arXiv subjects

Sean Yiu

Publications and source records attributed to Sean Yiu.

8 recordsLinked to original sources

arXiv2024

A Bayesian joint model of multiple longitudinal and categorical outcomes with application to multiple myeloma using permutation-based variable importance

Joint models have proven to be an effective approach for uncovering potentially hidden connections between various types of outcomes, mainly continuous, time-to-event, and binary. Typically, longitudinal continuous outcomes are characterized by linear mixed-effects models, survival outcomes are described by proportional hazards models, and the link between outcomes are captured by shared random effects. Other modeling variations include generalized linear mixed-effects models for longitudinal data and logistic regression when a binary outcome is present, rather than time until an event of interest. However, in a clinical research setting, one might be interested in modeling the physician's chosen treatment based on the patient's medical history to identify prognostic factors. In this situation, there are often multiple treatment options, requiring the use of a multiclass classification approach. Inspired by this context, we develop a Bayesian joint model for longitudinal and categorical data. In particular, our motivation comes from a multiple myeloma study, in which biomarkers display nonlinear trajectories that are well captured through bi-exponential submodels, where patient-level information is shared with the categorical submodel. We also present a variable importance strategy to rank prognostic factors. We apply our proposal and a competing model to the multiple myeloma data, compare the variable importance and inferential results for both models, and illustrate patient-level interpretations using our joint model.

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arXiv2024

A Bayesian joint model of multiple nonlinear longitudinal and competing risks outcomes for dynamic prediction in multiple myeloma: joint estimation and corrected two-stage approaches

Predicting cancer-associated clinical events is challenging in oncology. In Multiple Myeloma (MM), a cancer of plasma cells, disease progression is determined by changes in biomarkers, such as serum concentration of the paraprotein secreted by plasma cells (M-protein). Therefore, the time-dependent behaviour of M-protein and the transition across lines of therapy (LoT) that may be a consequence of disease progression should be accounted for in statistical models to predict relevant clinical outcomes. Furthermore, it is important to understand the contribution of the patterns of longitudinal biomarkers, upon each LoT initiation, to time-to-death or time-to-next-LoT. Motivated by these challenges, we propose a Bayesian joint model for trajectories of multiple longitudinal biomarkers, such as M-protein, and the competing risks of death and transition to next LoT. Additionally, we explore two estimation approaches for our joint model: simultaneous estimation of all parameters (joint estimation) and sequential estimation of parameters using a corrected two-stage strategy aiming to reduce computational time. Our proposed model and estimation methods are applied to a retrospective cohort study from a real-world database of patients diagnosed with MM in the US from January 2015 to February 2022. We split the data into training and test sets in order to validate the joint model using both estimation approaches and make dynamic predictions of times until clinical events of interest, informed by longitudinally measured biomarkers and baseline variables available up to the time of prediction.

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arXiv2023

Sequential linear regression for conditional mean imputation of longitudinal continuous outcomes under reference-based assumptions

In clinical trials of longitudinal continuous outcomes, reference based imputation (RBI) has commonly been applied to handle missing outcome data in settings where the estimand incorporates the effects of intercurrent events, e.g. treatment discontinuation. RBI was originally developed in the multiple imputation framework, however recently conditional mean imputation (CMI) combined with the jackknife estimator of the standard error was proposed as a way to obtain deterministic treatment effect estimates and correct frequentist inference. For both multiple and CMI, a mixed model for repeated measures (MMRM) is often used for the imputation model, but this can be computationally intensive to fit to multiple data sets (e.g. the jackknife samples) and lead to convergence issues with complex MMRM models with many parameters. Therefore, a step-wise approach based on sequential linear regression (SLR) of the outcomes at each visit was developed for the imputation model in the multiple imputation framework, but similar developments in the CMI framework are lacking. In this article, we fill this gap in the literature by proposing a SLR approach to implement RBI in the CMI framework, and justify its validity using theoretical results and simulations. We also illustrate our proposal on a real data application.

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arXiv2023

Accommodating informative visit times for analysing irregular longitudinal data: a sensitivity analysis approach with balancing weights estimators

Irregular longitudinal data with informative visit times arise when patients' visits are partly driven by concurrent disease outcomes. However, existing methods such as inverse intensity weighting (IIW), often overlook or have not adequately assess the influence of informative visit times on estimation and inference. Based on novel balancing weights estimators, we propose a new sensitivity analysis approach to addressing informative visit times within the IIW framework. The balancing weights are obtained by balancing observed history variable distributions over time and including a selection function with specified sensitivity parameters to characterise the additional influence of the concurrent outcome on the visit process. A calibration procedure is proposed to anchor the range of the sensitivity parameters to the amount of variation in the visit process that could be additionally explained by the concurrent outcome given the observed history and time. Simulations demonstrate that our balancing weights estimators outperform existing weighted estimators for robustness and efficiency. We provide an R Markdown tutorial of the proposed methods and apply them to analyse data from a clinic-based cohort of psoriatic arthritis.

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arXiv2021

Standard and reference-based conditional mean imputation

Clinical trials with longitudinal outcomes typically include missing data due to missed assessments or structural missingness of outcomes after intercurrent events handled with a hypothetical strategy. Approaches based on Bayesian random multiple imputation and Rubin's rule for pooling results across multiple imputed datasets are increasingly used in order to align the analysis of these trials with the targeted estimand. We propose and justify deterministic conditional mean imputation combined with the jackknife for inference as an alternative approach. The method is applicable to imputations under a missing-at-random assumption as well as for reference-based imputation approaches. In an application and a simulation study, we demonstrate that it provides consistent treatment effect estimates with the Bayesian approach and reliable frequentist inference with accurate standard error estimation and type I error control. A further advantage of the method is that it does not rely on random sampling and is therefore replicable and unaffected by Monte Carlo error.

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arXiv2018

Joint calibrated estimation of inverse probability of treatment and censoring weights for marginal structural models

Marginal structural models (MSMs) with inverse probability weighting offer an approach to estimating causal effects of treatment sequences on repeated outcome measures in the presence of time-varying confounding and dependent censoring. However, when weights are estimated by maximum likelihood, inverse probability weighted estimators (IPWEs) can be inefficient and unstable in practice. We propose a joint calibration approach for inverse probability of treatment and censoring weights to improve the efficiency and robustness of the IPWEs for MSMs with time-varying treatments of arbitrary (i.e., binary and non-binary) distributions. Specifically, novel calibration restrictions are derived by explicitly eliminating covariate associations with both the treatment assignment process and the censoring process after weighting the current sample (i.e., to optimise covariate balance in finite samples). A convex minimization procedure is developed to implement the calibration. Simulations show that IPWEs with calibrated weights perform better than IPWEs with weights from maximum likelihood. We apply our method to a natural history study of HIV for estimating the cumulative effect of highly active antiretroviral therapy on CD4 cell counts over time.

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arXiv2017

Clustered multi-state models with observation-level random effects, mover-stayer effects and dynamic covariates: Modelling transition intensities and sojourn times in a study of psoriatic arthritis

In psoriatic arthritis, it is important to understand the joint activity (represented by swelling and pain) and damage processes because both are related to severe physical disability. This paper aims to provide a comprehensive investigation in to both processes occurring over time, in particular their relationship, by specifying a joint multi-state model at the individual hand joint-level, which also accounts for many of their important features. As there are multiple hand joints, such an analysis will be based on the use of clustered multi-state models. Here we consider an observation-level random effects structure with dynamic covariates and allow for the possibility that a subpopulation of patients are at minimal risk of damage. Such an analysis is found to provide further understanding of the activity-damage relationship beyond that provided by previous analyses. Consideration is also given to the modelling of mean sojourn times and jump probabilities. In particular, a novel model parameterization which allows easily interpretable covariate effects to act on these quantities is proposed.

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arXiv2017

Two-part models with stochastic processes for modelling longitudinal semicontinuous data: computationally efficient inference and modelling the overall marginal mean

Several researchers have described two-part models with patient-specific stochastic processes for analysing longitudinal semicontinuous data. In theory, such models can offer greater flexibility than the standard two-part model with patient-specific random effects. However, in practice the high dimensional integrations involved in the marginal likelihood (i.e. integrated over the stochastic processes) significantly complicates model fitting. Thus non-standard computationally intensive procedures based on simulating the marginal likelihood have so far only been proposed. In this paper, we describe an efficient method of implementation by demonstrating how the high dimensional integrations involved in the marginal likelihood can be computed efficiently. Specifically, by using a property of the multivariate normal distribution and the standard marginal cumulative distribution function identity, we transform the marginal likelihood so that the high dimensional integrations are contained in the cumulative distribution function of a multivariate normal distribution, which can then be efficiently evaluated. Hence maximum likelihood estimation can be used to obtain parameter estimates and asymptotic standard errors (from the observed information matrix) of model parameters. We describe our proposed efficient implementation procedure for the standard two-part model parameterisation and when it is of interest to directly model the overall marginal mean. The methodology is applied on a psoriatic arthritis data set concerning functional disability.

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