Anytime parallel tempering

نویسندگان

چکیده

Developing efficient MCMC algorithms is indispensable in Bayesian inference. In parallel tempering, multiple interacting chains run to more efficiently explore the state space and improve performance. The advance independently through local moves, performance enhancement steps are exchange where pause their current sample amongst each other. To accelerate independent they may be performed simultaneously on processors. Another problem then encountered: depending implementation inference problem, moves can take a varying random amount of time complete. There also infrastructure-induced variations, such as competing jobs same processors, which arises cloud computing. Before exchanges occur, all must complete engaged avoid introducing potentially substantial bias (Proposition 2.1). solve this issue randomly move completion times multi-processor we adopt Anytime Monte Carlo framework Murray et al. (2016): impose real-time deadlines perform at these without any processor idling. We show our methodology for does not introduce leads significant enhancements over na\"ive approach idling until every processor's applied an ABC setting, tempering algorithm derived difficult task estimating parameters Lotka-Volterra predator-prey model, similar efficiency observed.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Likelihood-free parallel tempering

Approximate Bayesian Computational (ABC) methods, or likelihood-free methods, have appeared in the past fifteen years as useful methods to perform Bayesian analysis when the likelihood is analytically or computationally intractable. Several ABC methods have been proposed: MCMC methods have been developed by Marjoram et al. [2003] and by Bortot et al. [2007] for instance, and sequential methods ...

متن کامل

Parallel Tempering in Rosetta Practice

Parallel Tempering (PT) is an effective algorithm to overcome the slow convergence in low-temperature protein simulation by initiating multiple systems to run at multiple temperature levels and randomly switch with neighbor temperature levels. We implemented the PT scheme in the Rosetta to explore the rough energy landscape in protein folding and to improve the success rate of Rosetta in topolo...

متن کامل

Decentralized Replica Exchange Parallel Tempering: An Efficient Implementation of Parallel Tempering Using MPI and SPRNG

Parallel Tempering (PT), also known as Replica Exchange, is a powerful Markov Chain Monte Carlo sampling approach which aims at reducing the relaxation time in simulations of physical systems. In this paper, we present a novel implementation of PT, so-called decentralized replica exchange PT, using MPI and the Scalable Parallel Random Number Generators (SPRNG) libraries. By adjusting the replic...

متن کامل

Parallel tempering simulations of HP-36.

We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins...

متن کامل

Parallel tempering for strongly nonlinear geoacoustic inversion.

This paper applies parallel tempering within a Bayesian formulation for strongly nonlinear geoacoustic inverse problems. Bayesian geoacoustic inversion consists of sampling the posterior probability density (PPD) of seabed parameters to estimate integral properties, such as marginal probability distributions, based on ocean acoustic data and prior information. This sampling is usually carried o...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

ژورنال

عنوان ژورنال: Statistics and Computing

سال: 2021

ISSN: ['0960-3174', '1573-1375']

DOI: https://doi.org/10.1007/s11222-021-10048-0