Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.

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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space

The Gibbs sampler, the algorithm of Metropolis and similar iterative simulation methods are potentially very helpful for summarizing multivariate distributions. Used naively, however, iterative simulation can give misleading answers. Our methods are simple and generally applicable to the output of any iterative simulation; they are designed for researchers primarily interested in the science underlying the data and models they are analyzing, rather than for researchers interested in the probability theory underlying the iterative simulations themselves. Our recommended strategy is to use several independent sequences, with starting points sampled from an overdispersed distribution. At each step of the iterative simulation, we obtain, for each univariate estimand of interest, a distributional estimate and an estimate of how much sharper the distributional estimate might become if the simulations were continued indefinitely. Because our focus is on applied inference for Bayesian posterior distributions in real problems, which often tend toward normality after transformations and marginalization, we derive our results as normal-theory approximations to exact Bayesian inference, conditional on the observed simulations. The methods are illustrated on a random-effects mixture model applied to experimental measurements of reaction times of normal and schizophrenic patients.

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Inference from Iterative Simulation Using Multiple Sequences

Today's Web-enabled deluge of electronic data calls for automated methods of data analysis. Machine learning provides these, developing methods that can automatically detect patterns in data and then use the uncovered patterns to predict future data. This textbook offers a comprehensive and self-contained introduction to the field of machine learning, based on a unified, probabilistic approach. The coverage combines breadth and depth, offering necessary background material on such topics as probability, optimization, and linear algebra as well as discussion of recent developments in the field, including conditional random fields, L1 regularization, and deep learning. The book is written in an informal, accessible style, complete with pseudo-code for the most important algorithms. All topics are copiously illustrated with color images and worked examples drawn from such application domains as biology, text processing, computer vision, and robotics. Rather than providing a cookbook of different heuristic methods, the book stresses a principled model-based approach, often using the language of graphical models to specify models in a concise and intuitive way. Almost all the models described have been implemented in a MATLAB software package--PMTK (probabilistic modeling toolkit)--that is freely available online. The book is suitable for upper-level undergraduates with an introductory-level college math background and beginning graduate students.

Machine Learning : A Probabilistic Perspective

Statistics for Spatial Data.

Meyn & Tweedie is back! The bible on Markov chains in general state spaces has been brought up to date to reflect developments in the field since 1996 - many of them sparked by publication of the first edition. The pursuit of more efficient simulation algorithms for complex Markovian models, or algorithms for computation of optimal policies for controlled Markov models, has opened new directions for research on Markov chains. As a result, new applications have emerged across a wide range of topics including optimisation, statistics, and economics. New commentary and an epilogue by Sean Meyn summarise recent developments and references have been fully updated. This second edition reflects the same discipline and style that marked out the original and helped it to become a classic: proofs are rigorous and concise, the range of applications is broad and knowledgeable, and key ideas are accessible to practitioners with limited mathematical background.

Markov Chains and Stochastic Stability

This paper considers the problem of scaling the proposal distribution of a multidimensional random walk Metropolis algorithm in order to maximize the efficiency of the algorithm. The main result is a weak convergence result as the dimension of a sequence of target densities, n, converges to $\infty$. When the proposal variance is appropriately scaled according to n, the sequence of stochastic processes formed by the first component of each Markov chain converges to the appropriate limiting Langevin diffusion process. The limiting diffusion approximation admits a straightforward efficiency maximization problem, and the resulting asymptotically optimal policy is related to the asymptotic acceptance rate of proposed moves for the algorithm. The asymptotically optimal acceptance rate is 0.234 under quite general conditions. The main result is proved in the case where the target density has a symmetric product form. Extensions of the result are discussed.

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Weak convergence and optimal scaling of random walk Metropolis algorithms

The use of the Gibbs sampler for Bayesian computation is reviewed and illustrated in the context of some canonical examples Other Markov chain Monte Carlo simulation methods are also briefly described, and comments are made on the advantages of sample-based approaches for Bayesian inference summaries

https://rss.onlinelibrary.wiley.com/doi/pdf/10.1111/j.2517-6161.1993.tb01466.x

Bayesian Computation Via the Gibbs Sampler and Related Markov Chain Monte Carlo Methods

We review and extend results related to optimal scaling of Metropolis–Hastings algorithms. We present various theoretical results for the high-dimensional limit. We also present simulation studies which confirm the theoretical results in finite-dimensional contexts.

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Optimal scaling for various Metropolis-Hastings algorithms

In this paper we consider a continuous-time method of approximating a given distribution π using the Langevin diffusion d L t=dW t+1 2 ∇logπ(L t)dt . We find conditions under which this diffusion converges exponentially quickly to π or does not: in one dimension, these are essentially that for distributions with exponential tails of the form π (x)∝exp(-γ|x| β ) , 0 <β<∞ , exponential convergence occurs if and only if β ≥1 . We then consider conditions under which the discrete approximations to the diffusion converge. We first show that even when the diffusion itself converges, naive discretizations need not do so. We then consider a 'Metropolis-adjusted' version of the algorithm, and find conditions under which this also converges at an exponential rate: perhaps surprisingly, even the Metropolized version need not converge exponentially fast even if the diffusion does. We briefly discuss a truncated form of the algorithm which, in practice, should avoid the difficulties of the other forms.

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Exponential convergence of Langevin distributions and their discrete approximations

We investigate the use of adaptive MCMC algorithms to automatically tune the Markov chain parameters during a run. Examples include the Adaptive Metropolis (AM) multivariate algorithm of Haario, Saksman, and Tamminen (2001), Metropolis-within-Gibbs algorithms for nonconjugate hierarchical models, regionally adjusted Metropolis algorithms, and logarithmic scalings. Computer simulations indicate that the algorithms perform very well compared to nonadaptive algorithms, even in high dimension.

https://www.jstor.org/stable/pdf/25651249.pdf

Gareth O. Roberts

Papers

Weak convergence and optimal scaling of random walk Metropolis algorithms

Bayesian Computation Via the Gibbs Sampler and Related Markov Chain Monte Carlo Methods

Optimal scaling for various Metropolis-Hastings algorithms

Exponential convergence of Langevin distributions and their discrete approximations

Examples of Adaptive MCMC