Temporal Prediction of Future State Occupation in a Multistate Model from High-Dimensional Baseline Covariates via Pseudo-Value Regression

A pseudo-value regression approach for differential network analysis of co-expression data

BACKGROUND

The differential network (DN) analysis identifies changes in measures of association among genes under two or more experimental conditions. In this article, we introduce a pseudo-value regression approach for network analysis (PRANA). This is a novel method of differential network analysis that also adjusts for additional clinical covariates. We start from mutual information criteria, followed by pseudo-value calculations, which are then entered into a robust regression model.

RESULTS

This article assesses the model performances of PRANA in a multivariable setting, followed by a comparison to dnapath and DINGO in both univariable and multivariable settings through variety of simulations. Performance in terms of precision, recall, and F1 score of differentially connected (DC) genes is assessed. By and large, PRANA outperformed dnapath and DINGO, neither of which is equipped to adjust for available covariates such as patient-age. Lastly, we employ PRANA in a real data application from the Gene Expression Omnibus database to identify DC genes that are associated with chronic obstructive pulmonary disease to demonstrate its utility.

CONCLUSION

To the best of our knowledge, this is the first attempt of utilizing a regression modeling for DN analysis by collective gene expression levels between two or more groups with the inclusion of additional clinical covariates. By and large, adjusting for available covariates improves accuracy of a DN analysis.

Predicting COVID-19 progression in hospitalized patients in Belgium from a multi-state model

Objectives

To adopt a multi-state risk prediction model for critical disease/mortality outcomes among hospitalised COVID-19 patients using nationwide COVID-19 hospital surveillance data in Belgium.

Materials and methods

Information on 44,659 COVID-19 patients hospitalised between March 2020 and June 2021 with complete data on disease outcomes and candidate predictors was used to adopt a multi-state, multivariate Cox model to predict patients' probability of recovery, critical [transfer to intensive care units (ICU)] or fatal outcomes during hospital stay.

Results

Median length of hospital stay was 9 days (interquartile range: 5-14). After admission, approximately 82% of the COVID-19 patients were discharged alive, 15% of patients were admitted to ICU, and 15% died in the hospital. The main predictors of an increased probability for recovery were younger age, and to a lesser extent, a lower number of prevalent comorbidities. A patient's transition to ICU or in-hospital death had in common the following predictors: high levels of c-reactive protein (CRP) and lactate dehydrogenase (LDH), reporting lower respiratory complaints and male sex. Additionally predictors for a transfer to ICU included middle-age, obesity and reporting loss of appetite and staying at a university hospital, while advanced age and a higher number of prevalent comorbidities for in-hospital death. After ICU, younger age and low levels of CRP and LDH were the main predictors for recovery, while in-hospital death was predicted by advanced age and concurrent comorbidities.

Conclusion

As one of the very few, a multi-state model was adopted to identify key factors predicting COVID-19 progression to critical disease, and recovery or death.

A semiparametric modeling approach for analyzing clinical biomarkers restricted to limits of detection

Before biomarkers can be used in clinical trials or patients' management, the laboratory assays that measure their levels have to go through development and analytical validation. One of the most critical performance metrics for validation of any assay is related to the minimum amount of values that can be detected and any value below this limit is referred to as below the limit of detection (LOD). Most of the existing approaches that model such biomarkers, restricted by LOD, are parametric in nature. These parametric models, however, heavily depend on the distributional assumptions, and can result in loss of precision under the model or the distributional misspecifications. Using an example from a prostate cancer clinical trial, we show how a critical relationship between serum androgen biomarker and a prognostic factor of overall survival is completely missed by the widely used parametric Tobit model. Motivated by this example, we implement a semiparametric approach, through a pseudo-value technique, that effectively captures the important relationship between the LOD restricted serum androgen and the prognostic factor. Our simulations show that the pseudo-value based semiparametric model outperforms a commonly used parametric model for modeling below LOD biomarkers by having lower mean square errors of estimation.