Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Bayesian inference”

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 235 records · Page 13Linked to original sources
PubMed2006

Phylogenetic relationships and phylogeography of the Killifish species of the subgenus Chromaphyosemion (Radda, 1971) in West Africa, inferred from mitochondrial DNA sequences.

We have analyzed the phylogenetic relationships of 160 specimens from 88 samples representing all defined species of the African Aplocheiloid subgenus Chromaphyosemion in order to examine the monophyly of this group, the species interrelationships, and to reveal trends in chromosomal evolution and formulate hypotheses about their evolutionary history. The data set comprised 1153 total nucleotides from the mitochondrial 12S rRNA, cytochrome oxidase I, and D-loop. The molecular-based topologies were analyzed by maximum parsimony, maximum likelihood, distance method and Bayesian inference support the monophyly of the subgenus Chromaphyosemion. All populations with ambiguous taxonomic status were assigned to an already described species except A. sp. Rio Muni which corresponds to a still undescribed species. Aphyosemion alpha and A. lugens were in basal position in the different trees that indicate a possible origin of the subgenus Chromaphyosemion in the South Cameroon-North Gabon region. Furthermore, the South Cameroon region (between 2 degrees and 3 degrees of North latitude) that accommodates half of the Chromaphyosemion species is considered to have been a refuge zone during the late quaternary dry events that Africa experienced. Phylogenetic relationships among the subgenus also revealed that chromosomal evolution is complex and should be studied at the intraspecific level.

Africa, Western↗
PubMed2005

Molecular systematics of Middle American harvest mice Reithrodontomys (Muridae), estimated from mitochondrial cytochrome b gene sequences.

We estimated phylogenetic relationships among 16 species of harvest mice using sequences from the mitochondrial cytochrome b (cyt b) gene. Gene phylogenies constructed using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) optimality criteria were largely congruent and arranged taxa into two groups corresponding to the two recognized subgenera (Aporodon and Reithrodontomys). All analyses also recovered R. mexicanus and R. microdon as polyphyletic, although greater resolution was obtained using ML and BI approaches. Within R. mexicanus, three clades were identified with high nodal support (MP and ML bootstrap, Bremer decay and Bayesian posterior probabilities). One represented a subspecies of R. mexicanus from Costa Rica (R. m. cherrii) and a second was distributed in the Sierra Madre Oriental of Mexico. The third R. mexicanus clade consisted of mice from southern Mexico southward to South America. Polyphyly between the two moieties of R. microdon corresponded to the Isthmus of Tehuantepec in southern Mexico. Populations of R. microdon microdon to the east of the isthmus (Chiapas, Mexico) grouped with R. tenuirostris, whereas samples of R. m. albilabris to the west in Oaxaca, Mexico, formed a clade with R. bakeri. Within the subgenus Reithrodontomys, all analyses recovered R. montanus and R. raviventris as sister taxa, a finding consistent with earlier studies based on allozymes and cyt b data. There was also strong support (ML and BI criteria) for a clade consisting of ((R. megalotis, R. zacatecae) (R. sumichrasti)). In addition, cytb gene phylogenies (MP, ML, and BI) recovered R. fulvescens and R. hirsutus (ML and BI) as basal taxa within the subgenus Reithrodontomys. Constraint analyses demonstrated that tree topologies treating the two subgenera (Aporodon and Reithrodontomys) as monophyletic (ML criterion) was significantly better (p>0.036) and supported polyphyly of R. mexicanus (both ML and MP criteria - p>0.013) and R. microdon (MP criterion only for certain topologies; p>0.02). Although several species-level taxa were identified based on multiple, independent data sets, we recommended a conservative approach which will involve thorough analyses of museum specimens including material from type localities together with additional sampling and data from multiple, nuclear gene markers.

Animals↗
PubMed2006

Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown Clades.

Inference of evolutionary relationships between nematodes is severely hampered by their conserved morphology, the high frequency of homoplasy, and the scarcity of phylum-wide molecular data. To study the origin of nematode radiation and to unravel the phylogenetic relationships between distantly related species, 339 nearly full-length small-subunit rDNA sequences were analyzed from a diverse range of nematodes. Bayesian inference revealed a backbone comprising 12 consecutive dichotomies that subdivided the phylum Nematoda into 12 clades. The most basal clade is dominated by the subclass Enoplia, and members of the order Triplonchida occupy positions most close to the common ancestor of the nematodes. Crown Clades 8-12, a group formerly indicated as "Secernentea" that includes Caenorhabditis elegans and virtually all major plant and animal parasites, show significantly higher nucleotide substitution rates than the more basal Clades 1-7. Accelerated substitution rates are associated with parasitic lifestyles (Clades 8 and 12) or short generation times (Clades 9-11). The relatively high substitution rates in the distal clades resulted in numerous autapomorphies that allow in most cases DNA barcode-based species identification. Teratocephalus, a genus comprising terrestrial bacterivores, was shown to be most close to the starting point of Secernentean radiation. Notably, fungal feeding nematodes were exclusively found basal to or as sister taxon next to the 3 groups of plant parasitic nematodes, namely, Trichodoridae, Longidoridae, and Tylenchomorpha. The exclusive common presence of fungivorous and plant parasitic nematodes supports a long-standing hypothesis that states that plant parasitic nematodes arose from fungivorous ancestors.

Amino Acid Substitution↗
PubMed2003

Modelling the world in real time: how robots engineer information.

Programming robots and other autonomous systems to interact with the world in real time is bringing into sharp focus general questions about representation, inference and understanding. These artificial agents use digital computation to interpret the data gleaned from sensors and produce decisions and actions to guide their future behaviour. In a physical system, however, finite computational resources unavoidably impose the need to approximate and make selective use of the information available to reach prompt deductions. Recent research has led to widespread adoption of the methodology of Bayesian inference, which provides the absolute framework to understand this process fully via modelling as informed, fully acknowledged approximation. The performance of modern systems has improved greatly on the heuristic methods of the early days of artificial intelligence. We discuss the general problem of real-time inference and computation, and draw on examples from recent research in computer vision and robotics: specifically visual tracking and simultaneous localization and mapping.

Artificial Intelligence↗
PubMed2006

A molecular phylogeny for the large African orchid genus Disa.

Phylogenetic relationships were inferred for the African subtribe Disinae (Orchidoideae, Orchidaceae), which include the large genus Disa and the small genus Schizodium. One nuclear (ITS) gene region and two plastid (trnLF and matK) gene regions were sequenced for 136 ingroup, representing 70% of all known Disinae species, as well as for 7 outgroup taxa. The combined data matrix contained 4094 characters and was analysed using parsimony and Bayesian inference. Our results show that the generic status of Schizodium can no longer be supported, as it is deeply embedded within the genus Disa. Furthermore, the currently recognised subgenera do not reflect the phylogenetic relationships and should be rejected. Several of the currently recognised sections are monophyletic, others contain misplaced elements, while some are polyphyletic. Morphological divergence, rather than convergence, has hampered previous attempts at a phylogenetic classification of the Disinae. On the basis of our molecular phylogenetic hypothesis, we propose a monotypic subtribe Disinae and a subdivision of the genus Disa into 18 sections.

Africa↗
PubMed2005

Stochastic models of neuronal dynamics.

Cortical activity is the product of interactions among neuronal populations. Macroscopic electrophysiological phenomena are generated by these interactions. In principle, the mechanisms of these interactions afford constraints on biologically plausible models of electrophysiological responses. In other words, the macroscopic features of cortical activity can be modelled in terms of the microscopic behaviour of neurons. An evoked response potential (ERP) is the mean electrical potential measured from an electrode on the scalp, in response to some event. The purpose of this paper is to outline a population density approach to modelling ERPs. We propose a biologically plausible model of neuronal activity that enables the estimation of physiologically meaningful parameters from electrophysiological data. The model encompasses four basic characteristics of neuronal activity and organization: (i) neurons are dynamic units, (ii) driven by stochastic forces, (iii) organized into populations with similar biophysical properties and response characteristics and (iv) multiple populations interact to form functional networks. This leads to a formulation of population dynamics in terms of the Fokker-Planck equation. The solution of this equation is the temporal evolution of a probability density over state-space, representing the distribution of an ensemble of trajectories. Each trajectory corresponds to the changing state of a neuron. Measurements can be modelled by taking expectations over this density, e.g. mean membrane potential, firing rate or energy consumption per neuron. The key motivation behind our approach is that ERPs represent an average response over many neurons. This means it is sufficient to model the probability density over neurons, because this implicitly models their average state. Although the dynamics of each neuron can be highly stochastic, the dynamics of the density is not. This means we can use Bayesian inference and estimation tools that have already been established for deterministic systems. The potential importance of modelling density dynamics (as opposed to more conventional neural mass models) is that they include interactions among the moments of neuronal states (e.g. the mean depolarization may depend on the variance of synaptic currents through nonlinear mechanisms).Here, we formulate a population model, based on biologically informed model-neurons with spike-rate adaptation and synaptic dynamics. Neuronal sub-populations are coupled to form an observation model, with the aim of estimating and making inferences about coupling among sub-populations using real data. We approximate the time-dependent solution of the system using a bi-orthogonal set and first-order perturbation expansion. For didactic purposes, the model is developed first in the context of deterministic input, and then extended to include stochastic effects. The approach is demonstrated using synthetic data, where model parameters are identified using a Bayesian estimation scheme we have described previously.

Bayes Theorem↗
PubMed2005

Molecular phylogeny of lugworms (Annelida, Arenicolidae) inferred from three genes.

Arenicolids comprise a group of four genera in which about 30 nominal species are described. Whereas the biology of many arenicolids is well known, the phylogenetic relationships of these worms are inadequately studied. A close relationship of Arenicolidae and Maldanidae is generally accepted. The phylogenetic relationships of arenicolid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA gene, the nuclear 18S rRNA gene, and a small fraction of the nuclear 28S rRNA gene. Members of all described arenicolid genera are included in the data set. Phylogenetic analyses were conducted using Maximum Likelihood, Bayesian inference, and Maximum Parsimony. The monophyly of the Maldanidae, as well as of the Arenicolidae is supported by all conducted analyses. Two well supported major clades are highest ranked sister taxa in the Arenicolidae: one containing all Abarenicola species and one containing Arenicola, Arenicolides, and Branchiomaldane. Evidence is given for a closer relationship between the two investigated Branchiomaldane species and Arenicolides ecaudata in the combined analysis. In the light of the molecular data the best explanation for structural and morphological observations is that Branchiomaldane evolved by progenesis.

Animals↗
PubMedDate not supplied

Integration of form and motion within a generative model of visual cortex.

One of the challenges faced by the visual system is integrating cues within and across processing streams for inferring scene properties and structure. This is particularly apparent in the inference of object motion, where psychophysical experiments have shown that integration of motion signals, distributed across space, must also be integrated with form cues. This has led several to conclude that there exist mechanisms which enable form cues to 'veto' or completely suppress ambiguous motion signals. We describe a probabilistic approach which uses a generative network model for integrating form and motion cues using the machinery of belief propagation and Bayesian inference. We show, using computer simulations, that motion integration can be mediated via a local, probabilistic representation of contour ownership, which we have previously termed 'direction of figure'. The uncertainty of this inferred form cue is used to modulate the covariance matrix of network nodes representing local motion estimates in the motion stream. We show with results for two sets of stimuli that the model does not completely suppress ambiguous cues, but instead integrates them in a way that is a function of their underlying uncertainty. The result is that the model can account for the continuum of bias seen for motion coherence and perceived object motion in psychophysical experiments.

Bayes Theorem↗
PubMed2005

A Bayesian framework for SNP identification.

As evolutionary models for single-nucleotide polymorphisms (SNPs) become available, methods for using them in the context of evolutionary information and expert prior information is a necessity. We formulate a probability model for SNPs as a Bayesian inference problem. Using this framework we compare the individual and combined predictive ability of four evolutionary models of varying levels of specificity on three SNP databases (two specifically targeted at functional SNPs) by calculating posterior probabilities and generating Receiver Operating Characteristic (ROC) curves. We discover that none of the models do exceptionally well, in some cases no better than a random-guess model. However, we demonstrate that several properties of the Bayesian formulation improve the predictability of SNPs in the three databases, specifically the ability to utilize mixtures of evolutionary models and a prior based on the genetic code.

Bayes Theorem↗
PubMed2001

Predicting dose-time profiles of solar energetic particle events using Bayesian forecasting methods.

Bayesian inference techniques, coupled with Markov chain Monte Carlo sampling methods, are used to predict dose-time profiles for energetic solar particle events. Inputs into the predictive methodology are dose and dose-rate measurements obtained early in the event. Surrogate dose values are grouped in hierarchical models to express relationships among similar solar particle events. Models assume nonlinear, sigmoidal growth for dose throughout an event. Markov chain Monte Carlo methods are used to sample from Bayesian posterior predictive distributions for dose and dose rate. Example predictions are provided for the November 8, 2000, and August 12, 1989, solar particle events.

Bayes Theorem↗
PubMed1999

MDL and the statistical mechanics of protein potentials.

The combination of a wealth of structural data and impressive computational power provides detailed information pertaining to the structure and dynamics of biomacromolecules. A natural inclination is to incorporate this information into models to gain added predictive power on protein folding and stability. There has been considerable recent interest in developing "knowledge-based" potentials to describe internal interactions in proteins. In these approaches, probability distribution functions are inferred from existing knowledge. A common assumption has been the "quasi-chemical approximation" or "Boltzmann device". This method relates statistical mechanical probabilities to observed frequencies. The validity of this approach is discussed in detail from a statistical mechanics perspective. Because statistical mechanics is a form of statistical inference based on a lack of knowledge of the system, the "Boltzmann device" does not have a rigorous theoretical justification. In the present work, a statistical mechanics based on partial knowledge of the system is employed. This statistical mechanical scheme uses the minimum description length (MDL) of phase space as its main tool. With this approach, "knowledge-based" potentials can be derived in a rigorous fashion. In practical calculations, these potentials are best obtained using Bayesian inference methods similar to those used in image reconstruction.

Algorithms↗
PubMed2004

The plerocercus of Ditrachybothridium macrocephalum Rees, 1959 from two deep-sea elasmobranchs, with a molecular analysis of its position within the order Diphyllidea and a checklist of the hosts of larval diphyllideans.

New collections were made of Ditrachybothridium macrocephalum Rees, 1959 from the deep-sea elasmobranchs Apristurus laurussonii (Saemundsson) and cf. Rajella bigelowi (Stehmann) in the northern Atlantic Ocean, allowing studies of the morphology of its plerocercus. The material has also allowed an estimate of its position within the Diphyllidea inferred from molecular data for the first time. The plerocercus is withdrawn, but not invaginated, within a cyst with a thick vacuolated wall. The encysted strobila is distinct, with several putative segments and advanced genital anlagen, and the scolex is fully developed with a distinct apical pad. 28S rDNA (D1-D3 regions) sequences were generated from both encysted and excysted D. macrocephalum , as well as from other diphyllidean and pseudophyllidean (outgroup) taxa for use in phylogenetic analyses. Maximum parsimony and Bayesian inference analyses both showed that the diphyllidean genus Echinobothrium is paraphyletic without inclusion of the only two other diphyllidean genera, Ditrachybothridium Rees, 1959 and Macrobothridium Khalil & Abdul-Salam, 1989. A list of published records of larval diphyllideans, their hosts and localities is included.

Animals↗
PubMed2003

Inference of viral evolutionary rates from molecular sequences.

The processes of mutation and nucleotide substitution contribute to the observed variability in virulence, transmission and persistence of viral pathogens. Since most viruses evolve many times faster than their human hosts, we are in the unusual position of being able to measure these processes directly by comparing viral genes that have been isolated and sequenced at different points in time. The analysis of such data requires the use of specific statistical methods that take into account the shared ancestry of the sequences and the randomness inherent in the process of nucleotide substitution. In this paper we describe the various statistical methods for estimating evolutionary rates, which can be classified into three general approaches: linear regression, maximum likelihood, and Bayesian inference. We discuss the advantages and shortcomings of each approach and illustrate their use through the analysis of two example viruses; human immunodeficiency virus type 1 and dengue virus serotype 4. Reliable estimates of viral substitution rates have many important applications in population genetics and phylogenetics, including dating evolutionary events and divergence times, estimating demographic parameters such as population size and generation time, and investigating the effect of natural selection on molecular evolution.

Base Sequence↗
PubMed1985

The problem of multiple inference in studies designed to generate hypotheses.

Epidemiologic research often involves the simultaneous assessment of associations between many risk factors and several disease outcomes. In such situations, often designed to generate hypotheses, multiple univariate hypothesis-testing is not an appropriate basis for inference. The number of true positive associations in a collection of many associations can be estimated by comparing the observed distribution of p values for the positive associations to a theoretical uniform distribution, or to the observed distribution of negative associations, or to an empiric randomization distribution. None of these approaches, however, will distinguish the true from the false positive associations. Various criteria for selecting a subset of associations to report are considered by the authors, including Bonferoni adjustment of p values, splitting the sample for searching and testing, Bayesian inference, and decision theory. The authors prefer an approach in which all associations in the data are reported, whether significant or not, followed by a ranking in order of priority for investigation using empirical Bayes techniques. Methods are illustrated by application to preliminary data from a study aimed at identifying hitherto unsuspected occupational carcinogens.

Bayes Theorem↗
PubMed1998

The 'Ideal Homunculus': decoding neural population signals.

Information processing in the nervous system involves the activity of large populations of neurons. It is possible, however, to interpret the activity of relatively small numbers of cells in terms of meaningful aspects of the environment. 'Bayesian inference' provides a systematic and effective method of combining information from multiple cells to accomplish this. It is not a model of a neural mechanism (neither are alternative methods, such as the population vector approach) but a tool for analysing neural signals. It does not require difficult assumptions about the nature of the dimensions underlying cell selectivity, about the distribution and tuning of cell responses or about the way in which information is transmitted and processed. It can be applied to any parameter of neural activity (for example, firing rate or temporal pattern). In this review, we demonstrate the power of Bayesian analysis using examples of visual responses of neurons in primary visual and temporal cortices. We show that interaction between correlation in mean responses to different stimuli (signal) and correlation in response variability within stimuli (noise) can lead to marked improvement of stimulus discrimination using population responses.

Animals↗
PubMed2006

Genetic relationships among Anisakis species (Nematoda: Anisakidae) inferred from mitochondrial cox2 sequences, and comparison with allozyme data.

The genetic relationships among 9 taxa of Anisakis Dujardin, 1845 (A. simplex (sensu stricto), A. pegreffii, A. simplex C., A. typica, A. ziphidarum, A. physeteris, A. brevispiculata, A. paggiae, and Anisakis sp.) were inferred from sequence analysis (629 bp) of the mitochondrial cox2 gene. Genetic divergence among the considered taxa, estimated by p-distance, ranged from p = 0.055, between sibling species of the A. simplex complex, to p = 0.12, between morphologically differentiated species, i.e., A. ziphidarum and A. typica. The highest level was detected when comparing A. physeteris, A. brevispiculata, and A. paggiae versus A. simplex complex (on average p = 0.13) or versus A. typica (on average p = 0.14). Sequence data from the newly identified Anisakis sp. poorly aligned with other Anisakis species but was most similar to A. ziphidarum (p = 0.08). Phylogenetic analyses based upon Parsimony and Bayesian Inference, as well as phenetic analysis based upon Neighbor-Joining p-distance values, generated similar tree topologies, each well supported at major nodes. All analyses delineated two main claides, the first encompassing A. physeteris, A. brevispiculata, and A. paggiae as a sister group to all the remaining species, and the second comprising the species of the A. simplex complex (A. simplex (s.s.), A. pegreffii and A. simplex C), A. typica, A. ziphidarum, and Anisakis sp. In general, mtDNA-based tree topologies showed high congruence with those generated from nuclear data sets (19 enzyme-loci) and with morphological data delineating adult and larval stages of the Anisakis spp.; however, precise positioning of A. typica and A. ziphidarum remain poorly resolved, though they consistently clustered in the same clade as Anisakis sp. and the A. simplex complex. Comparison of anisakid data with those currently available for their cetacean-definitive hosts suggests parallelism between host and parasite phylogenetic tree topologies.

Animals↗
PubMed2003

Phylogeny and classification of the Digenea (Platyhelminthes: Trematoda).

Complete small subunit ribosomal RNA gene (ssrDNA) and partial (D1-D3) large subunit ribosomal RNA gene (lsrDNA) sequences were used to estimate the phylogeny of the Digenea via maximum parsimony and Bayesian inference. Here we contribute 80 new ssrDNA and 124 new lsrDNA sequences. Fully complementary data sets of the two genes were assembled from newly generated and previously published sequences and comprised 163 digenean taxa representing 77 nominal families and seven aspidogastrean outgroup taxa representing three families. Analyses were conducted on the genes independently as well as combined and separate analyses including only the higher plagiorchiidan taxa were performed using a reduced-taxon alignment including additional characters that could not be otherwise unambiguously aligned. The combined data analyses yielded the most strongly supported results and differences between the two methods of analysis were primarily in their degree of resolution. The Bayesian analysis including all taxa and characters, and incorporating a model of nucleotide substitution (general-time-reversible with among-site rate heterogeneity), was considered the best estimate of the phylogeny and was used to evaluate their classification and evolution. In broad terms, the Digenea forms a dichotomy that is split between a lineage leading to the Brachylaimoidea, Diplostomoidea and Schistosomatoidea (collectively the Diplostomida nomen novum (nom. nov.)) and the remainder of the Digenea (the Plagiorchiida), in which the Bivesiculata nom. nov. and Transversotremata nom. nov. form the two most basal lineages, followed by the Hemiurata. The remainder of the Plagiorchiida forms a large number of independent lineages leading to the crown clade Xiphidiata nom. nov. that comprises the Allocreadioidea, Gorgoderoidea, Microphalloidea and Plagiorchioidea, which are united by the presence of a penetrating stylet in their cercariae. Although a majority of families and to a lesser degree, superfamilies are supported as currently defined, the traditional divisions of the Echinostomida, Plagiorchiida and Strigeida were found to comprise non-natural assemblages. Therefore, the membership of established higher taxa are emended, new taxa erected and a revised, phylogenetically based classification proposed and discussed in light of ontogeny, morphology and taxonomic history.

Animals↗
PubMed2003

Prevalence estimates for paratuberculosis adjusted for test variability using Bayesian analysis.

The ELISA tests that are available to detect an infection with Mycobacterium avium subsp. paratuberculosis (MAP) have a limited validity expressed as the sensitivity (Se) and specificity (Sp). In many studies, the Se and Sp of the tests are treated as constants and this will result in an underestimation of the variability of the true prevalence (TP). Bayesian inference provided a natural framework for using information on the test variability (i.e., the uncertainty) in the estimates of test Se and Sp when estimating the TP. Data from two prevalence studies for MAP using an ELISA in several regions in two locations were available for the analyses. In location 1, all cattle of at least 3 years of age were sampled in approximately 90 randomly sampled herds in each of the four regions of the country. In location 2, in 30 randomly sampled herds in each of three regions, approximately 30 randomly selected cows were sampled. Information about the unknown test Se and Sp and MAP prevalence was incorporated into a Bayesian model by joint prior probability distributions. Posterior estimates were obtained by combining the actual likelihood with the prior distributions using Bayes' formula. The corrected cow-level TP (proportion of infected cows in a herd) was low, 5.8 and 3.6% in locations 1 and 2, respectively. Certain regions within a location differed significantly in herd-level TP (proportion of infected herds). The herd-level TP was 54.3% in location 1 (95% credible interval (CI) 46.1, 63.3%) and 32.9% in location 2 (95% CI: 14.4, 73.3%). The variation in the herd-level TP estimate for location 2 was more than three times as large as the variation in location 1 mainly because of the relatively small number of investigated herds in location 2. In future prevalence studies for MAP, sample size calculations should be based on a very low cow-level prevalence. Approximately 50 and 90% of the herds in the current study had an estimated cow-level TP below 4 and 10%, respectively.

Animals↗