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Bayesian color constancy.

The problem of color constancy may be solved if we can recover the physical properties of illuminants and surfaces from photosensor responses. We consider this problem within the framework of Bayesian decision theory. First, we model the relation among illuminants, surfaces, and photosensor responses. Second, we construct prior distributions that describe the probability that particular illuminants and surfaces exist in the world. Given a set of photosensor responses, we can then use Bayes's rule to compute the posterior distribution for the illuminants and the surfaces in the scene. There are two widely used methods for obtaining a single best estimate from a posterior distribution. These are maximum a posteriori (MAP) and minimum mean-square-error (MMSE) estimation. We argue that neither is appropriate for perception problems. We describe a new estimator, which we call the maximum local mass (MLM) estimate, that integrates local probability density. The new method uses an optimality criterion that is appropriate for perception tasks: It finds the most probable approximately correct answer. For the case of low observation noise, we provide an efficient approximation. We develop the MLM estimator for the color-constancy problem in which flat matte surfaces are uniformly illuminated. In simulations we show that the MLM method performs better than the MAP estimator and better than a number of standard color-constancy algorithms. We note conditions under which even the optimal estimator produces poor estimates: when the spectral properties of the surfaces in the scene are biased.

Color Perception↗

Inheritance of hypoadrenocorticism in bearded collies.

OBJECTIVE: To assess heritability and mode of inheritance for hypoadrenocorticism in Bearded Collies. ANIMALS: 635 Bearded Collies. PROCEDURES: Dogs were classified as affected by hypoadrenocorticism or unaffected. Phenotypic and pedigree data were analyzed. Heritability was estimated by use of Bayesian statistical methods. Regressive logistic models for complex segregation analyses were used to characterize mode of inheritance. RESULTS: Hypoadrenocorticism was diagnosed in 60 (9.4%) dogs. Heritability of hypoadrenocorticism was estimated to be 0.76 with both sexes affected with equal probability. Evaluation of the pedigrees did not support a Mendelian autosomal dominant mode of inheritance. Evidence from the complex segregation analysis for a single locus of large effect on hypoadrenocorticism was not convincing. CONCLUSIONS AND CLINICAL RELEVANCE: Hypoadrenocorticism in Bearded Collies is highly heritable. Although a precise genetic mechanism responsible for inheritance of the disorder remains undetermined, breeding decisions must include consideration of the genetic likelihood of passing on this deleterious disorder to offspring of affected dams and sires.

Adrenal Insufficiency↗

Genetic parameters of fertility in two lines of rabbits with different reproductive potential.

A Bayesian analysis with a threshold model was performed for fertility defined as a binary trait (1 = successful mating, 0 = unsuccessful mating) in two populations of rabbits of different reproductive potential and different genetic origin: Line P selected for litter size and Line C selected for growth rate. There were 20,793 records of natural mating (86.2% successful) in Line C between 1983 and 2003, and 17,548 records (80.5% successful) in Line P, between 1992 and 2003. Data related to 5,388 and 3,848 females and 1,021 and 685 males in Lines C and P, respectively. The pedigree included 6,409 and 4,533 individuals in Lines C and P, respectively. The binary response was modeled under a probit approach. The model for the latent variable included male and female additive genetic effects, male and female permanent environmental effects, and the year-season and physiological status of the female (nulliparous, multiparous lactating, or multiparous nonlactating) as systematic effects. Means (standard deviation in parentheses) of the estimated marginal posterior distribution (EMPD) of male heritability were 0.013 (0.006) and 0.010 (0.008) in Lines C and P, respectively, and those of EMPD of female heritability were 0.056 (0.013) and 0.062 (0.018) in Lines C and P, respectively. Means of the EMPD of the proportion of the phenotypic variance due to environmental male and female effects were, respectively, 0.031 (0.007) and 0.128 (0.018) in Line C and 0.053 (0.010) and 0.231 (0.024) in Line P. Means (standard deviations in parentheses) of the EMPD of genetic correlation between male and female fertility were 0.733 (0.197) in Line C and 0.434 (0.381) in Line P. The posterior distribution of genetic correlations presents a huge dispersion, and the estimates should be taken with caution because of the almost negligible estimate of the male genetic component. Results indicate that little genetic variation exists for female fertility, and practically none for male fertility. It would, therefore, be possible to improve reproductive performance by including female fertility in a breeding program, but response to selection would be very small.

Animals↗

Association analyses between the prion protein locus and reproductive and lamb weight traits in Ripollesa sheep.

The objective of this study was to analyze the association between the haplotypes of the prion protein (PrP) locus and several reproductive and lamb weight traits in Ripollesa sheep. Prion protein genotypes were available for a total of 310 sheep (7 rams, 114 ewes, and 189 lambs), all of them belonging to the purebred Ripollesa flock of the Universitat Autònoma of Barcelona, for which all sheep had a known pedigree. In addition, the genotype of 24 historical descendants of the previously genotyped adult individuals was reconstructed, provided that both parents were homozygous for PrP haplotypes. Only 3 haplotypes (ARR, ARQ, and ARH) were observed in the PrP locus of the sheep sampled. Reproductive traits included conception rate and litter size, whereas birth BW and 90-d BW were the lamb weight traits studied. The additive effect of PrP haplotypes was analyzed through Bayesian animal threshold and linear models, for reproduction and weight traits, respectively. Ewe reproductive data belonged to 89 ewes that gave 492 conception rate records and 440 litter size records. Analyses of BW at birth and at 90 d of age were made on 323 and 164 lamb records, respectively. No associations between PrP haplotypes and conception rate and BW traits were observed. For litter size, the effect of the ARH haplotype was greater than that of the ARQ haplotype. Differences between ARH and ARR haplotypes also suggested an advantage for the ARH. As a whole, our results indicated that the selection favorable to increase litter size in Ripollesa ewes may also increase the ARH haplotype frequency, which contradicts the recommendations of the current European Union legislation aiming to increase the genetic resistance to scrapie. As a consequence, scrapie genotyping needs to be included as a new selection criterion in the breed.

Animals↗

Evidence for use of coronary stents. A hierarchical bayesian meta-analysis.

BACKGROUND: Coronary stents are widely used in interventional cardiology, but a current quantitative systematic overview comparing routine coronary stenting with standard percutaneous transluminal coronary angioplasty (PTCA) and restricted stenting (provisional stenting) has not been published. PURPOSE: To summarize results from all randomized clinical trials comparing routine coronary stenting with standard PTCA. DATA SOURCES: Electronic databases were searched by using the key words angioplasty and stent. References from identified articles were also reviewed. In addition, several prominent general medical and cardiology journals were searched and agencies known to perform systematic reviews were consulted. STUDY SELECTION: All comparative randomized clinical trials were included, except those involving primary angioplasty for the treatment of acute myocardial infarction. DATA EXTRACTION: A specified protocol was followed, and two of the authors independently extracted the data. Outcomes assessed were total mortality, myocardial infarction, angiographic restenosis, coronary artery bypass surgery, repeated PTCA, and freedom from angina. DATA SYNTHESIS: The results were synthesized by using a Bayesian hierarchical random-effects model. A total of 29 trials involving 9918 patients were identified. There was no evidence for a difference between routine coronary stenting and standard PTCA in terms of deaths or myocardial infarctions (odds ratio, 0.90 [95% credible interval [CrI], 0.72 to 1.11]) or the need for coronary artery bypass surgery (odds ratio, 1.01 [CrI, 0.79 to 1.31]). Coronary stenting reduced the rate of restenosis (odds ratio, 0.52 [CrI, 0.37 to 0.69]) and the need for repeated PTCA (odds ratio, 0.59 [CrI, 0.50 to 0.68]). The trials showed a wide range of crossover rates from PTCA to stenting. By use of a multiplicative model, each 10% increase in crossover rate decreased the need for repeated angioplasty by approximately 8% (odds ratio multiplying factor, 1.08 [CrI, 0.98 to 1.18]). Routine stenting probably reduces the need for repeated angioplasty by fewer than 4 to 5 per 100 treated persons compared with PTCA with provisional stenting. Studies were not blinded and suggest a bias with a possible overestimation of this benefit. CONCLUSIONS: In the controlled environment of randomized clinical trials, routine coronary stenting is safe but probably not associated with important reductions in rates of mortality, acute myocardial infarction, or coronary artery bypass surgery compared with standard PTCA with provisional stenting. Coronary stenting is associated with substantial reductions in angiographic restenosis rates and the subsequent need for repeated PTCA, although this benefit may be overestimated because of trial designs. The incremental benefit of routine stenting for reducing repeated angioplasty diminishes as the crossover rate of stenting with conventional PTCA increases.

Aged↗

[Cancer incidence in Modena: 2002-2006 projections].

OBJECTIVE: Cancer incidence predictions for the period 2002-2006 in the Province of Modena applying a Bayesian APC (Age Period Cohort) model. DESIGN: Population based descriptive study. SETTING: Patients with cancer diagnosed between 1988 and 2001 recorded in Modena Cancer Registry. MAIN OUTCOME MEASURES: Number of cases, crude and standardized incidence rates. RESULTS: Cancer incidence in 2002-2006 is expected to increase in both sexes, with the exception of stomach cancer (males and females) and lung cancer in males, both expected to decrease. The difference between the number of cases predicted for 2002 and observed data was about 0.7%. CONCLUSION: Prediction based on APC model seems to be reliable for most of the cancer sites, but should be used cautiously. In particular, projected number of breast and prostate cancer cases is clearly overestimated due to diagnostic anticipation effect which gives rise to an excess in recent years.

Aged↗

[The effects of various factors on cerebrovascular disease mortality rates in the 20th century and future trends in Japan].

PURPOSES: To analyze the outcomes of measures designed to decrease cerebrovascular diseases (CVDs) in Japan and to project CVD mortality trends into the 21st century based on an analysis of rates observed in the 20th century. METHODS: The numbers of CVD deaths and population sizes from 1920 to 2003 (excluding 1940 to 1946) by sex, year, and 5-year age group (from 20 to 79 years old) were used and effects of various factors on CVD mortality rates were estimated using Nakamura's Bayesian age-period-cohort model. The numbers of CVD deaths up to the year 2050 were projected based on estimates of age, cohort, and future period effects under three scenarios: (i) values remaining constant after year 2003; (ii) linearly extrapolated values; and (iii) quadratically extrapolated values, we obtained using a regression line for period effects from 1995 to 2003. RESULTS: The age, cohort, and period effects on CVD mortality rates were large and in order of the magnitude of their ranges. There were small differences between males and females. The age effect increased with aging and the period effect started decreasing after 1970. The cohort effect was high for birth cohorts born from the 1840s to the 1890s and low for those born from the 1920s to the 1970s. There were some differences in the cohort effect between males and females for birth cohorts born after 1940s; for females there was a gradual decrease, while for males there was a slight increase, after which it remained almost constant. According to the three scenarios, CVD deaths: (i) had upward trends through the projected period and peaked at around 2025 and 2045; (ii) remained almost constant at the present level for males, and decreased slightly for females; (iii) decreased for both males and females. CONCLUSIONS: The outcomes of measures designed to decrease CVDs were observed as period effects after 1970. Exposure to these measures is associated with prevention of CVD deaths. Nevertheless, in the first half of the 21st century, the number of CVD deaths is projected to increase due to the aging of the baby boomers and upward trends in the cohort effect for males. It would be necessary to adopt and develop both population strategies to decrease future period effects and high-risk strategies to decrease cohort effects for younger males who are currently in their twenties and thirties.

Adult↗

Unsupervised learning with independent component analysis can identify patterns of glaucomatous visual field defects.

PURPOSE: We previously reported the use of clustering by unsupervised learning with machine learning classifiers to segment clusters of patterns in standard automated perimetry (SAP) for glaucoma. In this study, the process of unsupervised learning by independent component analysis decomposed SAP field patterns into axes, and the information represented by these axes was evaluated. METHODS: SAP fields were obtained with the Humphrey Visual Field Analyzer on 189 normal eyes and 156 eyes with glaucomatous optic neuropathy (GON) determined by masked review with stereoscopic optic disc photos. The variational Bayesian independent component analysis mixture model (vB-ICA-mm) partitioned the SAP fields into the most informative number of clusters. Simultaneously, it learned an optimal number of maximally independent axes for each cluster. RESULTS: The most informative number of clusters was two. vB-ICA-mm placed 68.6% of the SAP fields from eyes with GON in a cluster labeled G and 98.4% of the fields from eyes with normal optic discs in a cluster labeled N. Cluster G optimally contained six axes. Post hoc analysis of patterns generated at -1 SD and +2 SD from the cluster G mean on the six axes revealed defects similar to those identified by experts as indicative of glaucoma. SAP fields associated with an axis showed increasing severity as they were located farther in the positive direction from the cluster G mean. CONCLUSIONS: vB-ICA-mm represented the SAP fields with patterns that were meaningful for glaucoma experts. This process also captured severity in the patterns uncovered. These findings should validate vB-ICA-mm as a data mining technique for new and unfamiliar complex tests.

Artificial Intelligence↗

Human causal discovery from observational data.

Utilizing Bayesian belief networks as a model of causality, we examined medical students' ability to discover causal relationships from observational data. Nine sets of patient cases were generated from relatively simple causal belief networks by stochastic simulation. Twenty participants examined the data sets and attempted to discover the underlying causal relationships. Performance was poor in general, except at discovering the absence of a causal relationship. This work supports the potential for combining human and computer methods for causal discovery.

Bayes Theorem↗

Bayesian hypothesis testing of four-taxon topologies using molecular sequence data.

The reconstruction of phylogenetic trees from molecular sequences presents unusual problems for statistical inference. For example, three possible alternatives must be considered for four taxa when inferring the correct unrooted tree (referred to as a topology). In our view, classical hypothesis testing is poorly suited to this triangular set of alternative hypotheses. In this article, we develop Bayesian inference to determine the posterior probability that a four-taxon topology is correct given the sequence data and the evolutionary parsimony algorithm for phylogenetic reconstruction. We assess the frequency properties of our models in a large simulation study. Bayesian inference under the principles of evolutionary parsimony is shown to be well calibrated with reasonable discriminating power for a wide range of realistic conditions, including conditions that violate the assumptions of evolutionary parsimony.

Base Sequence↗

Recursive bayesian decoding of motor cortical signals by particle filtering.

The population vector (PV) algorithm and optimal linear estimation (OLE) have been used to reconstruct movement by combining signals from multiple neurons in the motor cortex. While these linear methods are effective, recursive Bayesian decoding schemes, which are nonlinear, can be more powerful when probability model assumptions are satisfied. We have implemented a recursive Bayesian algorithm for reconstructing hand movement from neurons in the motor cortex. The algorithm uses a recently developed numerical method known as "particle filtering" and follows the same general strategy as that used by Brown et al. to reconstruct the path of a foraging rat from hippocampal place cells. We investigated the method in a numerical simulation study in which neural firing rate was assumed to be positive, but otherwise a linear function of movement velocity, and preferred directions were not uniformly distributed. In terms of mean-squared error, the approach was approximately 10 times more efficient than the PV algorithm and 5 times more efficient than OLE. Thus use of recursive Bayesian decoding can achieve the accuracy of the PV algorithm (or OLE) with approximately 10 times (or 5 times) fewer neurons. The method was also used to reconstruct hand movement in an ellipse-drawing task from 258 cells in the ventral premotor cortex. Recursive Bayesian decoding was again more efficient than the PV and OLE methods, by factors of roughly seven and three, respectively.

Algorithms↗

Pharmacokinetics of dopamine in healthy male subjects.

BACKGROUND: Dopamine is an agonist of alpha, beta, and dopaminergic receptors with varying hemodynamic effects depending on the dose of drug being administered. The purpose of this study was to measure plasma concentrations of dopamine in a homogeneous group of healthy male subjects to develop a pharmacokinetic model for the drug. Our hypothesis was that dopamine concentrations can be predicted from the infusion dose using a population-based pharmacokinetic model. METHODS: Nine healthy male volunteers aged 23 to 45 yr were studied in a clinical research facility within our academic medical center. After placement of venous and arterial catheters, dopamine was infused at 10 microg x kg(-1) x min(-1) for 10 min, followed by a 30-min washout period. Subsequently, dopamine was infused at 3 microg x kg(-1) x min(-1) for 90 min, followed by another 30-min washout period. Timed arterial blood samples were centrifuged, and the plasma was analyzed by high-performance liquid chromatography. Mixed-effects pharmacokinetic models using NONMEM software (NONMEM Project Group, University of California, San Francisco, CA) were used to determine the optimal compartmental pharmacokinetic model for dopamine. RESULTS: Plasma concentrations of dopamine varied from 12,300 to 201,500 ng/l after 10 min of dopamine infusion at 10 microg x kg(-1) x min(-1). Similarly, steady-state dopamine concentrations varied from 1,880 to 18,300 ng/l in these same subjects receiving 3-microg x kg(-1) x min(-1) infusions for 90 min. A two-compartment model adjusted for body weight was the best model based on the Schwartz-Bayesian criterion. CONCLUSIONS: Despite a homogeneous population of healthy male subjects and weight-based dosing, there was 10- to 75-fold intersubject variability in plasma dopamine concentrations, making standard pharmacokinetic modeling of less utility than for other drugs. The data suggest marked intraindividual and interindividual variability in dopamine distribution and/or metabolism. Thus, plasma dopamine concentrations in patients receiving dopamine infusion at identical rates may vary profoundly. Our data suggest that dosing dopamine based on body weight does not yield predictable blood concentrations.

Adult↗

Genetic evaluation of dairy cattle using test-day models.

Recently there has been considerable interest in modeling individual test-day records (TDR) for genetic evaluation of dairy cattle as a replacement for the traditional use of estimated accumulated 305-d yields. Some advantages of test-day models (TDM) include the ability to account for environmental effects of each test day, the ability to model the trajectory of the lactation for individual genotypes or groups of animals, and the possibility of genetic evaluations for persistency of production. Also, the use of test-day models avoids the necessity of extending short lactations on culled animals and animals with records in progress. The disadvantages of TDM include computational difficulties associated with analyzing much larger datasets and the need to estimate many more parameters than in a traditional 305-d lactation model. Several different models have been proposed to model the trajectory of the lactation, including so-called "biological functions," various polynomials and character process models. At present, there is not universal agreement on which models to use in routine prediction of breeding values and better methods to compare models are desirable. Obtaining accurate estimates of the dispersion parameters to use in TDM remains a challenge. Methods used include a two-step procedure in which the dispersion parameters are estimated in a series of multivariate models followed by a reduction in order of fit using covariance functions, and a one-step procedure in which the parameters of TDM are estimated using restricted maximum likelihood or Bayesian methods in a random regression model. Further research should focus on including multiple lactation data and accounting for heterogeneity variance.

Algorithms↗

Estimation of uncertainty and variability in bacterial growth using Bayesian inference. Application to Listeria monocytogenes.

The usefulness of risk assessment is limited by its ability or inability to model and evaluate risk uncertainty and variability separately. A key factor of variability and uncertainty in microbial risk assessment could be growth variability between strains and growth model parameter uncertainty. In this paper, we propose a Bayesian procedure for growth parameter estimation which makes it possible to separate these two components by means of hyperparameters. This model incorporates in a single step the logistic equation with delay as a primary growth model and the cardinal temperature equation as a secondary growth model. The estimation of Listeria monocytogenes growth parameters in milk using literature data is proposed as a detailed application. While this model should be applied on genuine data, it is highlighted that the proposed approach may be convenient for estimating the variability and uncertainty of growth parameters separately, using a complete predictive microbiology model.

Animals↗

Risk-based integrity and inspection modeling (RBIIM) of process components/system.

Process plants deal with hazardous (highly flammable and toxic) chemicals at extreme conditions of temperature and pressure. Proper inspection and maintenance of these facilities is paramount for the maintenance of safe and continuous operation. This article proposes a risk-based methodology for integrity and inspection modeling (RBIIM) to ensure safe and fault-free operation of the facility. This methodology uses a gamma distribution to model the material degradation and a Bayesian updating method to improve the distribution based on actual inspection results. The method deals with the two cases of perfect and imperfect inspections. The measurement error resulting from imperfect inspections is modeled as a zero-mean, normally distributed random process. The risk is calculated using the probability of failure and the consequence is assessed in terms of cost as a function of time. The risk function is used to determine an optimal inspection and replacement interval. The calculated inspection and replacement interval is subsequently used in the design of an integrity inspection plan. Two case studies are presented: the maintenance of an autoclave and the maintenance of a pipeline segment. For the autoclave, the interval between two successive inspections is found to be 19 years. For the pipeline, the next inspection is due after 5 years from now. Measurements taken at inspections are used in estimating a new degradation rate that can then be used to update the failure distribution function.

Journal Article↗

An adaptive Gaussian model for satellite image deblurring.

The deconvolution of blurred and noisy satellite images is an ill-posed inverse problem, which can be regularized within a Bayesian context by using an a priori model of the reconstructed solution. Since real satellite data show spatially variant characteristics, we propose here to use an inhomogeneous model. We use the maximum likelihood estimator (MLE) to estimate its parameters and we show that the MLE computed on the corrupted image is not suitable for image deconvolution because it is not robust to noise. We then show that the estimation is correct only if it is made from the original image. Since this image is unknown, we need to compute an approximation of sufficiently good quality to provide useful estimation results. Such an approximation is provided by a wavelet-based deconvolution algorithm. Thus, a hybrid method is first used to estimate the space-variant parameters from this image and then to compute the regularized solution. The obtained results on high resolution satellite images simultaneously exhibit sharp edges, correctly restored textures, and a high SNR in homogeneous areas, since the proposed technique adapts to the local characteristics of the data.

Algorithms↗

Clustering ensembles of neural network models.

We show that large ensembles of (neural network) models, obtained e.g. in bootstrapping or sampling from (Bayesian) probability distributions, can be effectively summarized by a relatively small number of representative models. In some cases this summary may even yield better function estimates. We present a method to find representative models through clustering based on the models' outputs on a data set. We apply the method on an ensemble of neural network models obtained from bootstrapping on the Boston housing data, and use the results to discuss bootstrapping in terms of bias and variance. A parallel application is the prediction of newspaper sales, where we learn a series of parallel tasks. The results indicate that it is not necessary to store all samples in the ensembles: a small number of representative models generally matches, or even surpasses, the performance of the full ensemble. The clustered representation of the ensemble obtained thus is much better suitable for qualitative analysis, and will be shown to yield new insights into the data.

Algorithms↗

Use of repeated measures analysis for evaluation of genetic background of dairy cattle behavior in automatic milking systems.

Milking frequencies measured at official test days were used with repeated measurement analysis to reveal the environmental and genetic impact on the milking frequency of cows in automatic milking systems. Repeated measurements were 3 test-day observations per cow within days in milk (DIM) classes, with 1,216 cows in DIM class 1 (d 0 to 99), from 1,112 cows in DIM class 2 (d 100 to 199), and from 1,004 cows in DIM class 3 (d 200 to 299) kept in 15 farms. Selection criteria for models analyzing repeated measurements were Akaike and Schwarz Bayesian values, which favored the autoregressive [AR(1)] covariance structure over the compound symmetry model. Results from the AR(1) model indicated a significant impact of fixed herd and parity effects. Milking frequencies decreased with increasing parities and were greatest for first-parity cows. High daily milk yield was associated with higher milking frequencies. Heritabilities for milking frequency were 0.16, 0.19, and 0.22 in DIM classes 1, 2, and 3, respectively, from the AR(1) model. Higher heritabilities in the later stage of lactation were due to a substantial reduction of the residual variance. Genetic correlations between test-day milk yield and daily milking frequency were in the range of 0.46 to 0.57 for all DIM classes and between milking frequency and somatic cell score were near zero. For verification of results, milking frequencies of the same cows obtained from herd management programs were averaged within DIM classes. Heritabilities were slightly above the values from the AR(1) model. In conclusion, heritabilities for milking frequency in automatic milking systems are moderate enough to incorporate this behavioral trait in a combined breeding goal. The inevitable improvement of labor efficiency in dairy cattle farming demands such cows going easily and voluntarily in automatic milking systems.

Analysis of Variance↗