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.

We analyze algorithms that predict a binary value by combining the predictions of several prediction strategies, called experts. Our analysis is for worst-case situations, i.e., we make no assumptions about the way the sequence of bits to be predicted is generated. We measure the performance of the algorithm by the difference between the expected number of mistakes it makes on the bit sequence and the expected number of mistakes made by the best expert on this sequence, where the expectation is taken with respect to the randomization in the predictions. We show that the minimum achievable difference is on the order of the square root of the number of mistakes of the best expert, and we give efficient algorithms that achieve this. Our upper and lower bounds have matching leading constants in most cases. We then show howthis leads to certain kinds of pattern recognition/learning algorithms with performance bounds that improve on the best results currently known in this context. We also compare our analysis to the case in which log loss is used instead of the expected number of mistakes.

Graphical techniques for modeling the dependencies of random variables have been explored in a variety of di erent areas including statistics, statistical physics, arti-cial intelligence, speech recognition, image processing, and genetics. Formalisms for manipulating these models have been developed relatively independently in these research communities. In this paper we explore hidden Markov models (HMMs) and related structures within the general framework of probabilistic independence networks (PINs). The paper contains a self-contained review of the basic principles of PINs. It is shown that the well-known forward-backward (F-B) and Viterbi algorithms for HMMs are special cases of more general inference algorithms for arbitrary PINs. Furthermore, the existence of inference and estimation algorithms for more general graphical models provides a set of analysis tools for HMM practitioners who wish to explore a richer class of HMM structures. Examples of relatively complex models to handle sensor fusion and coarticulation in speech recognition are introduced and treated within the graphical model framework to illustrate the advantages of the general approach. 1

This paper reviews the principle of Minimum Description Length (MDL) for problems of model selection. By viewing statistical modeling as a means of generating descriptions of observed data, the MDL framework discriminates between competing models based on the complexity of each description. This approach began with Kolmogorov's theory of algorithmic complexity, matured in the literature on information theory, and has recently received renewed interest within the statistics community. In the pages that follow, we review both the practical as well as the theoretical aspects of MDL as a tool for model selection, emphasizing the rich connections between information theory and statistics. At the boundary between these two disciplines, we find many interesting interpretations of popular frequentist and Bayesian procedures. As we will see, MDL provides an objective umbrella under which rather disparate approaches to statistical modeling can co-exist and be compared. We illustrate th...

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. The points we emphasize are:- from Jeffreys's Bayesian point of view, the purpose of hypothesis testing is to evaluate the evidence in favor of a scientific theory;- Bayes factors offer a way of evaluating evidence in favor ofa null hypothesis;- Bayes factors provide a way of incorporating external information into the evaluation of evidence about a hypothesis;- Bayes factors are very general, and do not require alternative models to be nested;- several techniques are available for computing Bayes factors, including asymptotic approximations which are easy to compute using the output from standard packages that maximize likelihoods;- in "non-standard " statistical models that do not satisfy common regularity conditions, it can be technically simpler to calculate Bayes factors than to derive non-Bayesian significance

The relationship between the Bayesian approach and the minimum description length approach is established. We sharpen and clarify the general modeling principles MDL and MML, abstracted as the ideal MDL principle and defined from Bayes's rule by means of Kolmogorov complexity. The basic condition under which the ideal principle should be applied is encapsulated as the Fundamental Inequality, which in broad terms states that the principle is valid when the data are random, relative to every contemplated hypothesis and also these hypotheses are random relative to the (universal) prior. Basically, the ideal principle states that the prior probability associated with the hypothesis should be given by the algorithmic universal probability, and the sum of the log universal probability of the model plus the log of the probability of the data given the model should be minimized. If we restrict the model class to the finite sets then application of the ideal principle turns into Kolmogorov's mi...

We consider adaptive sequential prediction of arbitrary binary sequences when the performance is evaluated using a general loss function. The goal is to predict on each individual sequence nearly as well as the best prediction strategy in a given comparison class of (possibly adaptive) prediction strategies, called experts. By using a general loss function, we generalize previous work on universal prediction, forecasting, and data compression. However, here we restrict ourselves to the case when the comparison class is finite. For a given sequence, we define the regret as the total loss on the entire sequence suffered by the adaptive sequential predictor, minus the total loss suffered by the predictor in the comparison class that performs best on that particular sequence. We show that for a large class of loss functions, the minimax regret is either \Theta(log N) or \Omega\Gamma p ` log N ), depending on the loss function, where N is the number of predictors in the comparison class a...

this paper appeared in the Proceedings of the 2002 IEEE Information Theory Workshop [see Grnwald and Dawid (2002)]

this paper is somewhat different from the one just described. Assume that there are N experts E i , i = 1; : : : ; N , each trying to predict the outcomes y t as best they can. Let x t;i be the prediction of the ith expert E i about the

ses where the variance is known or taken as a parameter. 1. INTRODUCTION Although the term `hypothesis' in statistics is synonymous with that of a probability `model' as an explanation of data, hypothesis testing is not quite the same problem as model selection. This is because usually a particular hypothesis, called the `null hypothesis', has already been selected as a favorite model and it will be abandoned in favor of another model only when it clearly fails to explain the currently available data. In model selection, by contrast, all the models considered are regarded on the same footing and the objective is simply to pick the one that best explains the data. For the Bayesians certain models may be favored in terms of a prior probability, but in the minimum description length (MDL) approach to be outlined below, prior knowledge of any kind is to be used in selecting the tentative models, which in the end, unlike in the Bayesians' case, can and will be fitted to data