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Bayesian modeling

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https://www.readbyqxmd.com/read/29244824/a-backwards-glance-at-words-using-reversed-interior-masked-primes-to-test-models-of-visual-word-identification
#1
Colin J Davis, Stephen J Lupker
The experiments reported here used "Reversed-Interior" (RI) primes (e.g., cetupmor-COMPUTER) in three different masked priming paradigms in order to test between different models of orthographic coding/visual word recognition. The results of Experiment 1, using a standard masked priming methodology, showed no evidence of priming from RI primes, in contrast to the predictions of the Bayesian Reader and LTRS models. By contrast, Experiment 2, using a sandwich priming methodology, showed significant priming from RI primes, in contrast to the predictions of open bigram models, which predict that there should be no orthographic similarity between these primes and their targets...
2017: PloS One
https://www.readbyqxmd.com/read/29244811/impact-of-increased-influenza-vaccination-in-2-3-year-old-children-on-disease-burden-within-the-general-population-a-bayesian-model-based-approach
#2
Sankarasubramanian Rajaram, Witold Wiecek, Richard Lawson, Betina T Blak, Yanli Zhao, Judith Hackett, Robert Brody, Vishal Patel, Billy Amzal
INTRODUCTION: During the 2013-2014 influenza season, Public Health England extended routine influenza vaccination to all 2- and 3-year-old children in England. To estimate the impact of this change in policy on influenza-related morbidity and mortality, we developed a disease transmission and surveillance model informed by real-world data. METHODS: We combined real-world and literature data sources to construct a model of influenza transmission and surveillance in England...
2017: PloS One
https://www.readbyqxmd.com/read/29244177/online-bayesian-phylogenetic-inference-theoretical-foundations-via-sequential-monte-carlo
#3
Vu Dinh, Aaron E Darling, Frederick A Matsen Iv
Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a posterior distribution on trees, have become a popular if computationally expensive means of doing phylogenetics. Modern data collection technologies are quickly adding new sequences to already substantial databases. With all current techniques for Bayesian phylogenetics, computation must start anew each time a sequence becomes available, making it costly to maintain an up-to-date estimate of a phylogenetic posterior...
December 13, 2017: Systematic Biology
https://www.readbyqxmd.com/read/29244162/efficacy-and-safety-of-biologics-targeting-interleukin-6-12-23-and-17-pathways-for-peripheral-psoriatic-arthritis-a-network-meta-analysis
#4
Dongze Wu, Jiang Yue, Lai-Shan Tam
Objective: To investigate the comparative efficacy, safety and tolerability of IL-6, IL-12/23 and IL-17 inhibitors for patients with active PsA. Methods: Randomized controlled trials evaluating the efficacy, safety and tolerability of IL-6, IL-12/23 and IL-17 inhibitors were identified by a comprehensive systematic literature review. Pairwise meta-analyses and Bayesian network meta-analyses using the random effects model were performed to estimate pooled odds ratios (ORs) and 95% credible intervals of attaining a 20% or 50% improvement in ACR criteria (ACR20 and ACR50, respectively) across trials...
December 13, 2017: Rheumatology
https://www.readbyqxmd.com/read/29243391/bayesian-molecular-dating-opening-up-the-black-box
#5
Lindell Bromham, Sebastián Duchêne, Xia Hua, Andrew M Ritchie, David A Duchêne, Simon Y W Ho
Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a 'molecular clock'. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account...
December 15, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29243250/a-camera-based-method-for-estimating-absolute-density-in-animals-displaying-home-range-behaviour
#6
Andrea Campos-Candela, Miquel Palmer, Salvador Balle, Josep Alós
1.The measurement of animal density may take advantage of recent technological achievements in wildlife video recording. Fostering the theoretical links between the patterns depicted by cameras and absolute density is required to exploit this potential. 2.We explore the applicability of the Hutchinson-Waser's postulate (i.e., when animal density is stationary at a given temporal and spatial scale, the absolute density is given by the average number of animals counted per frame), which is a counter-intuitive statement for most ecologists and managers who are concerned with counting the same individual more than once...
December 15, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/29242838/a-dirichlet-multinomial-bayes-classifier-for-disease-diagnosis-with-microbial-compositions
#7
Xiang Gao, Huaiying Lin, Qunfeng Dong
Dysbiosis of microbial communities is associated with various human diseases, raising the possibility of using microbial compositions as biomarkers for disease diagnosis. We have developed a Bayes classifier by modeling microbial compositions with Dirichlet-multinomial distributions, which are widely used to model multicategorical count data with extra variation. The parameters of the Dirichlet-multinomial distributions are estimated from training microbiome data sets based on maximum likelihood. The posterior probability of a microbiome sample belonging to a disease or healthy category is calculated based on Bayes' theorem, using the likelihood values computed from the estimated Dirichlet-multinomial distribution, as well as a prior probability estimated from the training microbiome data set or previously published information on disease prevalence...
November 2017: MSphere
https://www.readbyqxmd.com/read/29242828/machine-learning-unifies-the-modeling-of-materials-and-molecules
#8
Albert P Bartók, Sandip De, Carl Poelking, Noam Bernstein, James R Kermode, Gábor Csányi, Michele Ceriotti
Determining the stability of molecules and condensed phases is the cornerstone of atomistic modeling, underpinning our understanding of chemical and materials properties and transformations. We show that a machine-learning model, based on a local description of chemical environments and Bayesian statistical learning, provides a unified framework to predict atomic-scale properties. It captures the quantum mechanical effects governing the complex surface reconstructions of silicon, predicts the stability of different classes of molecules with chemical accuracy, and distinguishes active and inactive protein ligands with more than 99% reliability...
December 2017: Science Advances
https://www.readbyqxmd.com/read/29242741/bayesian-joint-models-with-inla-exploring-marine-mobile-predator-prey-and-competitor-species-habitat-overlap
#9
Dinara Sadykova, Beth E Scott, Michela De Dominicis, Sarah L Wakelin, Alexander Sadykov, Judith Wolf
Understanding spatial physical habitat selection driven by competition and/or predator-prey interactions of mobile marine species is a fundamental goal of spatial ecology. However, spatial counts or density data for highly mobile animals often (1) include excess zeros, (2) have spatial correlation, and (3) have highly nonlinear relationships with physical habitat variables, which results in the need for complex joint spatial models. In this paper, we test the use of Bayesian hierarchical hurdle and zero-inflated joint models with integrated nested Laplace approximation (INLA), to fit complex joint models to spatial patterns of eight mobile marine species (grey seal, harbor seal, harbor porpoise, common guillemot, black-legged kittiwake, northern gannet, herring, and sandeels)...
July 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29242718/a-bayesian-assessment-of-real-world-behavior-during-multitasking
#10
Jeroen H M Bergmann, Joan Fei, David A Green, Amir Hussain, Newton Howard
Multitasking is common in everyday life, but its effect on activities of daily living is not well understood. Critical appraisal of performance for both healthy individuals and patients is required. Motor activities during meal preparation were monitored in healthy individuals with a wearable sensor network during single and multitask conditions. Motor performance was quantified by the median frequencies (fm) of hand trajectories and wrist accelerations. The probability that multitasking occurred based on the obtained motor information was estimated using a Naïve Bayes Model, with a specific focus on the single and triple loading conditions...
2017: Cognitive Computation
https://www.readbyqxmd.com/read/29241887/basal-insulin-regimens-for-adults-with-type-1-diabetes-mellitus-a-cost-utility-analysis
#11
Dalia Dawoud, Elisabetta Fenu, Bernard Higgins, David Wonderling, Stephanie A Amiel
OBJECTIVES: To assess the cost-effectiveness of basal insulin regimens for adults with type 1 diabetes mellitus in England. METHODS: A cost-utility analysis was conducted in accordance with the National Institute for Health and Care Excellence reference case. The UK National Health Service and personal and social services perspective was used and a 3.5% discount rate was applied for both costs and outcomes. Relative effectiveness estimates were based on a systematic review of published trials and a Bayesian network meta-analysis...
December 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/29241659/a-novel-method-for-predicting-kidney-stone-type-using-ensemble-learning
#12
Yassaman Kazemi, Seyed Abolghasem Mirroshandel
The high morbidity rate associated with kidney stone disease, which is a silent killer, is one of the main concerns in healthcare systems all over the world. Advanced data mining techniques such as classification can help in the early prediction of this disease and reduce its incidence and associated costs. The objective of the present study is to derive a model for the early detection of the type of kidney stone and the most influential parameters with the aim of providing a decision-support system. Information was collected from 936 patients with nephrolithiasis at the kidney center of the Razi Hospital in Rasht from 2012 through 2016...
December 11, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/29241658/spatiotemporal-bayesian-networks-for-malaria-prediction
#13
Peter Haddawy, A H M Imrul Hasan, Rangwan Kasantikul, Saranath Lawpoolsri, Patiwat Sa-Angchai, Jaranit Kaewkungwal, Pratap Singhasivanon
Targeted intervention and resource allocation are essential for effective malaria control, particularly in remote areas, with predictive models providing important information for decision making. While a diversity of modeling technique have been used to create predictive models of malaria, no work has made use of Bayesian networks. Bayes nets are attractive due to their ability to represent uncertainty, model time lagged and nonlinear relations, and provide explanations. This paper explores the use of Bayesian networks to model malaria, demonstrating the approach by creating village level models with weekly temporal resolution for Tha Song Yang district in northern Thailand...
December 11, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/29241620/trends-in-and-projections-of-indicators-of-universal-health-coverage-in-bangladesh-1995-2030-a-bayesian-analysis-of-population-based-household-data
#14
Md Shafiur Rahman, Md Mizanur Rahman, Stuart Gilmour, Khin Thet Swe, Sarah Krull Abe, Kenji Shibuya
BACKGROUND: Many countries are implementing health system reforms to achieve universal health coverage (UHC) by 2030. To understand the progress towards UHC in Bangladesh, we estimated trends in indicators of the health service and of financial risk protection. We also estimated the probability of Bangladesh's achieving of UHC targets of 80% essential health-service coverage and 100% financial risk protection by 2030. METHODS: We estimated the coverage of UHC indicators-13 prevention indicators and four treatment indicators-from 19 nationally representative population-based household surveys done in Bangladesh from Jan 1, 1991, to Dec 31, 2014...
January 2018: Lancet Global Health
https://www.readbyqxmd.com/read/29241588/reanalyzing-neurocognitive-data-on-the-role-of-the-motor-system-in-speech-perception-within-cosmo-a-bayesian-perceptuo-motor-model-of-speech-communication
#15
Marie-Lou Barnaud, Pierre Bessière, Julien Diard, Jean-Luc Schwartz
While neurocognitive data provide clear evidence for the involvement of the motor system in speech perception, its precise role and the way motor information is involved in perceptual decision remain unclear. In this paper, we discuss some recent experimental results in light of COSMO, a Bayesian perceptuo-motor model of speech communication. COSMO enables us to model both speech perception and speech production with probability distributions relating phonological units with sensory and motor variables. Speech perception is conceived as a sensory-motor architecture combining an auditory and a motor decoder thanks to a Bayesian fusion process...
December 11, 2017: Brain and Language
https://www.readbyqxmd.com/read/29241400/bayesian-nonparametric-inference-for-the-three-class-youden-index-and-its-associated-optimal-cutoff-points
#16
Vanda Inácio de Carvalho, Adam J Branscum
The three-class Youden index serves both as a measure of medical test accuracy and a criterion to choose the optimal pair of cutoff values for classifying subjects into three ordinal disease categories (e.g. no disease, mild disease, advanced disease). We present a Bayesian nonparametric approach for estimating the three-class Youden index and its corresponding optimal cutoff values based on Dirichlet process mixtures, which are robust models that can handle intricate features of distributions for complex data...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/29239808/drug-class-renal-elimination-and-outcomes-of-direct-oral-anticoagulants-in-asian-patients-a-meta-analysis
#17
Kang-Ling Wang, Chun-Chih Chiu, Robert P Giugliano, Doreen Su-Yin Tan, Chun-Yi Lin, En-Yu Lai, Shinya Goto, Chern-En Chiang
BACKGROUND: Direct oral anticoagulants (DOACs) have a better risk benefit profile in Asian patients with atrial fibrillation (AF). Whether treatment effects could be modified by drug class and dependency on renal elimination of studied agents has not yet been explored. METHODS: We searched PubMed, CENTRAL, and CINAHL databases through November 2016 for phase III randomized controlled trials comparing DOACs with warfarin in patients with AF. Efficacy and safety outcomes were pooled according to drug class and dependency on renal elimination of DOACs and were compared with the Mantel-Haenszel fixed-effects model...
November 24, 2017: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
https://www.readbyqxmd.com/read/29239658/working-memory-training-in-older-adults-bayesian-evidence-supporting-the-absence-of-transfer
#18
Sabrina Guye, Claudia C von Bastian
The question of whether working memory training leads to generalized improvements in untrained cognitive abilities is a longstanding and heatedly debated one. Previous research provides mostly ambiguous evidence regarding the presence or absence of transfer effects in older adults. Thus, to draw decisive conclusions regarding the effectiveness of working memory training interventions, methodologically sound studies with larger sample sizes are needed. In this study, we investigated whether or not a computer-based working memory training intervention induced near and far transfer in a large sample of 142 healthy older adults (65 to 80 years)...
December 2017: Psychology and Aging
https://www.readbyqxmd.com/read/29239571/spatial-temporal-analysis-of-prostate-cancer-incidence-from-the-pennsylvania-cancer-registry-2000-2011
#19
Ming Wang, Stephen A Matthews, Khaled Iskandarani, Yimei Li, Zheng Li, Vernon M Chinchilli, Lijun Zhang
Prostate cancer is the most common cancer diagnosed among males, and the incidence in Pennsylvania, USA is considerably higher than nationally. Knowledge of regional differences and time trends in prostate cancer incidence may contribute to a better understanding of aetiologic factors and racial disparities in outcomes, and to improvements in preventive intervention and screening efforts. We used Pennsylvania Cancer Registry data on reported prostate cancer diagnoses between 2000 and 2011 to study the regional distribution and temporal trends of prostate cancer incidence in both Pennsylvania White males and Philadelphia metropolitan area Black males...
November 28, 2017: Geospatial Health
https://www.readbyqxmd.com/read/29239568/spatiotemporal-transmission-and-socio-climatic-factors-related-to-paediatric-tuberculosis-in-north-western-ethiopia
#20
Kefyalew Addis Alene, Kerri Viney, Emma S McBryde, Archie C A Clements
The burden of tuberculosis (TB) in children reflects continuing and recent transmission within a population. This study aimed to identify spatiotemporal and socio-climatic factors associated with paediatric TB in north-western Ethiopia. Multivariate Poisson regression models were computed using a Bayesian framework. Estimates of parameters were generated using Markov chain Monte Carlo simulation. A total of 2,240 children aged under 15 years diagnosed with TB during the years 2013- 2016 were included in the analysis...
November 27, 2017: Geospatial Health
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