J Integr Bioinform - Analyzing phylogenetic trees with timed and probabilistic model checking: the lactose persistence case study.

Tópicos

{ model(3404) distribut(989) bayesian(671) }
{ concept(1167) ontolog(924) domain(897) }
{ algorithm(1844) comput(1787) effici(935) }
{ control(1307) perform(991) simul(935) }
{ medic(1828) order(1363) alert(1069) }
{ analysi(2126) use(1163) compon(1037) }
{ can(774) often(719) complex(702) }
{ network(2748) neural(1063) input(814) }
{ motion(1329) object(1292) video(1091) }
{ framework(1458) process(801) describ(734) }
{ method(1557) propos(1049) approach(1037) }
{ research(1085) discuss(1038) issu(1018) }
{ ehr(2073) health(1662) electron(1139) }
{ survey(1388) particip(1329) question(1065) }
{ detect(2391) sensit(1101) algorithm(908) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ error(1145) method(1030) estim(1020) }
{ design(1359) user(1324) use(1319) }
{ care(1570) inform(1187) nurs(1089) }
{ search(2224) databas(1162) retriev(909) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ state(1844) use(1261) util(961) }
{ age(1611) year(1155) adult(843) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ activ(1452) weight(1219) physic(1104) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ take(945) account(800) differ(722) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ learn(2355) train(1041) set(1003) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ data(1714) softwar(1251) tool(1186) }
{ model(2220) cell(1177) simul(1124) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

Model checking is a generic verification technique that allows the phylogeneticist to focus on models and specifications instead of on implementation issues. Phylogenetic trees are considered as transition systems over which we interrogate phylogenetic questions written as formulas of temporal logic. Nonetheless, standard logics become insufficient for certain practices of phylogenetic analysis since they do not allow the inclusion of explicit time and probabilities. The aim of this paper is to extend the application of model checking techniques beyond qualitative phylogenetic properties and adapt the existing logical extensions and tools to the field of phylogeny. The introduction of time and probabilities in phylogenetic specifications is motivated by the study of a real example: the analysis of the ratio of lactose intolerance in some populations and the date of appearance of this phenotype.

Resumo Limpo

model check generic verif techniqu allow phylogeneticist focus model specif instead implement issu phylogenet tree consid transit system interrog phylogenet question written formula tempor logic nonetheless standard logic becom insuffici certain practic phylogenet analysi sinc allow inclus explicit time probabl aim paper extend applic model check techniqu beyond qualit phylogenet properti adapt exist logic extens tool field phylogeni introduct time probabl phylogenet specif motiv studi real exampl analysi ratio lactos intoler popul date appear phenotyp

Resumos Similares

J. Comput. Biol. - Computational methods for a class of network models. ( 0,716608498687955 )
Neural Comput - A semiparametric Bayesian model for detecting synchrony among multiple neurons. ( 0,708618616848159 )
Neural Comput - Efficient Markov chain Monte Carlo methods for decoding neural spike trains. ( 0,703244081955881 )
Spat Spatiotemporal Epidemiol - Goodness-of-fit measures for individual-level models of infectious disease in a Bayesian framework. ( 0,689486001672302 )
Comput. Biol. Med. - Formal specification and analysis of intelligent agents for model-based medicine usage management. ( 0,683393756941799 )
Lifetime Data Anal - Bayesian nonparametric models for ranked set sampling. ( 0,671494931245753 )
Med Decis Making - Calibration of complex models through Bayesian evidence synthesis: a demonstration and tutorial. ( 0,671388550425119 )
IEEE Trans Neural Netw Learn Syst - Variational Bayesian Inference Algorithms for Infinite Relational Model of Network Data. ( 0,666743981771077 )
Comput Math Methods Med - Inference for ecological dynamical systems: a case study of two endemic diseases. ( 0,666540205778827 )
Med Decis Making - Bayesian calibration of a natural history model with application to a population model for colorectal cancer. ( 0,664218806958009 )
Brief. Bioinformatics - CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. ( 0,660319032256755 )
Res Synth Methods - A Bayesian nonparametric meta-analysis model. ( 0,656549076111149 )
Spat Spatiotemporal Epidemiol - Bayesian hierarchical modeling of the dynamics of spatio-temporal influenza season outbreaks. ( 0,655555555555556 )
IEEE Trans Image Process - Bayesian robust principal component analysis. ( 0,654645556694145 )
IEEE Trans Pattern Anal Mach Intell - Are Gibbs-Type Priors the Most Natural Generalization of the Dirichlet Process? ( 0,651738185488437 )
Med Decis Making - Linear regression metamodeling as a tool to summarize and present simulation model results. ( 0,650832457473146 )
J. Comput. Biol. - A spatial haplotype copying model with applications to genotype imputation. ( 0,645594650558838 )
Comput. Biol. Med. - Expectation-maximization technique for fibro-glandular discs detection in mammography images. ( 0,64071086373529 )
Comput Math Methods Med - Bayesian inference of the Weibull model based on interval-censored survival data. ( 0,640303173868259 )
J. Comput. Biol. - On the inference of dirichlet mixture priors for protein sequence comparison. ( 0,639820642036048 )
Res Synth Methods - Bayesian model selection for meta-analysis of diagnostic test accuracy data: Application to Ddimer for deep vein thrombosis. ( 0,63867714592901 )
IEEE Trans Image Process - Studentized dynamical system for robust object tracking. ( 0,633373091540696 )
IEEE Trans Image Process - Probabilistic image modeling with an extended chain graph for human activity recognition and image segmentation. ( 0,625402126274665 )
Med Decis Making - Not simply more of the same: distinguishing between patient heterogeneity and parameter uncertainty. ( 0,622954962834349 )
IEEE Trans Image Process - Variational Bayesian method for Retinex. ( 0,618172326462547 )
IEEE Trans Neural Netw Learn Syst - Incorporating Wind Power Forecast Uncertainties Into Stochastic Unit Commitment Using Neural Network-Based Prediction Intervals. ( 0,61690852781206 )
Lifetime Data Anal - Bayesian semiparametric modeling for stochastic precedence, with applications in epidemiology and survival analysis. ( 0,614187993008902 )
AMIA Annu Symp Proc - Learning to predict post-hospitalization VTE risk from EHR data. ( 0,613321502399942 )
Comput Methods Programs Biomed - Identification of an integrated mathematical model of standard oral glucose tolerance test for characterization of insulin potentiation in health. ( 0,612241267603301 )
IEEE Trans Pattern Anal Mach Intell - Causal Inference on Discrete Data using Additive Noise Models. ( 0,611155787022749 )
IEEE Trans Image Process - A Bayesian framework for image segmentation with spatially varying mixtures. ( 0,610181455528153 )
Lifetime Data Anal - Bayesian local influence for survival models. ( 0,609998618060858 )
Spat Spatiotemporal Epidemiol - Inference from ecological models: estimating the relative risk of stroke from air pollution exposure using small area data. ( 0,609576644033196 )
Artif Intell Med - Impact of precision of Bayesian network parameters on accuracy of medical diagnostic systems. ( 0,609426752106908 )
Spat Spatiotemporal Epidemiol - Mapping gender variation in the spatial pattern of alcohol-related mortality: a Bayesian analysis using data from South Yorkshire, United Kingdom. ( 0,60712731267189 )
J. Comput. Biol. - Characterizing the empirical distribution of prokaryotic genome n-mers in the presence of nullomers. ( 0,607007849167938 )
Comput Math Methods Med - Bayesian hierarchical modeling for categorical longitudinal data from sedation measurements. ( 0,606788036412138 )
Neural Comput - The neural representation of time: an information-theoretic perspective. ( 0,60499014198202 )
IEEE Trans Pattern Anal Mach Intell - Modeling Natural Images Using Gated MRFs. ( 0,604152298679729 )
Neural Comput - Attention as reward-driven optimization of sensory processing. ( 0,602580577789633 )
Res Synth Methods - Critical interpretation of Cochran's Q test depends on power and prior assumptions about heterogeneity. ( 0,601798453895099 )
AMIA Annu Symp Proc - Testing the calibration of classification models from first principles. ( 0,60037727299719 )
IEEE Trans Neural Netw Learn Syst - Context Dependent Encoding Using Convolutional Dynamic Networks. ( 0,599376623208311 )
J. Comput. Biol. - Expectation-maximization algorithm for determining natural selection of Y-linked genes through two-sex branching processes. ( 0,599320882634663 )
Comput Math Methods Med - An empirical Bayes optimal discovery procedure based on semiparametric hierarchical mixture models. ( 0,599265881661799 )
Neural Comput - Approximate, computationally efficient online learning in Bayesian spiking neurons. ( 0,599176957851287 )
Comput Methods Programs Biomed - A Bayesian multilevel model for fMRI data analysis. ( 0,5931195913753 )
Spat Spatiotemporal Epidemiol - A Bayesian space-time model for discrete spread processes on a lattice. ( 0,592348877759092 )
IEEE J Biomed Health Inform - Sparsity-inspired nonparametric probability characterization for radio propagation in body area networks. ( 0,592025616899944 )
Neural Comput - Formal modeling of robot behavior with learning. ( 0,59186837283824 )
IEEE Trans Image Process - Computationally tractable stochastic image modeling based on symmetric Markov mesh random fields. ( 0,58965076298104 )
Med Decis Making - A framework for addressing structural uncertainty in decision models. ( 0,583524603929549 )
IEEE Trans Image Process - Generative Bayesian image super resolution with natural image prior. ( 0,582589855465614 )
Neural Comput - Learning coefficient of generalization error in Bayesian estimation and vandermonde matrix-type singularity. ( 0,582511756492928 )
IEEE Trans Pattern Anal Mach Intell - Negative Binomial Process Count and Mixture Modeling. ( 0,580180595857466 )
Res Synth Methods - Random-effects meta-analysis of time-to-event data using the expectation-maximisation algorithm and shrinkage estimators. ( 0,579864599078293 )
IEEE Trans Pattern Anal Mach Intell - Articulated Human Detection with Flexible Mixtures-of-Parts. ( 0,577519478970844 )
Comput Methods Programs Biomed - The exponentiated exponential mixture and non-mixture cure rate model in the presence of covariates. ( 0,577363272427636 )
IEEE Trans Vis Comput Graph - The Perception of Visual Uncertainty Representation by Non-Experts. ( 0,576410916470701 )
IEEE Trans Pattern Anal Mach Intell - Temporal Analysis of Motif Mixtures using Dirichlet Processes. ( 0,57527399640534 )
Neural Comput - Universal approximation depth and errors of narrow belief networks with discrete units. ( 0,575113515365059 )
Med Decis Making - Assessing uncertainties surrounding combined endpoints for use in economic models. ( 0,574552705693956 )
Int J Neural Syst - Closed-loop control of the thalamocortical relay neuron's Parkinsonian state based on slow variable. ( 0,574411281586144 )
IEEE Trans Image Process - Posterior-mean super-resolution with a causal Gaussian Markov random field prior. ( 0,573611279059854 )
IEEE Trans Image Process - Blind separation of time/position varying mixtures. ( 0,57320860290535 )
J Biomed Inform - Link-topic model for biomedical abbreviation disambiguation. ( 0,572360032801709 )
IEEE Trans Image Process - A Bayesian hierarchical factorization model for vector fields. ( 0,572009896450601 )
Comput Biol Chem - Abstract Next Subvolume Method: a logical process-based approach for spatial stochastic simulation of chemical reactions. ( 0,570905070275201 )
Med Decis Making - Comparing Bayesian and frequentist approaches for multiple outcome mixed treatment comparisons. ( 0,570559373330339 )
J Biomed Inform - Semantic concept-enriched dependence model for medical information retrieval. ( 0,570352084108539 )
IEEE Trans Image Process - Bayesian estimation of linear mixtures using the normal compositional model. Application to hyperspectral imagery. ( 0,56916659888292 )
Neural Comput - Learning quadratic receptive fields from neural responses to natural stimuli. ( 0,567776222133428 )
Neural Comput - A finite-sample, distribution-free, probabilistic lower bound on mutual information. ( 0,567026867252456 )
Neural Comput - Efficient sensory encoding and Bayesian inference with heterogeneous neural populations. ( 0,566696255194692 )
Comput Math Methods Med - Immune response to a variable pathogen: a stochastic model with two interlocked Darwinian entities. ( 0,566294243466099 )
Neural Comput - Determination and the no-free-lunch paradox. ( 0,565045146956902 )
IEEE Trans Image Process - A study of multiplicative watermark detection in the contourlet domain using alpha-stable distributions. ( 0,56182553725195 )
Med Decis Making - Accounting for methodological, structural, and parameter uncertainty in decision-analytic models: a practical guide. ( 0,561632096068437 )
Res Synth Methods - A basic introduction to fixed-effect and random-effects models for meta-analysis. ( 0,560537617151627 )
Artif Intell Med - On the interplay of machine learning and background knowledge in image interpretation by Bayesian networks. ( 0,558372718345544 )
Comput Methods Programs Biomed - On the prediction of glucose concentration under intra-patient variability in type 1 diabetes: a monotone systems approach. ( 0,557530612191599 )
IEEE Trans Pattern Anal Mach Intell - Fast Inference with Min-Sum Matrix Product. ( 0,557302457438545 )
IEEE Trans Image Process - Foreground object detection using top-down information based on EM framework. ( 0,556590724282208 )
IEEE Trans Image Process - Cross-camera knowledge transfer for multiview people counting. ( 0,55352094475615 )
Med Biol Eng Comput - A poisson process model for hip fracture risk. ( 0,553286186222586 )
Med Biol Eng Comput - Fundamental principles of data assimilation underlying the Verdandi library: applications to biophysical model personalization within euHeart. ( 0,553286186222586 )
Res Synth Methods - Automating network meta-analysis. ( 0,552235030049625 )
Comput. Biol. Med. - BootstRatio: A web-based statistical analysis of fold-change in qPCR and RT-qPCR data using resampling methods. ( 0,551207087202074 )
IEEE Trans Image Process - Modeling and classifying human activities from trajectories using a class of space-varying parametric motion fields. ( 0,550512045127657 )
Spat Spatiotemporal Epidemiol - The detection of spatially localised outbreaks in campylobacteriosis notification data. ( 0,549431832672068 )
Int J Health Geogr - Gumbel based p-value approximations for spatial scan statistics. ( 0,548845476216369 )
Artif Intell Med - Temporal abstraction and temporal Bayesian networks in clinical domains: a survey. ( 0,54821793766748 )
Neural Comput - Bayesian community detection. ( 0,547996624351191 )
IEEE Trans Neural Netw Learn Syst - Robust Novelty Detection via Worst Case CVaR Minimization. ( 0,545993482123633 )
Med Decis Making - Exploring model uncertainty in economic evaluation of health interventions: the example of rotavirus vaccination in Vietnam. ( 0,545829926815333 )
Comput Methods Programs Biomed - NIMROD: a program for inference via a normal approximation of the posterior in models with random effects based on ordinary differential equations. ( 0,545806813972719 )
IEEE Trans Image Process - Blind image quality assessment: a natural scene statistics approach in the DCT domain. ( 0,543958096693949 )
Comput Math Methods Med - In silico modelling of tumour margin diffusion and infiltration: review of current status. ( 0,542610193850535 )
Spat Spatiotemporal Epidemiol - A space-time point process model for analyzing and predicting case patterns of diarrheal disease in northwestern Ecuador. ( 0,541555260840801 )
Comput Methods Programs Biomed - Application of probabilistic and fuzzy cognitive approaches in semantic web framework for medical decision support. ( 0,540691988184545 )