Discussion of "Is Bayes Posterior just Quick and Dirty Confidence?" by D. A.
S. Fraser [arXiv:1112.5582].
This report is a collection of comments on the Read Paper of Fearnhead and
Prangle (2011), to appear in the Journal of the Royal Statistical Society
Series B, along with a reply from the authors.
While some of the enclosed already is a well-known derivation, and the
remaining may have been obtained in earlier publications, this note computes
the first two moments of a Student's variate truncated at zero and of an
absolute (or folded) Student's variate.
This note is an extended review of the book Error and Inference, edited by
Deborah Mayo and Aris Spanos, about their frequentist and philosophical
perspective on testing of hypothesis and on the criticisms of alternatives like
the Bayesian approach.
For many decades, statisticians have made attempts to prepare the Bayesian
omelette without breaking the Bayesian eggs; that is, to obtain probabilistic
likelihood-based inferences without relying on informative prior distributions.
A recent example is Murray Aitkin's recent book, {\em Statistical Inference},
which presents an approach to statistical hypothesis testing based on
comparisons of posterior distributions of likelihoods under competing models.
Aitkin develops and illustrates his method using some simple examples of
inference from iid data and two-way tests of independence.
The missionary zeal of many Bayesians has been matched, in the other
direction, by a view among some theoreticians that Bayesian methods are
absurd-not merely misguided but obviously wrong in principle. We consider
several examples, beginning with Feller's classic text on probability theory
and continuing with more recent cases such as the perceived Bayesian nature of
the so-called doomsday argument.
Approximate Bayesian computation (ABC) have become a essential tool for the
analysis of complex stochastic models. Earlier, Grelaud et al. (2009) advocated
the use of ABC for Bayesian model choice in the specific case of Gibbs random
fields, relying on a inter-model sufficiency property to show that the
approximation was legitimate.
Also known as likelihood-free methods, approximate Bayesian computational
(ABC) methods have appeared in the past ten years as the most satisfactory
approach to untractable likelihood problems, first in genetics then in a
broader spectrum of applications. However, these methods suffer to some degree
from calibration difficulties that make them rather volatile in their
implementation and thus render them suspicious to the users of more traditional
Monte Carlo methods.
The Adaptive Multiple Importance Sampling (AMIS) algorithm is aimed at an
optimal recycling of past simulations in an iterated importance sampling
scheme. The difference with earlier adaptive importance sampling
implementations like Population Monte Carlo is that the importance weights of
all simulated values, past as well as present, are recomputed at each
iteration, following the technique of the deterministic multiple mixture
estimator of Owen and Zhou (2000).
This is a collection of discussions of `Riemann manifold Langevin and
Hamiltonian Monte Carlo methods" by Girolami and Calderhead, to appear in the
Journal of the Royal Statistical Society, Series B.
In this paper, we show how a complete and exact Bayesian analysis of a
parametric mixture model is possible in some cases when components of the
mixture are taken from exponential families and when conjugate priors are used.
This restricted set-up allows us to show the relevance of the Bayesian approach
as well as to exhibit the limitations of a complete analysis, namely that it is
impossible to conduct this analysis when the sample size is too large, when the
data are not from an exponential family, or when priors that are more complex
than conjugate priors are used.
In this paper, we consider the implications of the fact that parallel
raw-power can be exploited by a generic Metropolis--Hastings algorithm if the
proposed values are independent. In particular, we present improvements to the
independent Metropolis--Hastings algorithm that significantly decrease the
variance of any estimator derived from the MCMC output, for a null computing
cost since those improvements are based on a fixed number of target density
evaluations.
We propose a global noninformative approach for Bayesian variable selection
that builds on Zellner's g-priors and is similar to Liang et al. (2008). Our
proposal does not require any kind of calibration. In the case of a benchmark,
we compare Bayesian and frequentist regularization approaches under a low
informative constraint when the number of variables is almost equal to the
number of observations. The simulated and real dataset experiments we present
here highlight the appeal of Bayesian regularization methods, when compared
with alternatives.
In Templeton (2010), the Approximate Bayesian Computation (ABC) algorithm
(see, e.g., Pritchard et al., 1999, Beaumont et al., 2002, Marjoram et al.,
2003, Ratmann et al., 2009) is criticised on mathematical and logical grounds:
"the [Bayesian] inference is mathematically incorrect and formally illogical".
Since those criticisms turn out to be bearing on Bayesian foundations rather
than on the computational methodology they are primarily directed at, we
endeavour to point out in this note the statistical errors and inconsistencies
in Templeton (2010), refering to Beaumont et al.
This document is the aggregation of several discussions of Lopes et al.
(2010) we submitted to the proceedings of the Ninth Valencia Meeting, held in
Benidorm, Spain, on June 3-8, 2010, in conjunction with Hedibert Lopes' talk at
this meeting. The main point in those discussions is the potential for
degeneracy in the particle learning methodology, related with the exponential
forgetting of the past simulations. We illustrate the resulting difficulties in
the case of mixtures.
"Evidence and Evolution: the Logic behind the Science" was published in 2008
by Elliott Sober. It examines the philosophical foundations of the statistical
arguments used to evaluate hypotheses in evolutionary biology, based on simple
examples and likelihood ratios. The difficulty with reading the book from a
statistician's perspective is the reluctance of the author to engage into model
building and even less into parameter estimation.
The book A Treatise on Probability was published by John Maynard Keynes in
1921. It contains a critical assessment of the foundations of probability and
of the current statistical methodology. As a modern reader, we review here the
aspects that are most related with statistics, avoiding a neophyte's
perspective on the philosophical issues. In particular, the book is quite
critical of the Bayesian approach and we examine the arguments provided by
Keynes, as well as the alternative he proposes.
While Robert and Rousseau (2010) addressed the foundational aspects of
Bayesian analysis, the current chapter details its practical aspects through a
review of the computational methods available for approximating Bayesian
procedures. Recent innovations like Monte Carlo Markov chain, sequential Monte
Carlo methods and more recently Approximate Bayesian Computation techniques
have considerably increased the potential for Bayesian applications and they
have also opened new avenues for Bayesian inference, first and foremost
Bayesian model choice.
In this chapter, we will first present the most standard computational
challenges met in Bayesian Statistics, focussing primarily on mixture
estimation and on model choice issues, and then relate these problems with
computational solutions. Of course, this chapter is only a terse introduction
to the problems and solutions related to Bayesian computations. For more
complete references, see Robert and Casella (2004, 2009), or Marin and Robert
(2007), among others.
This chapter provides a overview of Bayesian inference, mostly emphasising
that it is a universal method for summarising uncertainty and making estimates
and predictions using probability statements conditional on observed data and
an assumed model (Gelman 2008).
The book The Search for Certainty published in 2009 by Krzysztof Burdzy
examines the "philosophical duopoly" at the foundation of statistics and find
it missing. We point out in this review the weakness of the scholarly arguments
presented in the book, we question the relevance of introducing a new set of
probability axioms, and we conclude on the lack of impact of this book on
statistical foundations and on Bayesian statistics in particular.
This introduction to Bayesian statistics presents the main concepts as well
as the principal reasons advocated in favour of a Bayesian modelling. We cover
the various approaches to prior determination as well as the basis asymptotic
arguments in favour of using Bayes estimators. The testing aspects of Bayesian
inference are also examined in details.
This is the solution manual to the odd-numbered exercises in our book
"Introducing Monte Carlo Methods with R", published by Springer Verlag on
December 10, 2009, and made freely available to everyone.
Published exactly seventy years ago, Jeffreys's Theory of Probability (1939)
has had a unique impact on the Bayesian community and is now considered to be
one of the main classics in Bayesian Statistics as well as the initiator of the
objective Bayes school. In particular, its advances on the derivation of
noninformative priors as well as on the scaling of Bayes factors have had a
lasting impact on the field. However, the book reflects the characteristics of
the time, especially in terms of mathematical rigor.
Every reversible Markov chain defines an operator whose spectrum encodes the
convergence properties of the chain. When the state space is finite, the
spectrum is just the set of eigenvalues of the corresponding Markov transition
matrix. However, when the state space is infinite, the spectrum may be
uncountable, and is nearly always impossible to calculate. In most applications
of the data augmentation (DA) algorithm, the state space of the DA Markov chain
is infinite.
This is the compilation of our comments submitted to the Journal of the Royal
Statistical Society, Series B, to be published within the discussion of the
Read Paper of Andrieu, Doucet and Hollenstein.
Casella and Robert (1996) presented a general Rao--Blackwellisation principle
for accept-reject and Metropolis-Hastings schemes that leads to significant
decreases in the variance of the resulting estimators, but at a high cost in
computing and storage. Adopting a completely different perspective, we
introduce instead a universal scheme that guarantees variance reductions in all
Metropolis-Hastings based estimators while keeping the computing cost under
control.
This solution manual contains the unabridged and original solutions to all
the exercises proposed in Bayesian Core, along with R programs when necessary.
This paper surveys some well-established approaches on the approximation of
Bayes factors used in Bayesian model choice, mostly as covered in Chen et al.
(2000). Our focus here is on methods that are based on importance sampling
strategies rather than variable dimension techniques like reversible jump MCMC,
including: crude Monte Carlo, maximum likelihood based importance sampling,
bridge and harmonic mean sampling, as well as Chib's method based on the
exploitation of a functional equality.
The new perspectives on ABC and Bayesian model criticisms presented in
Ratmann et al.(2009) are challenging standard approaches to Bayesian model
choice. We discuss here some issues arising from the authors' approach,
including prior influence, model assessment and criticism, and the meaning of
error in ABC.
We argue here about the relevance and the ultimate unity of the Bayesian
approach in a non-conflicting and non-antagonistic manner. Our main theme is
that Bayesian data analysis is an effective tool for handling complex models,
as proven by the increasing proportion of Bayesian studies in the applied
sciences. We disregard in this essay the philosophical debates on the deeper
meaning of probability and on the random nature of parameters as things of the
past that do a disservice to the approach and are incomprehensible to most
bystanders.
We are grateful to all discussants (Bernardo, Gelman, Kass, Lindley, Senn,
and Zellner) of our re-visitation for their strong support in our enterprise
and for their overall agreement with our perspective. Further discussions with
them and other leading statisticians showed that the legacy of Theory of
Probability is alive and lasting.
We are grateful to all discussants (Bernardo, Gelman, Kass, Lindley, Senn,
and Zellner) of our re-visitation for their strong support in our enterprise
and for their overall agreement with our perspective. Further discussions with
them and other leading statisticians showed that the legacy of Theory of
Probability is alive and lasting.
Monte Carlo methods are now an essential part of the statistician's toolbox,
to the point of being more familiar to graduate students than the measure
theoretic notions upon which they are based! We recall in this note some of the
advances made in the design of Monte Carlo techniques towards their use in
Statistics, referring to Robert and Casella (2004,2010) for an in-depth
coverage.