Detecting change points and monitoring biomedical data

Bayesian and likelihood approaches to on-line detecting change points in time series are discussed and applied to analyze biomedical data. Using a linear dynamic model, the Bayesian analysis outputs the conditional posterior probability of a change at time t ? 1, given the data up to time t and the status of changes occurred before time t ? 1. The likelihood method is based on a change-point regression model and tests whether there is no change-point.     

Change-Point Detection With Non-Parametric Regression

We consider the regression model y_i = ?(x_i ) + ε in which the function ? or its pth derivative ?^(p) may have a discontinuity at some unknown point τ. By fitting local polynomials from the left and right, we test the null that ?^(p) is continuous against the alternative that ?^(p)(τ?) ≠ ?^(p)(τ+). We obtain Darling-Erdös type limit theorems for the test statistics under the null hypothesis of no change, as well as their limits in probability under the alternative. Consistency of the related change-point estimators is also established.     

Maximum likelihood estimator in a multi-phase random regression model

We consider a random regression model with several-fold change-points. The results for one change-point are generalized. The maximum likelihood estimator of the parameters is shown to be consistent, and the asymptotic distribution for the estimators of the coefficients is shown to be Gaussian. The estimators of the change-points converge, with n ^?1 rate, to the vector whose components are the left end points of the maximizing interval with respect to each change-point. The likelihood process is asymptotically equivalent to the sum of independent compound Poisson processes.     

Rank-based multiple change-point detection

Abstract

A nonparametric procedure is proposed to estimate multiple change-points of location changes in a univariate data sequence by using ranks instead of the raw data. While existing rank-based multiple change-point detection methods are mostly based on sequential tests, we treat it as a model selection problem. We derive the corresponding Schwarz’s information criterion for rank-statistics, theoretically prove the consistency of the change-point estimator and use a pruned dynamic programing algorithm to achieve the change-point estimator. Simulation studies show our method’s robustness, effectiveness and efficiency in detecting mean-changes. We also apply the method to a gene dataset as an illustration.     

Change-point detection in a shape-restricted regression model

A regression model with a possible structural change and with a small number of measurements is considered. A priori information about the shape of the regression function is used to formulate the model as a linear regression model with inequality constraints and a likelihood ratio test for the presence of a change-point is constructed. The exact null distribution of the test statistic is given. Consistency of the test is proved when the noise level goes to zero. Numerical approximations to the powers against various alternatives are given and compared with the powers of the k-linear-r-ahead recursive residuals tests and CUSUM tests. Performance of four different estimators of the change-point is studied in a Monte Carlo experiment. An application of the procedures to some real data is also presented.     

Approximations to the p-values of tests for a change-point under non-standard conditions

Three test statistics for a change-point in a linear model, variants of those considered by Andrews and Ploberger [Optimal tests when a nusiance parameter is present only under the alternative. Econometrica. 1994;62:1383–1414]: the sup-likelihood ratio (LR) statistic; a weighted average of the exponential of LR-statistics and a weighted average of LR-statistics, are studied. Critical values for the statistics with time trend regressors, obtained via simulation, are found to vary considerably, depending on conditions on the error terms. The performance of the bootstrap in approximating p-values of the distributions is assessed in a simulation study. A sample approximation to asymptotic analytical expressions extending those of Kim and Siegmund [The likelihood ratio test for a change-point in simple linear regression. Biometrika. 1989;76:409–423] in the case of the sup-LR test is also assessed. The approximations and bootstrap are applied to the Quandt data [The estimation of a parameter of a linear regression system obeying two separate regimes. J Amer Statist Assoc. 1958;53:873–880] and real data concerning a change-point in oxygen uptake during incremental exercise testing and the bootstrap gives reasonable results.     

On computing estimates of a change-point in the Weibull regression hazard model

The hazard function describes the instantaneous rate of failure at a time t, given that the individual survives up to t. In applications, the effect of covariates produce changes in the hazard function. When dealing with survival analysis, it is of interest to identify where a change point in time has occurred. In this work, covariates and censored variables are considered in order to estimate a change-point in the Weibull regression hazard model, which is a generalization of the exponential model. For this more general model, it is possible to obtain maximum likelihood estimators for the change-point and for the parameters involved. A Monte Carlo simulation study shows that indeed, it is possible to implement this model in practice. An application with clinical trial data coming from a treatment of chronic granulomatous disease is also included.     

THE COVERAGE PROBABILITY OF CONFIDENCE INTERVALS IN 2r FACTORIAL EXPERIMENTS AFTER PRELIMINARY HYPOTHESIS TESTING

We consider a 2^r factorial experiment with at least two replicates. Our aim is to find a confidence interval for θ, a specified linear combination of the regression parameters (for the model written as a regression, with factor levels coded as ?1 and 1). We suppose that preliminary hypothesis tests are carried out sequentially, beginning with the rth‐order interaction. After these preliminary hypothesis tests, a confidence interval for θ with nominal coverage 1 ?α is constructed under the assumption that the selected model had been given to us a priori. We describe a new efficient Monte Carlo method, which employs conditioning for variance reduction, for estimating the minimum coverage probability of the resulting confidence interval. The application of this method is demonstrated in the context of a 2³ factorial experiment with two replicates and a particular contrast θ of interest. The preliminary hypothesis tests consist of the following two‐step procedure. We first test the null hypothesis that the third‐order interaction is zero against the alternative hypothesis that it is non‐zero. If this null hypothesis is accepted, we assume that this interaction is zero and proceed to the second step; otherwise, we stop. In the second step, for each of the second‐order interactions we test the null hypothesis that the interaction is zero against the alternative hypothesis that it is non‐zero. If this null hypothesis is accepted, we assume that this interaction is zero. The resulting confidence interval, with nominal coverage probability 0.95, has a minimum coverage probability that is, to a good approximation, 0.464. This shows that this confidence interval is completely inadequate.     

A permutation test for umbrella alternatives

There is a wide variety of stochastic ordering problems where K groups (typically ordered with respect to time) are observed along with a (continuous) response. The interest of the study may be on finding the change-point group, i.e. the group where an inversion of trend of the variable under study is observed. A change point is not merely a maximum (or a minimum) of the time-series function, but a further requirement is that the trend of the time-series is monotonically increasing before that point, and monotonically decreasing afterwards. A suitable solution can be provided within a conditional approach, i.e. by considering some suitable nonparametric combination of dependent tests for simple stochastic ordering problems. The proposed procedure is very flexible and can be extended to trend and/or repeated measure problems. Some comparisons through simulations and examples with the well known Mack & Wolfe test for umbrella alternative and with Page’s test for trend problems with correlated data are investigated.     

Change-Point Detection in Two-Phase Regression with Inequality Constraints on the Regression Parameters

Two-phase regression models with inequality constraints on the regression coefficients and with a small number of measurements is considered. A new test based on the likelihood ratio in linear model with inequality constraints for the presence of a change-point is proposed. Numerical approximations to the powers against various alternatives are given and compared with the powers of the likelihood ratio test in the two-phase regression models without inequality constraints, the backwards CUSUM test, and the k-linear-r-ahead recursive residuals tests. Performance of related likelihood based estimators of the change-point is briefly studied in a Monte Carlo experiment.     

A backward procedure for change-point detection with applications to copy number variation detection

Change-point detection regains much attention recently for analyzing array or sequencing data for copy number variation (CNV) detection. In such applications, the true signals are typically very short and buried in the long data sequence, which makes it challenging to identify the variations efficiently and accurately. In this article, we propose a new change-point detection method, a backward procedure, which is not only fast and simple enough to exploit high-dimensional data but also performs very well for detecting short signals. Although motivated by CNV detection, the backward procedure is generally applicable to assorted change-point problems that arise in a variety of scientific applications. It is illustrated by both simulated and real CNV data that the backward detection has clear advantages over other competing methods, especially when the true signal is short. The Canadian Journal of Statistics 48: 366–385; 2020 © 2020 Statistical Society of Canada     

A Bayesian wavelet approach to estimation of a change-point in a nonlinear multivariate time series

ABSTRACT

We propose a semiparametric approach to estimate the existence and location of a statistical change-point to a nonlinear multivariate time series contaminated with an additive noise component. In particular, we consider a p-dimensional stochastic process of independent multivariate normal observations where the mean function varies smoothly except at a single change-point. Our approach involves conducting a Bayesian analysis on the empirical detail coefficients of the original time series after a wavelet transform. If the mean function of our time series can be expressed as a multivariate step function, we find our Bayesian-wavelet method performs comparably with classical parametric methods such as maximum likelihood estimation. The advantage of our multivariate change-point method is seen in how it applies to a much larger class of mean functions that require only general smoothness conditions.     

Identifying change-point in polynomial profiles based on data-segmentation

Profile monitoring is the use of control charts for cases in which the quality of a process or product can be characterized by a functional relationship between a response variable and one or more explanatory variables. Unlike the linear profile's simple structure, the nonlinear profile has relatively less attainment because of high complexity. Regression model is the initial method to analyze the phase I of nonlinear profiles, but it lacks sensitivity for local characteristic changes. This article presents a strategy comprising two major components: data-segmentation, to concisely detect the location of local change by overlaying grid points onto horizontal axis, and change-point detection via the maximum likelihood estimate. Simulated data set of a polynomial profile is used to illustrate the effectiveness of the proposed strategy, and is compared with Williams' T² multi-variable statistics.     

Visualizing main effects and interaction in multiple non-symmetric correspondence analysis

Non-symmetric correspondence analysis (NSCA) is a useful technique for analysing a two-way contingency table. Frequently, the predictor variables are more than one; in this paper, we consider two categorical variables as predictor variables and one response variable. Interaction represents the joint effects of predictor variables on the response variable. When interaction is present, the interpretation of the main effects is incomplete or misleading. To separate the main effects and the interaction term, we introduce a method that, starting from the coordinates of multiple NSCA and using a two-way analysis of variance without interaction, allows a better interpretation of the impact of the predictor variable on the response variable. The proposed method has been applied on a well-known three-way contingency table proposed by Bockenholt and Bockenholt in which they cross-classify subjects by person's attitude towards abortion, number of years of education and religion. We analyse the case where the variables education and religion influence a person's attitude towards abortion.     

Fitting multiplicative models by robust alternating regressions

In this paper a robust approach for fitting multiplicative models is presented. Focus is on the factor analysis model, where we will estimate factor loadings and scores by a robust alternating regression algorithm. The approach is highly robust, and also works well when there are more variables than observations. The technique yields a robust biplot, depicting the interaction structure between individuals and variables. This biplot is not predetermined by outliers, which can be retrieved from the residual plot. Also provided is an accompanying robust R ²-plot to determine the appropriate number of factors. The approach is illustrated by real and artificial examples and compared with factor analysis based on robust covariance matrix estimators. The same estimation technique can fit models with both additive and multiplicative effects (FANOVA models) to two-way tables, thereby extending the median polish technique.     

The LAD estimation of the change-point linear model with randomly censored data

Abstract

In this paper, a change-point linear model with randomly censored data is investigated. We propose the least absolute deviation estimation procedure for regression and change-point parameters simultaneously. The asymptotic properties of the change-point and regression parameter estimators are obtained. We show that the resulting regression parameter estimator is asymptotically normal, and the change-point estimator converges weakly to the minimizer of a given random process. The extensive simulation studies and the analysis of an acute myocardial infarction data set are conducted to illustrate the finite sample performance of the proposed method.     

A Bayesian analysis of the change-point problem for directional data

In this paper, we discuss a simple fully Bayesian analysis of the change-point problem for the directional data in the parametric framework with von Mises or circular normal distribution as the underlying distribution. We first discuss the problem of detecting change in the mean direction of the circular normal distribution using a latent variable approach when the concentration parameter is unknown. Then, a simpler approach, beginning with proper priors for all the unknown parameters – the sampling importance resampling technique – is used to obtain the posterior marginal distribution of the change-point. The method is illustrated using the wind data [E.P. Weijers, A. Van Delden, H.F. Vugts and A.G.C.A. Meesters, The composite horizontal wind field within convective structures of the atmospheric surface layer, J. Atmos. Sci. 52 (1995. 3866–3878]. The method can be adapted for a variety of situations involving both angular and linear data and can be used with profit in the context of statistical process control in Phase I of control charting and also in Phase II in conjunction with control charts.     

A binary control chart to detect small jumps

The classic N p-chart gives a signal if the number of successes in a sequence of independent binary variables exceeds a control limit. Motivated by engineering applications in industrial image processing and, to some extent, financial statistics, we study a simple modification of this chart, which uses only the most recent observations. Our aim is to construct a control chart for detecting a shift of an unknown size, allowing for an unknown distribution of the error terms. Simulation studies indicate that the proposed chart is superior in terms of out-of-control average run length, when one is interested in the detection of very small shifts. We provide a (functional) central limit theorem under a change-point model with local alternatives, which explains that unexpected and interesting behaviour. Since real observations are often not independent, the question arises whether these results still hold true for the dependent case. Indeed, our asymptotic results work under the fairly general condition that the observations form a martingale difference array. This enlarges the applicability of our results considerably, first, to a large class of time series models, and, second, to locally dependent image data, as we demonstrate by an example.     

KENDALL'S TAU AND CONTINGENCY TABLES

Kendall's tau is a coefficient of concordance between two rankings of n objects. Its definition and large sample normal approximation are easily extended to the case where one of the rankings contains ties. In this paper, definition and normal approximation are extended further to the case where both rankings contain ties. The results are applied to give a fully distribution-free test for two-way contingency tables with ordered categories.     

A comparative simulation study of the small sample powers of several goodness fit test

Eight goodness of fit tests are compared with respect to their simulated small sample power of detecting an inbreeding alternative to the Hardy-Weinberg null hypothesis. The Pearson's x ² test is found to be most powerful, and the small rample levels of this test are close to the nominal (x ²) significance levels. The use of conditional expectations, rather than expected frequencies based on ML estimates, increases the power and improves thc x ² fit to the true significance level. The small sample powers are also compared to the asymptotic (Pitman) pourer, based on the noncenlral x ² distribution.