Bridged parametric survival models: General paradigm and speed improvements. (July 2021)

• Record Type: Journal Article
• Authors: Swihart, Bruce J.; Bandyopadhyay, Dipankar
• Is Part Of: Computer methods and programs in biomedicine. Volume 206(2021)
• Publication Date: 2021-07
• Subjects: Accelerated failure time -- Likelihood -- Marginal -- Parametric survival models -- Positive stable distribution -- Proportional hazard -- Hougaard; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2021.106115
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: Currently marginal survival model fits are slow for large data with many clusters. Bridged-survival models allow for population-average and subject-specific analyses. Our implementation is 12x faster than currently available R software. Our implementation is 2400x faster than SAS. Marginal and conditional hazard ratios can be directly estimated. Marginal and conditional acceleration factors can be directly estimated. Abstract: Background and objective: With the recent surge in availability of large biomedical databases mostly derived from electronic health records, the need for the development of scalable marginal survival models with faster implementation cannot be more timely. The presence of clustering renders computational complexity, especially when the number of clusters is high. Marginalizing conditional survival models can violate the proportional hazards assumption for some frailty distributions, disrupting the connection to a conditional model. While theoretical connections between proportional hazard and accelerated failure time models exist, a computational framework to produce both for either marginal or conditional perspectives is lacking. Our objective is to provide fast, scalable bridged-survival models contained in a unified framework from which the effects and standard errors for the conditional hazard ratio, the marginal hazard ratio, the conditional acceleration factor, and the marginal acceleration factor can be estimated, and related to one another in a transparent fashion. Methods We formulate a Weibull parametric frailty likelihood for clustered survival times that can directly estimate the four estimands. Under a nonlinear mixed model specification with positive stable frailties powered by Gaussian quadrature, we put forth a novel closed form of the integrated likelihood that lowered the computational threshold for fitting these models. The method is illustrated on a real dataset generated from electronic health records examining tooth-loss. Results: Our novel closed form of the integrated likelihood significantly lowered the computational threshold for fitting these models by a factor of 12 (36 compared to 3 min) for the R package parfm, and a factor of 2400 for Gaussian Quadrature (4.6 days compared to 3 min) in SAS. Moreover, each of these estimands are connected by simple relationships of the parameters and the proportional hazards assumption is preserved for the marginal model. Our framework provides a flow of analysis enabling the fit of any/all of the 4 perspective-parameterization combinations. Conclusions We see the potential usefulness of our framework of bridged parametric survival models fitted with the Static-Stirling closed form likelihood. Bridged-survival models provide insights on subject-specific and population-level survival effects when their relation is transparent. SAS and R codes, along with implementation details on a pseudo data are provided.