36,165 research outputs found
A Bayesian semiparametric latent variable model for mixed responses
In this article we introduce a latent variable model (LVM) for mixed ordinal and continuous responses, where covariate effects on the continuous latent variables are modelled through a flexible semiparametric predictor. We extend existing LVM with simple linear covariate effects by including nonparametric components for nonlinear effects of continuous covariates and interactions with other covariates as well as spatial effects. Full Bayesian modelling is based on penalized spline and Markov random field priors and is performed by computationally efficient Markov chain Monte Carlo (MCMC) methods. We apply our approach to a large German social science survey which motivated our methodological development
netgwas: An R Package for Network-Based Genome-Wide Association Studies
Graphical models are powerful tools for modeling and making statistical
inferences regarding complex associations among variables in multivariate data.
In this paper we introduce the R package netgwas, which is designed based on
undirected graphical models to accomplish three important and interrelated
goals in genetics: constructing linkage map, reconstructing linkage
disequilibrium (LD) networks from multi-loci genotype data, and detecting
high-dimensional genotype-phenotype networks. The netgwas package deals with
species with any chromosome copy number in a unified way, unlike other
software. It implements recent improvements in both linkage map construction
(Behrouzi and Wit, 2018), and reconstructing conditional independence network
for non-Gaussian continuous data, discrete data, and mixed
discrete-and-continuous data (Behrouzi and Wit, 2017). Such datasets routinely
occur in genetics and genomics such as genotype data, and genotype-phenotype
data. We demonstrate the value of our package functionality by applying it to
various multivariate example datasets taken from the literature. We show, in
particular, that our package allows a more realistic analysis of data, as it
adjusts for the effect of all other variables while performing pairwise
associations. This feature controls for spurious associations between variables
that can arise from classical multiple testing approach. This paper includes a
brief overview of the statistical methods which have been implemented in the
package. The main body of the paper explains how to use the package. The
package uses a parallelization strategy on multi-core processors to speed-up
computations for large datasets. In addition, it contains several functions for
simulation and visualization. The netgwas package is freely available at
https://cran.r-project.org/web/packages/netgwasComment: 32 pages, 9 figures; due to the limitation "The abstract field cannot
be longer than 1,920 characters", the abstract appearing here is slightly
shorter than that in the PDF fil
Herding as a Learning System with Edge-of-Chaos Dynamics
Herding defines a deterministic dynamical system at the edge of chaos. It
generates a sequence of model states and parameters by alternating parameter
perturbations with state maximizations, where the sequence of states can be
interpreted as "samples" from an associated MRF model. Herding differs from
maximum likelihood estimation in that the sequence of parameters does not
converge to a fixed point and differs from an MCMC posterior sampling approach
in that the sequence of states is generated deterministically. Herding may be
interpreted as a"perturb and map" method where the parameter perturbations are
generated using a deterministic nonlinear dynamical system rather than randomly
from a Gumbel distribution. This chapter studies the distinct statistical
characteristics of the herding algorithm and shows that the fast convergence
rate of the controlled moments may be attributed to edge of chaos dynamics. The
herding algorithm can also be generalized to models with latent variables and
to a discriminative learning setting. The perceptron cycling theorem ensures
that the fast moment matching property is preserved in the more general
framework
Julian Ernst Besag, 26 March 1945 -- 6 August 2010, a biographical memoir
Julian Besag was an outstanding statistical scientist, distinguished for his
pioneering work on the statistical theory and analysis of spatial processes,
especially conditional lattice systems. His work has been seminal in
statistical developments over the last several decades ranging from image
analysis to Markov chain Monte Carlo methods. He clarified the role of
auto-logistic and auto-normal models as instances of Markov random fields and
paved the way for their use in diverse applications. Later work included
investigations into the efficacy of nearest neighbour models to accommodate
spatial dependence in the analysis of data from agricultural field trials,
image restoration from noisy data, and texture generation using lattice models.Comment: 26 pages, 14 figures; minor revisions, omission of full bibliograph
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