Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Bayesian computational modeling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,009 records · Page 56Linked to original sources
PubMed2006

Likelihood ratio tests in behavioral genetics: problems and solutions.

The likelihood ratio test of nested models for family data plays an important role in the assessment of genetic and environmental influences on the variation in traits. The test is routinely based on the assumption that the test statistic follows a chi-square distribution under the null, with the number of restricted parameters as degrees of freedom. However, tests of variance components constrained to be non-negative correspond to tests of parameters on the boundary of the parameter space. In this situation the standard test procedure provides too large p-values and the use of the Akaike Information Criterion (AIC) or the Bayesian Information Criterion (BIC) for model selection is problematic. Focusing on the classical ACE twin model for univariate traits, we adapt existing theory to show that the asymptotic distribution for the likelihood ratio statistic is a mixture of chi-square distributions, and we derive the mixing probabilities. We conclude that when testing the AE or the CE model against the ACE model, the p-values obtained from using the chi(2)(1 df) as the reference distribution should be halved. When the E model is tested against the ACE model, a mixture of chi(2)(0 df), chi(2)(1 df) and chi(2)(2 df) should be used as the reference distribution, and we provide a simple formula to compute the mixing probabilities. Similar results for tests of the AE, DE and E models against the ADE model are also derived. Failing to use the appropriate reference distribution can lead to invalid conclusions.

Analysis of Variance↗
PubMed1978

General problems in medical decision making with comments on ROC analysis.

Medical decision-making studies continue to focus on two questions: How do physicians make decisions? How should physicians make decisions? Researchers pursuing the first question emphasize human cognitive processes and the programming of symbol systems to model observed human behavior. Those researchers concentrating on the second question assume that there is a standard of performance against which the physician's decisions can be judged, and to help the physician improve his performance, an array of tools is proposed. These tools include decision trees, Bayesian analysis, decision matrices, receiver operating characteristics (ROC) analysis, and cost-benefit considerations including utility measures. Medical decision-making questions must be answered in an ethical context where ethics and decision analysis are interviewed.

Bayes Theorem↗
PubMed2006

Bayesian-based selection of metabolic objective functions.

MOTIVATION: A critical component of in silico analysis of underdetermined metabolic systems is the identification of the appropriate objective function. A common assumption is that the objective of the cell is to maximize growth. This objective function has been shown to be consistent in a few limited experimental cases, but may not be universally appropriate. Here a method is presented to quantitatively determine the most probable objective function. RESULTS: The genome-scale metabolism of Escherichia coli growing on succinate was used as a case-study for analysis. Five different objective functions, including maximization of growth rate, were chosen based on biological plausibility. A combination of flux balance analysis and linear programming was used to simulate cellular metabolism, which was then compared to independent experimental data using a Bayesian objective function discrimination technique. After comparing rates of oxygen uptake and acetate production, minimization of the production rate of redox potential was determined to be the most probable objective function. Given the appropriate reaction network and experimental data, the discrimination technique can be applied to any bacterium to test a variety of different possible objective functions. SUPPLEMENTARY INFORMATION: Additional files, code and a program for carrying out model discrimination are available at http://www.engr.uconn.edu/~srivasta/modisc.html.

Algorithms↗
PubMed2006

Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains.

BACKGROUND: The subcellular location of a protein is closely related to its function. It would be worthwhile to develop a method to predict the subcellular location for a given protein when only the amino acid sequence of the protein is known. Although many efforts have been made to predict subcellular location from sequence information only, there is the need for further research to improve the accuracy of prediction. RESULTS: A novel method called HensBC is introduced to predict protein subcellular location. HensBC is a recursive algorithm which constructs a hierarchical ensemble of classifiers. The classifiers used are Bayesian classifiers based on Markov chain models. We tested our method on six various datasets; among them are Gram-negative bacteria dataset, data for discriminating outer membrane proteins and apoptosis proteins dataset. We observed that our method can predict the subcellular location with high accuracy. Another advantage of the proposed method is that it can improve the accuracy of the prediction of some classes with few sequences in training and is therefore useful for datasets with imbalanced distribution of classes. CONCLUSION: This study introduces an algorithm which uses only the primary sequence of a protein to predict its subcellular location. The proposed recursive scheme represents an interesting methodology for learning and combining classifiers. The method is computationally efficient and competitive with the previously reported approaches in terms of prediction accuracies as empirical results indicate. The code for the software is available upon request.

Amino Acid Sequence↗
PubMed2006

Bayesian analysis of the linear reaction norm model with unknown covariates.

The reaction norm model is becoming a popular approach for the analysis of genotype x environment interactions. In a classical reaction norm model, the expression of a genotype in different environments is described as a linear function (a reaction norm) of an environmental gradient or value. An environmental value is typically defined as the mean performance of all genotypes in the environment, which is usually unknown. One approximation is to estimate the mean phenotypic performance in each environment and then treat these estimates as known covariates in the model. However, a more satisfactory alternative is to infer environmental values simultaneously with the other parameters of the model. This study describes a method and its Bayesian Markov Chain Monte Carlo implementation that makes this possible. Frequentist properties of the proposed method are tested in a simulation study. Estimates of parameters of interest agree well with the true values. Further, inferences about genetic parameters from the proposed method are similar to those derived from a reaction norm model using true environmental values. On the other hand, using phenotypic means as proxies for environmental values results in poor inferences.

Bayes Theorem↗
PubMedDate not supplied

[Non-parametric estimation of pharmacokinetic parameters of amikacin in patients with non-insulin-dependent diabetes mellitus].

To establish a reference for MAP Bayesian adaptive control of amikacin therapy in non-insulin-dependent diabetic patients, 30 patients (age: 63.5 +/- 10.1 years) were studied. Weight (84.2 +/- 15.4 kg) and body mass index (28.0 +/- 4.3 kg/m2 for males and 30.5 +/- 6.4 kg/m2 for females) were stable during treatment. Creatinine clearance (CCr) was 70.3 +/- 27.2 ml/min/1.73 m2 before treatment and 69.6 +/- 24.3 ml/min/1.73 m2 (NS) at the end of treatment (2 to 15 days). 129 serum concentrations were drawn (4.8 +/- 2.6 levels per patient). The one-compartment model was parameterized as having Vs (l.kg-1) and Kslope (min/ml.h) for each unit of CCr (Kel = Kintercept + Kslope x CCr). The non-renal Kintercept was fixed at 0.00693 h-1. The NPEM computes the joint probability densities. The mean, median, and SD were respectively: Vs = 0.3574, 0.3654, 0.0825 l.kg-1; Kslope = 0.0026, 0.0027, 0.0007 min/ml.h. For the a priori first doses determination, precision is higher with the new population. No difference in adaptive control was observed. In additive, the full joint density probability should be used to develop stochastic multiple model linear quadratic (MMLQ) adaptive control strategies.

Amikacin↗
PubMed1996

Problems in pharmacokinetic analysis of alcohol disposition: a trial of the Bayesian least-squares method.

The technical problems of the pharmacokinetic analysis of alcohol disposition were studied using the Michaelis-Menten elimination kinetic model. This model was defined by two forms of equations: differential and integrated, with the latter being derived by integration of the differential equation. We compared the parameter values, estimated by one-line curve-fitting, using these two equation forms. We concluded that, for the kinetic analysis of alcohol disposition, curve-fitting with the differential equation was superior to that with the integrated equation. We also studied the methodological problems involved in one-line fitting. The ordinary least-squares (OLS) method was compared with the Bayesian least-squares (BLS) method. Correlation between the Vmax and beta (ethanol elimination rate) values, and between the Vmax and K(m) values was seen when the parameter values were estimated by the OLS method. These results suggested that one-line fitting by the OLS method was not adequate for Michaelis-Menten-type elimination kinetic analysis. BLS analysis resulted in no correlation between the estimated parameter values that did not change with the level of the dose. The BLS method seemed to be more useful than the OLS method for the estimation of individual pharmacokinetic parameter values.

Animals↗
PubMed2005

Active concept learning in image databases.

Concept learning in content-based image retrieval systems is a challenging task. This paper presents an active concept learning approach based on the mixture model to deal with the two basic aspects of a database system: the changing (image insertion or removal) nature of a database and user queries. To achieve concept learning, we a) propose a new user directed semi-supervised expectation-maximization algorithm for mixture parameter estimation, and b) develop a novel model selection method based on Bayesian analysis that evaluates the consistency of hypothesized models with the available information. The analysis of exploitation versus exploration in the search space helps to find the optimal model efficiently. Our concept knowledge transduction approach is able to deal with the cases of image insertion and query images being outside the database. The system handles the situation where users may mislabel images during relevance feedback. Experimental results on Corel database show the efficacy of our active concept learning approach and the improvement in retrieval performance by concept transduction.

Algorithms↗
PubMed2005

Bayesian inference for stochastic kinetic models using a diffusion approximation.

This article is concerned with the Bayesian estimation of stochastic rate constants in the context of dynamic models of intracellular processes. The underlying discrete stochastic kinetic model is replaced by a diffusion approximation (or stochastic differential equation approach) where a white noise term models stochastic behavior and the model is identified using equispaced time course data. The estimation framework involves the introduction of m- 1 latent data points between every pair of observations. MCMC methods are then used to sample the posterior distribution of the latent process and the model parameters. The methodology is applied to the estimation of parameters in a prokaryotic autoregulatory gene network.

Bayes Theorem↗
PubMed2005

Automatic image orientation detection via confidence-based integration of low-level and semantic cues.

Automatic image orientation detection for natural images is a useful, yet challenging research topic. Humans use scene context and semantic object recognition to identify the correct image orientation. However, it is difficult for a computer to perform the task in the same way because current object recognition algorithms are extremely limited in their scope and robustness. As a result, existing orientation detection methods were built upon low-level vision features such as spatial distributions of color and texture. Discrepant detection rates have been reported for these methods in the literature. We have developed a probabilistic approach to image orientation detection via confidence-based integration of low-level and semantic cues within a Bayesian framework. Our current accuracy is 90 percent for unconstrained consumer photos, impressive given the findings of a psychophysical study conducted recently. The proposed framework is an attempt to bridge the gap between computer and human vision systems and is applicable to other problems involving semantic scene content understanding.

Algorithms↗
PubMed2002

Application of pharmacokinetic modelling to the routine therapeutic drug monitoring of anticancer drugs.

Over the last 10 years, proofs of the clinical interest of therapeutic drug monitoring (TDM) of certain anticancer drugs have been established. Numerous studies have shown that TDM is an efficient tool for controlling the toxicity of therapeutic drugs, and a few trials have even demonstrated that it can improve their efficacy. This article critically reviews TDM tools based on pharmacokinetic modelling of anticancer drugs. The administered dose of anticancer drugs is sometimes adjusted individually using either a priori or a posteriori methods. The most frequent clinical application of a priori formulae concerns carboplatin and allows the computation of the first dose based on biometrical and biological data such as weight, age, gender, creatinine clearance and glomerular filtration rate. A posteriori methods use drug plasma concentrations to adjust the subsequent dose(s). Thus, nomograms allowing dose adjustment on the basis of blood concentration are routinely used for 5-fluorouracil given as long continuous infusions. Multilinear regression models have been developed, for example for etoposide, doxorubicin. carboplatin, cyclophosphamide and irinotecan, to predict a single exposure variable [such as area under concentration-time curve (AUC)] from a small number of plasma concentrations obtained at predetermined times after a standard dose. These models can only be applied by using the same dose and schedule as the original study. Bayesian estimation offers more flexibility in blood sampling times and, owing to its precision and to the amount of information provided, is the method of choice for ensuring that a given patient benefits from the desired systemic exposure. Unlike the other a posteriori methods, Bayesian estimation is based on population pharmacokinetic studies and can take into account the effects of different individual factors on the pharmacokinetics of the drug. Bayesian estimators have been used to determine maximum tolerated systemic exposure thresholds (e.g. for topotecan or teniposide) as well as for the routine monitoring of drugs characterized by a very high interindividual pharmacokinetic variability such as methotrexate or carboplatin. The development of these methods has contributed to improving cancer chemotherapy in terms of patient outcome and survival and should be pursued.

Antineoplastic Agents↗
PubMed2006

Adaptive dose selection using efficacy-toxicity trade-offs: illustrations and practical considerations.

The purpose of this paper is to describe and illustrate an outcome-adaptive Bayesian procedure, proposed by Thall and Cook (2004), for assigning doses of an experimental treatment to successive cohorts of patients. The method uses elicited (efficacy, toxicity) probability pairs to construct a family of trade-off contours that are used to quantify the desirability of each dose. This provides a basis for determining a best dose for each cohort. The method combines the goals of conventional Phase I and Phase II trials, and thus may be called a "Phase I-II" design. We first give a general review of the probability model and dose-finding algorithm. We next describe an application to a trial of a biologic agent for treatment of acute myelogenous leukemia, including a computer simulation study to assess the design's average behavior. To illustrate how the method may work in practice, we present a cohort-by-cohort example of a particular trial. We close with a discussion of some practical issues that may arise during implementation.

Algorithms↗
PubMedDate not supplied

Estimation of markov chain transition probabilities and rates from fully and partially observed data: uncertainty propagation, evidence synthesis, and model calibration.

Markov transition models are frequently used to model disease progression. The authors show how the solution to Kolmogorov's forward equations can be exploited to map between transition rates and probabilities from probability data in multistate models. They provide a uniform, Bayesian treatment of estimation and propagation of uncertainty of transition rates and probabilities when 1) observations are available on all transitions and exact time at risk in each state (fully observed data) and 2) observations are on initial state and final state after a fixed interval of time but not on the sequence of transitions (partially observed data). The authors show how underlying transition rates can be recovered from partially observed data using Markov chain Monte Carlo methods in WinBUGS, and they suggest diagnostics to investigate inconsistencies between evidence from different starting states. An illustrative example for a 3-state model is given, which shows how the methods extend to more complex Markov models using the software WBDiff to compute solutions. Finally, the authors illustrate how to statistically combine data from multiple sources, including partially observed data at several follow-up times and also how to calibrate a Markov model to be consistent with data from one specific study.

Calibration↗
PubMed2006

Bayesian models for pooling microarray studies with multiple sources of replications.

BACKGROUND: Biologists often conduct multiple but different cDNA microarray studies that all target the same biological system or pathway. Within each study, replicate slides within repeated identical experiments are often produced. Pooling information across studies can help more accurately identify true target genes. Here, we introduce a method to integrate multiple independent studies efficiently. RESULTS: We introduce a Bayesian hierarchical model to pool cDNA microarray data across multiple independent studies to identify highly expressed genes. Each study has multiple sources of variation, i.e. replicate slides within repeated identical experiments. Our model produces the gene-specific posterior probability of differential expression, which provides a direct method for ranking genes, and provides Bayesian estimates of false discovery rates (FDR). In simulations combining two and five independent studies, with fixed FDR levels, we observed large increases in the number of discovered genes in pooled versus individual analyses. When the number of output genes is fixed (e.g., top 100), the pooled model found appreciably more truly differentially expressed genes than the individual studies. We were also able to identify more differentially expressed genes from pooling two independent studies in Bacillus subtilis than from each individual data set. Finally, we observed that in our simulation studies our Bayesian FDR estimates tracked the true FDRs very well. CONCLUSION: Our method provides a cohesive framework for combining multiple but not identical microarray studies with several sources of replication, with data produced from the same platform. We assume that each study contains only two conditions: an experimental and a control sample. We demonstrated our model's suitability for a small number of studies that have been either pre-scaled or have no outliers.

Bacillus subtilis↗
PubMed2005

A control study to evaluate a computer-based microarray experiment design recommendation system for gene-regulation pathways discovery.

The main topic of this paper is evaluating a system that uses the expected value of experimentation for discovering causal pathways in gene expression data. By experimentation we mean both interventions (e.g., a gene knock-out experiment) and observations (e.g., passively observing the expression level of a "wild-type" gene). We introduce a system called GEEVE (causal discovery in Gene Expression data using Expected Value of Experimentation), which implements expected value of experimentation in discovering causal pathways using gene expression data. GEEVE provides the following assistance, which is intended to help biologists in their quest to discover gene-regulation pathways: Recommending which experiments to perform (with a focus on "knock-out" experiments) using an expected value of experimentation (EVE) method. Recommending the number of measurements (observational and experimental) to include in the experimental design, again using an EVE method. Providing a Bayesian analysis that combines prior knowledge with the results of recent microarray experimental results to derive posterior probabilities of gene regulation relationships. In recommending which experiments to perform (and how many times to repeat them) the EVE approach considers the biologist's preferences for which genes to focus the discovery process. Also, since exact EVE calculations are exponential in time, GEEVE incorporates approximation methods. GEEVE is able to combine data from knock-out experiments with data from wild-type experiments to suggest additional experiments to perform and then to analyze the results of those microarray experimental results. It models the possibility that unmeasured (latent) variables may be responsible for some of the statistical associations among the expression levels of the genes under study. To evaluate the GEEVE system, we used a gene expression simulator to generate data from specified models of gene regulation. Using the simulator, we evaluated the GEEVE system using a randomized control study that involved 10 biologists, some of whom used GEEVE and some of whom did not. The results show that biologists who used GEEVE reached correct causal assessments about gene regulation more often than did those biologists who did not use GEEVE. The GEEVE users also reached their assessments in a more cost-effective manner.

Animals↗
PubMed1992

Drug delivery optimization through Bayesian networks.

This paper describes how Bayesian Networks can be used in combination with compartmental models to plan Recombinant Human Erythropoietin (r-HuEPO) delivery in the treatment of anemia of chronic uremic patients. Past measurements of hematocrit or hemoglobin concentration in a patient during the therapy can be exploited to adjust the parameters of a compartmental model of the erythropoiesis. This adaptive process allows more accurate patient-specific predictions, and hence a more rational dosage planning. We describe a drug delivery optimization protocol, based on our approach. Some results obtained on real data are presented.

Anemia↗
PubMed2005

GOR V server for protein secondary structure prediction.

SUMMARY: We have created the GOR V web server for protein secondary structure prediction. The GOR V algorithm combines information theory, Bayesian statistics and evolutionary information. In its fifth version, the GOR method reached (with the full jack-knife procedure) an accuracy of prediction Q3 of 73.5%. Although GOR V has been among the most successful methods, its online unavailability has been a deterrent to its popularity. Here, we remedy this situation by creating the GOR V server.

Algorithms↗
PubMed2005

Posterior probability support vector machines for unbalanced data.

This paper proposes a complete framework of posterior probability support vector machines (PPSVMs) for weighted training samples using modified concepts of risks, linear separability, margin, and optimal hyperplane. Within this framework, a new optimization problem for unbalanced classification problems is formulated and a new concept of support vectors established. Furthermore, a soft PPSVM with an interpretable parameter v is obtained which is similar to the v-SVM developed by Schölkopf et al., and an empirical method for determining the posterior probability is proposed as a new approach to determine v. The main advantage of an PPSVM classifier lies in that fact that it is closer to the Bayes optimal without knowing the distributions. To validate the proposed method, two synthetic classification examples are used to illustrate the logical correctness of PPSVMs and their relationship to regular SVMs and Bayesian methods. Several other classification experiments are conducted to demonstrate that the performance of PPSVMs is better than regular SVMs in some cases. Compared with fuzzy support vector machines (FSVMs), the proposed PPSVM is a natural and an analytical extension of regular SVMs based on the statistical learning theory.

Algorithms↗