International Journal of Biostatistics

Few systematic comparisons of methods for constructing survival trees and forests exist in the literature. Importantly, when the goal is to predict a survival time or estimate a survival function, the optimal choice of method is unclear. We use an extensive simulation study to systematically investigate various factors that influence survival forest performance - forest construction method, censoring, sample size, distribution of the response, structure of the linear predictor, and presence of correlated or noisy covariates...

Impulse noised outliers are data points that differ significantly from other observations. They are generally removed from the data set through local regression or the Kalman filter algorithm. However, these methods, or their generalizations, are not well suited when the number of outliers is of the same order as the number of low-noise data (often called nominal measurement ). In this article, we propose a new model for impulsed noise outliers. It is based on a hierarchical model and a simple linear Gaussian process as with the Kalman Filter...

Many cohort studies in survival analysis have imbedded in them subcohorts consisting of incident cases and prevalent cases. Instead of analysing the data from the incident and prevalent cohorts alone, there are surely advantages to combining the data from these two subcohorts. In this paper, we discuss a survival function nonparametric maximum likelihood estimator (NPMLE) using both length-biased right-censored prevalent cohort data and right-censored incident cohort data. We establish the asymptotic properties of the survival function NPMLE and utilize the NPMLE to estimate the distribution for time spent in a Montreal area hospital...

Individual level models are a class of mechanistic models that are widely used to infer infectious disease transmission dynamics. These models incorporate individual level covariate information accounting for population heterogeneity and are generally fitted in a Bayesian Markov chain Monte Carlo (MCMC) framework. However, Bayesian MCMC methods of inference are computationally expensive for large data sets. This issue becomes more severe when applied to infectious disease data collected from spatially heterogeneous populations, as the number of covariates increases...

The mean residual lifetime (MRL) of a unit in a population at a given time t , is the average remaining lifetime among those population units still alive at the time t . In some applications, it is reasonable to assume that MRL function is a decreasing function over time. Thus, one natural way to improve the estimation of MRL function is to use this assumption in estimation process. In this paper, we develop an MRL estimator in ranked set sampling (RSS) which, enjoys the monotonicity property. We prove that it is a strongly uniformly consistent estimator of true MRL function...

Agreement between methods for quantitative measurements are typically assessed by computing limits of agreement between pairs of methods and/or by illustration through Bland-Altman plots. We consider the situation where the observed measurement methods are considered a random sample from a population of possible methods, and discuss how the underlying linear mixed effects model can be extended to this situation. This is relevant when, for example, the methods represent raters/judges that are used to score specific individuals or items...

In many applications, it is of interest to identify a parsimonious set of features, or panel, from multiple candidates that achieves a desired level of performance in predicting a response. This task is often complicated in practice by missing data arising from the sampling design or other random mechanisms. Most recent work on variable selection in missing data contexts relies in some part on a finite-dimensional statistical model, e.g., a generalized or penalized linear model. In cases where this model is misspecified, the selected variables may not all be truly scientifically relevant and can result in panels with suboptimal classification performance...

Studying a large number of variables measured on the same observations and organized in blocks - denoted multiblock data - is becoming standard in several domains especially in biology. To explore the relationships between all these variables - at the block- and the variable-level - several exploratory multiblock methods were proposed. However, most of them are only designed for numeric variables. In reality, some data sets contain variables of different measurement levels (i.e., numeric, nominal, ordinal)...

In randomized trials, repeated measures of the outcome are routinely collected. The mixed model for repeated measures (MMRM) leverages the information from these repeated outcome measures, and is often used for the primary analysis to estimate the average treatment effect at the primary endpoint. MMRM, however, can suffer from bias and precision loss when it models intermediate outcomes incorrectly, and hence fails to use the post-randomization information harmlessly. This paper proposes an extension of the commonly used MMRM, called IMMRM, that improves the robustness and optimizes the precision gain from covariate adjustment, stratified randomization, and adjustment for intermediate outcome measures...

Incomplete data is a prevalent complication in longitudinal studies due to individuals' drop-out before intended completion time. Currently available methods via commercial software for analyzing incomplete longitudinal data at best rely on the ignorability of the drop-outs. If the underlying missing mechanism was non-ignorable, potential bias arises in the statistical inferences. To remove the bias when the drop-out is non-ignorable, joint complete-data and drop-out models have been proposed which involve computational difficulties and untestable assumptions...

Model-based component-wise gradient boosting is a popular tool for data-driven variable selection. In order to improve its prediction and selection qualities even further, several modifications of the original algorithm have been developed, that mainly focus on different stopping criteria, leaving the actual variable selection mechanism untouched. We investigate different prediction-based mechanisms for the variable selection step in model-based component-wise gradient boosting. These approaches include Akaikes Information Criterion (AIC) as well as a selection rule relying on the component-wise test error computed via cross-validation...

Data description is the first step for understanding the nature of the problem at hand. Usually, it is a simple task that does not require any particular assumption. However, the interpretation of the used descriptive measures can be a source of confusion and misunderstanding. The incidence rate is the quotient between the number of observed events and the sum of time that the studied population was at risk of having this event (person-time). Despite this apparently simple definition, its interpretation is not free of complexity...

In genome-wide association studies (GWAS), logistic regression is one of the most popular analytics methods for binary traits. Multinomial regression is an extension of binary logistic regression that allows for multiple categories. However, many GWAS methods have been limited application to binary traits. These methods have improperly often been used to account for ordinal traits, which causes inappropriate type I error rates and poor statistical power. Owing to the lack of analysis methods, GWAS of ordinal traits has been known to be problematic and gaining attention...

Differentiated care delivery aims to simplify care of people living with HIV, reflect their preferences, reduce burdens on the healthcare system, maintain care quality and preserve resources. However, assessing program effectiveness using observational data is difficult due to confounding by indication and randomized trials may be infeasible. Also, benefits can reach patients directly, through enrollment in the program, and indirectly, by increasing quality of and accessibility to care. Low-risk express care (LREC), the program under evaluation, is a nurse-centered model which assigns patients stable on ART to a nurse every two months and a clinician every third visit, reducing annual clinician visits by two thirds...

Consider the one-sided binomial confidence interval <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"> <mml:mfenced><mml:mrow><mml:mi>L</mml:mi> <mml:mo>,</mml:mo> <mml:mn>1</mml:mn></mml:mrow> </mml:mfenced> </mml:math> containing the unknown parameter p when all n trials are successful, and the significance level α to be five or one percent. We develop two functions (one for each level) that represent approximations within <mml:math xmlns:mml="https://www...

Simulation studies are promising in medical research in particular to improve drug development. For instance, one can aim to develop In Silico Clinical Trial in order to challenge trial's design parameters in terms of feasibility and probability of success of the trial. Approaches based on agent-based models draw on a particularly useful framework to simulate patients evolution. In this paper, an approach based on agent-based modeling is described and discussed in the context of medical research. An R-vine copula model is used to represent the multivariate distribution of the data...

Network meta-analysis is gaining prominence in clinical epidemiology and health technology assessments that enable comprehensive assessment of comparative effectiveness for multiple available treatments. In network meta-analysis, Bayesian methods have been one of the standard approaches for the arm-based approach and are widely applied in practical data analyses. Also, for most cases in these applications, proper noninformative priors are adopted, which does not incorporate subjective prior knowledge into the analyses, and reference Bayesian analyses are major choices...

Although they remain little used in the field of Health Care Economics, Agent Based Models (ABM) are potentially powerful decision-making tools that open up great prospects. The reasons for this lack of popularity are essentially to be found in a methodology that should be further clarified. This article hence aims to illustrate the methodology by means of two applications to medical examples. The first example of ABM illustrates the construction of a Baseline Data Cohort by means of a Virtual Baseline Generator...

In clinical trials that are subject to noncompliance, the commonly used intention-to-treat estimand is valid as a causal effect of treatment assignment but is sensitive to the level of compliance. An alternative estimand, the complier average causal effect ( CACE ), measures the average effect of treatment received in the latent subset of subjects who would comply with either assigned treatment. Because the principal stratum of compliers can vary with the circumstances of the trial, CACE too depends on the compliance fraction...

There is widespread interest in using deep learning to build prediction models for medical imaging data. These deep learning methods capture the local structure of the image and require no manual feature extraction. Despite the importance of modeling survival in the context of medical data analysis, research on deep learning methods for modeling the relationship of imaging and time-to-event data is still under-developed. We provide an overview of deep learning methods for time-to-event outcomes and compare several deep learning methods to Cox model based methods through the analysis of a histology dataset of gliomas...