7,764 research outputs found
A nonparametric Bayesian approach to the rare type match problem
The "rare type match problem" is the situation in which the suspect's DNA
profile, matching the DNA profile of the crime stain, is not in the database of
reference. The evaluation of this match in the light of the two competing
hypotheses (the crime stain has been left by the suspect or by another person)
is based on the calculation of the likelihood ratio and depends on the
population proportions of the DNA profiles, that are unknown. We propose a
Bayesian nonparametric method that uses a two-parameter Poisson Dirichlet
distribution as a prior over the ranked population proportions, and discards
the information about the names of the different DNA profiles. This fits very
well the data coming from European Y-STR DNA profiles, and the calculation of
the likelihood ratio becomes quite simple thanks to a justified Empirical Bayes
approach.Comment: arXiv admin note: text overlap with arXiv:1506.0844
Bayesian nonparametric dependent model for partially replicated data: the influence of fuel spills on species diversity
We introduce a dependent Bayesian nonparametric model for the probabilistic
modeling of membership of subgroups in a community based on partially
replicated data. The focus here is on species-by-site data, i.e. community data
where observations at different sites are classified in distinct species. Our
aim is to study the impact of additional covariates, for instance environmental
variables, on the data structure, and in particular on the community diversity.
To that purpose, we introduce dependence a priori across the covariates, and
show that it improves posterior inference. We use a dependent version of the
Griffiths-Engen-McCloskey distribution defined via the stick-breaking
construction. This distribution is obtained by transforming a Gaussian process
whose covariance function controls the desired dependence. The resulting
posterior distribution is sampled by Markov chain Monte Carlo. We illustrate
the application of our model to a soil microbial dataset acquired across a
hydrocarbon contamination gradient at the site of a fuel spill in Antarctica.
This method allows for inference on a number of quantities of interest in
ecotoxicology, such as diversity or effective concentrations, and is broadly
applicable to the general problem of communities response to environmental
variables.Comment: Main Paper: 22 pages, 6 figures. Supplementary Material: 11 pages, 1
figur
Philosophy and the practice of Bayesian statistics
A substantial school in the philosophy of science identifies Bayesian
inference with inductive inference and even rationality as such, and seems to
be strengthened by the rise and practical success of Bayesian statistics. We
argue that the most successful forms of Bayesian statistics do not actually
support that particular philosophy but rather accord much better with
sophisticated forms of hypothetico-deductivism. We examine the actual role
played by prior distributions in Bayesian models, and the crucial aspects of
model checking and model revision, which fall outside the scope of Bayesian
confirmation theory. We draw on the literature on the consistency of Bayesian
updating and also on our experience of applied work in social science.
Clarity about these matters should benefit not just philosophy of science,
but also statistical practice. At best, the inductivist view has encouraged
researchers to fit and compare models without checking them; at worst,
theorists have actively discouraged practitioners from performing model
checking because it does not fit into their framework.Comment: 36 pages, 5 figures. v2: Fixed typo in caption of figure 1. v3:
Further typo fixes. v4: Revised in response to referee
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