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At least 1,189 records · Page 66Linked to original sources
PubMed2006

Locally Bayesian learning with applications to retrospective revaluation and highlighting.

A scheme is described for locally Bayesian parameter updating in models structured as successions of component functions. The essential idea is to back-propagate the target data to interior modules, such that an interior component's target is the input to the next component that maximizes the probability of the next component's target. Each layer then does locally Bayesian learning. The approach assumes online trial-by-trial learning. The resulting parameter updating is not globally Bayesian but can better capture human behavior. The approach is implemented for an associative learning model that first maps inputs to attentionally filtered inputs and then maps attentionally filtered inputs to outputs. The Bayesian updating allows the associative model to exhibit retrospective revaluation effects such as backward blocking and unovershadowing, which have been challenging for associative learning models. The back-propagation of target values to attention allows the model to show trial-order effects, including highlighting and differences in magnitude of forward and backward blocking, which have been challenging for Bayesian learning models.

Attention↗
PubMed2004

A bayesian approach to parameter estimation for a crayfish (Procambarus spp.) bioaccumulation model.

Bioaccumulation models are used to describe chemical uptake and clearances by organisms. Averaged input parameter values are traditionally used and yield point estimates of model outputs. Hence, the uncertainty and variability of model predictions are ignored. Probabilistic modeling approaches, such as Monte Carlo simulation and the Bayesian method, have been recommended by the U.S. Environmental Protection Agency to provide a quantitative description of the degree of uncertainty and/or variability in risk estimates in ecological hazards and human health effects. In this study, a Bayesian analysis was conducted to account for the combined uncertainty and variability of model parameters in a crayfish bioaccumulation model. After a 5-d exposure in the LaBranche Wetlands (LA, USA), crayfish were analyzed for polycyclic aromatic hydrocarbon concentrations and lipid fractions. The posterior distribution of model parameters were derived from the joint posterior parameter distributions using a Markov chain Monte Carlo approach and the experimental data. The results were then used to predict the distribution of chrysene concentration versus time in the crayfish to compare the predicted ranges at the different study sites.

Animals↗
PubMed1998

Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model.

This paper tests the performance of a simple empirical scoring function on a set of candidate designs produced by a de novo design package. The scoring function calculates approximate ligand-receptor binding affinities given a putative binding geometry. To our knowledge this is the first substantial test of an empirical scoring function of this type on a set of molecular designs which were then subsequently synthesised and assayed. The performance illustrates that the methods used to construct the scoring function and the reliance on plausible, yet potentially false, binding modes can lead to significant over-prediction of binding affinity in bad cases. This is anticipated on theoretical grounds and provides caveats on the reliance which can be placed when using the scoring function as a screen in the choice of molecular designs. To improve the predictability of the scoring function and to understand experimental results, it is important to perform subsequent Quantitative Structure-Activity Relationship (QSAR) studies. In this paper, Bayesian regression is performed to improve the predictability of the scoring function in the light of the assay results. Bayesian regression provides a rigorous mathematical framework for the incorporation of prior information, in this case information from the original training set, into a regression on the assay results of the candidate molecular designs. The results indicate that Bayesian regression is a useful and practical technique when relevant prior knowledge is available and that the constraints embodied in the prior information can be used to improve the robustness and accuracy of regression models. We believe this to be the first application of Bayesian regression to QSAR analysis in chemistry.

Bayes Theorem↗
PubMed2002

Bayesian analysis and inference from QSAR predictive model results.

QSAR models have been under development for decades but acceptance and utilization of model results have been slow, in part, because there is no widely accepted metric for assessing their reliability. We reapply a method commonly used in quantitative epidemiology and medical decision-making for evaluating the results of screening tests to assess reliability of a QSAR model. It quantifies the accuracy (expressed as sensitivity and specificity) of QSAR models as conditional probabilities of correct and incorrect classification of chemical characteristic, given a true characteristic. Using Bayes formula, these conditional probabilities are combined with prior information to generate a posterior distribution to determine the probability a specific chemical has a particular characteristic, given a model prediction. As an example, we apply this approach to evaluate the predictive reliability of a CATABOL model and base on it a "ready" and "not ready" biodegradability classification. Finally, we show how predictive capability of the model can be improved by sequential use of two models, the first one with high sensitivity and the second with high specificity.

Bayes Theorem↗
PubMed2005

Bayesian analysis of hierarchical pattern-mixture models for clinical trials data with attrition and comparisons to commonly used ad-hoc and model-based approaches.

This article addresses the problem of making scientifically sound inferences from clinical trials data with attrition, when reasons of attrition seem related to the outcomes of interest. The problem is particularly difficult when the effect of a covariate is to be estimated and if the dropout mechanism appears to operate differently at different levels of the covariate. In this context, multiple imputation under a multilevel pattern-mixture model that allows random variation across dropout groups is presented. Using simulated data generated around an alcoholic hepatitis trial, we compare the performance of this model and commonly used ad-hoc and model-based approaches.

Algorithms↗
PubMed2001

Estimating the posterior probability of LTP failure by sequential Bayesian analysis of an imperfect Bernoulli trial model.

A tetanically stimulated (TS) neuron is said to have failed to fire if its voltage-clamped excitatory postsynaptic current (EPSC) measurement is devoid of a long-term potentiation (LTP) response. This paper provides a method for evaluating the posterior probability of "failure" for TS neurons. A sequential Bayes algorithm is employed on an imperfect Bernoulli trial model to refine the posterior with each EPSC data record processed. The method is applied to both real and simulated LTP data and is shown to be consistent with the theoretical Beta-distributed posterior and the reported in vitro voltage-clamped EPSC failure rates.

Algorithms↗
PubMed2003

Bayesian meta-analysis for longitudinal data models using multivariate mixture priors.

We propose a class of longitudinal data models with random effects that generalizes currently used models in two important ways. First, the random-effects model is a flexible mixture of multivariate normals, accommodating population heterogeneity, outliers, and nonlinearity in the regression on subject-specific covariates. Second, the model includes a hierarchical extension to allow for meta-analysis over related studies. The random-effects distributions are decomposed into one part that is common across all related studies (common measure), and one part that is specific to each study and that captures the variability intrinsic between patients within the same study. Both the common measure and the study-specific measures are parameterized as mixture-of-normals models. We carry out inference using reversible jump posterior simulation to allow a random number of terms in the mixtures. The sampler takes advantage of the small number of entertained models. The motivating application is the analysis of two studies carried out by the Cancer and Leukemia Group B (CALGB). In both studies, we record for each patient white blood cell counts (WBC) over time to characterize the toxic effects of treatment. The WBCs are modeled through a nonlinear hierarchical model that gathers the information from both studies.

Bayes Theorem↗
PubMed2003

Bayesian estimation of parameters of a structural model for genetic covariances between milk yield in five regions of the United States.

Inference about genetic covariance matrices using multiple-trait models is often hindered by lack of information. This leads to imprecise estimates of genetic parameters and of breeding values. Patterns in a genetic covariance matrix can be exploited to reduce the number of parameters and to increase quality of inferences. A structural model for genetic covariances was developed and fitted to milk yield data in five regions of the United States. This was compared with a standard multiple-trait analysis using a deviance information criterion, a measure of quality of fit. Data consisted of 3,465,334 Holstein first-lactation records from daughters of 43,755 sires in five regions of the United States (Midwest, Northeast, Northwest, Southeast, Southwest). Parameters of the structural model included an intercept and effects of measures of genetic and of management similarity on genetic covariances. Genetic similarity depended on the number of records contributed by sires that were common to a pair of regions. Management similarity was a function of the quantity of concentrate used to produce 1000 kg of milk in each pair of regions. The structural and the multiple-trait models gave similar estimates of genetic covariances, but the number of parameters was 8 in the former vs. 15 in the latter. Hence, estimates of genetic covariances were more precise with the structural model. A deviance information criterion suggested a slight superiority of the multiple-trait model, although probably within sampling error. For both models, genetic correlations between milk yield in five regions of the United States were larger than 0.93.

Analysis of Variance↗
PubMed2006

Modelling SF-6D health state preference data using a nonparametric Bayesian method.

This paper reports on the findings from applying a new approach to modelling health state valuation data. The approach applies a nonparametric model to estimate SF-6D health state utility values using Bayesian methods. The data set is the UK SF-6D valuation study where a sample of 249 states defined by the SF-6D (a derivative of the SF-36) was valued by a representative sample of the UK general population using standard gamble. The paper presents the results from applying the nonparametric model and comparing it to the original model estimated using a conventional parametric random effects model. The two models are compared theoretically and in terms of empirical performance. The paper discusses the implications of these results for future applications of the SF-6D and further work in this field.

Bayes Theorem↗
PubMed2005

A semi-parametric Bayesian analysis of survival data based on Lévy-driven processes.

In the presence of covariate information, the proportional hazards model is one of the most popular models. In this paper, in a Bayesian nonparametric framework, we use a Markov (Lévy-driven) process to model the baseline hazard rate. Previous Bayesian nonparametric models have been based on neutral to the right processes, which have a number of drawbacks, such as discreteness of the cumulative hazard function. We allow the covariates to be time dependent functions and develop a full posterior analysis via substitution sampling. A detailed illustration is presented.

Bayes Theorem↗
PubMed2000

A quantitative structure--activity relationships model for the acute toxicity of substituted benzenes to Tetrahymena pyriformis using Bayesian-regularized neural networks.

We have used a new, robust structure-activity mapping technique, a Bayesian-regularized neural network, to develop a quantitative structure-activity relationships (QSAR) model for the toxicity of 278 substituted benzenes toward Tetrahymena pyriformis. The independent variables used in the modeling were derived solely from the molecular structure, and the model was tested on 20% of the data set selected from the whole set by cluster analysis and which had not been used in training the network. The results show that the method is robust and reliable and give results for mixed class compounds which are comparable to earlier QSAR work on single-chemical class subsets of the 278 compounds and which employed measured physicochemical parameters as independent variables. Comparisons of Bayesian neural net models with those derived by classical PLS analysis showed the superiority of our method. The method appears to be able to model more diverse chemical classes and more than one mechanism of toxicity.

Animals↗
PubMed2000

Iron stores and coronary artery disease: a clinical application of a method to incorporate measurement error of the exposure in a logistic regression model.

Rates of coronary artery disease (CAD) increase sharply after menopause. We examined the hypotheses that high iron stores, as measured by plasma ferritin levels, are a risk factor for CAD and that the increase in iron stores after menopause is at least in part responsible for the rise in CAD in women. We also investigated measurement error of plasma ferritin using a Bayesian conditional independence model and incorporated it into the estimation of the odds ratio (OR) for males. Cases had >/=1 coronary artery stenosis >/=70%. Controls had no visible coronary lesions on angiography. The median plasma ferritin level was 48 mg/L (interquartile range: 28 to 86) among 244 cases and 45 mg/l (24 to 85) among 140 controls. The multivariate analyses among females, males, and females and males combined did not support an association between plasma ferritin levels and CAD (OR for one unit change in log ferritin 1.01, 95% CI 0.71-1.44, OR 0.95, 95% CI 0.66-1.37 and OR 0.95, 95% CI 0.75-1.21, respectively). Accounting for the measurement error of ferritin in males slightly improved the precision of the estimate of the OR but did not unmask an association (OR: 0.94, 95% CI 0.69-1.30). We conclude that high ferritin levels before or after menopause are not associated with CAD. Measurement error might be considered in situations where a one-time measurement is assumed to be representative of long-term exposure.

Aged↗
PubMed2000

Bayesian methods for a growth-curve degradation model with repeated measures.

The increasing reliability of some manufactured products has led to fewer observed failures in reliability testing. Thus, useful inference on the distribution of failure times is often not possible using traditional survival analysis methods. Partly as a result of this difficulty, there has been increasing interest in inference from degradation measurements made on products prior to failure. In the degradation literature inference is commonly based on large-sample theory and, if the degradation path model is nonlinear, their implementation can be complicated by the need for approximations. In this paper we review existing methods and then describe a fully Bayesian approach which allows approximation-free inference. We focus on predicting the failure time distribution of both future units and those that are currently under test. The methods are illustrated using fatigue crack growth data.

Bayes Theorem↗
PubMed2004

Bayesian analysis of signaling networks governing embryonic stem cell fate decisions.

MOTIVATION: Signaling events that direct mouse embryonic stem (ES) cell self-renewal and differentiation are complex and accordingly difficult to understand in an integrated manner. We address this problem by adapting a Bayesian network learning algorithm to model proteomic signaling data for ES cell fate responses to external cues. Using this model we were able to characterize the signaling pathway influences as quantitative, logic-circuit type interactions. Our experimental dataset includes measurements for 28 signaling protein phosphorylation states across 16 different factorial combinations of cytokine and matrix stimuli as reported previously. RESULTS: The Bayesian network modeling approach allows us to uncover previously reported signaling activities related to mouse ES cell self-renewal, such as the roles of LIF and STAT3 in maintaining undifferentiated ES cell populations. Furthermore, the network predicts novel influences such as between ERK phosphorylation and differentiation, or RAF phosphorylation and differentiated cell proliferation. Visualization of the influences detected by the Bayesian network provides intuition about the underlying physiology of the signaling pathways. We demonstrate that the Bayesian networks can capture the linear, nonlinear and multistate logic interactions that connect extracellular cues, intracellular signals and consequent cell functional responses.

Algorithms↗
PubMed2003

Identification of land use with water quality data in stormwater using a neural network.

To control stormwater pollution effectively, development of innovative, land-use-related control strategies will be required. An approach that could differentiate land-use types from stormwater quality would be the first step to solving this problem. We propose a neural network approach to examine the relationship between stormwater water quality and various types of land use. The neural network model can be used to identify land-use types for future known and unknown cases. The neural model uses a Bayesian network and has 10 water quality input variables, four neurons in the hidden layer, and five land-use target variables (commercial, industrial, residential, transportation, and vacant). We obtained 92.3 percent of correct classification and 0.157 root-mean-squared error on test files. Based on the neural model, simulations were performed to predict the land-use type of a known data set, which was not used when developing the model. The simulation accurately described the behavior of the new data set. This study demonstrates that a neural network can be effectively used to produce land-use type classification with water quality data.

Agriculture↗
PubMed2005

A method and software for segmentation of anatomic object ensembles by deformable m-reps.

Deformable shape models (DSMs) comprise a general approach that shows great promise for automatic image segmentation. Published studies by others and our own research results strongly suggest that segmentation of a normal or near-normal object from 3D medical images will be most successful when the DSM approach uses (1) knowledge of the geometry of not only the target anatomic object but also the ensemble of objects providing context for the target object and (2) knowledge of the image intensities to be expected relative to the geometry of the target and contextual objects. The segmentation will be most efficient when the deformation operates at multiple object-related scales and uses deformations that include not just local translations but the biologically important transformations of bending and twisting, i.e., local rotation, and local magnification. In computer vision an important class of DSM methods uses explicit geometric models in a Bayesian statistical framework to provide a priori information used in posterior optimization to match the DSM against a target image. In this approach a DSM of the object to be segmented is placed in the target image data and undergoes a series of rigid and nonrigid transformations that deform the model to closely match the target object. The deformation process is driven by optimizing an objective function that has terms for the geometric typicality and model-to-image match for each instance of the deformed model. The success of this approach depends strongly on the object representation, i.e., the structural details and parameter set for the DSM, which in turn determines the analytic form of the objective function. This paper describes a form of DSM called m-reps that has or allows these properties, and a method of segmentation consisting of large to small scale posterior optimization of m-reps. Segmentation by deformable m-reps, together with the appropriate data representations, visualizations, and user interface, has been implemented in software that accomplishes 3D segmentations in a few minutes. Software for building and training models has also been developed. The methods underlying this software and its abilities are the subject of this paper.

Algorithms↗