Survival analysis is one of the most important fields of statistics in medicine and the biological sciences. In addition, the computational advances in the last decades have favoured the use of Bayesian methods in this context, providing a flexible and powerful alternative to the traditional frequentist approach. The objective of this paper is to summarise some of the most popular Bayesian survival models, such as accelerated failure time, proportional hazards, mixture cure, competing risks, frailty, and joint models of longitudinal and survival data. Moreover, an implementation of each presented model is provided using a BUGS syntax that can be run with JAGS from the R programming language. Reference to other Bayesian R-packages are also discussed.
Many phase II clinical trials have used survival outcomes as the primary endpoints in recent decades. Suppose the radiotherapy is evaluated in a phase II trial using survival outcomes. In that case, the competing risk issue often arises because the time to disease progression can be censored by the time to normal tissue complications, and vice versa. Besides, much literature has examined that patients receiving the same radiotherapy dose may yield distinct responses due to their heterogeneous radiation susceptibility statuses. Therefore, the "one-dose-fit-all" strategy often fails, and it is m…
Patient-level health economic data collected alongside clinical trials are an important component of the process of technology appraisal, with a view to informing resource allocation decisions. For end of life treatments, such as cancer treatments, modelling of cost-effectiveness/utility data may involve some form of partitioned survival analysis, where measures of health-related quality of life and survival time for both pre- and post-progression periods are combined to generate some aggregate measure of clinical benefits (e.g. quality-adjusted survival). In addition, resource use data are of…
Cricketing knowledge tells us batting is more difficult early in a player's innings but becomes easier as a player familiarizes themselves with the conditions. In this paper, we develop a Bayesian survival analysis method to predict the Test Match batting abilities for international cricketers. The model is applied in two stages, firstly to individual players, allowing us to quantify players' initial and equilibrium batting abilities, and the rate of transition between the two. This is followed by implementing the model using a hierarchical structure, providing us with more general inference c…
Bayesian generalized method of moments applied to pseudo-observations in survival analysis
Oncostat U1018, Inserm（Inserm）；University Paris-Saclay（巴黎萨克雷大学）；Ipsen Innovation, Clinical Development Organisation（益普生创新）；I-Biostat；KU-Leuven（荷语鲁汶大学）；Department of Statistics and Actuarial Science（统计学与精算学系）；The University of Hong Kong（香港大学）；F. Hoffmann-La Roche AG（罗氏制药）
Spatial survival analysis has received a great deal of attention over the last 20 years due to the important role that geographical information can play in predicting survival. This paper provides an introduction to a set of programs for implementing some Bayesian spatial survival models in R using the package spBayesSurv. The function survregbayes includes the three most commonly-used semiparametric models: proportional hazards, proportional odds, and accelerated failure time. All manner of censored survival times are simultaneously accommodated including uncensored, interval censored, curren…
There has been increasing interest in modeling survival data using deep learning methods in medical research. In this paper, we proposed a Bayesian hierarchical deep neural networks model for modeling and prediction of survival data. Compared with previously studied methods, the new proposal can provide not only point estimate of survival probability but also quantification of the corresponding uncertainty, which can be of crucial importance in predictive modeling and subsequent decision making. The favorable statistical properties of point and uncertainty estimates were demonstrated by simula…
Survival data is encountered in a range of disciplines, most notably health and medical research. Although Bayesian approaches to the analysis of survival data can provide a number of benefits, they are less widely used than classical (e.g. likelihood-based) approaches. This may be in part due to a relative absence of user-friendly implementations of Bayesian survival models. In this article we describe how the rstanarm R package can be used to fit a wide range of Bayesian survival models. The rstanarm package facilitates Bayesian regression modelling by providing a user-friendly interface (us…
Illness-death models are a class of stochastic models inside the multi-state framework. In those models, individuals are allowed to move over time between different states related to illness and death. They are of special interest when working with non-terminal diseases, as they not only consider the competing risk of death but also allow to study progression from illness to death. The intensity of each transition can be modelled including both fixed and random effects of covariates. In particular, spatially structured random effects or their multivariate versions can be used to assess spatial…
McCombs School of Business（麦克库姆斯商学院）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）
We propose Lomax delegate racing (LDR) to explicitly model the mechanism of survival under competing risks and to interpret how the covariates accelerate or decelerate the time to event. LDR explains non-monotonic covariate effects by racing a potentially infinite number of sub-risks, and consequently relaxes the ubiquitous proportional-hazards assumption which may be too restrictive. Moreover, LDR is naturally able to model not only censoring, but also missing event times or event types. For inference, we develop a Gibbs sampler under data augmentation for moderately sized data, along with a …
We overview Bayesian estimation, hypothesis testing, and model-averaging and illustrate how they benefit parametric survival analysis. We contrast the Bayesian framework to the currently dominant frequentist approach and highlight advantages, such as seamless incorporation of historical data, continuous monitoring of evidence, and incorporating uncertainty about the true data generating process. We illustrate the application of the Bayesian approaches on an example data set from a colon cancer trial. We compare the Bayesian parametric survival analysis and frequentist models with AIC/BIC model…
When Method Choice Changes Statistical Inference: A Comparison of a Baseline Two-Stage Approach and Bayesian Joint Modeling for Longitudinal and Survival Data in an HIV Clinical Trial
Bayes linear kinematics and Bayes linear Bayes graphical models provide an extension of Bayes linear methods so that full conditional updates may be combined with Bayes linear belief adjustment. In this paper we investigate the application of this approach to a more complicated problem: namely survival analysis with time-dependent covariate effects. We use a piecewise-constant hazard function with a prior in which covariate effects are correlated over time. The need for computationally intensive methods is avoided and the relatively simple structure facilitates interpretation. Our approach eli…
Stochastic volatility often implies increasing risks that are difficult to capture given the dynamic nature of real-world applications. We propose using arc length, a mathematical concept, to quantify cumulative variations (the total variability over time) to more fully characterize stochastic volatility. The hazard rate, as defined by the Cox proportional hazards model in survival analysis, is assumed to be impacted by the instantaneous value of a longitudinal variable. However, when cumulative variations pose a significant impact on the hazard, this assumption is questionable. Our proposed B…
We introduce a novel procedure to perform Bayesian non-parametric inference with right-censored data, the \emph{beta-Stacy bootstrap}. This approximates the posterior law of summaries of the survival distribution (e.g. the mean survival time). More precisely, our procedure approximates the joint posterior law of functionals of the beta-Stacy process, a non-parametric process prior that generalizes the Dirichlet process and that is widely used in survival analysis. The beta-Stacy bootstrap generalizes and unifies other common Bayesian bootstraps for complete or censored data based on non-parame…
In this paper, we develop a family of bivariate beta distributions that encapsulate both positive and negative correlations, and which can be of general interest for Bayesian inference. We then invoke a use of these bivariate distributions in two contexts. The first is diagnostic testing in medicine, threat detection, and signal processing. The second is system survivability assessment, relevant to engineering reliability, and to survival analysis in biomedicine. In diagnostic testing one encounters two parameters that characterize the efficacy of the testing mechanism, {\it test sensitivity},…
Datasets containing large samples of time-to-event data arising from several small heterogeneous groups are commonly encountered in statistics. This presents problems as they cannot be pooled directly due to their heterogeneity or analyzed individually because of their small sample size. Bayesian nonparametric modelling approaches can be used to model such datasets given their ability to flexibly share information across groups. In this paper, we will compare three popular Bayesian nonparametric methods for modelling the survival functions of heterogeneous groups. Specifically, we will first c…
Recently, the Bayesian nonparametric approach in survival studies attracts much more attentions. Because of multi modality in survival data, the mixture models are very common in this field. One of the famous priors on Bayesian nonparametric models is Dirichlet process prior. In this paper we introduce a Bayesian nonparametric mixture model with Burr distribution(Burr type XII) as the kernel of mixture model. Since the Burr distribution shares good properties of common distributions on survival analysis, it has more flexibility than other distributions. By applying this model to simulated and …
In decision modelling with time to event data, there are a variety of parametric models which could be used to extrapolate the survivor function. Each of these implies a different hazard function and in situations where there is moderate censoring, they can result in quite different extrapolations. Expert opinion on the long-term survival or other quantities could reduce model uncertainty. We present a general and easily implementable approach for including a variety of types of expert opinions. Expert opinion is incorporated by penalizing the likelihood function. Inference is performed in a B…
Popular parametric and semiparametric hazards regression models for clustered survival data are inappropriate and inadequate when the unknown effects of different covariates and clustering are complex. This calls for a flexible modeling framework to yield efficient survival prediction. Moreover, for some survival studies involving time to occurrence of some asymptomatic events, survival times are typically interval censored between consecutive clinical inspections. In this article, we propose a robust semiparametric model for clustered interval-censored survival data under a paradigm of Bayesi…
Extended cure survival models enable to separate covariates that affect the probability of an event (or `long-term' survival) from those only affecting the event timing (or `short-term' survival). We propose to generalize the bounded cumulative hazard model to handle additive terms for time-varying (exogenous) covariates jointly impacting long- and short-term survival. The selection of the penalty parameters is a challenge in that framework. A fast algorithm based on Laplace approximations in Bayesian P-spline models is proposed. The methodology is motivated by fertility studies where women's …
We study objective Bayesian inference for linear regression models with residual errors distributed according to the class of two-piece scale mixtures of normal distributions. These models allow for capturing departures from the usual assumption of normality of the errors in terms of heavy tails, asymmetry, and certain types of heteroscedasticity. We propose a general noninformative, scale-invariant, prior structure and provide sufficient conditions for the propriety of the posterior distribution of the model parameters, which cover cases when the response variables are censored. These results…
To better understand effects of exposure to food allergens, food challenge studies are designed to slowly increase the dose of an allergen delivered to allergic individuals until an objective reaction occurs. These dose-to-failure studies are used to determine acceptable intake levels and are analyzed using parametric failure time models. Though these models can provide estimates of the survival curve, their parametric form may misrepresent the survival function for doses of interest, and different models that describe the data similarly may produce different dose-to-failure estimates. Motivat…
In this paper we utilize a survival analysis methodology incorporating Bayesian additive regression trees to account for nonlinear and additive covariate effects. We compare the performance of Bayesian additive regression trees, Cox proportional hazards and random survival forests models for censored survival data, using simulation studies and survival analysis for breast cancer with U.S. SEER database for the year 2005. In simulation studies, we compare the three models across varying sample sizes and censoring rates on the basis of bias and prediction accuracy. In survival analysis for breas…
Conventional survival analysis approaches estimate risk scores or individualized time-to-event distributions conditioned on covariates. In practice, there is often great population-level phenotypic heterogeneity, resulting from (unknown) subpopulations with diverse risk profiles or survival distributions. As a result, there is an unmet need in survival analysis for identifying subpopulations with distinct risk profiles, while jointly accounting for accurate individualized time-to-event predictions. An approach that addresses this need is likely to improve characterization of individual outcome…
Bayesian joint modeling of longitudinal patient-reported outcomes and survival: an application to chronic obstructive pulmonary disease
Basque Center for Applied Mathematics BCAM（巴斯克应用数学中心）；University of the Basque Country UPV/EHU（巴斯克大学）；MRC Biostatistics Unit, University of Cambridge（剑桥大学医学研究委员会生物统计学单位）；IE University（IE大学）
We present a general approach to synthesizing evidence of time-to-event endpoints in meta-analyses of aggregate data (AD). Our work goes beyond most previous meta-analytic research by using reconstructed survival data as a source of information. A Bayesian multilevel regression model, called the "meta-analysis of reconstructed survival data" (MARS), is introduced, by modeling and integrating reconstructed survival information with other types of summary data, to estimate the hazard ratio function and survival probabilities. The method attempts to reduce selection bias, and relaxes the presumpt…
We study Bayesian linear regression models with skew-symmetric scale mixtures of normal error distributions. These kinds of models can be used to capture departures from the usual assumption of normality of the errors in terms of heavy tails and asymmetry. We propose a general non-informative prior structure for these regression models and show that the corresponding posterior distribution is proper under mild conditions. We extend these propriety results to cases where the response variables are censored. The latter scenario is of interest in the context of accelerated failure time models, wh…
The proportional hazards (PH), proportional odds (PO) and accelerated failure time (AFT) models have been widely used in different applications of survival analysis. Despite their popularity, these models are not suitable to handle lifetime data with crossing survival curves. In 2005, Yang and Prentice proposed a semiparametric two-sample strategy (YP model), including the PH and PO frameworks as particular cases, to deal with this type of data. Assuming a general regression setting, the present paper proposes an unified approach to fit the YP model by employing Bernstein polynomials to manage…
Missing data occur in many types of studies and typically complicate the analysis. Multiple imputation, either using joint modelling or the more flexible fully conditional specification approach, are popular and work well in standard settings. In settings involving non-linear associations or interactions, however, incompatibility of the imputation model with the analysis model is an issue often resulting in bias. Similarly, complex outcomes such as longitudinal or survival outcomes cannot be adequately handled by standard implementations. In this paper, we introduce the R package JointAI, whic…
Intrusion Detection Systems are an important component of many organizations' cyber defense and resiliency strategies. However, one downside of these systems is their reliance on known attack signatures for detection of malicious network events. When it comes to unknown attack types and zero-day exploits, modern Intrusion Detection Systems often fall short. In this paper, we introduce an unconventional approach to identifying network traffic features that influence novelty detection based on survival analysis techniques. Specifically, we combine several Cox proportional hazards models and impl…
Cystic fibrosis is a chronic lung disease which requires frequent patient monitoring to maintain lung function over time and minimize onset of acute respiratory events known as pulmonary exacerbations. From the clinical point of view it is important to characterize the association between key biomarkers such as $FEV_1$ and time-to first exacerbation. Progression of the disease is heterogeneous, yielding different sub-groups in the population exhibiting distinct longitudinal profiles. It is desirable to categorize these unobserved sub-groups (latent classes) according to their distinctive traje…
While the study of a single network is well-established, technological advances now allow for the collection of multiple networks with relative ease. Increasingly, anywhere from several to thousands of networks can be created from brain imaging, gene co-expression data, or microbiome measurements. And these networks, in turn, are being looked to as potentially powerful features to be used in modeling. However, with networks being non-Euclidean in nature, how best to incorporate them into standard modeling tasks is not obvious. In this paper, we propose a Bayesian modeling framework that provid…
Objective: To provide guidance for the use of the main functions available in R for performing post hoc Bayesian analysis of a randomized clinical trial with a survival endpoint using proportional hazard models. Study Design and Setting: Data derived from the ALLOZITHRO trial, conducted with 465 patients after allograft to prevent pulmonary complications and allocated between azithromycin and placebo; airflow decline-free survival at 2 years after randomization was the main endpoint. Results: Despite heterogeneity in modeling assumptions, in particular for the baseline hazard (parametric or no…
In this work, we propose a new Bayesian spatial homogeneity pursuit method for survival data under the proportional hazards model to detect spatially clustered patterns in baseline hazard and regression coefficients. Specially, regression coefficients and baseline hazard are assumed to have spatial homogeneity pattern over space. To capture such homogeneity, we develop a geographically weighted Chinese restaurant process prior to simultaneously estimate coefficients and baseline hazards and their uncertainty measures. An efficient Markov chain Monte Carlo (MCMC) algorithm is designed for our p…
