44,370 research outputs found
Inference for reaction networks using the Linear Noise Approximation
We consider inference for the reaction rates in discretely observed networks
such as those found in models for systems biology, population ecology and
epidemics. Most such networks are neither slow enough nor small enough for
inference via the true state-dependent Markov jump process to be feasible.
Typically, inference is conducted by approximating the dynamics through an
ordinary differential equation (ODE), or a stochastic differential equation
(SDE). The former ignores the stochasticity in the true model, and can lead to
inaccurate inferences. The latter is more accurate but is harder to implement
as the transition density of the SDE model is generally unknown. The Linear
Noise Approximation (LNA) is a first order Taylor expansion of the
approximating SDE about a deterministic solution and can be viewed as a
compromise between the ODE and SDE models. It is a stochastic model, but
discrete time transition probabilities for the LNA are available through the
solution of a series of ordinary differential equations. We describe how a
restarting LNA can be efficiently used to perform inference for a general class
of reaction networks; evaluate the accuracy of such an approach; and show how
and when this approach is either statistically or computationally more
efficient than ODE or SDE methods. We apply the LNA to analyse Google Flu
Trends data from the North and South Islands of New Zealand, and are able to
obtain more accurate short-term forecasts of new flu cases than another
recently proposed method, although at a greater computational cost
A shared-parameter continuous-time hidden Markov and survival model for longitudinal data with informative dropout
A shared-parameter approach for jointly modeling longitudinal and survival data is proposed. With respect to available approaches, it allows for time-varying random effects that affect both the longitudinal and the survival processes. The distribution of these random effects is modeled according to a continuous-time hidden Markov chain so that transitions may occur at any time point. For maximum likelihood estimation, we propose an algorithm based on a discretization of time until censoring in an arbitrary number of time windows. The observed information matrix is used to obtain standard errors. We illustrate the approach by simulation, even with respect to the effect of the number of time windows on the precision of the estimates, and by an application to data about patients suffering from mildly dilated cardiomyopathy
Stochastic Approximation and Modern Model-Based Designs for Dose-Finding Clinical Trials
In 1951 Robbins and Monro published the seminal article on stochastic
approximation and made a specific reference to its application to the
"estimation of a quantal using response, nonresponse data." Since the 1990s,
statistical methodology for dose-finding studies has grown into an active area
of research. The dose-finding problem is at its core a percentile estimation
problem and is in line with what the Robbins--Monro method sets out to solve.
In this light, it is quite surprising that the dose-finding literature has
developed rather independently of the older stochastic approximation
literature. The fact that stochastic approximation has seldom been used in
actual clinical studies stands in stark contrast with its constant application
in engineering and finance. In this article, I explore similarities and
differences between the dose-finding and the stochastic approximation
literatures. This review also sheds light on the present and future relevance
of stochastic approximation to dose-finding clinical trials. Such connections
will in turn steer dose-finding methodology on a rigorous course and extend its
ability to handle increasingly complex clinical situations.Comment: Published in at http://dx.doi.org/10.1214/10-STS334 the Statistical
Science (http://www.imstat.org/sts/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Maximally selected chi-square statistics and binary splits of nominal variables
We address the problem of maximally selected chi-square statistics in the case of a binary Y variable and a nominal X variable with several categories. The distribution of the maximally selected chi-square statistic has already been derived when the best cutpoint is chosen from a continuous or an ordinal X, but not when the best split is chosen from a nominal X. In this paper, we derive the exact distribution of the maximally selected chi-square statistic in this case using a combinatorial approach. Applications of the derived distribution to variable selection and hypothesis testing are discussed based on simulations. As an illustration, our method is applied to a pregnancy and birth data set
A latent factor model for spatial data with informative missingness
A large amount of data is typically collected during a periodontal exam.
Analyzing these data poses several challenges. Several types of measurements
are taken at many locations throughout the mouth. These spatially-referenced
data are a mix of binary and continuous responses, making joint modeling
difficult. Also, most patients have missing teeth. Periodontal disease is a
leading cause of tooth loss, so it is likely that the number and location of
missing teeth informs about the patient's periodontal health. In this paper we
develop a multivariate spatial framework for these data which jointly models
the binary and continuous responses as a function of a single latent spatial
process representing general periodontal health. We also use the latent spatial
process to model the location of missing teeth. We show using simulated and
real data that exploiting spatial associations and jointly modeling the
responses and locations of missing teeth mitigates the problems presented by
these data.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS278 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Maximally selected chi-square statistics and umbrella orderings
Binary outcomes that depend on an ordinal predictor in a non-monotonic way are common in medical data analysis. Such patterns can be addressed in terms of cutpoints: for example, one looks for two cutpoints that define an interval in the range of the ordinal predictor for which the probability of a positive outcome is particularly high (or low). A chi-square test may then be performed to compare the proportions of positive outcomes in and outside this interval. However, if the two cutpoints are chosen to maximize the chi-square statistic, referring the obtained chi-square statistic to the standard chi-square distribution is an inappropriate approach. It is then necessary to correct the p-value for multiple comparisons by considering the distribution of the maximally selected chi-square statistic instead of the nominal chi-square distribution. Here, we derive the exact distribution of the chi-square statistic obtained by the optimal two cutpoints. We suggest a combinatorial computation method and illustrate our approach by a simulation study and an application to varicella data
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