Bayesian clustering of multiple zero-inflated outcomes

Several applications involving counts present a large proportion of zeros (excess-of-zeros data). A popular model for such data is the hurdle model, which explicitly models the probability of a zero count, while assuming a sampling distribution on the positive integers. We consider data from multiple count processes. In this context, it is of interest to study the patterns of counts and cluster the subjects accordingly. We introduce a novel Bayesian approach to cluster multiple, possibly related, zero-inflated processes. We propose a joint model for zero-inflated counts, specifying a hurdle model for each process with a shifted Negative Binomial sampling distribution. Conditionally on the model parameters, the different processes are assumed independent, leading to a substantial reduction in the number of parameters as compared with traditional multivariate approaches. The subject-specific probabilities of zero-inflation and the parameters of the sampling distribution are flexibly modelled via an enriched finite mixture with random number of components. This induces a two-level clustering of the subjects based on the zero/non-zero patterns (outer clustering) and on the sampling distribution (inner clustering). Posterior inference is performed through tailored Markov chain Monte Carlo schemes. We demonstrate the proposed approach on an application involving the use of the messaging service WhatsApp. This article is part of the theme issue 'Bayesian inference: challenges, perspectives, and prospects'.

Joint modelling of mental health markers through pregnancy: a Bayesian semi-parametric approach

Maternal depression and anxiety through pregnancy have lasting societal impacts. It is thus crucial to understand the trajectories of its progression from preconception to postnatal period, and the risk factors associated with it. Within the Bayesian framework, we propose to jointly model seven outcomes, of which two are physiological and five non-physiological indicators of maternal depression and anxiety over time. We model the former two by a Gaussian process and the latter by an autoregressive model, while imposing a multidimensional Dirichlet process prior on the subject-specific random effects to account for subject heterogeneity and induce clustering. The model allows for the inclusion of covariates through a regression term. Our findings reveal four distinct clusters of trajectories of the seven health outcomes, characterising women's mental health progression from before to after pregnancy. Importantly, our results caution against the loose use of hair corticosteroids as a biomarker, or even a causal factor, for pregnancy mental health progression. Additionally, the regression analysis reveals a range of preconception determinants and risk factors for depressive and anxiety symptoms during pregnancy.

Mutual information: Measuring nonlinear dependence in longitudinal epidemiological data

Given a large clinical database of longitudinal patient information including many covariates, it is computationally prohibitive to consider all types of interdependence between patient variables of interest. This challenge motivates the use of mutual information (MI), a statistical summary of data interdependence with appealing properties that make it a suitable alternative or addition to correlation for identifying relationships in data. MI: (i) captures all types of dependence, both linear and nonlinear, (ii) is zero only when random variables are independent, (iii) serves as a measure of relationship strength (similar to but more general than R2), and (iv) is interpreted the same way for numerical and categorical data. Unfortunately, MI typically receives little to no attention in introductory statistics courses and is more difficult than correlation to estimate from data. In this article, we motivate the use of MI in the analyses of epidemiologic data, while providing a general introduction to estimation and interpretation. We illustrate its utility through a retrospective study relating intraoperative heart rate (HR) and mean arterial pressure (MAP). We: (i) show postoperative mortality is associated with decreased MI between HR and MAP and (ii) improve existing postoperative mortality risk assessment by including MI and additional hemodynamic statistics.

Bayesian inference on the number of recurrent events: A joint model of recurrence and survival

The number of recurrent events before a terminating event is often of interest. For instance, death terminates an individual's process of rehospitalizations and the number of rehospitalizations is an important indicator of economic cost. We propose a model in which the number of recurrences before termination is a random variable of interest, enabling inference and prediction on it. Then, conditionally on this number, we specify a joint distribution for recurrence and survival. This novel conditional approach induces dependence between recurrence and survival, which is often present, for instance, due to frailty that affects both. Additional dependence between recurrence and survival is introduced by the specification of a joint distribution on their respective frailty terms. Moreover, through the introduction of an autoregressive model, our approach is able to capture the temporal dependence in the recurrent events trajectory. A non-parametric random effects distribution for the frailty terms accommodates population heterogeneity and allows for data-driven clustering of the subjects. A tailored Gibbs sampler involving reversible jump and slice sampling steps implements posterior inference. We illustrate our model on colorectal cancer data, compare its performance with existing approaches and provide appropriate inference on the number of recurrent events.

Trust and Trade-Offs in Sharing Data for Precision Medicine: A National Survey of Singapore

BACKGROUND

Precision medicine (PM) programs typically use broad consent. This approach requires maintenance of the social license and public trust. The ultimate success of PM programs will thus likely be contingent upon understanding public expectations about data sharing and establishing appropriate governance structures. There is a lack of data on public attitudes towards PM in Asia.

METHODS

The aim of the research was to measure the priorities and preferences of Singaporeans for sharing health-related data for PM. We used adaptive choice-based conjoint analysis (ACBC) with four attributes: uses, users, data sensitivity and consent. We recruited a representative sample of n = 1000 respondents for an in-person household survey.

RESULTS

Of the 1000 respondents, 52% were female and majority were in the age range of 40-59 years (40%), followed by 21-39 years (33%) and 60 years and above (27%). A total of 64% were generally willing to share de-identified health data for IRB-approved research without re-consent for each study. Government agencies and public institutions were the most trusted users of data. The importance of the four attributes on respondents' willingness to share data were: users (39.5%), uses (28.5%), data sensitivity (19.5%), consent (12.6%). Most respondents found it acceptable for government agencies and hospitals to use de-identified data for health research with broad consent. Our sample was consistent with official government data on the target population with 52% being female and majority in the age range of 40-59 years (40%), followed by 21-39 years (33%) and 60 years and above (27%).

CONCLUSIONS

While a significant body of prior research focuses on preferences for consent, our conjoint analysis found consent was the least important attribute for sharing data. Our findings suggest the social license for PM data sharing in Singapore currently supports linking health and genomic data, sharing with public institutions for health research and quality improvement; but does not support sharing with private health insurers or for private commercial use.

The Search for Optimal Oxygen Saturation Targets in Critically Ill Patients: Observational Data From Large ICU Databases

BACKGROUND

Although low oxygen saturations are generally regarded as deleterious, recent studies in ICU patients have shown that a liberal oxygen strategy increases mortality. However, the optimal oxygen saturation target remains unclear. The goal of this study was to determine the optimal range by using real-world data.

METHODS

Replicate retrospective analyses were conducted of two electronic medical record databases: the eICU Collaborative Research Database (eICU-CRD) and the Medical Information Mart for Intensive Care III database (MIMIC). Only patients with at least 48 h of oxygen therapy were included. Nonlinear regression was used to analyze the association between median pulse oximetry-derived oxygen saturation (Spo₂) and hospital mortality. We derived an optimal range of Spo₂ and analyzed the association between the percentage of time within the optimal range of Spo₂ and hospital mortality. All models adjusted for age, BMI, sex, and Sequential Organ Failure Assessment score. Subgroup analyses included ICU types, main diagnosis, and comorbidities.

RESULTS

The analysis identified 26,723 patients from eICU-CRD and 8,564 patients from MIMIC. The optimal range of Spo₂ was 94% to 98% in both databases. The percentage of time patients were within the optimal range of Spo₂ was associated with decreased hospital mortality (OR of 80% vs 40% of the measurements within the optimal range, 0.42 [95% CI, 0.40-0.43] for eICU-CRD and 0.53 [95% CI, 0.50-0.55] for MIMIC). This association was consistent across subgroup analyses.

CONCLUSIONS

The optimal range of Spo₂ was 94% to 98% and should inform future trials of oxygen therapy.

Extrema-weighted feature extraction for functional data

Motivation

Although there is a rich literature on methods for assessing the impact of functional predictors, the focus has been on approaches for dimension reduction that do not suit certain applications. Examples of standard approaches include functional linear models, functional principal components regression and cluster-based approaches, such as latent trajectory analysis. This article is motivated by applications in which the dynamics in a predictor, across times when the value is relatively extreme, are particularly informative about the response. For example, physicians are interested in relating the dynamics of blood pressure changes during surgery to post-surgery adverse outcomes, and it is thought that the dynamics are more important when blood pressure is significantly elevated or lowered.

Results

We propose a novel class of extrema-weighted feature (XWF) extraction models. Key components in defining XWFs include the marginal density of the predictor, a function up-weighting values at extreme quantiles of this marginal, and functionals characterizing local dynamics. Algorithms are proposed for fitting of XWF-based regression and classification models, and are compared with current methods for functional predictors in simulations and a blood pressure during surgery application. XWFs find features of intraoperative blood pressure trajectories that are predictive of postoperative mortality. By their nature, most of these features cannot be found by previous methods.

Availability and implementation

The R package 'xwf' is available at the CRAN repository: https://cran.r-project.org/package=xwf.

Supplementary information

Supplementary data are available at Bioinformatics online.

Effect of A1C and Glucose on Postoperative Mortality in Noncardiac and Cardiac Surgeries

OBJECTIVE

Hemoglobin A_1c (A1C) is used in assessment of patients for elective surgeries because hyperglycemia increases risk of adverse events. However, the interplay of A1C, glucose, and surgical outcomes remains unclarified, with often only two of these three factors considered simultaneously. We assessed the association of preoperative A1C with perioperative glucose control and their relationship with 30-day mortality.

RESEARCH DESIGN AND METHODS

Retrospective analysis on 431,480 surgeries within the Duke University Health System determined the association of preoperative A1C with perioperative glucose (averaged over the first 3 postoperative days) and 30-day mortality among 6,684 noncardiac and 6,393 cardiac surgeries with A1C and glucose measurements. A generalized additive model was used, enabling nonlinear relationships.

RESULTS

A1C and glucose were strongly associated. Glucose and mortality were positively associated for noncardiac cases: 1.0% mortality at mean glucose of 100 mg/dL and 1.6% at mean glucose of 200 mg/dL. For cardiac procedures, there was a striking U-shaped relationship between glucose and mortality, ranging from 4.5% at 100 mg/dL to a nadir of 1.5% at 140 mg/dL and rising again to 6.9% at 200 mg/dL. A1C and 30-day mortality were not associated when controlling for glucose in noncardiac or cardiac procedures.

CONCLUSIONS

Although A1C is positively associated with perioperative glucose, it is not associated with increased 30-day mortality after controlling for glucose. Perioperative glucose predicts 30-day mortality, linearly in noncardiac and nonlinearly in cardiac procedures. This confirms that perioperative glucose control is related to surgical outcomes but that A1C, reflecting antecedent glycemia, is a less useful predictor.