J. Comput. Biol. - Population model-based inter-diplotype similarity measure for accurate diplotype clustering.

Tópicos

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

Resumo

Classification of the individuals' genotype data is important in various kinds of biomedical research. There are many sophisticated clustering algorithms, but most of them require some appropriate similarity measure between objects to be clustered. Hence, accurate inter-diplotype similarity measures are always required for classification of diplotypes. In this article, we propose a new accurate inter-diplotype similarity measure that we call the population model-based distance (PMD), so that we can cluster individuals with diplotype SNPs data (i.e., unphased-diplotypes) with higher accuracies. For unphased-diplotypes, the allele sharing distance (ASD) has been the standard to measure the genetic distance between the diplotypes of individuals. To achieve higher clustering accuracies, our new measure PMD makes good use of a given appropriate population model which has never been utilized in the ASD. As the population model, we propose to use an hidden Markov model (HMM)-based model. We call the PMD based on the model the HHD (HIT HMM-based Distance). We demonstrate the impact of the HHD on the diplotype classification through comprehensive large-scale experiments over the genome-wide 8930 data sets derived from the HapMap SNPs database. The experiments revealed that the HHD enables significantly more accurate clustering than the ASD.

Resumo Limpo

classif individu genotyp data import various kind biomed research mani sophist cluster algorithm requir appropri similar measur object cluster henc accur interdiplotyp similar measur alway requir classif diplotyp articl propos new accur interdiplotyp similar measur call popul modelbas distanc pmd can cluster individu diplotyp snps data ie unphaseddiplotyp higher accuraci unphaseddiplotyp allel share distanc asd standard measur genet distanc diplotyp individu achiev higher cluster accuraci new measur pmd make good use given appropri popul model never util asd popul model propos use hidden markov model hmmbase model call pmd base model hhd hit hmmbase distanc demonstr impact hhd diplotyp classif comprehens largescal experi genomewid data set deriv hapmap snps databas experi reveal hhd enabl signific accur cluster asd

Resumos Similares

IEEE Trans Image Process - View-based discriminative probabilistic modeling for 3D object retrieval and recognition. ( 0,662482070013565 )
IEEE Trans Image Process - Co-transduction for shape retrieval. ( 0,662049006472729 )
Neural Comput - A new class of metrics for spike trains. ( 0,662042916428048 )
IEEE Trans Vis Comput Graph - Enhanced Spatial Stability with Hilbert and Moore Treemaps. ( 0,630967494662575 )
Comput. Biol. Med. - Similarity measure for quality control of dental CAD/CAM-applications. ( 0,621037745455768 )
Neural Comput - Exploitation of pairwise class distances for ordinal classification. ( 0,615919210952017 )
IEEE Trans Image Process - Two-dimensional approach to full-reference image quality assessment based on positional structural information. ( 0,612114293769347 )
IEEE Trans Vis Comput Graph - Scheduling in Heterogeneous Computing Environments for Proximity Queries. ( 0,606391758020765 )
Neural Comput - Markov chain Monte Carlo methods for state-space models with point process observations. ( 0,599401775059785 )
IEEE Trans Vis Comput Graph - A Structure-Based Distance Metric for High-Dimensional Space Exploration with Multi-Dimensional Scaling. ( 0,584885543822099 )
Comput Methods Programs Biomed - METRADISC-XL: a program for meta-analysis of multidimensional ranked discovery oriented datasets including microarrays. ( 0,582320033609524 )
Med Decis Making - Evaluation of markers and risk prediction models: overview of relationships between NRI and decision-analytic measures. ( 0,573976911083245 )
Res Synth Methods - Selecting the best scale for measuring treatment effect in a network meta-analysis: a case study in childhood nocturnal enuresis. ( 0,573036513005293 )
IEEE Trans Image Process - A multisize superpixel approach for salient object detection based on multivariate normal distribution estimation. ( 0,571928345010493 )
J Biomed Inform - Quantifying the determinants of outbreak detection performance through simulation and machine learning. ( 0,566596327955734 )
IEEE Trans Image Process - Image quality assessment using multi-method fusion. ( 0,565720139394682 )
J. Comput. Biol. - A new constant memory recursion for hidden Markov models. ( 0,560480921684088 )
AMIA Annu Symp Proc - Shortest Path Edit Distance for Enhancing UMLS Integration and Audit. ( 0,556076745900765 )
Neural Comput - Causal discovery via reproducing kernel Hilbert space embeddings. ( 0,555924883255888 )
Lifetime Data Anal - Bayesian local influence for survival models. ( 0,550139056880711 )
IEEE Trans Image Process - Evaluating combinational illumination estimation methods on real-world images. ( 0,547928219358739 )
Int J Health Geogr - Mapping amyotrophic lateral sclerosis lake risk factors across northern New England. ( 0,546408027018126 )
Int J Health Geogr - Estimating the reproductive number in the presence of spatial heterogeneity of transmission patterns. ( 0,5426282546612 )
IEEE Trans Image Process - 3-D object retrieval and recognition with hypergraph analysis. ( 0,542037653376564 )
Res Synth Methods - Meta-analysis inside and outside particle physics: two traditions that should converge? ( 0,541414051516612 )
IEEE Trans Image Process - Two-direction nonlocal model for image denoising. ( 0,539567414507795 )
Res Synth Methods - Random-effects meta-analysis of time-to-event data using the expectation-maximisation algorithm and shrinkage estimators. ( 0,538479027808 )
Comput Biol Chem - Complexity measures for the evolutionary categorization of organisms. ( 0,537621338000461 )
Int J Comput Assist Radiol Surg - Three-dimensional skeletonization and symbolic description in vascular imaging: preliminary results. ( 0,536417861272307 )
IEEE Trans Image Process - A novel video dataset for change detection benchmarking. ( 0,532290996142201 )
IEEE Trans Image Process - Inverse halftoning based on the bayesian theorem. ( 0,529557836349793 )
J. Comput. Biol. - Order of precedence and age of Y-DNA haplotypes. ( 0,526365703199233 )
J Chem Inf Model - Prediction of active site cleft using support vector machines. ( 0,526361528199237 )
Brief. Bioinformatics - Evaluating template-based and template-free protein-protein complex structure prediction. ( 0,522175176694867 )
Res Synth Methods - The use of meta-analytic statistical significance testing. ( 0,51956472798072 )
Artif Intell Med - Improved cosine similarity measures of simplified neutrosophic sets for medical diagnoses. ( 0,519068495586099 )
Spat Spatiotemporal Epidemiol - Comparing spatio-temporal clusters of arthropod-borne infections using administrative medical claims and state reported surveillance data. ( 0,517896590773017 )
Neural Comput - Improved similarity measures for small sets of spike trains. ( 0,514687509140441 )
AMIA Annu Symp Proc - Using RxNorm for cross-institutional formulary data normalization within a distributed grid-computing environment. ( 0,51406432333343 )
IEEE Trans Image Process - Spatial statistics of image features for performance comparison. ( 0,512981303720031 )
IEEE Trans Image Process - The segmentation of 3D images using the random walking technique on a randomly created image adjacency graph. ( 0,512886075374465 )
Med Biol Eng Comput - A mathematical method for constraint-based cluster analysis towards optimized constrictive diameter smoothing of saphenous vein grafts. ( 0,512280092280475 )
IEEE Trans Image Process - Linear time distances between fuzzy sets with applications to pattern matching and classification. ( 0,511844909064472 )
Brief. Bioinformatics - Letter to the editor: Stability of Random Forest importance measures. ( 0,511136968398078 )
Comput Math Methods Med - Developing image processing meta-algorithms with data mining of multiple metrics. ( 0,510745507527378 )
Med Biol Eng Comput - Experimental comparison of connectivity measures with simulated EEG signals. ( 0,510273340194076 )
J Chem Inf Model - Assessing relative bioactivity of chemical substances using quantitative molecular network topology analysis. ( 0,510044941763693 )
J. Med. Internet Res. - De-identification methods for open health data: the case of the Heritage Health Prize claims dataset. ( 0,509928620586034 )
J Chem Inf Model - Large-scale learning of structure-activity relationships using a linear support vector machine and problem-specific metrics. ( 0,508336657818911 )
Comput. Biol. Med. - Towards automatic detection of atrial fibrillation: A hybrid computational approach. ( 0,506205155768472 )
IEEE Trans Image Process - Toward an impairment metric for stereoscopic video: a full-reference video quality metric to assess compressed stereoscopic video. ( 0,503780534578272 )
IEEE Trans Image Process - Decomposition-based transfer distance metric learning for image classification. ( 0,503677658835651 )
IEEE Trans Pattern Anal Mach Intell - Improved Iris Recognition Through Fusion of Hamming Distance and Fragile Bit Distance. ( 0,503293708295581 )
IEEE Trans Pattern Anal Mach Intell - Iterative Discovery of Multiple Alternative Clustering Views. ( 0,502807536162232 )
IEEE Trans Image Process - Homogeneity localization using particle filters with application to noise estimation. ( 0,502661333750612 )
IEEE Trans Image Process - Structural texture similarity metrics for image analysis and retrieval. ( 0,502483039493285 )
Comput Biol Chem - Ranking of microRNA target prediction scores by Pareto front analysis. ( 0,501779319048026 )
J Chem Inf Model - Applicability domains for classification problems: Benchmarking of distance to models for Ames mutagenicity set. ( 0,5015855847819 )
IEEE Trans Image Process - S3: a spectral and spatial measure of local perceived sharpness in natural images. ( 0,500276528300765 )
Int J Comput Assist Radiol Surg - Automatic scoring of virtual mastoidectomies using expert examples. ( 0,499600021792714 )
IEEE Trans Image Process - Data-dependent hashing based on p-stable distribution. ( 0,498083978762163 )
J Biomed Inform - Complementary ensemble clustering of biomedical data. ( 0,495948980966073 )
IEEE Trans Neural Netw Learn Syst - A Distributed Approach Toward Discriminative Distance Metric Learning. ( 0,495690086059145 )
Med Biol Eng Comput - Risk stratification of cardiac autonomic neuropathy based on multi-lag Tone-Entropy. ( 0,493291725067473 )
Comput Math Methods Med - A review on the computational methods for emotional state estimation from the human EEG. ( 0,493041369276013 )
AMIA Annu Symp Proc - Knowledge-based method for determining the meaning of ambiguous biomedical terms using information content measures of similarity. ( 0,491688090046675 )
IEEE Trans Image Process - Multimodal graph-based reranking for web image search. ( 0,489051128777674 )
J Biomed Inform - An ontology-based similarity measure for biomedical data-application to radiology reports. ( 0,486447717417356 )
IEEE Trans Image Process - Implicit polynomial representation through a fast fitting error estimation. ( 0,486064119521167 )
Comput Methods Programs Biomed - A multi-task learning approach for the extraction of single-trial evoked potentials. ( 0,485221703180459 )
Int J Health Geogr - An open source software for fast grid-based data-mining in spatial epidemiology (FGBASE). ( 0,484802947610882 )
Neural Comput - Neural decoding with kernel-based metric learning. ( 0,483305840890217 )
Comput. Biol. Med. - Retinal vessel extraction using Lattice Neural Networks with Dendritic Processing. ( 0,482715441113085 )
Neural Comput - Neural representation of spatial topology in the rodent hippocampus. ( 0,482694068909744 )
Neural Comput - Conditional association. ( 0,482240737561241 )
J. Comput. Biol. - Phylogeny inference based on spectral graph clustering. ( 0,481187245002373 )
AMIA Annu Symp Proc - Data-driven order set generation and evaluation in the pediatric environment. ( 0,480829394731913 )
IEEE J Biomed Health Inform - Identifying Similar Cases in Document Networks using Cross-reference Structures. ( 0,480569290933523 )
J Chem Inf Model - Interpretable, probability-based confidence metric for continuous quantitative structure-activity relationship models. ( 0,480219922122458 )
Comput. Biol. Med. - A classification study of kinematic gait trajectories in hip osteoarthritis. ( 0,479853241899206 )
Comput. Aided Surg. - Fast GPU-based CT reconstruction applied in ablation treatment for hepatocellular carcinoma. ( 0,478902958670428 )
IEEE Trans Image Process - Distance regularized level set evolution and its application to image segmentation. ( 0,478670428447397 )
Comput. Biol. Med. - Empirical evaluation of consistency and accuracy of methods to detect differentially expressed genes based on microarray data. ( 0,476352315897952 )
IEEE J Biomed Health Inform - Identifying mammalian MicroRNA targets based on supervised distance metric learning. ( 0,476205474079527 )
IEEE Trans Image Process - Efficient particle filtering via sparse kernel density estimation. ( 0,474504255140472 )
Methods Inf Med - Motor Unit Tracking?Using High Density Surface Electromyography (HDsEMG)?. Automated Correction of Electrode Displacement Errors. ( 0,474409087714965 )
AMIA Annu Symp Proc - Statistical machine translation for biomedical text: are we there yet? ( 0,473474244410851 )
Int J Comput Assist Radiol Surg - Statistical atlas-based morphological variation analysis of the asian humerus: towards consistent allometric implant positioning. ( 0,472648029632424 )
J Chem Inf Model - DEKOIS: demanding evaluation kits for objective in silico screening--a versatile tool for benchmarking docking programs and scoring functions. ( 0,472339647627757 )
J Chem Inf Model - Analysis of commercial and public bioactivity databases. ( 0,470298009395462 )
Comput Biol Chem - Multi objective SNP selection using pareto optimality. ( 0,46926799364421 )
J Biomed Inform - Statistical file matching of flow cytometry data. ( 0,468536947708666 )
IEEE Trans Vis Comput Graph - Exact and Adaptive Signed Distance Fields Computation for Rigid and Deformable Models on GPUs. ( 0,468352727272863 )
J. Comput. Biol. - Bayesian blind source separation for data with network structure. ( 0,468332543079791 )
IEEE Trans Pattern Anal Mach Intell - A Link-Based Approach to the Cluster Ensemble Problem. ( 0,468059915504022 )
J Med Syst - Distance-constrained orthogonal Latin squares for brain-computer interface. ( 0,465866079933686 )
IEEE Trans Neural Netw Learn Syst - Synchronization of chaotic Lur'e systems with time delays using sampled-data control. ( 0,46580723261104 )
Comput Methods Programs Biomed - Estimating postprandial glucose fluxes using hierarchical Bayes modelling. ( 0,464090202862458 )
IEEE Trans Pattern Anal Mach Intell - Online Multiple Kernel Similarity Learning for Visual Search. ( 0,463552663542501 )
Comput Methods Programs Biomed - Independent cohort cross-validation of the real-time DISTq estimation of insulin sensitivity. ( 0,46284009080245 )