A changepoint statistic with uniform type I error probabilities

ABSTRACT

Likelihood ratio tests for a change in mean in a sequence of independent, normal random variables are based on the maximum two-sample t-statistic, where the maximum is taken over all possible changepoints. The maximum t-statistic has the undesirable characteristic that Type I errors are not uniformly distributed across possible changepoints. False positives occur more frequently near the ends of the sequence and occur less frequently near the middle of the sequence. In this paper we describe an alternative statistic that is based upon a minimum p-value, where the minimum is taken over all possible changepoints. The p-value at any particular changepoint is based upon both the two-sample t-statistic at that changepoint and the probability that the maximum two-sample t-statistic is achieved at that changepoint. The new statistic has a more uniform distribution of Type I errors across potential changepoints and it compares favorably with respect to statistical power, false discovery rates, and the mean square error of changepoint estimates.     

Bayesian binary segmentation procedure for detecting streakiness in sports

Summary.  When an individual player or team enjoys periods of good form, and when these occur, is a widely observed phenomenon typically called 'streakiness'. It is interesting to assess which team is a streaky team, or who is a streaky player in sports. Such competitors might have a large number of successes during some periods and few or no successes during other periods. Thus, their success rate is not constant over time. We provide a Bayesian binary segmentation procedure for locating changepoints and the associated success rates simultaneously for these competitors. The procedure is based on a series of nested hypothesis tests each using the Bayes factor or the Bayesian information criterion. At each stage, we only need to compare a model with one changepoint with a model based on a constant success rate. Thus, the method circumvents the computational complexity that we would normally face in problems with an unknown number of changepoints. We apply the procedure to data corresponding to sports teams and players from basketball, golf and baseball.     

A computationally efficient nonparametric approach for changepoint detection

In this paper we build on an approach proposed by Zou et al. (2014) for nonparametric changepoint detection. This approach defines the best segmentation for a data set as the one which minimises a penalised cost function, with the cost function defined in term of minus a non-parametric log-likelihood for data within each segment. Minimising this cost function is possible using dynamic programming, but their algorithm had a computational cost that is cubic in the length of the data set. To speed up computation, Zou et al. (2014) resorted to a screening procedure which means that the estimated segmentation is no longer guaranteed to be the global minimum of the cost function. We show that the screening procedure adversely affects the accuracy of the changepoint detection method, and show how a faster dynamic programming algorithm, pruned exact linear time (PELT) (Killick et al. 2012), can be used to find the optimal segmentation with a computational cost that can be close to linear in the amount of data. PELT requires a penalty to avoid under/over-fitting the model which can have a detrimental effect on the quality of the detected changepoints. To overcome this issue we use a relatively new method, changepoints over a range of penalties (Haynes et al. 2016), which finds all of the optimal segmentations for multiple penalty values over a continuous range. We apply our method to detect changes in heart-rate during physical activity.     

Exact and efficient Bayesian inference for multiple changepoint problems

We demonstrate how to perform direct simulation from the posterior distribution of a class of multiple changepoint models where the number of changepoints is unknown. The class of models assumes independence between the posterior distribution of the parameters associated with segments of data between successive changepoints. This approach is based on the use of recursions, and is related to work on product partition models. The computational complexity of the approach is quadratic in the number of observations, but an approximate version, which introduces negligible error, and whose computational cost is roughly linear in the number of observations, is also possible. Our approach can be useful, for example within an MCMC algorithm, even when the independence assumptions do not hold. We demonstrate our approach on coal-mining disaster data and on well-log data. Our method can cope with a range of models, and exact simulation from the posterior distribution is possible in a matter of minutes.     

Efficient Bayesian analysis of multiple changepoint models with dependence across segments

We consider Bayesian analysis of a class of multiple changepoint models. While there are a variety of efficient ways to analyse these models if the parameters associated with each segment are independent, there are few general approaches for models where the parameters are dependent. Under the assumption that the dependence is Markov, we propose an efficient online algorithm for sampling from an approximation to the posterior distribution of the number and position of the changepoints. In a simulation study, we show that the approximation introduced is negligible. We illustrate the power of our approach through fitting piecewise polynomial models to data, under a model which allows for either continuity or discontinuity of the underlying curve at each changepoint. This method is competitive with, or outperform, other methods for inferring curves from noisy data; and uniquely it allows for inference of the locations of discontinuities in the underlying curve.     

Variable dimension via stochastic volatility model using FX rates

In this paper, changepoint analysis is applied to stochastic volatility (SV) models which aim to understand the locations and movements of high frequency FX financial time series. Bayesian inference using the Markov Chain Monte Carlo method is performed using a process called variable dimension for SV parameters. Interesting results are that FX series have locations where one or more positions of the sequence correspond to systemic changes, and overall non-stationarity, in the returns process. Furthermore, we found that the changepoint locations provide an informative estimate for all FX series. Importantly in most cases, the detected changepoints can be identified with economic factors relevant to the country concerned. This helps support the fact that macroeconomics news and the movement in financial price are positively related.     

Mixtures of regressions with changepoints

We introduce an extension to the mixture of linear regressions model where changepoints are present. Such a model provides greater flexibility over a standard changepoint regression model if the data are believed to not only have changepoints present, but are also believed to belong to two or more unobservable categories. This model can provide additional insight into data that are already modeled using mixtures of regressions, but where the presence of changepoints has not yet been investigated. After discussing the mixture of regressions with changepoints model, we then develop an Expectation/Conditional Maximization (ECM) algorithm for maximum likelihood estimation. Two simulation studies illustrate the performance of our ECM algorithm and we analyze a real dataset.     

Segmental modeling of changing immunologic response for CD4 data with skewness,missingness and dropout

In clinical practice, the profile of each subject's CD4 response from a longitudinal study may follow a ‘broken stick’ like trajectory, indicating multiple phases of increase and/or decline in response. Such multiple phases (changepoints) may be important indicators to help quantify treatment effect and improve management of patient care. Although it is a common practice to analyze complex AIDS longitudinal data using nonlinear mixed-effects (NLME) or nonparametric mixed-effects (NPME) models in the literature, NLME or NPME models become a challenge to estimate changepoint due to complicated structures of model formulations. In this paper, we propose a changepoint mixed-effects model with random subject-specific parameters, including the changepoint for the analysis of longitudinal CD4 cell counts for HIV infected subjects following highly active antiretroviral treatment. The longitudinal CD4 data in this study may exhibit departures from symmetry, may encounter missing observations due to various reasons, which are likely to be non-ignorable in the sense that missingness may be related to the missing values, and may be censored at the time of the subject going off study-treatment, which is a potentially informative dropout mechanism. Inferential procedures can be complicated dramatically when longitudinal CD4 data with asymmetry (skewness), incompleteness and informative dropout are observed in conjunction with an unknown changepoint. Our objective is to address the simultaneous impact of skewness, missingness and informative censoring by jointly modeling the CD4 response and dropout time processes under a Bayesian framework. The method is illustrated using a real AIDS data set to compare potential models with various scenarios, and some interested results are presented.     

Change-points in stochastic ordering

This article studies the problem of testing and locating changepoints in stochas¬tic ordering. We propose a sequential process to detect the changepoints from two multinomial distributions. We also obtain the maximum likelihood estimators of two multinomial probability vectors under the assumption that the cumulative distribu¬tions have a changepoint. Asymptotically unbiased Akaike's information criterion is used to estimate the changepoints of two discrete probability distributions. Finally. we demonstrate our procedure by studying a data set pertaining to average daily insulin dose from the Boston Collaborative Drug Surveillance Program and locate the changepoints in stochastic ordering.     

Bayesian Single Changepoint Estimation in a Parameter‐driven Model

In this paper, we consider the problem of estimating a single changepoint in a parameter‐driven model. The model – an extension of the Poisson regression model – accounts for serial correlation through a latent process incorporated in its mean function. Emphasis is placed on the changepoint characterization with changes in the parameters of the model. The model is fully implemented within the Bayesian framework. We develop a RJMCMC algorithm for parameter estimation and model determination. The algorithm embeds well‐devised Metropolis–Hastings procedures for estimating the missing values of the latent process through data augmentation and the changepoint. The methodology is illustrated using data on monthly counts of claimants collecting wage loss benefit for injuries in the workplace and an analysis of presidential uses of force in the USA.     

Modelling growth and decline in lung function in Duchenne's muscular dystrophy with an augmented linear mixed effects model

Summary.  Longitudinal modelling of lung function in Duchenne's muscular dystrophy is complicated by a mixture of both growth and decline in lung function within each subject, an unknown point of separation between these phases and significant heterogeneity between individual trajectories. Linear mixed effects models can be used, assuming a single changepoint for all cases; however, this assumption may be incorrect. The paper describes an extension of linear mixed effects modelling in which random changepoints are integrated into the model as parameters and estimated by using a stochastic EM algorithm. We find that use of this 'mixture modelling' approach improves the fit significantly.     

Generalized bent-cable methodology for changepoint data: a Bayesian approach

The choice of the model framework in a regression setting depends on the nature of the data. The focus of this study is on changepoint data, exhibiting three phases: incoming and outgoing, both of which are linear, joined by a curved transition. Bent-cable regression is an appealing statistical tool to characterize such trajectories, quantifying the nature of the transition between the two linear phases by modeling the transition as a quadratic phase with unknown width. We demonstrate that a quadratic function may not be appropriate to adequately describe many changepoint data. We then propose a generalization of the bent-cable model by relaxing the assumption of the quadratic bend. The properties of the generalized model are discussed and a Bayesian approach for inference is proposed. The generalized model is demonstrated with applications to three data sets taken from environmental science and economics. We also consider a comparison among the quadratic bent-cable, generalized bent-cable and piecewise linear models in terms of goodness of fit in analyzing both real-world and simulated data. This study suggests that the proposed generalization of the bent-cable model can be valuable in adequately describing changepoint data that exhibit either an abrupt or gradual transition over time.     

Bayesian hierarchical regression models for detecting QTLs in plant experiments

Quantitative trait loci (QTL) mapping is a growing field in statistical genetics. In plants, QTL detection experiments often feature replicates or clones within a specific genetic line. In this work, a Bayesian hierarchical regression model is applied to simulated QTL data and to a dataset from the Arabidopsis thaliana plants for locating the QTL mapping associated with cotyledon opening. A conditional model search strategy based on Bayesian model averaging is utilized to reduce the computational burden.     

Dynamic changepoint detection in count time series: a particle filter approach

We study Bayesian dynamic models for detecting changepoints in count time series that present structural breaks. As the inferential approach, we develop a parameter learning version of the algorithm proposed by Chopin [Chopin N. Dynamic detection of changepoints in long time series. Annals of the Institute of Statistical Mathematics 2007;59:349–366.], called the Chopin filter with parameter learning, which allows us to estimate the static parameters in the model. In this extension, the static parameters are addressed by using the kernel smoothing approximations proposed by Liu and West [Liu J, West M. Combined parameters and state estimation in simulation-based filtering. In: Doucet A, de Freitas N, Gordon N, editors. Sequential Monte Carlo methods in practice. New York: Springer-Verlag; 2001]. The proposed methodology is then applied to both simulated and real data sets and the time series models include distributions that allow for overdispersion and/or zero inflation. Since our procedure is general, robust and naturally adaptive because the particle filter approach does not require restrictive specifications to ensure its validity and effectiveness, we believe it is a valuable alternative for dealing with the problem of detecting changepoints in count time series. The proposed methodology is also suitable for count time series with no changepoints and for independent count data.     

A Bayesian approach for misclassified ordinal response data

ABSTRACT

Motivated by a longitudinal oral health study, the Signal-Tandmobiel^® study, a Bayesian approach has been developed to model misclassified ordinal response data. Two regression models have been considered to incorporate misclassification in the categorical response. Specifically, probit and logit models have been developed. The computational difficulties have been avoided by using data augmentation. This idea is exploited to derive efficient Markov chain Monte Carlo methods. Although the method is proposed for ordered categories, it can also be implemented for unordered ones in a simple way. The model performance is shown through a simulation-based example and the analysis of the motivating study.     

Hidden Markov model for discrete circular–linear wind data time series

ABSTRACT

In this work, we deal with a bivariate time series of wind speed and direction. Our observed data have peculiar features, such as informative missing values, non-reliable measures under a specific condition and interval-censored data, that we take into account in the model specification. We analyse the time series with a non-parametric Bayesian hidden Markov model, introducing a new emission distribution, suitable to model our data, based on the invariant wrapped Poisson, the Poisson and the hurdle density. The model is estimated on simulated datasets and on the real data example that motivated this work.     

A Bayesian semi-parametric approach to the ordinal calibration problem

ABSTRACT

We introduce a semi-parametric Bayesian approach based on skewed Dirichlet processes priors for location parameters in the ordinal calibration problem. This approach allows the modeling of asymmetrical error distributions. Conditional posterior distributions are implemented, thus allowing the use of Markov chains Monte Carlo to generate the posterior distributions. The methodology is applied to both simulated and real data.     

Bayesian estimation and prediction of the intensity of the power law process

In analyzing failure data pertaining to a repairable system, perhaps the most widely used parametric model is a nonhomogeneous Poisson process with Weibull intensity, more commonly referred to as the Power Law Process (PLP) model. Investigations relating to inference of parameters of the PLP under a frequentist framework abound in the literature. The focus of this article is to supplement those findings from a Bayesian perspective, which has thus far been explored to a limited extent in this context. Main emphasis is on the inference of the intensity function of the PLP. Both estimation and future prediction are considered under traditional as well as more complex censoring schemes. Modern computational tools such as Markov Chain Monte Carlo are exploited efficiently to facilitate the numerical evaluation process. Results from the Bayesian inference are contrasted with the corresponding findings from a frequentist analysis, both from a qualitative and a quantitative viewpoint. The developed methodology is implemented in analyzing interval-censored failure data of equipments in a fleet of marine vessels.     

Non-homogeneous Markov models in the analysis of survival after breast cancer

A cohort of 300 women with breast cancer who were submitted for surgery is analysed by using a non-homogeneous Markov process. Three states are onsidered: no relapse, relapse and death. As relapse times change over time, we have extended previous approaches for a time homogeneous model to a non omogeneous multistate process. The trends of the hazard rate functions of transitions between states increase and then decrease, showing that a changepoint can be considered. Piecewise Weibull distributions are introduced as transition intensity functions. Covariates corresponding to treatments are incorporated in the model multiplicatively via these functions. The likelihood function is built for a general model with k changepoints and applied to the data set, the parameters are estimated and life-table and transition probabilities for treatments in different periods of time are given. The survival probability functions for different treatments are plotted and compared with the corresponding function for the homogeneous model. The survival functions for the various cohorts submitted for treatment are fitted to the mpirical survival functions.