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PubMed1985

Extrapolation from large-scale radiation exposures: cancer.

Even though much is known about cancer risk associated with exposure to ionizing radiation, societal demands for detailed risk assessment go far beyond our ability to satisfy them according to customary standards of scientific accuracy. Society's requirement, however, is for the best information available, however good it may be, and not necessarily for the definitive solution to the problem posed. Bayesian methods may be useful for presenting incomplete and varied data and informed scientific opinion in a form suitable for use in societal decision making, while at the same time providing a disciplinary framework for incorporating opinion into scientific recommendations. Inferences about individual cases and their relationship to risk of radiation carcinogenesis provide an especially severe test of the completeness of our understanding of the relationship between exposure and risk. This is particularly true with respect to the distribution of excess risk over time following exposure. Recent work suggests that a standard model often used for projection of risk forward in time, the constant relative excess model, may give a surprisingly accurate picture of time to tumor for a number of cancer sites.

Breast Neoplasms↗
PubMed2005

A probabilistic approach to the joint evaluation of firearm evidence and gunshot residues.

The present paper addresses issues that affect both the separate as well as the joint evaluation of firearm evidence (i.e., marks) and gunshot residues (GSR). Mark evidence will be used as a basis to discriminate among barrels through which a bullet in question might have been shot whereas GSR will be used to draw inferences about the distance of firing. Particular attention is drawn to the coherent handling of uncertainties associated with the various parameters considered within each item of evidence. The proposed analysis relies on a probabilistic viewpoint that uses graphical models (i.e., Bayesian networks) as an aid to cope with the complexity induced by the number of variables considered. The paper discusses how an approach based on a probabilistic network environment can be used for the formal analysis and construction of arguments. Emphasis is made on the gain of insight into structural dependencies that may be uncovered when the evaluative process is extended beyond single items of scientific evidence.

Bayes Theorem↗
PubMed2003

Statistical inversion for medical x-ray tomography with few radiographs: II. Application to dental radiology.

Diagnostic and operational tasks in dental radiology often require three-dimensional information that is difficult or impossible to see in a projection image. A CT-scan provides the dentist with comprehensive three-dimensional data. However, often CT-scan is impractical and, instead, only a few projection radiographs with sparsely distributed projection directions are available. Statistical (Bayesian) inversion is well-suited approach for reconstruction from such incomplete data. In statistical inversion, a priori information is used to compensate for the incomplete information of the data. The inverse problem is recast in the form of statistical inference from the posterior probability distribution that is based on statistical models of the projection data and the a priori information of the tissue. In this paper, a statistical model for three-dimensional imaging of dentomaxillofacial structures is proposed. Optimization and MCMC algorithms are implemented for the computation of posterior statistics. Results are given with in vitro projection data that were taken with a commercial intraoral x-ray sensor. Examples include limited-angle tomography and full-angle tomography with sparse projection data. Reconstructions with traditional tomographic reconstruction methods are given as reference for the assessment of the estimates that are based on the statistical model.

Algorithms↗
PubMed2003

A software package for cDNA microarray data normalization and assessing confidence intervals.

DNA microarray data are affected by variations from a number of sources. Before these data can be used to infer biological information, the extent of these variations must be assessed. Here we describe an open source software package, lcDNA, that provides tools for filtering, normalizing, and assessing the statistical significance of cDNA microarray data. The program employs a hierarchical Bayesian model and Markov Chain Monte Carlo simulation to estimate gene-specific confidence intervals for each gene in a cDNA microarray data set. This program is designed to perform these primary analytical operations on data from two-channel spotted, or in situ synthesized, DNA microarrays.

Bayes Theorem↗
PubMed2004

Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes.

Many phylogenetic analyses that include numerous terminals but few genes show high resolution and branch support for relatively recently diverged clades, but lack of resolution and/or support for "basal" clades of the tree. The various benefits of increased taxon and character sampling have been widely discussed in the literature, albeit primarily based on simulations rather than empirical data. In this study, we used a well-sampled gene-tree analysis (based on 100 mitochondrial genomes of higher teleost fishes) to test empirically the efficiency of different methods of data sampling and phylogenetic inference to "correctly" resolve the basal clades of a tree (based on congruence with the reference tree constructed using all 100 taxa and 7990 characters). By itself, increased character sampling was an inefficient method by which to decrease the likelihood of "incorrect" resolution (i.e., incongruence with the reference tree) for parsimony analyses. Although increased taxon sampling was a powerful approach to alleviate "incorrect" resolution for parsimony analyses, it had the general effect of increasing the number of, and support for, "incorrectly" resolved clades in the Bayesian analyses. For both the parsimony and Bayesian analyses, increased taxon sampling, by itself, was insufficient to help resolve the basal clades, making this sampling strategy ineffective for that purpose. For this empirical study, the most efficient of the six approaches considered to resolve the basal clades when adding nucleotides to a dataset that consists of a single gene sampled for a small, but representative, number of taxa, is to increase character sampling and analyze the characters using the Bayesian method.

Animals↗
PubMed2003

Time flies, a new molecular time-scale for brachyceran fly evolution without a clock.

The insect order Diptera, the true flies, contains one of the four largest Mesozoic insect radiations within its suborder Brachycera. Estimates of phylogenetic relationships and divergence dates among the major brachyceran lineages have been problematic or vague because of a lack of consistent evidence and the rarity of well-preserved fossils. Here, we combine new evidence from nucleotide sequence data, morphological reinterpretations, and fossils to improve estimates of brachyceran evolutionary relationships and ages. The 28S ribosomal DNA (rDNA) gene was sequenced for a broad diversity of taxa, and the data were combined with recently published morphological scorings for a parsimony-based phylogenetic analysis. The phylogenetic topology inferred from the combined 28S rDNA and morphology data set supports brachyceran monophyly and the monophyly of the four major brachyceran infraorders and suggests relationships largely consistent with previous classifications. Weak support was found for a basal brachyceran clade comprising the infraorders Stratiomyomorpha (soldier flies and relatives), Xylophagomorpha (xylophagid flies), and Tabanomorpha (horse flies, snipe flies, and relatives). This topology and similar alternative arrangements were used to obtain Bayesian estimates of divergence times, both with and without the assumption of a constant evolutionary rate. The estimated times were relatively robust to the choice of prior distributions. Divergence times based on the 28S rDNA and several fossil constraints indicate that the Brachycera originated in the late Triassic or earliest Mesozoic and that all major lower brachyceran fly lineages had near contemporaneous origins in the mid-Jurassic prior to the origin of flowering plants (angiosperms). This study provides increased resolution of brachyceran phylogeny, and our revised estimates of fly ages should improve the temporal context of evolutionary inferences and genomic comparisons between fly model organisms.

Animals↗
PubMed2006

Bayesian theories of conditioning in a changing world.

The recent flowering of Bayesian approaches invites the re-examination of classic issues in behavior, even in areas as venerable as Pavlovian conditioning. A statistical account can offer a new, principled interpretation of behavior, and previous experiments and theories can inform many unexplored aspects of the Bayesian enterprise. Here we consider one such issue: the finding that surprising events provoke animals to learn faster. We suggest that, in a statistical account of conditioning, surprise signals change and therefore uncertainty and the need for new learning. We discuss inference in a world that changes and show how experimental results involving surprise can be interpreted from this perspective, and also how, thus understood, these phenomena help constrain statistical theories of animal and human learning.

Animals↗
PubMed2003

Phylogenetic relationships among calyptraeid gastropods and their implications for the biogeography of marine speciation.

Although calyptraeid gastropods are not well understood taxonomically, in part because their simple plastic shells are the primary taxonomic character, they provide an ideal system to examine questions about evolution in the marine environment. I conducted a phylogenetic analysis of calyptraeid gastropods using DNA sequence data from mitochondrial cytochrome oxidase I (COI) and 16S genes and the nuclear 28S gene. The resultant phylogeny was used to examine the biogeographic patterns of speciation in the Calyptraeidae. Parsimony and Bayesian analyses of the combined data sets for 94 calyptraeid operational taxonomic units and 24 outgroups produced well-resolved phylogenies. Both approaches resulted in identical sister-species relationships, and the few differences in deeper topology did not affect biogeographic inferences. The geographic distribution of the species included here demonstrate numerous dispersal events both between the Pacific and Atlantic oceans and across the equator. When parsimony is used to reconstruct the movement from the Pacific to the Atlantic oceans on the phylogeny, there are 12 transitions between oceans, primarily from the Pacific to the Atlantic. When the latitude is coded as north versus south of the equator, the most-parsimonious reconstruction gives the origin of calyptraeids in the north followed by 15 dispersal events to regions south of the equator and no returns to the north. Many clades of the most closely related species are either sympatric or occur along a single coastline. Closely related species can, however, occur in such divergent regions as Southern California and South Africa. There is little evidence for sister-species pairs or larger clades having been split by the Isthmus of Panama or the Benguela upwelling, but the East Pacific Barrier appears to separate the most basal taxa from the rest of the family.

Animals↗
PubMed2005

Extracting a maximum of useful information from statistical research data.

The practice of statistical inference in psychological research is critically reviewed. Particular emphasis is put on the fast pace of change from the sole reliance on null hypothesis significance testing (NHST) to the inclusion of effect size estimates, confidence intervals, and an interest in the Bayesian approach. We conclude that these developments are helpful for psychologists seeking to extract a maximum of useful information from statistical research data, and that seven decades of criticism against NHST is finally having an effect.

Bayes Theorem↗
PubMed2002

Deductive and inductive reasoning in obsessive-compulsive disorder.

OBJECTIVES: This study tested the hypothesis that people with obsessive-compulsive disorder (OCD) show an inductive reasoning style distinct from people with generalized anxiety disorder (GAD) and from participants in a non-anxious (NA) control group. DESIGN: The experimental procedure consisted of administering a range of six deductive and inductive tasks and a probabilistic task in order to compare reasoning processes between groups. METHODS: Recruitment was in the Montreal area within a French-speaking population. The participants were 12 people with OCD, 12 NA controls and 10 people with GAD. Participants completed a series of written and oral reasoning tasks including the Wason Selection Task, a Bayesian probability task and other inductive tasks, designed by the authors. RESULTS: There were no differences between groups in deductive reasoning. On an inductive "bridging task", the participants with OCD always took longer than the NA control and GAD groups to infer a link between two statements and to elaborate on this possible link. The OCD group alone showed a significant decrease in their degree of conviction about an arbitrary statement after inductively generating reasons to support this statement. Differences in probabilistic reasoning replicated those of previous authors. CONCLUSIONS: The results pinpoint the importance of examining inference processes in people with OCD in order to further refine the clinical applications of behavioural-cognitive therapy for this disorder.

Adult↗
PubMed1996

Decision-support systems in dentistry.

Decision-support systems hold a specialized body of knowledge in computerized form such that the non- specialist can obtain expert-level information. The goal of these systems in clinical sciences is usually to assist patient care by providing the clinician with improved diagnosis or treatment planning. Decision-support systems consist of three components: the user interface through which the clinician or patient enters signs or symptoms, the set of data describing clinical knowledge in the domain of the program, and an inference engine to manipulate the data set in light of a patient's specific signs or symptoms to arrive at a diagnosis or treatment plan. Such systems usually use one of three mechanisms of analysis alone or in combination: classification trees, Bayesian conditional probabilities, or rule-based (heuristic) systems. Numerous problems must be solved before decision-support systems will become commonplace in clinical practice. Data entry of patients' signs and symptoms is often tedious. The quality of the clinician's initial observations is of great importance in determining the quality of the output. It is also often difficult to convey to a program the subtlety of clinical information observed. Knowledge required in clinical data bases is often unavailable or imprecise. As these and other challenges are addressed we can anticipate increased utility of decision support programs in the future.

Algorithms↗
PubMed2004

Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes.

The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological homoplasy. Analysis of the mechanisms generating such homoplasy requires an independent molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, and performed partitioned and unpartitioned Bayesian, maximum likelihood, and maximum parsimony phylogenetic analyses. We explored four dataset partitioning strategies to account for evolutionary process heterogeneity among genes and codon positions, all of which yielded increased model likelihoods and decreased numbers of supported nodes in the topologies (Bayesian posterior probability >0.95) relative to the unpartitioned analysis. Our phylogenetic analyses yielded congruent trees that contrast with the traditional morphology-based taxonomy; the monophyly of three of four major groups is rejected. Reanalysis of current hypotheses in light of these evolutionary relationships suggests that (i) a larval life history stage reevolved from a direct-developing ancestor multiple times; (ii) there is no phylogenetic support for the "Out of Appalachia" hypothesis of plethodontid origins; and (iii) novel scenarios must be reconstructed for the convergent evolution of projectile tongues, reduction in toe number, and specialization for defensive tail loss. Some of these scenarios imply morphological transformation series that proceed in the opposite direction than was previously thought. In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative.

Animals↗
PubMed2025

Parallel algorithms for phylogenetic inference under a structured coalescent approximation.

While advances in molecular epidemiology and computational modeling have enhanced our capacity to track pathogen evolution, the accurate reconstruction of spatiotemporal transmission dynamics remains essential for developing epidemic preparedness frameworks and implementing outbreak response measures. Structured coalescent models offer a phylogeographic framework by restricting lineage coalescence events to geographically proximate host populations. Although the Bayesian structured coalescent approximation (BASTA) provides a tractable approach, contemporary phylogeographic analyses involving dozens of geographic localities and hundreds to thousands of viral genomes substantially exceed the computational capacity of existing implementations. The BASTA likelihood scales cubically with deme count and quadratically with sequence count due to matrix exponentiation and pairwise coalescent probability calculations. Here, we introduce a comprehensive algorithmic restructuring of the structured coalescent likelihood that eliminates redundancies, optimizes memory access, and exposes parallelization opportunities. Our approach reorganizes computations along three dimensions: (i) independent calculation of deme-transition probability matrices across time intervals; (ii) simultaneous evaluation of partial likelihood vectors within temporal slices; and (iii) concurrent aggregation of coalescent probabilities. Algorithmic restructuring cuts average coalescent likelihood computation by 7-8 fold, and parallelization further boosts performance to 10-26 fold, enabling joint phylogeographic analyses of dengue virus across 10 South American countries and H5N1 avian influenza across 20 Eurasian regions to finish in a fraction of prior time. This computational efficiency also enables comparison between backward-in-time structured coalescent approximations and forward-in-time phylogeographic methods, revealing that the former provides appropriately conservative posterior estimates, particularly at intermediate phylogenetic depths. We integrate our implementation into the popular BEAST X and BEAGLE software packages, with an accompanying interface in BEAUti X to easily set up the analyses, providing researchers with an accessible and scalable tool for real-time phylogeographic surveillance of rapidly evolving pathogens.

Journal Article↗
PubMed2004

Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences.

To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.

Animals↗
PubMed2005

Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Hypermastigea.

Small subunit rRNA gene sequences were identified without cultivation from parabasalid symbionts of termites belonging to the hypermastigid orders Trichonymphida (the genera Hoplonympha, Staurojoenina, Teranympha, and Eucomonympha) and Spirotrichonymphida (Spirotrichonymphella), and from four yet-unidentified parabasalid symbionts of the termite Incisitermes minor. All these new sequences were analyzed by Bayesian, likelihood, and parsimony methods in a broad phylogeny including all identified parabasalid sequences available in databases and some as yet unidentified sequences probably derived from hypermastigids. A salient point of our study focused on hypermastigids was the polyphyly of this class. We also noted a clear dichotomy between Trichonymphida and the other parabasalid taxa. However, this hypermastigid order was apparently polyphyletic, probably reflecting its morphological diversity. Among Trichonymphida, Teranympha (Teranymphidae) grouped together with the members of the family Eucomonymphidae, suggesting that its family status is ambiguous. The monophyletic lineage composed by Spirotrichonymphida exhibited a narrower branching pattern than Trichonymphida. The root of parabasalids was examined but could not be discerned accurately.

Animals↗
PubMed1995

Assessing probability of paternity and the product rule in DNA systems.

The genetic resolution of paternity disputes begins with an intricate detection of inherited traits and finishes with a statistical inference (the probability of paternity, W). Notwithstanding some initial fanfare, statistical inference is a necessary component of DNA-based paternity tests because band patterns may be rare but not yet unique, and even rare events in a vacuum are meaningless. The genetic match must be combined with other evidence for relevancy, thus a Bayesian approach is preferred when computing W. This paper reviews the standard model used to compute W and discusses the model's various properties and assumptions. The standard model is extended to include DNA systems in which alleles are operationally continuous due to measurement error. This extension avoids problems associated with 'matched/non-matched' binned decisions. After outlining the model assumptions for a single DNA system, particular attention is given to the product rule-the procedure of multiplying intermediate probabilities across genetic loci to form a combined W. An empirical alternative to the product rule is also assessed and correlated with standard procedures.

Alleles↗
PubMed2006

Enabling a powerful marine and offshore decision-support solution through Bayesian network technique.

A powerful practical solution is by far the most desired output when making decisions under the realm of uncertainty on any safety-critical marine or offshore units and their systems. With data and information typically being obtained incrementally, adopting Bayesian network (BN) is shown to realistically deal with the random uncertainties while at the same time making risk assessments easier to build and to check. A well-matched methodology is proposed to formalize the reasoning in which the focal mechanism of inference processing relies on the sound Bayes's rule/theorem that permits the logic. Expanding one or more influencing nodal parameters with decision and utility node(s) also yields an influence diagram (ID). BN and ID feasibility is shown in a marine evacuation scenario and that of authorized vessels to floating, production, storage, and offloading collision, developed via a commercial computer tool. Sensitivity analysis and validation of the produced results are also presented.

Accidents, Occupational↗
PubMed2006

Bootstrap model averaging in time series studies of particulate matter air pollution and mortality.

The consensus from time series studies that have investigated the mortality effects of particulate matter air pollution (PM) is that increases in PM are associated with increases in daily mortality. However, recently concerns have been raised that the observed positive association between PM and mortality may be an artefact of model selection due to multiple hypothesis testing. This problem arises when a number of models are investigated, but only the "best" model is reported and all subsequent inference is based on this model, ignoring the model selection process. In this paper, we introduce the use of the bootstrap as a means of addressing the problems of model selection in PM mortality time series studies. Using the bootstrap to perform inference about the effect of PM on mortality is a process based on a set of models rather than on a single model. It is shown that using the bootstrap to overcome the problems of model selection is competitive with the existing methodology of Bayesian model averaging.

Air Pollutants↗