J. Comput. Biol. - Phylogeny inference based on spectral graph clustering.

Tópicos

{ algorithm(1844) comput(1787) effici(935) }
{ problem(2511) optim(1539) algorithm(950) }
{ structur(1116) can(940) graph(676) }
{ model(3404) distribut(989) bayesian(671) }
{ learn(2355) train(1041) set(1003) }
{ perform(999) metric(946) measur(919) }
{ data(1737) use(1416) pattern(1282) }
{ general(901) number(790) one(736) }
{ method(2212) result(1239) propos(1039) }
{ can(774) often(719) complex(702) }
{ state(1844) use(1261) util(961) }
{ error(1145) method(1030) estim(1020) }
{ model(2220) cell(1177) simul(1124) }
{ studi(1410) differ(1259) use(1210) }
{ research(1085) discuss(1038) issu(1018) }
{ studi(1119) effect(1106) posit(819) }
{ signal(2180) analysi(812) frequenc(800) }
{ gene(2352) biolog(1181) express(1162) }
{ implement(1333) system(1263) develop(1122) }
{ method(1969) cluster(1462) data(1082) }
{ detect(2391) sensit(1101) algorithm(908) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ imag(2830) propos(1344) filter(1198) }
{ method(1557) propos(1049) approach(1037) }
{ control(1307) perform(991) simul(935) }
{ howev(809) still(633) remain(590) }
{ import(1318) role(1303) understand(862) }
{ perform(1367) use(1326) method(1137) }
{ ehr(2073) health(1662) electron(1139) }
{ medic(1828) order(1363) alert(1069) }
{ can(981) present(881) function(850) }
{ use(1733) differ(960) four(931) }
{ result(1111) use(1088) new(759) }
{ activ(1452) weight(1219) physic(1104) }
{ imag(1947) propos(1133) code(1026) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ 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) }
{ chang(1828) time(1643) increas(1301) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ 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) }
{ data(3963) clinic(1234) research(1004) }
{ risk(3053) factor(974) diseas(938) }
{ system(1050) medic(1026) inform(1018) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ 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) }
{ age(1611) year(1155) adult(843) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ 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) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ 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) }

Resumo

Phylogeny inference is an importance issue in computational biology. Some early approaches based on characteristics such as the maximum parsimony algorithm and the maximum likelihood algorithm will become intractable when the number of taxonomic units is large. Recent algorithms based on distance data which adopt an agglomerative scheme are widely used for phylogeny inference. However, they have to recursively merge the nearest pair of taxa and estimate a distance matrix; this may enlarge the error gradually, and lead to an inaccurate tree topology. In this study, a splitting algorithm is proposed for phylogeny inference by using the spectral graph clustering (SGC) technique. The SGC algorithm splits graphs by using the maximum cut criterion and circumvents optimization problems through solving a generalized eigenvalue system. The promising features of the proposed algorithm are the following: (i) using a heuristic strategy for constructing phylogenies from certain distance functions, which are not even additive; (ii) distance matrices do not have to be estimated recursively; (iii) inferring a more accurate tree topology than that of the Neighbor-joining (NJ) algorithm on simulated datasets; and (iv) strongly supporting hypotheses induced by other methods for Baculovirus genomes. Our numerical experiments confirm that the SGC algorithm is efficient for phylogeny inference.

Resumo Limpo

phylogeni infer import issu comput biolog earli approach base characterist maximum parsimoni algorithm maximum likelihood algorithm will becom intract number taxonom unit larg recent algorithm base distanc data adopt agglom scheme wide use phylogeni infer howev recurs merg nearest pair taxa estim distanc matrix may enlarg error gradual lead inaccur tree topolog studi split algorithm propos phylogeni infer use spectral graph cluster sgc techniqu sgc algorithm split graph use maximum cut criterion circumv optim problem solv general eigenvalu system promis featur propos algorithm follow use heurist strategi construct phylogeni certain distanc function even addit ii distanc matric estim recurs iii infer accur tree topolog neighborjoin nj algorithm simul dataset iv strong support hypothes induc method baculovirus genom numer experi confirm sgc algorithm effici phylogeni infer

Resumos Similares

Comput Math Methods Med - The new and computationally efficient MIL-SOM algorithm: potential benefits for visualization and analysis of a large-scale high-dimensional clinically acquired geographic data. ( 0,699896443346215 )
IEEE Trans Image Process - Minimization of monotonically levelable higher order MRF energies via graph cuts. ( 0,695541036474009 )
Artif Intell Med - Scalable approximate policies for Markov decision process models of hospital elective admissions. ( 0,667611307695887 )
J. Comput. Biol. - Finding maximum colorful subtrees in practice. ( 0,664746962307593 )
Neural Comput - Information-theoretic semi-supervised metric learning via entropy regularization. ( 0,664490282039116 )
IEEE Trans Pattern Anal Mach Intell - Fast Inference with Min-Sum Matrix Product. ( 0,661950986392079 )
IEEE Trans Neural Netw Learn Syst - Fick's Law Assisted Propagation for Semisupervised Learning. ( 0,65884069803547 )
Comput. Biol. Med. - A fast hierarchical clustering algorithm for large-scale protein sequence data sets. ( 0,654528862966309 )
Comput Methods Programs Biomed - On the prediction of glucose concentration under intra-patient variability in type 1 diabetes: a monotone systems approach. ( 0,65221495316284 )
IEEE Trans Pattern Anal Mach Intell - C^4: Exploring Multiple Solutions in Graphical Models by Cluster Sampling. ( 0,637804057503953 )
Neural Comput - Approximate, computationally efficient online learning in Bayesian spiking neurons. ( 0,633212401843235 )
Comput Biol Chem - Quick path finding--quick algorithmic solution for unambiguous labeling of phylogenetic tree nodes. ( 0,630040284390434 )
IEEE Trans Pattern Anal Mach Intell - Construction of Iso-Contours, Bisectors, and Voronoi Diagrams on Triangulated Surfaces. ( 0,626826755916866 )
IEEE Trans Vis Comput Graph - Hybrid Long-Range Collision Avoidance for Crowd Simulation. ( 0,622714798236459 )
IEEE Trans Neural Netw Learn Syst - MTC: A Fast and Robust Graph-Based Transductive Learning Method. ( 0,620764286603758 )
IEEE Trans Vis Comput Graph - Scheduling in Heterogeneous Computing Environments for Proximity Queries. ( 0,612333368947004 )
IEEE Trans Vis Comput Graph - Memory-Scalable GPU Spatial Hierarchy Construction. ( 0,609782333712224 )
IEEE Trans Vis Comput Graph - Computing Reeb Graphs as a Union of Contour Trees. ( 0,609208774036369 )
IEEE Trans Vis Comput Graph - Exact and Adaptive Signed Distance Fields Computation for Rigid and Deformable Models on GPUs. ( 0,60687455213586 )
J. Comput. Biol. - A new constant memory recursion for hidden Markov models. ( 0,60224626660278 )
IEEE Trans Image Process - Artistic image analysis using graph-based learning approaches. ( 0,601982216042138 )
Neural Comput - Multiple spectral kernel learning and a gaussian complexity computation. ( 0,599388267913918 )
J. Comput. Biol. - Comparing pedigree graphs. ( 0,598256686786616 )
Comput Biol Chem - Deposition and extension approach to find longest common subsequence for thousands of long sequences. ( 0,597253064405395 )
Neural Comput - A DC programming approach for finding communities in networks. ( 0,597087821992231 )
J Chem Inf Model - Exact parallel maximum clique algorithm for general and protein graphs. ( 0,593616729989898 )
Neural Comput - Conditional association. ( 0,593462687693873 )
Neural Comput - Learning rates of lq coefficient regularization learning with gaussian kernel. ( 0,591787733736845 )
IEEE Trans Image Process - A generalized accelerated proximal gradient approach for total-variation-based image restoration. ( 0,589823012811113 )
IEEE Trans Image Process - Fast model-based X-ray CT reconstruction using spatially nonhomogeneous ICD optimization. ( 0,588824720769494 )
J. Comput. Biol. - A Bayesian sampler for optimization of protein domain hierarchies. ( 0,586249395182045 )
AMIA Annu Symp Proc - Shortest Path Edit Distance for Enhancing UMLS Integration and Audit. ( 0,586238362495238 )
Comput Methods Programs Biomed - Parallel evolutionary computation in bioinformatics applications. ( 0,584019664706534 )
Comput Biol Chem - Heuristic energy landscape paving for protein folding problem in the three-dimensional HP lattice model. ( 0,583426988601633 )
Int J Neural Syst - An optimization spiking neural p system for approximately solving combinatorial optimization problems. ( 0,582688159209146 )
IEEE Trans Image Process - Learning smooth pattern transformation manifolds. ( 0,577492219694366 )
IEEE Trans Pattern Anal Mach Intell - What Is Optimized in Convex Relaxations for Multi-Label Problems: Connecting Discrete and Continuously-Inspired MAP Inference. ( 0,575045781844648 )
Comput Biol Chem - ProteinLasso: A Lasso regression approach to protein inference problem in shotgun proteomics. ( 0,574344366959464 )
Comput. Biol. Med. - Frequent patterns mining in multiple biological sequences. ( 0,572440088087037 )
Comput Methods Programs Biomed - CUDA optimization strategies for compute- and memory-bound neuroimaging algorithms. ( 0,571857635812101 )
IEEE Trans Neural Netw Learn Syst - A Deterministic Analysis of an Online Convex Mixture of Experts Algorithm. ( 0,571812009096536 )
Neural Comput - Efficient Markov chain Monte Carlo methods for decoding neural spike trains. ( 0,571377071778642 )
J. Comput. Biol. - Quantifying hybridization in realistic time. ( 0,571284638726254 )
IEEE Trans Image Process - Efficient semidefinite spectral clustering via lagrange duality. ( 0,569678765362574 )
IEEE Trans Image Process - Efficient algorithm for level set method preserving distance function. ( 0,56885640699772 )
IEEE Trans Image Process - Recovering missing slices of the discrete Fourier transform using Ghosts. ( 0,568500150651997 )
IEEE Trans Vis Comput Graph - Scalable Collision Detection using p-Partition Fronts on Many-core Processors. ( 0,567741096158542 )
IEEE Trans Image Process - FAST rate allocation through steepest descent for JPEG2000 video transmission. ( 0,56715432465774 )
IEEE Trans Pattern Anal Mach Intell - Matching by Tone Mapping: Photometric Invariant Template Matching. ( 0,565970250117229 )
Comput Biol Chem - Identification of gene knockout strategies using a hybrid of an ant colony optimization algorithm and flux balance analysis to optimize microbial strains. ( 0,56594191008656 )
IEEE Trans Neural Netw Learn Syst - Kernel reconstruction ICA for sparse representation. ( 0,564433730890326 )
IEEE Trans Pattern Anal Mach Intell - Fast Exact Euclidean Distance (FEED): A New Class of Adaptable Distance Transforms. ( 0,564182093326377 )
IEEE Trans Image Process - Distributed dictionary learning for sparse representation in sensor networks. ( 0,563539674451798 )
Comput Methods Programs Biomed - Real time emotion aware applications: a case study employing emotion evocative pictures and neuro-physiological sensing enhanced by Graphic Processor Units. ( 0,562810430352733 )
J Integr Bioinform - Efficient mapping of genomic sequences to optimize multiple pairwise alignment in hybrid cluster platforms. ( 0,561906354612106 )
J. Comput. Biol. - Efficient error-correcting pooling designs constructed from pseudo-symplectic spaces over a finite field. ( 0,561811764057936 )
IEEE Trans Image Process - Graph cuts for curvature based image denoising. ( 0,560238631042132 )
IEEE Trans Image Process - Real-time discriminative background subtraction. ( 0,559776933001458 )
IEEE Trans Image Process - Multirate-based fast parallel algorithms for 2-D DHT-based real-valued discrete Gabor transform. ( 0,558103395055896 )
IEEE Trans Image Process - Shape-based normalized cuts using spectral relaxation for biomedical segmentation. ( 0,557314966403723 )
IEEE Trans Pattern Anal Mach Intell - Performance Evaluation of Full Search Equivalent Pattern Matching Algorithms. ( 0,55728220261987 )
Neural Comput - A novel iterative method for computing generalized inverse. ( 0,556861784185203 )
Comput Biol Chem - Abstract Next Subvolume Method: a logical process-based approach for spatial stochastic simulation of chemical reactions. ( 0,556548740612436 )
J Chem Inf Model - The generation of fullerenes. ( 0,556485704055734 )
IEEE Trans Image Process - Distance regularized level set evolution and its application to image segmentation. ( 0,55617556442737 )
IEEE Trans Pattern Anal Mach Intell - Constrained Nonnegative Matrix Factorization for Image Representation. ( 0,556008345668809 )
IEEE Trans Image Process - Sparse approximation using M-term pursuit and application in image and video coding. ( 0,555826648323618 )
IEEE Trans Image Process - Determinant and exchange algorithms for observation subset selection. ( 0,555337325260465 )
IEEE Trans Pattern Anal Mach Intell - An Extended Path Following Algorithm for Graph-Matching Problem. ( 0,555009012519369 )
IEEE Trans Pattern Anal Mach Intell - Automatic Generation of Co-Embeddings from Relational Data with Adaptive Shaping. ( 0,554974043612015 )
IEEE Trans Pattern Anal Mach Intell - Iterative Quantization: A Procrustean Approach to Learning Binary Codes for Large-scale Image Retrieval. ( 0,553963206026739 )
Comput. Biol. Med. - A pattern-oriented specification of gene network inference processes. ( 0,553332571416164 )
IEEE Trans Vis Comput Graph - Fast Construction of SAH BVHs on the Intel Many Integrated Core (MIC) Architecture. ( 0,552262763873819 )
IEEE Trans Image Process - Inductive robust principal component analysis. ( 0,551519921982584 )
Comput Methods Programs Biomed - Fast computation of sample entropy and approximate entropy in biomedicine. ( 0,551148979238627 )
IEEE Trans Vis Comput Graph - Efficient Rasterization for Outdoor Radio Wave Propagation. ( 0,550791740951667 )
IEEE Trans Image Process - A 124 Mpixels/s VLSI design for histogram-based joint bilateral filtering. ( 0,550746734823408 )
Comput Math Methods Med - A 3D finite-difference BiCG iterative solver with the Fourier-Jacobi preconditioner for the anisotropic EIT/EEG forward problem. ( 0,550424865680994 )
Brief. Bioinformatics - Fighting against uncertainty: an essential issue in bioinformatics. ( 0,55024080905198 )
IEEE Trans Image Process - Decomposition-based transfer distance metric learning for image classification. ( 0,549212583770789 )
J. Comput. Biol. - Computational methods for a class of network models. ( 0,548428490628094 )
Comput Methods Programs Biomed - Fast box-counting algorithm on GPU. ( 0,547290955252031 )
IEEE Trans Image Process - Fast approximation of algebraic reconstruction methods for tomography. ( 0,546827416640755 )
Neural Comput - A general likelihood framework for characterizing the time course of neural activity. ( 0,545469492808443 )
IEEE Trans Image Process - Super-resolution image reconstruction using non-parametric Bayesian INLA approximation. ( 0,545037469394225 )
Neural Comput - Refined rademacher chaos complexity bounds with applications to the multikernel learning problem. ( 0,544192832204597 )
IEEE Trans Neural Netw Learn Syst - On recursive edit distance kernels with application to time series classification. ( 0,543151821807549 )
J Med Syst - ACO for the surgical cases assignment problem. ( 0,54307193949608 )
IEEE Trans Image Process - Parallel proximal algorithm for image restoration using hybrid regularization. ( 0,542351068658037 )
Artif Intell Med - Memetic algorithms for de novo motif-finding in biomedical sequences. ( 0,540637702608397 )
J Am Med Inform Assoc - Efficient sequential and parallel algorithms for record linkage. ( 0,540603042786516 )
Comput Methods Programs Biomed - Accelerated event-by-event Monte Carlo microdosimetric calculations of electrons and protons tracks on a multi-core CPU and a CUDA-enabled GPU. ( 0,540568488920178 )
J. Comput. Biol. - Determining protein structures from NOESY distance constraints by semidefinite programming. ( 0,539605765478571 )
IEEE Trans Pattern Anal Mach Intell - Consistent Latent Position Estimation and Vertex Classification for Random Dot Product Graphs. ( 0,539511534267157 )
IEEE Trans Image Process - Fitting multiple connected ellipses to an image silhouette hierarchically. ( 0,538132891027026 )
IEEE Trans Pattern Anal Mach Intell - Causal Inference on Discrete Data using Additive Noise Models. ( 0,537815590331708 )
Neural Comput - A network of spiking neurons for computing sparse representations in an energy-efficient way. ( 0,537141979223969 )
IEEE Trans Vis Comput Graph - Memory-Hazard-Aware K-Buffer Algorithm for Order-Independent Transparency Rendering. ( 0,537015915300996 )
IEEE Trans Image Process - Fast and memory efficient 2-D connected components using linked lists of line segments. ( 0,536454913503347 )
IEEE Trans Image Process - Two efficient label-equivalence-based connected-component labeling algorithms for 3-D binary images. ( 0,536260703275716 )