In a 1935 paper, and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P -values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this paper we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology and psychology.

Spanning seven orders of magnitude: a challenge for

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This paper is also the originator of the Markov Chain Monte Carlo methods developed in the following chapters. The potential of these two simultaneous innovations has been discovered much latter by statisticians (Hastings 1970; Geman and Geman 1984) than by of physicists (see also Kirkpatrick et al. 1983). 5.5.5 ] PROBLEMS 211

Probabilistic inference is an attractive approach to uncertain reasoning and empirical learning in artificial intelligence. Computational difculties arise, however, because probabilistic models with the necessary realism and flexibility lead to complex distributions over high-dimensional spaces. Related problems in other fields have been tackled using Monte Carlo methods based on sampling using Markov chains, providing a rich array of techniques that can be applied to problems in artificial intelligence. The "Metropolis algorithm" has been used to solve difficult problems in statistical physics for over forty years, and, in the last few years, the related method of "Gibbs sampling" has been applied to problems of statistical inference. Concurrently, an alternative method for solving problems in statistical physics by means of dynamical simulation has been developed as well, and has recently been unified with the Metropolis algorithm to produce the "hybrid Monte Carlo" method. In computer science, Markov chain sampling is the basis of the heuristic optimization technique of "simulated annealing", and has recently been used in randomized algorithms for approximate counting of large sets. In this review, I outline the role of probabilistic inference in artificial intelligence, and present the theory of Markov chains, and describe various Markov chain Monte Carlo algorithms, along with a number of supporting techniques. I try to present a comprehensive picture of the range of methods that have been developed, including techniques from the varied literature that have not yet seen wide application in artificial intelligence, but which appear relevant. As illustrative examples, I use the problems of probabilitic inference in expert systems, discovery of latent classes from data, and Bayesian learning for neural networks.

Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EF-hand calcium binding motif. In each case the parameters of an HMM are estimated from a training set of unaligned sequences. After the HMM is built, it is used to obtain a multiple alignment of all the training sequences. It is also used to search the. SWISS-PROT 22 database for other sequences. that are members of the given protein family, or contain the given domain. The Hi " produces multiple alignments of good quality that agree closely with the alignments produced by programs that incorporate threedimensional structural information. When employed in discrimination tests (by examining how closely the sequences in a database fit the globin, kinase and EF-hand HMMs), the '\ HMM is able to distinguish members of these families from non-members with a high degree of accuracy. Both the HMM and PROFILESEARCH (a technique used to search for relationships between a protein sequence and multiply aligned sequences) perform better in these tests than PROSITE (a dictionary of sites and patterns in proteins). The HMM appecvs to have a slight advantage over PROFILESEARCH in terms of lower rates of false

Although Bayesian analysis has been in use since Laplace, the Bayesian method of model--comparison has only recently been developed in depth. In this paper, the Bayesian approach to regularisation and model--comparison is demonstrated by studying the inference problem of interpolating noisy data. The concepts and methods described are quite general and can be applied to many other problems. Regularising constants are set by examining their posterior probability distribution. Alternative regularisers (priors) and alternative basis sets are objectively compared by evaluating the evidence for them. `Occam's razor' is automatically embodied by this framework. The way in which Bayes infers the values of regularising constants and noise levels has an elegant interpretation in terms of the effective number of parameters determined by the data set. This framework is due to Gull and Skilling. 1 Data modelling and Occam's razor In science, a central task is to develop and compare models to a...

Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and bio-sequence analysis, and KFMs have been used for problems ranging from tracking planes and missiles to predicting the economy. However, HMMs and KFMs are limited in their “expressive power”. Dynamic Bayesian Networks (DBNs) generalize HMMs by allowing the state space to be represented in factored form, instead of as a single discrete random variable. DBNs generalize KFMs by allowing arbitrary probability distributions, not just (unimodal) linear-Gaussian. In this thesis, I will discuss how to represent many different kinds of models as DBNs, how to perform exact and approximate inference in DBNs, and how to learn DBN models from sequential data. In particular, the main novel technical contributions of this thesis are as follows: a way of representing Hierarchical HMMs as DBNs, which enables inference to be done in O(T) time instead of O(T 3), where T is the length of the sequence; an exact smoothing algorithm that takes O(log T) space instead of O(T); a simple way of using the junction tree algorithm for online inference in DBNs; new complexity bounds on exact online inference in DBNs; a new deterministic approximate inference algorithm called factored frontier; an analysis of the relationship between the BK algorithm and loopy belief propagation; a way of applying Rao-Blackwellised particle filtering to DBNs in general, and the SLAM (simultaneous localization and mapping) problem in particular; a way of extending the structural EM algorithm to DBNs; and a variety of different applications of DBNs. However, perhaps the main value of the thesis is its catholic presentation of the field of sequential data modelling.

We show a learning-based method for low-level vision problems. We set-up a Markov network of patches of the image and the underlying scene. A factorization approximation allows us to easily learn the parameters of the Markov network from synthetic examples of image/scene pairs, and to e ciently propagate image information. Monte Carlo simulations justify this approximation. We apply this to the \super-resolution " problem (estimating high frequency details from a low-resolution image), showing good results. For the motion estimation problem, we show resolution of the aperture problem and lling-in arising from application of the same probabilistic machinery.

This paper introduces a general Bayesian framework for obtaining sparse solutions to regression and classication tasks utilising models linear in the parameters. Although this framework is fully general, we illustrate our approach with a particular specialisation that we denote the `relevance vector machine' (RVM), a model of identical functional form to the popular and state-of-the-art `support vector machine' (SVM). We demonstrate that by exploiting a probabilistic Bayesian learning framework, we can derive accurate prediction models which typically utilise dramatically fewer basis functions than a comparable SVM while oering a number of additional advantages. These include the benets of probabilistic predictions, automatic estimation of `nuisance' parameters, and the facility to utilise arbitrary basis functions (e.g. non-`Mercer' kernels).