Adaptive MCMC for Bayesian variable selection in generalised linear models and survival models

Abstract

Developing an efficient computational scheme for high-dimensional Bayesian variable selection in generalised linear models and survival models has always been a challenging problem due to the absence of closed-form solutions for the marginal likelihood. The RJMCMC approach can be employed to samples model and coefficients jointly, but effective design of the transdimensional jumps of RJMCMC can be challenge, making it hard to implement. Alternatively, the marginal likelihood can be derived using data-augmentation scheme e.g. Polya-gamma data argumentation for logistic regression) or through other estimation methods. However, suitable data-augmentation schemes are not available for every generalised linear and survival models, and using estimations such as Laplace approximation or correlated pseudo-marginal to derive marginal likelihood within a locally informed proposal can be computationally expensive in the "large n, large p" settings. In this paper, three main contributions are presented. Firstly, we present an extended Point-wise implementation of Adaptive Random Neighbourhood Informed proposal (PARNI) to efficiently sample models directly from the marginal posterior distribution in both generalised linear models and survival models. Secondly, in the light of the approximate Laplace approximation, we also describe an efficient and accurate estimation method for the marginal likelihood which involves adaptive parameters. Additionally, we describe a new method to adapt the algorithmic tuning parameters of the PARNI proposal by replacing the Rao-Blackwellised estimates with the combination of a warm-start estimate and an ergodic average. We present numerous numerical results from simulated data and 8 high-dimensional gene fine mapping data-sets to showcase the efficiency of the novel PARNI proposal compared to the baseline add-delete-swap proposal