40,498 research outputs found
A Statistical Modeling Approach to Computer-Aided Quantification of Dental Biofilm
Biofilm is a formation of microbial material on tooth substrata. Several
methods to quantify dental biofilm coverage have recently been reported in the
literature, but at best they provide a semi-automated approach to
quantification with significant input from a human grader that comes with the
graders bias of what are foreground, background, biofilm, and tooth.
Additionally, human assessment indices limit the resolution of the
quantification scale; most commercial scales use five levels of quantification
for biofilm coverage (0%, 25%, 50%, 75%, and 100%). On the other hand, current
state-of-the-art techniques in automatic plaque quantification fail to make
their way into practical applications owing to their inability to incorporate
human input to handle misclassifications. This paper proposes a new interactive
method for biofilm quantification in Quantitative light-induced fluorescence
(QLF) images of canine teeth that is independent of the perceptual bias of the
grader. The method partitions a QLF image into segments of uniform texture and
intensity called superpixels; every superpixel is statistically modeled as a
realization of a single 2D Gaussian Markov random field (GMRF) whose parameters
are estimated; the superpixel is then assigned to one of three classes
(background, biofilm, tooth substratum) based on the training set of data. The
quantification results show a high degree of consistency and precision. At the
same time, the proposed method gives pathologists full control to post-process
the automatic quantification by flipping misclassified superpixels to a
different state (background, tooth, biofilm) with a single click, providing
greater usability than simply marking the boundaries of biofilm and tooth as
done by current state-of-the-art methods.Comment: 10 pages, 7 figures, Journal of Biomedical and Health Informatics
2014. keywords: {Biomedical imaging;Calibration;Dentistry;Estimation;Image
segmentation;Manuals;Teeth},
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6758338&isnumber=636350
Learning loopy graphical models with latent variables: Efficient methods and guarantees
The problem of structure estimation in graphical models with latent variables
is considered. We characterize conditions for tractable graph estimation and
develop efficient methods with provable guarantees. We consider models where
the underlying Markov graph is locally tree-like, and the model is in the
regime of correlation decay. For the special case of the Ising model, the
number of samples required for structural consistency of our method scales
as , where p is the
number of variables, is the minimum edge potential, is
the depth (i.e., distance from a hidden node to the nearest observed nodes),
and is a parameter which depends on the bounds on node and edge
potentials in the Ising model. Necessary conditions for structural consistency
under any algorithm are derived and our method nearly matches the lower bound
on sample requirements. Further, the proposed method is practical to implement
and provides flexibility to control the number of latent variables and the
cycle lengths in the output graph.Comment: Published in at http://dx.doi.org/10.1214/12-AOS1070 the Annals of
Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical
Statistics (http://www.imstat.org
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.
Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite of models. Consequently, users of these software packages are simultaneously forced to use a number of programs for a given study, while also lacking the freedom to explore models that have not been implemented by the developers of those programs. We developed a new open-source software package, RevBayes, to address these problems. RevBayes is entirely based on probabilistic graphical models, a powerful generic framework for specifying and analyzing statistical models. Phylogenetic-graphical models can be specified interactively in RevBayes, piece by piece, using a new succinct and intuitive language called Rev. Rev is similar to the R language and the BUGS model-specification language, and should be easy to learn for most users. The strength of RevBayes is the simplicity with which one can design, specify, and implement new and complex models. Fortunately, this tremendous flexibility does not come at the cost of slower computation; as we demonstrate, RevBayes outperforms competing software for several standard analyses. Compared with other programs, RevBayes has fewer black-box elements. Users need to explicitly specify each part of the model and analysis. Although this explicitness may initially be unfamiliar, we are convinced that this transparency will improve understanding of phylogenetic models in our field. Moreover, it will motivate the search for improvements to existing methods by brazenly exposing the model choices that we make to critical scrutiny. RevBayes is freely available at http://www.RevBayes.com [Bayesian inference; Graphical models; MCMC; statistical phylogenetics.]
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