J. Comput. Biol. - Detecting non-uniform clusters in large-scale interaction graphs.

Tópicos

{ method(1969) cluster(1462) data(1082) }
{ structur(1116) can(940) graph(676) }
{ network(2748) neural(1063) input(814) }
{ sampl(1606) size(1419) use(1276) }
{ detect(2391) sensit(1101) algorithm(908) }
{ bind(1733) structur(1185) ligand(1036) }
{ imag(2830) propos(1344) filter(1198) }
{ general(901) number(790) one(736) }
{ studi(1410) differ(1259) use(1210) }
{ import(1318) role(1303) understand(862) }
{ data(2317) use(1299) case(1017) }
{ data(3008) multipl(1320) sourc(1022) }
{ can(981) present(881) function(850) }
{ use(976) code(926) identifi(902) }
{ result(1111) use(1088) new(759) }
{ model(3404) distribut(989) bayesian(671) }
{ method(1219) similar(1157) match(930) }
{ patient(2315) diseas(1263) diabet(1191) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ algorithm(1844) comput(1787) effici(935) }
{ method(1557) propos(1049) approach(1037) }
{ search(2224) databas(1162) retriev(909) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ perform(999) metric(946) measur(919) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ ehr(2073) health(1662) electron(1139) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ activ(1452) weight(1219) physic(1104) }
{ method(2212) result(1239) propos(1039) }
{ can(774) often(719) complex(702) }
{ 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) }
{ sequenc(1873) structur(1644) protein(1328) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2675) segment(2577) method(1081) }
{ 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) }
{ learn(2355) train(1041) set(1003) }
{ 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) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ method(984) reconstruct(947) comput(926) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ risk(3053) factor(974) diseas(938) }
{ research(1085) discuss(1038) issu(1018) }
{ 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) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ gene(2352) biolog(1181) express(1162) }
{ 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(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }

Resumo

Graph clustering becomes difficult as the graph size and complexity increase. In particular, in interaction graphs, the clusters are small and the data on the underlying interaction are not only complex, but also noisy due to the lack of information and experimental errors. The graphs representing such data consist of (possibly overlapping) clusters of non-uniform size with some false positive and false negative links. In this article, we propose a new approach, assuming that clusters in the graphs of protein-protein interaction (PPI) networks resemble corrupted cliques. Therefore, the problem can be reduced to looking for clusters only among nodes of approximately similar degrees. This idea was implemented using a soft version of the Farthest-Point-First (FPF) clustering algorithm with the Jaccard distance function modified to perform on slightly overlapping clusters. The StripClust program developed by us was tested on a synthetic network and on the yeast PPI network.

Resumo Limpo

graph cluster becom difficult graph size complex increas particular interact graph cluster small data under interact complex also noisi due lack inform experiment error graph repres data consist possibl overlap cluster nonuniform size fals posit fals negat link articl propos new approach assum cluster graph proteinprotein interact ppi network resembl corrupt cliqu therefor problem can reduc look cluster among node approxim similar degre idea implement use soft version farthestpointfirst fpf cluster algorithm jaccard distanc function modifi perform slight overlap cluster stripclust program develop us test synthet network yeast ppi network

Resumos Similares

Neural Comput - Spontaneous clustering via minimum -divergence. ( 0,781582802470328 )
Int J Neural Syst - Adaptive k-means algorithm for overlapped graph clustering. ( 0,701451448474054 )
Comput Math Methods Med - How the statistical validation of functional connectivity patterns can prevent erroneous definition of small-world properties of a brain connectivity network. ( 0,6872088959012 )
Neural Comput - A network of spiking neurons for computing sparse representations in an energy-efficient way. ( 0,67993834753164 )
IEEE Trans Image Process - A Geometric Framework for Rectangular Shape Detection. ( 0,658563520028495 )
IEEE Trans Image Process - A comparative review of component tree computation algorithms. ( 0,649632741635592 )
BMC Med Inform Decis Mak - Spatial cluster detection using dynamic programming. ( 0,627741912044352 )
IEEE Trans Pattern Anal Mach Intell - A Link-Based Approach to the Cluster Ensemble Problem. ( 0,627288244645628 )
IEEE Trans Vis Comput Graph - GPU-based Multilevel Clustering. ( 0,624295594521553 )
Neural Comput - Encoding through patterns: regression tree-based neuronal population models. ( 0,619894160496253 )
IEEE Trans Vis Comput Graph - Visual Analysis of Large Graphs Using (X,Y)-clustering and Hybrid Visualizations. ( 0,616604646431516 )
Spat Spatiotemporal Epidemiol - Optimal selection of the spatial scan parameters for cluster detection: a simulation study. ( 0,598961243748954 )
Int J Neural Syst - A genetic graph-based approach for partitional clustering. ( 0,598630277345896 )
IEEE Trans Neural Netw Learn Syst - Optimization of a multilayer neural network by using minimal redundancy maximal relevance-partial mutual information clustering with least square regression. ( 0,597278681019915 )
IEEE Trans Image Process - A co-saliency model of image pairs. ( 0,595914572452309 )
IEEE Trans Neural Netw Learn Syst - Improved Fault Classification in Series Compensated Transmission Line: Comparative Evaluation of Chebyshev Neural Network Training Algorithms. ( 0,594875522336514 )
J. Comput. Biol. - Exactly computing the parsimony scores on phylogenetic networks using dynamic programming. ( 0,59305378629809 )
Int J Health Geogr - A binary-based approach for detecting irregularly shaped clusters. ( 0,592207193913984 )
IEEE Trans Vis Comput Graph - An Intrinsic Algorithm for Parallel Poisson Disk Sampling on Arbitrary Surfaces. ( 0,591635194154872 )
Comput Biol Chem - Global energy minimization of alanine dipeptide via barrier function methods. ( 0,588530508303504 )
Comput Methods Programs Biomed - Automatic detection and characterisation of retinal vessel tree bifurcations and crossovers in eye fundus images. ( 0,585383962187307 )
Int J Comput Assist Radiol Surg - Complete fully automatic model-based segmentation of normal and pathological lymph nodes in CT data. ( 0,58172581131833 )
IEEE Trans Image Process - Enhancing Low-Rank Subspace Clustering by Manifold Regularization. ( 0,576924998933738 )
Brief. Bioinformatics - Hive plots--rational approach to visualizing networks. ( 0,576159730055871 )
Int J Health Geogr - Voronoi distance based prospective space-time scans for point data sets: a dengue fever cluster analysis in a southeast Brazilian town. ( 0,575133497314983 )
J Am Med Inform Assoc - Privacy-preserving heterogeneous health data sharing. ( 0,573567868261889 )
IEEE Trans Vis Comput Graph - Point-Based Visualization for Large Hierarchies. ( 0,572502265128609 )
IEEE Trans Vis Comput Graph - Dynamic Network Visualization with Extended Massive Sequence Views. ( 0,571880572839323 )
IEEE Trans Pattern Anal Mach Intell - C^4: Exploring Multiple Solutions in Graphical Models by Cluster Sampling. ( 0,571554041960776 )
J Biomed Inform - FALCON or how to compute measures time efficiently on dynamically evolving dense complex networks? ( 0,569147382827923 )
Artif Intell Med - Multi-test decision tree and its application to microarray data classification. ( 0,569108064558203 )
Int J Comput Assist Radiol Surg - A Hessian-based filter for vascular segmentation of noisy hepatic CT scans. ( 0,568358349946274 )
IEEE Trans Image Process - 3-D curvilinear structure detection filter via structure-ball analysis. ( 0,566797472443157 )
Res Synth Methods - Less is less: a systematic review of graph use in meta-analyses. ( 0,566760480450746 )
Neural Comput - Parametric inference in the large data limit using maximally informative models. ( 0,563157151628143 )
Comput Math Methods Med - Decimative spectral estimation with unconstrained model order. ( 0,563100926972337 )
Int J Health Geogr - Detecting activity locations from raw GPS data: a novel kernel-based algorithm. ( 0,557523058886795 )
Neural Comput - Intrinsic graph structure estimation using graph Laplacian. ( 0,557038592507488 )
Artif Intell Med - Weighted spherical 1-mean with phase shift and its application in electrocardiogram discord detection. ( 0,556745210415777 )
Comput. Biol. Med. - Probing brain connectivity by combined analysis of diffusion MRI tractography and electrocorticography. ( 0,555464337453289 )
Comput Methods Programs Biomed - Fuzzy and hard clustering analysis for thyroid disease. ( 0,553335819459597 )
J Chem Inf Model - New Markov-autocorrelation indices for re-evaluation of links in chemical and biological complex networks used in metabolomics, parasitology, neurosciences, and epidemiology. ( 0,549200682315308 )
AMIA Annu Symp Proc - Using hierarchical mixture of experts model for fusion of outbreak detection methods. ( 0,548446662144621 )
Comput. Aided Surg. - The Equidistant Method - a novel hip joint simulation algorithm for detection of femoroacetabular impingement. ( 0,548289187169689 )
Comput Math Methods Med - The effect of edge definition of complex networks on protein structure identification. ( 0,548188397632539 )
Neural Comput - System identification of mGluR-dependent long-term depression. ( 0,54807725878022 )
Comput Methods Programs Biomed - Use of graph theory measures to identify errors in record linkage. ( 0,546317741758195 )
Int J Health Geogr - Detection of clusters of a rare disease over a large territory: performance of cluster detection methods. ( 0,546064939142033 )
IEEE Trans Image Process - Constrained and dimensionality-independent path openings. ( 0,545517165803234 )
J. Comput. Biol. - A theoretical model for whole genome alignment. ( 0,545392386711681 )
J Biomed Inform - Enabling the use of hereditary information from pedigree tools in medical knowledge-based systems. ( 0,544749058223573 )
J. Comput. Biol. - The approximability of shortest path-based graph orientations of protein-protein interaction networks. ( 0,544619579726856 )
J Chem Inf Model - Composition and topology of activity cliff clusters formed by bioactive compounds. ( 0,543728917645884 )
Comput Methods Programs Biomed - Classification of intelligence quotient via brainwave sub-band power ratio features and artificial neural network. ( 0,539864448703781 )
Comput Math Methods Med - A wavelet relational fuzzy C-means algorithm for 2D gel image segmentation. ( 0,536301077078354 )
IEEE Trans Neural Netw Learn Syst - Generalized single-hidden layer feedforward networks for regression problems. ( 0,536145158268927 )
Brief. Bioinformatics - Computational methods for Gene Orthology inference. ( 0,53442467447438 )
Int J Health Geogr - Detection of arbitrarily-shaped clusters using a neighbor-expanding approach: a case study on murine typhus in south Texas. ( 0,532679794665454 )
IEEE Trans Image Process - Ridge network detection in crumpled paper via graph density maximization. ( 0,531674262573892 )
IEEE J Biomed Health Inform - Identifying Similar Cases in Document Networks using Cross-reference Structures. ( 0,530567712974199 )
Comput Methods Programs Biomed - TreeVis: a MATLAB-based tool for tree visualization. ( 0,529839301023234 )
Neural Comput - Nearly extensive sequential memory lifetime achieved by coupled nonlinear neurons. ( 0,529466456004035 )
IEEE Trans Image Process - Boundary operation of 2-D nonseparable linear-phase paraunitary filter banks. ( 0,52856491882334 )
Comput Biol Chem - A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification. ( 0,528016804644555 )
IEEE Trans Image Process - Edge detecting for range data using Laplacian operators. ( 0,527771999619239 )
IEEE Trans Pattern Anal Mach Intell - Fast Detection of Dense Subgraphs with Iterative Shrinking and Expansion. ( 0,526330667027698 )
J. Comput. Biol. - Modeling alternative splicing variants from RNA-Seq data with isoform graphs. ( 0,526300154220517 )
IEEE Trans Vis Comput Graph - Visualization of High Dimensional Point Clouds Using their Density Distribution's Topology. ( 0,525588371873241 )
Int J Health Geogr - Maximum linkage space-time permutation scan statistics for disease outbreak detection. ( 0,52507494011242 )
J Chem Inf Model - Comparison of combinatorial clustering methods on pharmacological data sets represented by machine learning-selected real molecular descriptors. ( 0,525064390357222 )
Int J Neural Syst - Hardware implementation of stochastic spiking neural networks. ( 0,521103592192201 )
IEEE Trans Neural Netw Learn Syst - Second-order global consensus in multiagent networks with random directional link failure. ( 0,520426226407682 )
Med Biol Eng Comput - Estimating the time scale and anatomical location of atrial fibrillation spontaneous termination in a biophysical model. ( 0,518745876765331 )
Med Decis Making - Multiple imputation methods for handling missing data in cost-effectiveness analyses that use data from hierarchical studies: an application to cluster randomized trials. ( 0,518379434274379 )
Comput Math Methods Med - Novel harmonic regularization approach for variable selection in Cox's proportional hazards model. ( 0,516869954467744 )
J Chem Inf Model - Benchmark data sets for structure-based computational target prediction. ( 0,516828810006856 )
J Chem Inf Model - Stereochemically consistent reaction mapping and identification of multiple reaction mechanisms through integer linear optimization. ( 0,515846955039432 )
J Chem Inf Model - Metabolism site prediction based on xenobiotic structural formulas and PASS prediction algorithm. ( 0,515625706693319 )
Neural Comput - Stability against fluctuations: scaling, bifurcations, and spontaneous symmetry breaking in stochastic models of synaptic plasticity. ( 0,51535018092002 )
Med Decis Making - Developing appropriate methods for cost-effectiveness analysis of cluster randomized trials. ( 0,515268073774123 )
J. Comput. Biol. - Computing fragmentation trees from metabolite multiple mass spectrometry data. ( 0,515026536840072 )
Neural Comput - Discovering functional neuronal connectivity from serial patterns in spike train data. ( 0,513449350878145 )
Neural Comput - Direct learning of sparse changes in Markov networks by density ratio estimation. ( 0,512871258734467 )
Res Synth Methods - Combining randomized and non-randomized evidence in clinical research: a review of methods and applications. ( 0,511049750775335 )
Comput Math Methods Med - A pipeline for neuron reconstruction based on spatial sliding volume filter seeding. ( 0,510699358484372 )
Brief. Bioinformatics - Ultrafast clustering algorithms for metagenomic sequence analysis. ( 0,510045172626933 )
J Biomed Inform - Tree kernel-based protein-protein interaction extraction from biomedical literature. ( 0,509429937664893 )
J Med Syst - Employing post-DEA cross-evaluation and cluster analysis in a sample of Greek NHS hospitals. ( 0,506675680222764 )
J. Comput. Biol. - A geometric clustering algorithm with applications to structural data. ( 0,506288041073659 )
Comput Methods Programs Biomed - Characterizing electrical signals evoked by acupuncture through complex network mapping: a new perspective on acupuncture. ( 0,505121756479775 )
Neural Comput - Short-term memory capacity in networks via the restricted isometry property. ( 0,50468477592269 )
Brief. Bioinformatics - Estimating the divisibility of complex biological networks by sparseness indices. ( 0,504347817100261 )
Int J Health Geogr - Penalized likelihood and multi-objective spatial scans for the detection and inference of irregular clusters. ( 0,503906466623072 )
Artif Intell Med - Missing data imputation using statistical and machine learning methods in a real breast cancer problem. ( 0,503109229324551 )
IEEE Trans Pattern Anal Mach Intell - Semi-Supervised Kernel Mean Shift Clustering. ( 0,503019391527194 )
Comput. Biol. Med. - Effective connectivity analysis of fMRI and MEG data collected under identical paradigms. ( 0,502873375161906 )
J. Med. Internet Res. - Security analysis and improvements to the PsychoPass method. ( 0,502487442045974 )
Neural Comput - Effects of multiplicative power law neural noise in visual information processing. ( 0,502095930203218 )
Neural Comput - A framework for simulating and estimating the state and functional topology of complex dynamic geometric networks. ( 0,501121447414474 )
J Chem Inf Model - BFMP: a method for discretizing and visualizing pyranose conformations. ( 0,500894721860851 )