952 research outputs found
Mixtures of Regression Models for Time-Course Gene Expression Data: Evaluation of Initialization and Random Effects
Finite mixture models are routinely applied to time course microarray data.
Due to the complexity and size of this type of data the choice of good starting values plays
an important role. So far initialization strategies have only been investigated for data
from a mixture of multivariate normal distributions. In this work several initialization
procedures are evaluated for mixtures of regression models with and without random
effects in an extensive simulation study on different artificial datasets. Finally these
procedures are also applied to a real dataset from E. coli
A bi-dimensional finite mixture model for longitudinal data subject to dropout
In longitudinal studies, subjects may be lost to follow-up, or miss some of
the planned visits, leading to incomplete response sequences. When the
probability of non-response, conditional on the available covariates and the
observed responses, still depends on unobserved outcomes, the dropout mechanism
is said to be non ignorable. A common objective is to build a reliable
association structure to account for dependence between the longitudinal and
the dropout processes. Starting from the existing literature, we introduce a
random coefficient based dropout model where the association between outcomes
is modeled through discrete latent effects. These effects are outcome-specific
and account for heterogeneity in the univariate profiles. Dependence between
profiles is introduced by using a bi-dimensional representation for the
corresponding distribution. In this way, we define a flexible latent class
structure which allows to efficiently describe both dependence within the two
margins of interest and dependence between them. By using this representation
we show that, unlike standard (unidimensional) finite mixture models, the non
ignorable dropout model properly nests its ignorable counterpart. We detail the
proposed modeling approach by analyzing data from a longitudinal study on the
dynamics of cognitive functioning in the elderly. Further, the effects of
assumptions about non ignorability of the dropout process on model parameter
estimates are (locally) investigated using the index of (local) sensitivity to
non-ignorability
A variational Bayesian method for inverse problems with impulsive noise
We propose a novel numerical method for solving inverse problems subject to
impulsive noises which possibly contain a large number of outliers. The
approach is of Bayesian type, and it exploits a heavy-tailed t distribution for
data noise to achieve robustness with respect to outliers. A hierarchical model
with all hyper-parameters automatically determined from the given data is
described. An algorithm of variational type by minimizing the Kullback-Leibler
divergence between the true posteriori distribution and a separable
approximation is developed. The numerical method is illustrated on several one-
and two-dimensional linear and nonlinear inverse problems arising from heat
conduction, including estimating boundary temperature, heat flux and heat
transfer coefficient. The results show its robustness to outliers and the fast
and steady convergence of the algorithm.Comment: 20 pages, to appear in J. Comput. Phy
FASTLens (FAst STatistics for weak Lensing) : Fast method for Weak Lensing Statistics and map making
With increasingly large data sets, weak lensing measurements are able to
measure cosmological parameters with ever greater precision. However this
increased accuracy also places greater demands on the statistical tools used to
extract the available information. To date, the majority of lensing analyses
use the two point-statistics of the cosmic shear field. These can either be
studied directly using the two-point correlation function, or in Fourier space,
using the power spectrum. But analyzing weak lensing data inevitably involves
the masking out of regions or example to remove bright stars from the field.
Masking out the stars is common practice but the gaps in the data need proper
handling. In this paper, we show how an inpainting technique allows us to
properly fill in these gaps with only operations, leading to a new
image from which we can compute straight forwardly and with a very good
accuracy both the pow er spectrum and the bispectrum. We propose then a new
method to compute the bispectrum with a polar FFT algorithm, which has the main
advantage of avoiding any interpolation in the Fourier domain. Finally we
propose a new method for dark matter mass map reconstruction from shear
observations which integrates this new inpainting concept. A range of examples
based on 3D N-body simulations illustrates the results.Comment: Final version accepted by MNRAS. The FASTLens software is available
from the following link : http://irfu.cea.fr/Ast/fastlens.software.ph
Bayesian Centroid Estimation for Motif Discovery
Biological sequences may contain patterns that are signal important
biomolecular functions; a classical example is regulation of gene expression by
transcription factors that bind to specific patterns in genomic promoter
regions. In motif discovery we are given a set of sequences that share a common
motif and aim to identify not only the motif composition, but also the binding
sites in each sequence of the set. We present a Bayesian model that is an
extended version of the model adopted by the Gibbs motif sampler, and propose a
new centroid estimator that arises from a refined and meaningful loss function
for binding site inference. We discuss the main advantages of centroid
estimation for motif discovery, including computational convenience, and how
its principled derivation offers further insights about the posterior
distribution of binding site configurations. We also illustrate, using
simulated and real datasets, that the centroid estimator can differ from the
maximum a posteriori estimator.Comment: 24 pages, 9 figure
An exploratory cluster randomised trial of a university halls of residence based social norms marketing campaign to reduce alcohol consumption among 1st year students
<p>Aims: This exploratory trial examines the feasibility of implementing a social norms marketing campaign to reduce student drinking in universities in Wales, and evaluating it using cluster randomised trial methodology.</p>
<p>Methods: Fifty residence halls in 4 universities in Wales were randomly assigned to intervention or control arms. Web and paper surveys were distributed to students within these halls (n = 3800), assessing exposure/contamination, recall of and evaluative responses to intervention messages, perceived drinking norms and personal drinking behaviour. Measures included the Drinking Norms Rating Form, the Daily Drinking Questionnaire and AUDIT-C.</p>
<p>Results: A response rate of 15% (n = 554) was achieved, varying substantially between sites. Intervention posters were seen by 80% and 43% of students in intervention and control halls respectively, with most remaining materials seen by a minority in both groups. Intervention messages were rated as credible and relevant by little more than half of students, though fewer felt they would influence their behaviour, with lighter drinkers more likely to perceive messages as credible. No differences in perceived norms were observed between intervention and control groups. Students reporting having seen intervention materials reported lower descriptive and injunctive norms than those who did not.</p>
<p>Conclusions: Attention is needed to enhancing exposure, credibility and perceived relevance of intervention messages, particularly among heavier drinkers, before definitive evaluation can be recommended. A definitive evaluation would need to consider how it would achieve sufficient response rates, whilst hall-level cluster randomisation appears subject to a significant degree of contamination.</p>
Exenatide Improves Bone Quality in a Murine Model of Genetically Inherited Type 2 Diabetes Mellitus
Type 2 diabetes mellitus (T2DM) is associated with skeletal complications, including an
increased risk of fractures. Reduced blood supply and bone strength may contribute to
this skeletal fragility. We hypothesized that long-term administration of Exenatide, a glucagon-
like peptide-1 receptor agonist, would improve bone architecture and strength of
T2DM mice by increasing blood flow to bone, thereby stimulating bone formation. In this study, we used a model of obesity and severe T2DM, the leptin receptor-deficient db/db mouse to assess alterations in bone quality and hindlimb blood flow and to examine the beneficial effects of 4 weeks administration of Exenatide. As expected, diabetic mice showed marked alterations in bone structure, remodeling and strength, and basal vascular tone compared with lean mice. Exenatide treatment improved trabecular bone mass and architecture by increasing bone formation rate, but only in diabetic mice. Although there was no effect on hindlimb perfusion at the end of this treatment, exenatide administration acutely increased tibial blood flow. While Exenatide treatment did not restore the
impaired bone strength, intrinsic properties of the matrix, such as collagen maturity, were improved. The effects of Exenatide on in vitro bone formation were further investigated in primary osteoblasts cultured under high-glucose conditions, showing that Exenatide
reversed the impairment in bone formation induced by glucose. In conclusion, Exenatide improves trabecular bone mass by increasing bone formation and could protect against the development of skeletal complications associated with T2DM
Graphical Markov models, unifying results and their interpretation
Graphical Markov models combine conditional independence constraints with
graphical representations of stepwise data generating processes.The models
started to be formulated about 40 years ago and vigorous development is
ongoing. Longitudinal observational studies as well as intervention studies are
best modeled via a subclass called regression graph models and, especially
traceable regressions. Regression graphs include two types of undirected graph
and directed acyclic graphs in ordered sequences of joint responses. Response
components may correspond to discrete or continuous random variables and may
depend exclusively on variables which have been generated earlier. These
aspects are essential when causal hypothesis are the motivation for the
planning of empirical studies.
To turn the graphs into useful tools for tracing developmental pathways and
for predicting structure in alternative models, the generated distributions
have to mimic some properties of joint Gaussian distributions. Here, relevant
results concerning these aspects are spelled out and illustrated by examples.
With regression graph models, it becomes feasible, for the first time, to
derive structural effects of (1) ignoring some of the variables, of (2)
selecting subpopulations via fixed levels of some other variables or of (3)
changing the order in which the variables might get generated. Thus, the most
important future applications of these models will aim at the best possible
integration of knowledge from related studies.Comment: 34 Pages, 11 figures, 1 tabl
Why are we not flooded by involuntary thoughts about the past and future? Testing the cognitive inhibition dependency hypothesis
© The Author(s) 2018In everyday life, involuntary thoughts about future plans and events occur as often as involuntary thoughts about the past. However, compared to involuntary autobiographical memories (IAMs), such episodic involuntary future thoughts (IFTs) have become a focus of study only recently. The aim of the present investigation was to examine why we are not constantly flooded by IFTs and IAMs given that they are often triggered by incidental cues while performing undemanding activities. One possibility is that activated thoughts are suppressed by the inhibitory control mechanism, and therefore depleting inhibitory control should enhance the frequency of both IFTs and IAMs. We report an experiment with a between-subjects design, in which participants in the depleted inhibition condition performed a 60-min high-conflict Stroop task before completing a laboratory vigilance task measuring the frequency of IFTs and IAMs. Participants in the intact inhibition condition performed a version of the Stroop task that did not deplete inhibitory control. To control for physical and mental fatigue resulting from performing the 60-min Stroop tasks in experimental conditions, participants in the control condition completed only the vigilance task. Contrary to predictions, the number of IFTs and IAMs reported during the vigilance task, using the probe-caught method, did not differ across conditions. However, manipulation checks showed that participants’ inhibitory resources were reduced in the depleted inhibition condition, and participants were more tired in the experimental than in the control conditions. These initial findings suggest that neither inhibitory control nor physical and mental fatigue affect the frequency of IFTs and IAMs.Peer reviewedFinal Published versio
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