Abstract
In this technical note we compare the performance of four gradient-free MCMC samplers (random walk Metropolis sampling, slice-sampling, adaptive MCMC sampling and population-based MCMC sampling with tempering) in terms of the number of independent samples they can produce per unit computational time. For the Bayesian inversion of a single-node neural mass model, both adaptive and population-based samplers are more efficient compared with random walk Metropolis sampler or slice-sampling; yet adaptive MCMC sampling is more promising in terms of compute time. Slice-sampling yields the highest number of independent samples from the target density - albeit at almost 1000% increase in computational time, in comparison to the most efficient algorithm (i.e., the adaptive MCMC sampler).
References
Nov 24, 1986·Physical Review Letters·R H Swendsen, J S Wang
Sep 4, 1999·Statistics in Medicine·L Tierney, A Mira
Sep 2, 2003·NeuroImage·K J FristonW Penny
Mar 9, 2006·Systematic Biology·Nicolas Lartillot, Hervé Philippe
Apr 25, 2006·NeuroImage·Olivier DavidKarl J Friston
Oct 24, 2006·NeuroImage·Karl FristonWill Penny
Sep 22, 2007·NeuroImage·Justin R ChumbleyStefan J Kiebel
Dec 7, 2005·Physical Chemistry Chemical Physics : PCCP·David J Earl, Michael W Deem
Jun 1, 1984·IEEE Transactions on Pattern Analysis and Machine Intelligence·S Geman, D Geman
Mar 18, 2015·NeuroImage·Biswa SenguptaWill D Penny
Citations
Jul 28, 2015·NeuroImage·Biswa SenguptaWill D Penny
Jul 30, 2015·NeuroImage·Gerald K CoorayKarl Friston
Nov 17, 2015·NeuroImage·Karl J FristonPeter Zeidman
Sep 20, 2015·Journal of Neuroscience Methods·Eduardo A AponteJakob Heinzle
Apr 27, 2016·NeuroImage·Dirk Ostwald, Ludger Starke
May 5, 2016·Journal of Neuroscience Methods·Sudhir RamanKlaas Enno Stephan
Mar 18, 2015·NeuroImage·Biswa SenguptaWill D Penny
Jan 26, 2018·Wiley Interdisciplinary Reviews. Cognitive Science·Stefan FrässleKlaas E Stephan
Aug 5, 2018·Brain Topography·Fadi N Karameh, Ziad Nahas
Mar 5, 2016·PLoS Computational Biology·Will Penny, Biswa Sengupta
Feb 23, 2019·Network Neuroscience·Natalia Z BielczykJan K Buitelaar
Feb 8, 2018·NeuroImage·Stanisław AdaszewskiPiotr Bogorodzki
May 11, 2021·Wellcome Open Research·Karl J FristonChristian Lambert
May 11, 2020·NeuroImage·M HashemiV K Jirsa
Jun 22, 2021·Frontiers in Psychiatry·Stefan FrässleKlaas E Stephan
Jul 15, 2021·PLoS Computational Biology·Meysam HashemiViktor K Jirsa