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At least 433 records · Page 24Linked to original sources
PubMed2005

Bayesian analysis for generalized linear models with nonignorably missing covariates.

We propose Bayesian methods for estimating parameters in generalized linear models (GLMs) with nonignorably missing covariate data. We show that when improper uniform priors are used for the regression coefficients, phi, of the multinomial selection model for the missing data mechanism, the resulting joint posterior will always be improper if (i) all missing covariates are discrete and an intercept is included in the selection model for the missing data mechanism, or (ii) at least one of the covariates is continuous and unbounded. This impropriety will result regardless of whether proper or improper priors are specified for the regression parameters, beta, of the GLM or the parameters, alpha, of the covariate distribution. To overcome this problem, we propose a novel class of proper priors for the regression coefficients, phi, in the selection model for the missing data mechanism. These priors are robust and computationally attractive in the sense that inferences about beta are not sensitive to the choice of the hyperparameters of the prior for phi and they facilitate a Gibbs sampling scheme that leads to accelerated convergence. In addition, we extend the model assessment criterion of Chen, Dey, and Ibrahim (2004a, Biometrika 91, 45-63), called the weighted L measure, to GLMs and missing data problems as well as extend the deviance information criterion (DIC) of Spiegelhalter et al. (2002, Journal of the Royal Statistical Society B 64, 583-639) for assessing whether the missing data mechanism is ignorable or nonignorable. A novel Markov chain Monte Carlo sampling algorithm is also developed for carrying out posterior computation. Several simulations are given to investigate the performance of the proposed Bayesian criteria as well as the sensitivity of the prior specification. Real datasets from a melanoma cancer clinical trial and a liver cancer study are presented to further illustrate the proposed methods.

Bayes Theorem↗
PubMed1998

Biases in three-dimensional structure-from-motion arise from noise in the early visual system.

The projected pattern of retinal-image motion supplies the human visual system with valuable information about properties of the three-dimensional environment. How well three-dimensional properties can be recovered depends both on the accuracy with which the early motion system estimates retinal motion, and on the way later processes interpret this retinal motion. Here we combine both early and late stages of the computational process to account for the hitherto puzzling phenomenon of systematic biases in three-dimensional shape perception. We present data showing how the perceived depth of a hinged plane ('an open book') can be systematically biased by the extent over which it rotates. We then present a Bayesian model that combines early measurement noise with geometric reconstruction of the three-dimensional scene. Although this model has no in-built bias towards particular three-dimensional shapes, it accounts for the data well. Our analysis suggests that the biases stem largely from the geometric constraints imposed on what three-dimensional scenes are compatible with the (noisy) early motion measurements. Given these findings, we suggest that the visual system may act as an optimal estimator of three-dimensional structure-from-motion.

Computer Simulation↗
PubMed2005

The ProDom database of protein domain families: more emphasis on 3D.

ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics.

Computer Graphics↗
PubMed1994

Design of dosage regimens: a multiple model stochastic control approach.

This paper presents a general stochastic control framework for determining drug dosage regimens where the sample times, dosing times, desired goals, etc., occur at different times and in an asynchronous fashion. In the special case of multiple models with linear dynamics and quadratic cost (MMLQ), it is shown that the optimal open-loop stochastic control with linear control/state constraints can be solved exactly and efficiently as a quadratic program. This provides a simple and flexible method for computing open-loop feedback designs of drug dosage regimens. An implementation of the MMLQ adaptive control approach is demonstrated on a Lidocaine infusion process. For this example, the resulting MMLQ regimen is more effective than the MAP Bayesian regimen at reducing interpatient variability and keeping patients in the therapeutic range.

Drug Administration Schedule↗
PubMedDate not supplied

Bayesian analysis of ROC curves using Markov-chain Monte Carlo methods.

The authors introduce a Bayesian approach to generalized linear regression models for rating data observed in the evaluation of a diagnostic technology. Such models were previously studied using a non-Bayesian approach. In a Bayesian analysis, the difficulties inherent in an ordinal rating scale are circumvented by using data-augmentation techniques. Posterior distributions for the regression parameters- and thereby for receiver operating characteristic (ROC) curve parameters and values, for the area under a ROC curve, differences between areas, etc.-may then be computed by Markov-chain Monte Carlo methods. Inferences are made in standard Bayesian ways. The methods are exemplified by a study of ultrasonography rating data for the detection of hepatic metastases in patients with colon or breast cancer (previously analyzed) and the results compared.

Bayes Theorem↗
PubMed1999

Motion transparency: making models of motion perception transparent.

In daily life our visual system is bombarded with motion information. We see cars driving by, flocks of birds flying in the sky, clouds passing behind trees that are dancing in the wind. Vision science has a good understanding of the first stage of visual motion processing, that is, the mechanism underlying the detection of local motions. Currently, research is focused on the processes that occur beyond the first stage. At this level, local motions have to be integrated to form objects, define the boundaries between them, construct surfaces and so on. An interesting, if complicated case is known as motion transparency: the situation in which two overlapping surfaces move transparently over each other. In that case two motions have to be assigned to the same retinal location. Several researchers have tried to solve this problem from a computational point of view, using physiological and psychophysical results as a guideline. We will discuss two models: one uses the traditional idea known as 'filter selection' and the other a relatively new approach based on Bayesian inference. Predictions from these models are compared with our own visual behaviour and that of the neural substrates that are presumed to underlie these perceptions.

Journal Article↗
PubMed2006

Large-scale neural models and dynamic causal modelling.

Dynamic causal modelling (DCM) is a method for estimating and making inferences about the coupling among small numbers of brain areas, and the influence of experimental manipulations on that coupling [Friston, K.J., Harrison, L., Penny, W., 2003 Dynamic causal modelling. Neuroimage 19, 1273-1302]. Large-scale neural modelling aims to construct neurobiologically grounded computational models with emergent behaviours that inform our understanding of neuronal systems. One such model has been used to simulate region-specific BOLD time-series [Horwitz, B., Friston, K.J., Taylor, J.G., 2000. Neural modeling and functional brain imaging: an overview. Neural Netw. 13, 829-846]. DCM was used to make inferences about effective connectivity using data generated by a model implementing a visual delayed match-to-sample task [Tagamets, M.A., Horwitz, B., 1998. Integrating electrophysiological and anatomical experimental data to create a large-scale model that simulates a delayed match-to-sample human brain imaging study. Cereb. Cortex 8, 310-320]. The aim was to explore the validity of inferences made using DCM about the connectivity structure and task-dependent modulatory effects, in a system with a known connectivity structure. We also examined the effects of misspecifying regions of interest. Models with hierarchical connectivity and reciprocal connections were examined using DCM and Bayesian Model Comparison [Penny, W.D., Stephan, K.E., Mechelli, A., Friston, K.J., 2004. Comparing dynamic causal models. Neuroimage 22, 1157-1172]. This approach revealed strong evidence for those models with correctly specified anatomical connectivity. Furthermore, Bayesian model comparison favoured those models when bilinear effects corresponded to their implementation in the neural model. These findings generalised to an extended model with two additional areas and reentrant circuits. The conditional uncertainty of coupling parameter estimates increased in proportion to the number of incorrectly specified regions. These results highlight the role of neural models in establishing the validity of estimation and inference schemes. Specifically, Bayesian model comparison confirms the validity of DCM in relation to a well-characterised and comprehensive neuronal model.

Bayes Theorem↗
PubMed2005

Bayesian solutions and performance analysis in bioelectric inverse problems.

In bioelectric inverse problems, one seeks to recover bioelectric sources from remote measurements using a mathematical model that relates the sources to the measurements. Due to attenuation and spatial smoothing in the medium between the sources and the measurements, bioelectric inverse problems are generally ill-posed. Bayesian methodology has received increasing attention recently to combat this ill-posedness, since it offers a general formulation of regularization constraints and additionally provides statistical performance analysis tools. These tools include the estimation error covariance and the marginal probability density of the measurements (known as the "evidence") that allow one to predictively quantify and compare experimental designs. These performance analysis tools have been previously applied in inverse electroencephalography and magnetoencephalography, but only in relatively simple scenarios. The main motivation here was to extend the utility of Bayesian estimation techniques and performance analysis tools in bioelectric inverse problems, with a particular focus on electrocardiography. In a simulation study we first investigated whether Bayesian error covariance, computed without knowledge of the true sources and based on instead statistical assumptions, accurately predicted the actual reconstruction error. Our study showed that error variance was a reasonably reliable qualitative and quantitative predictor of estimation performance even when there was error in the prior model. We also examined whether the evidence statistic accurately predicted relative estimation performance when distinct priors were used. In a simple scenario our results support the hypothesis that the prior model that maximizes the evidence is a good choice for inverse reconstructions.

Algorithms↗
PubMed2001

Bias reduction for risk ratio and vaccine effect estimators.

We examine the structural bias for established estimators of vaccine effects on susceptibility and for newer estimates of vaccine effects on infectiousness. We then propose and analyse new bias corrections for vaccine effect estimators of both susceptibility and infectiousness, as well as their combined effect on infection transmission. Each estimator is evaluated empirically with computer simulations. Of the estimators examined in this paper, those with the least bias and root mean squared error are computed by adding one to the positive count in the placebo population. We also identify a source of bias for a standard Bayesian estimator of risk ratios.

Bayes Theorem↗
PubMed2005

Assessing uncertainty in simulation-based maritime risk assessment.

Recent work in the assessment of risk in maritime transportation systems has used simulation-based probabilistic risk assessment techniques. In the Prince William Sound and Washington State Ferries risk assessments, the studies' recommendations were backed up by estimates of their impact made using such techniques and all recommendations were implemented. However, the level of uncertainty about these estimates was not available, leaving the decisionmakers unsure whether the evidence was sufficient to assess specific risks and benefits. The first step toward assessing the impact of uncertainty in maritime risk assessments is to model the uncertainty in the simulation models used. In this article, a study of the impact of proposed ferry service expansions in San Francisco Bay is used as a case study to demonstrate the use of Bayesian simulation techniques to propagate uncertainty throughout the analysis. The conclusions drawn in the original study are shown, in this case, to be robust to the inherent uncertainties. The main intellectual merit of this work is the development of Bayesian simulation technique to model uncertainty in the assessment of maritime risk. However, Bayesian simulations have been implemented only as theoretical demonstrations. Their use in a large, complex system may be considered state of the art in the field of computational sciences.

Journal Article↗
PubMed1999

On Bayesian calculations for mixture likelihoods and priors.

We present methodology for calculating Bayes factors between models as well as posterior probabilities of the models when the indicator variables of the models are integrated out of the posterior before Markov chain Monte Carlo (MCMC) computations. Standard methodology would include the indicator functions as part of the MCMC computations. We demonstrate that our methodology can give substantially greater accuracy than the traditional approach. We illustrate the methodology using the model selection prior of George and McCulloch applied to logistic regression and to a mixture model for observations in a hierarchical random effects model.

Bayes Theorem↗
PubMed2026

Diagnosing scientific replicability through probabilistic distinguishability.

MOTIVATION: Despite the widely recognized importance of replicability in biological research, computational methods to quantify irreplicability and identify irreplicable instances remain underdeveloped. This article presents an efficient and robust computational framework to address this gap. RESULTS: To tackle the challenge of defining an acceptable level of intrinsic heterogeneity among replicable studies, we introduce a distinguishability criterion, ensuring that replicable effects, while potentially heterogeneous, can be distinguished from zero effects and maintain consistent directions with high probability. We implement a Bayesian model criticism approach, reporting a Bayesian P-value to identify potential irreplicable instances. Through numerical experiments, we demonstrate the efficacy of the proposed methods in detecting batch effects in high-throughput experiments and identifying instances of the publication bias. Finally, we apply the framework to multi-tissue eQTL data from the GTEx consortium, uncovering tissue-specific eQTLs that represent biological heterogeneity across tissues. AVAILABILITY AND IMPLEMENTATION: An R package DiscRep implementing our method is available on GitHub (https://github.com/PengWang96/DiscRep).

Bayes Theorem↗
PubMed2004

An empirical comparison of information-theoretic selection criteria for multivariate behavior genetic models.

Information theory provides an attractive basis for statistical inference and model selection. However, little is known about the relative performance of different information-theoretic criteria in covariance structure modeling, especially in behavioral genetic contexts. To explore these issues, information-theoretic fit criteria were compared with regard to their ability to discriminate between multivariate behavioral genetic models under various model, distribution, and sample size conditions. Results indicate that performance depends on sample size, model complexity, and distributional specification. The Bayesian Information Criterion (BIC) is more robust to distributional misspecification than Akaike's Information Criterion (AIC) under certain conditions, and outperforms AIC in larger samples and when comparing more complex models. An approximation to the Minimum Description Length (MDL; Rissanen, J. (1996). IEEE Transactions on Information Theory 42:40-47, Rissanen, J. (2001). IEEE Transactions on Information Theory 47:1712-1717) criterion, involving the empirical Fisher information matrix, exhibits variable patterns of performance due to the complexity of estimating Fisher information matrices. Results indicate that a relatively new information-theoretic criterion, Draper's Information Criterion (DIC; Draper, 1995), which shares features of the Bayesian and MDL criteria, performs similarly to or better than BIC. Results emphasize the importance of further research into theory and computation of information-theoretic criteria.

Bayes Theorem↗
PubMed2004

A Bayesian approach to reconstructing genetic regulatory networks with hidden factors.

MOTIVATION: We have used state-space models (SSMs) to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a well-established model of T cell activation. SSMs are a class of dynamic Bayesian networks in which the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics. These hidden variables can capture effects that cannot be directly measured in a gene expression profiling experiment, for example: genes that have not been included in the microarray, levels of regulatory proteins, the effects of mRNA and protein degradation, etc. RESULTS: We have approached the problem of inferring the model structure of these state-space models using both classical and Bayesian methods. In our previous work, a bootstrap procedure was used to derive classical confidence intervals for parameters representing 'gene-gene' interactions over time. In this article, variational approximations are used to perform the analogous model selection task in the Bayesian context. Certain interactions are present in both the classical and the Bayesian analyses of these regulatory networks. The resulting models place JunB and JunD at the centre of the mechanisms that control apoptosis and proliferation. These mechanisms are key for clonal expansion and for controlling the long term behavior (e.g. programmed cell death) of these cells. AVAILABILITY: Supplementary data is available at http://public.kgi.edu/wild/index.htm and Matlab source code for variational Bayesian learning of SSMs is available at http://www.cse.ebuffalo.edu/faculty/mbeal/software.html.

Bayes Theorem↗
PubMed1993

Computer dosing program for the initiation of vancomycin therapy.

The predictive performance of a computer dosing program used for initiating vancomycin therapy was studied. Initial serum vancomycin concentrations in 31 adult patients receiving vancomycin were estimated by using a computer program (T.D.M.S.) incorporating a two-compartment open model. Sixty-two serum vancomycin concentrations at steady state (Css) were obtained before and after one-hour infusions and compared with estimated Css values. Bias and precision were evaluated by calculating median error (ME) and median absolute error (MAE), respectively. Population-based estimates of volume of distribution (V) and clearance (CL) were compared with those obtained by fitting each patient's data set by using Bayesian analysis (BA) and non-linear least-squares regression (NLLS). Median (mean +/- S.D.) bias and precision for peak Css were 7.7 (10.2 +/- 10.8) and 7.7 (10.6 +/- 10.5) mg/L, and for trough Css were 7.4 (7.7 +/- 7.6) and 7.4 (8.8 +/- 6.2) mg/L. The medians were significantly different from zero. Estimated median (mean +/- S.D.) V, CL, and half-life were 0.72 L/kg, 0.60 (0.67 +/- 0.21) mL/min/kg, and 11.59 (12.87 +/- 3.91) hours. Median (mean +/- S.D.) CL values determined by BA and NLLS were 0.86 (0.89 +/- 0.32) and 0.85 (0.92 +/- 0.34) mL/min/kg, respectively. Both CL values were significantly greater than the population-based estimate. However, median V values determined by BA and NLLS did not differ from the population-based estimate. A revised clearance model derived from Bayesian analysis of data for the first 21 patients was tested in the 10 other patients and appeared to improve the predictive performance of the a priori model.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2004

A Bayesian analysis of the 4-year follow-up data of the Wisconsin epidemiologic study of diabetic retinopathy.

The Wisconsin epidemiologic study of diabetic retinopathy (WESDR) is a population-based epidemiologic study carried out in Southern Wisconsin during the 1980s of the last century. The resulting data were analysed by different statisticians and ophthalmologists during the last two decades. Most of the analyses were carried out on the baseline data, although there were two follow-up studies on the same population. In this present paper, we provide a Bayesian analysis of the first follow-up data which were taken 4 years after the baseline study. Our Bayesian analysis provides estimates of the associated covariate effects. Choice of the best model in terms of the covariate inclusion is also performed. The baseline data were used to set the prior for the parameters. Extensive numerical computations illustrate our present methodology.

Bayes Theorem↗
PubMed2006

Selection of generative models in classification.

This paper is concerned with the selection of a generative model for supervised classification. Classical criteria for model selection assess the fit of a model rather than its ability to produce a low classification error rate. A new criterion, the Bayesian Entropy Criterion (BEC), is proposed. This criterion takes into account the decisional purpose of a model by minimizing the integrated classification entropy. It provides an interesting alternative to the cross-validated error rate which is computationally expensive. The asymptotic behavior of the BEC criterion is presented. Numerical experiments on both simulated and real data sets show that BEC performs better than the BIC criterion to select a model minimizing the classification error rate and provides analogous performance to the cross-validated error rate.

Algorithms↗
PubMedDate not supplied

Solitary pulmonary nodules: Part II. Evaluation of the indeterminate nodule.

Various strategies may be used to evaluate indeterminate solitary pulmonary nodules. Growth rate assessment is an important and cost-effective step in the evaluation of these nodules. Clinical features (eg, patient age, history of prior malignancy, presenting symptoms, smoking history) can be useful in suggesting the diagnosis and aiding in management planning. Bayesian analysis allows more precise determination of the probability of malignancy (pCa). Decision analysis models suggest that the most cost-effective management strategy depends on the pCa for a given nodule. At contrast material-enhanced computed tomography, nodular enhancement of less than 15 HU is strongly predictive of a benign lesion, whereas enhancement of more than 20 HU typically indicates malignancy. At 2-[fluorine-18]fluoro-2-deoxy-D-glucose (FDG) positron emission tomography, lesions with low FDG uptake are typically benign, whereas those with increased FDG uptake are typically malignant. Results of transthoracic needle aspiration biopsy influence management in approximately 50% of cases and, in indeterminate lesions with a pCa between 0.05 and 0.6, is the best initial diagnostic procedure. It is optimally used in peripheral nodules and has been reported to establish a benign diagnosis in up to 91% of cases. Although there is no one correct management approach, the ability to distinguish benign from malignant solitary pulmonary lesions has improved with the use of these strategies.

Bayes Theorem↗