the fixed step size regime, a fascinating trilemma concerning the convergence rate, statistical error rate, and regret is observed. With an optimal choice of step size we achieve an optimal regret of $O(\sqrt{T})$. Furthermore, we extend our analysis to the adaptive setting where the horizon T is unknown. In this case, we demonstrate that by employing different step sizes, we can attain a statistically optimal error rate along with a regret of $O(\log T)$. To validate our theoretical claims, we provide numerical results that corroborate our findings and support our assertions.
Kernel survival analysis models estimate individual survival distributions with the help of a kernel function, which measures the similarity between any two data points. Such a kernel function can be learned using deep kernel survival models. In this paper, we present a new deep kernel survival model called a survival kernet, which scales to large datasets in a manner that is amenable to model interpretation and also theoretical analysis. Specifically, the training data are partitioned into clusters based on a recently developed training set compression scheme for classification and regression called kernel netting that we extend to the survival analysis setting. At test time, each data point is represented as a weighted combination of these clusters, and each such cluster can be visualized. For a special case of survival kernets, we establish a finite-sample error bound on predicted survival distributions that is, up to a log factor, optimal. Whereas scalability at test time is achieved using the aforementioned kernel netting compression strategy, scalability during training is achieved by a warm-start procedure based on tree ensembles such as XGBoost and a heuristic approach to accelerating neural architecture search. On four standard survival analysis datasets of varying sizes (up to roughly 3 million data points), we show that survival kernets are highly competitive compared to various baselines tested in terms of time-dependent concordance index. Our code is available at: //github.com/georgehc/survival-kernets
Consider a diffusion process X=(X_t), with t in [0,1], observed at discrete times and high frequency, solution of a stochastic differential equation whose drift and diffusion coefficients are assumed to be unknown. In this article, we focus on the nonparametric esstimation of the diffusion coefficient. We propose ridge estimators of the square of the diffusion coefficient from discrete observations of X and that are obtained by minimization of the least squares contrast. We prove that the estimators are consistent and derive rates of convergence as the size of the sample paths tends to infinity, and the discretization step of the time interval [0,1] tend to zero. The theoretical results are completed with a numerical study over synthetic data.
This paper presents a novel Importance Sampling (IS) scheme for estimating distribution tails of performance measures modeled with a rich set of tools such as linear programs, integer linear programs, piecewise linear/quadratic objectives, feature maps specified with deep neural networks, etc. The conventional approach of explicitly identifying efficient changes of measure suffers from feasibility and scalability concerns beyond highly stylized models, due to their need to be tailored intricately to the objective and the underlying probability distribution. This bottleneck is overcome in the proposed scheme with an elementary transformation which is capable of implicitly inducing an effective IS distribution in a variety of models by replicating the concentration properties observed in less rare samples. This novel approach is guided by developing a large deviations principle that brings out the phenomenon of self-similarity of optimal IS distributions. The proposed sampler is the first to attain asymptotically optimal variance reduction across a spectrum of multivariate distributions despite being oblivious to the specifics of the underlying model. Its applicability is illustrated with contextual shortest path and portfolio credit risk models informed by neural networks