Search results for "bayesian"

Multivariate versus univariate calibration for nonlinear chemiluminescence data

2001

Abstract Multivariate calibration is tested as an alternative to model chromium(III) concentration versus chemiluminescence registers obtained from luminol-hydrogen peroxide reaction. The multivariate calibration approaches included have been: conventional linear methods (principal component regression (PCR) and partial least squares (PLS)), nonlinear methods (nonlinear variants and variants of locally weighted regression) and linear methods combined with variable selection performed in the original or in the transformed data (stepwise multiple linear regression procedure). Both the direct and inverse univariate approaches have been also tested. The use of a double logarithmic transformatio…

Order statistics-based parametric classification for multi-dimensional distributions

2013

Traditionally, in the field of Pattern Recognition (PR), the moments of the class-conditional densities of the respective classes have been used to perform classification. However, the use of phenomena that utilized the properties of the Order Statistics (OS) were not reported. Recently, in [10,8], we proposed a new paradigm named CMOS, Classification by the Moments of Order Statistics, which specifically used these quantifiers. It is fascinating that CMOS is essentially ''anti''-Bayesian in its nature because the classification is performed in a counter-intuitive manner, i.e., by comparing the testing sample to a few samples distant from the mean, as opposed to the Bayesian approach in whi…

Model averaging estimation of generalized linear models with imputed covariates

2015

a b s t r a c t We address the problem of estimating generalized linear models when some covariate values are missing but imputations are available to fill-in the missing values. This situation generates a bias-precision trade- off in the estimation of the model parameters. Extending the generalized missing-indicator method proposed by Dardanoni et al. (2011) for linear regression, we handle this trade-off as a problem of model uncertainty using Bayesian averaging of classical maximum likelihood estimators (BAML). We also propose a block model averaging strategy that incorporates information on the missing-data patterns and is computationally simple. An empirical application illustrates our…

Weighted-average least squares estimation of generalized linear models

2018

The weighted-average least squares (WALS) approach, introduced by Magnus et al. (2010) in the context of Gaussian linear models, has been shown to enjoy important advantages over other strictly Bayesian and strictly frequentist model averaging estimators when accounting for problems of uncertainty in the choice of the regressors. In this paper we extend the WALS approach to deal with uncertainty about the specification of the linear predictor in the wider class of generalized linear models (GLMs). We study the large-sample properties of the WALS estimator for GLMs under a local misspecification framework that allows the development of asymptotic model averaging theory. We also investigate t…

2020

Piping erosion is one form of water erosion that leads to significant changes in the landscape and environmental degradation. In the present study, we evaluated piping erosion modeling in the Zarandieh watershed of Markazi province in Iran based on random forest (RF), support vector machine (SVM), and Bayesian generalized linear models (Bayesian GLM) machine learning algorithms. For this goal, due to the importance of various geo-environmental and soil properties in the evolution and creation of piping erosion, 18 variables were considered for modeling the piping erosion susceptibility in the Zarandieh watershed. A total of 152 points of piping erosion were recognized in the study area that…

Modern taurine cattle descended from small number of near-eastern founders.

2012

Archaeozoological and genetic data indicate that taurine cattle were first domesticated from local wild ox (aurochs) in the Near East some 10,500 years ago. However, while modern mitochondrial DNA (mtDNA) variation indicates early Holocene founding event(s), a lack of ancient DNA data from the region of origin, variation in mutation rate estimates, and limited application of appropriate inference methodologies have resulted in uncertainty on the number of animals first domesticated. A large number would be expected if cattle domestication was a technologically straightforward and unexacting region-wide phenomenon, while a smaller number would be consistent with a more complex and challengin…

SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models

2015

The discovery of single nucleotide variants (SNVs) from next-generation sequencing (NGS) data typically works by aligning reads to a given genome and then creating an alignment map to interpret the presence of SNVs. Various approaches have been developed to call whether germline SNVs (or SNPs) in normal cells or somatic SNVs in cancer/tumor cells. Nonetheless, efficient callers for both germline and somatic SNVs have not yet been extensively investigated. In this paper, we present SNVSniffer, an integrated caller for germline and somatic SNVs from NGS data based on Bayesian probabilistic models. In SNVSniffer, our germline SNV calling models allele counts per site as a multinomial condition…

A Phylogenetic Analysis of Human Syntenies Revealed by Chromosome Painting in Euarchontoglires Orders

2010

To search for cytogenetic signatures that can help to clarify evolutionary affinities among the five orders within the Euarchontoglires clade, we focused on associations of conserved syntenic blocks that have been accumulated in the karyotypes of Primates (Strepsirhini and Haplorhini), five families of Rodentia, Scandentia (Tupaia belangeri), Dermoptera (Galeopterus variegatus) and Lagomorpha (Oryctolagus cuniculus). We examined available chromosome painting data to identify conserved chromosomes and chromosomal segments, and syntenic associations likely to have characterized the ancestral eutherian karyotype. The data set includes 161 characters that have been subjected to a concatenated a…

Selective phenotyping, entropy reduction, and the mastermind game.

2011

Abstract Background With the advance of genome sequencing technologies, phenotyping, rather than genotyping, is becoming the most expensive task when mapping genetic traits. The need for efficient selective phenotyping strategies, i.e. methods to select a subset of genotyped individuals for phenotyping, therefore increases. Current methods have focused either on improving the detection of causative genetic variants or their precise genomic location separately. Results Here we recognize selective phenotyping as a Bayesian model discrimination problem and introduce SPARE (Selective Phenotyping Approach by Reduction of Entropy). Unlike previous methods, SPARE can integrate the information of p…

2021

The domestication and spreading of grapevine as well as the gene flow history had been described in many studies. We used a high-quality 7k SNP dataset of 1,038 Eurasian grape varieties with unique profiles to assess the population genetic diversity, structure, and relatedness, and to infer the most likely migration events. Comparisons of putative scenarios of gene flow throughout Europe from Caucasus helped to fit the more reliable migration routes around the Mediterranean Basin. Approximate Bayesian computation (ABC) approach made possible to provide a response to several questions so far remaining unsolved. Firstly, the assessment of genetic diversity and population structure within a we…