Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Graph”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,531 records · Page 85Linked to original sources

Statistical mechanics of topological phase transitions in networks.

We provide a phenomenological theory for topological transitions in restructuring networks. In this statistical mechanical approach energy is assigned to the different network topologies and temperature is used as a quantity referring to the level of noise during the rewiring of the edges. The associated microscopic dynamics satisfies the detailed balance condition and is equivalent to a lattice gas model on the edge-dual graph of a fully connected network. In our studies-based on an exact enumeration method, Monte Carlo simulations, and theoretical considerations-we find a rich variety of topological phase transitions when the temperature is varied. These transitions signal singular changes in the essential features of the global structure of the network. Depending on the energy function chosen, the observed transitions can be best monitored using the order parameters Phi(s)=s(max)/M, i.e., the size of the largest connected component divided by the number of edges, or Phi(k)=k(max)/M, the largest degree in the network divided by the number of edges. If, for example, the energy is chosen to be E=-s(max), the observed transition is analogous to the percolation phase transition of random graphs. For this choice of the energy, the phase diagram in the ( ,T) plane is constructed. Single-vertex energies of the form E= summation operator (i)f(k(i)), where k(i) is the degree of vertex i, are also studied. Depending on the form of f(k(i)), first-order and continuous phase transitions can be observed. In case of f(k(i))=-(k(i)+alpha)ln(k(i)), the transition is continuous, and at the critical temperature scale-free graphs can be recovered. Finally, by abruptly decreasing the temperature, nonequilibrium processes (e.g., nucleation and growth of particular topological phases) can also be interpreted by the present approach.

Journal Article↗

Clustering analysis of the ground-state structure of the vertex-cover problem.

Vertex cover is one of the classical NP-complete problems in theoretical computer science. A vertex cover of a graph is a subset of vertices such that for each edge at least one of the two endpoints is contained in the subset. When studied on Erdo s-Re nyi random graphs (with connectivity c) one observes a threshold behavior: In the thermodynamic limit the size of the minimal vertex cover is independent of the specific graph. Recent analytical studies show that on the phase boundary, for small connectivities c<e , the system is replica symmetric, while for larger connectivities replica symmetry breaking occurs. This change coincides with a change of the typical running time of algorithms from polynomial to exponential. To understand the reasons for this behavior and to compare with the analytical results, we numerically analyze the structure of the solution landscape. For this purpose, we have also developed an algorithm, which allows the calculation of the backbone, without the need to enumerate all solutions. We study exact solutions found with a branch-and-bound algorithm as well as configurations obtained via a Monte Carlo simulation. We analyze the cluster structure of the solution landscape by direct clustering of the states, by analyzing the eigenvalue spectrum of correlation matrices and by using a hierarchical clustering method. All results are compatible with a change at c=e . For small connectivities, the solutions are collected in a finite small number of clusters, while the number of clusters diverges slowly with system size for larger connectivities and replica symmetry breaking, but not one-step replica symmetry breaking (1-RSB) occurs.

Journal Article↗

Systematic identification of statistically significant network measures.

We present a graph embedding space (i.e., a set of measures on graphs) for performing statistical analyses of networks. Key improvements over existing approaches include discovery of "motif hubs" (multiple overlapping significant subgraphs), computational efficiency relative to subgraph census, and flexibility (the method is easily generalizable to weighted and signed graphs). The embedding space is based on scalars, functionals of the adjacency matrix representing the network. Scalars are global, involving all nodes; although they can be related to subgraph enumeration, there is not a one-to-one mapping between scalars and subgraphs. Improvements in network randomization and significance testing--we learn the distribution rather than assuming Gaussianity--are also presented. The resulting algorithm establishes a systematic approach to the identification of the most significant scalars and suggests machine-learning techniques for network classification.

Algorithms↗

Adaptive walk on complex networks.

We investigate the properties of adaptive walks on an uncorrelated fitness landscape which is established in sequence spaces of complex structure. In particular, we perform numerical simulations of adaptive walks on random graphs and scale-free networks. For the former, we also derive some analytical approximations for the density of local optima of the fitness landscape and the mean length walk. We compare our results with those obtained for regular lattices. We obtain that the density of local optima decreases as 1/z, where z is the mean connectivity, for all networks we have investigated. In random graphs, the mean length walk L reaches the asymptotic value e - 1 for large z, which corresponds to the result for regular networks. Although we could not find an exact estimate, we derive an underestimated value for L. Unlike random graphs, scale-free networks show an upper asymptotic value of L.

Adaptation, Physiological↗

From simple to complex networks: inherent structures, barriers, and valleys in the context of spin glasses.

Given discrete degrees of freedom (spins) on a graph interacting via an energy function, what can be said about the energy local minima and associated inherent structures? Using the lid algorithm in the context of a spin glass energy function, we investigate the properties of the energy landscape for a variety of graph topologies. First, we find that the multiplicity N(s) of the inherent structures generically has a log-normal distribution. In addition, the large volume limit of ln / differs from unity, except for the Sherrington-Kirkpatrick model. Second, we find simple scaling laws for the growth of the height of the energy barrier between the two degenerate ground states and the size of the associated valleys. For finite connectivity models, changing the topology of the underlying graph does not modify qualitatively the energy landscape, but at the quantitative level the models can differ substantially.

Journal Article↗

Fractal structure in the collision of vector solitons

We study the collision of two orthogonally polarized and equal-amplitude vector solitons in the nonintegrable coupled nonlinear Schrodinger equations. We show that the separation velocity versus collision velocity graph has a fractal structure. When we zoom into this graph, we get a structure qualitatively identical to the original one. In addition, collision dynamics in the zoomed-in windows is intimately related to that in the original graph. We explain this fractal dependence of the collision by a resonance mechanism between the translational motion of vector solitons and internal oscillations inside a vector soliton.

Journal Article↗

Exactly solvable model with two conductor-insulator transitions driven by impurities.

We present an exact analysis of two conductor-insulator transitions in the random graph model where low connectivity means high impurity concentration. The adjacency matrix of the random graph is used as a hopping Hamiltonian. We compute the height of the delta peak at zero energy in its spectrum exactly and describe analytically the structure and contribution of localized eigenvectors. The system is a conductor for average connectivities between 1.421 529ellipsis and 3.154 985ellipsis but an insulator in the other regimes. We explain the spectral singularity at average connectivity e = 2.718 281ellipsis and relate it to other enumerative problems in random graph theory.

Journal Article↗

Magnetization reversal in spin patterns with complex geometry.

We study field-driven dynamics of spins with antiferromagnetic interactions along the links of a complex substrate geometry, which is modeled by graphs of a controlled connectivity distribution. The magnetization reversal occurs in avalanches of spin flips, which are pinned by the topological constraints of the underlying graph. The hysteresis loop and avalanche sizes are analyzed and classified in terms of the graph's connectivity and clustering. The results are relevant for magnets with a hierarchical spatial inhomogeneity and for design of nanoscale magnetic devices.

Journal Article↗

Hydrogen-bonding motifs in 4-carboxyphenylammonium nitrate and perchlorate monohydrate, and in bis(4-carboxyphenylammonium) sulfate.

In the title compounds, C7H8NO2+.NO3-, (I), C7H8NO2+.ClO4-.H2O, (II), and 2C7H8NO2+.SO4(2-), (III), the carboxyl planes of the 4-carboxyphenylammonium cations are twisted from the aromatic plane. A homonuclear C(8) hydrogen-bonding motif of 4-carboxyphenylammonium cations is observed in both (I) and (II), leading to ;head-to-tail' layers. The cations in (III) form carboxyl group dimers, making a graph-set motif of R2(2)(8). In all the structures, anions connect the cationic layers and an infinite chain running along the c axis is observed, having the C2(2)(6) graph-set motif. Interestingly, in (II), the anions are connected through weak hydrogen bonds involving the water molecules, leading to a graph-set motif of R4(4)(12). Alternate hydrophobic and hydrophilic layers are observed in all three compounds as a result of the column-like arrangement of the aromatic rings of the cations and the anions. Furthermore, in (I), head-to-tail N-H...O interactions and interactions linking the cations and anions form an R6(4)(16) hydrogen-bonding motif, resulting in a pseudo-inversion centre at (1/2, 1/2, 0).

4-Aminobenzoic Acid↗

Inhibitor of HIV-1 reverse transcriptase: N'-(5-bromo-2-pyridyl)-N-[2-(2,5-dimethoxyphenyl)ethyl]thiourea.

The crystal structure of the title compound, C16H18Br-N3O2S (HI-236), a potent non-nucleoside inhibitor of HIV-1 reverse transcriptase, revealed an intramolecular hydrogen bond between a thiourea N atom and the pyridyl-N atom [N-H...N = 2.671 (3) A, graph-set motif S1(1)(6)] that imparts a more rigid conformation to the molecule. A second hydrogen bond between a thiourea N atom and the thiocarbonyl-S atom [N-H2...S = 3.403 (2) A, graph-set motif R2(2)(8)] was observed between inversion-related molecules of HI-236. The first-level hydrogen-bond graph-set notation for HI-236 was determined to be S1(1)(6)R2(2)(8).

Crystallography, X-Ray↗

A method for hierarchical comparative analysis of crystal structures.

A geometrical-topological description of crystal structure as a three-dimensional graph with coloured nodes, weighted and coloured edges is used to generate a hierarchical sequence of the structure representations. The solid angles of Voronoi-Dirichlet polyhedra of atoms are used as the edge weights and the nodes and edges are coloured according to chemical reasons. Two operations are defined to derive the representations: contracting an atom to other atoms keeping the local connectivity, and removing an atom together with all its bonds. The atoms of the crystal structure are called origin, removed, contracted or target according to their roles in the operations. Each structure representation is described as a labelled quotient graph and determined by (i) colours of the graph nodes and edges, (ii) some level for edge weights, and (iii) an arrangement of atoms according to their roles. The computer enumeration and topological comparative analysis of all representations for crystal structures of any composition and complexity are implemented into the TOPOS program package. The advantages of the method are shown by the analysis of typical inorganic compounds and a molecular packing.

Journal Article↗

A computer-aided approach to the structural analysis and modification of a large circulatory system model.

The purpose of this study is to show an approach to making an intelligent support system for understanding and modifying a large circulatory system model using techniques of system analysis. Structural analysis makes it possible to visualize hierarchies of Coleman's circulatory model Human. Two techniques are successively applied for structural analysis, model reduction and graph analysis by interpretative structural modeling (ISM). First, the analysis for model reduction removes input-output relations with an input-output gain less than a given threshold, and second, the ISM technique applied to the reduced model of Human provides hierarchical directed graphs. The proposed approach: 1) enables visualization of a hierarchy graph of cause and effect relations of the large circulatory model, 2) suggests control and diagnostic information to the model by tracing back a path in the hierarchy, and 3) allows the user to modify the circulatory model. The efficiency and performance of the proposed approach demonstrates technical indications of success in analyzing and justifying experimental evidences with the online help of the system.

Algorithms↗

Methods for robust clustering of epileptic EEG spikes.

We investigate algorithms for clustering of epileptic electroencephalogram (EEG) spikes. Such a method is useful prior to averaging and inverse computations since the spikes of a patient often belong to a few distinct classes. Data sets often contain outliers, which makes algorithms with robust performance desirable. We compare the fuzzy C-means (FCM) algorithm and a graph-theoretic algorithm. We give criteria for determination of the correct level of outlier contamination. The performance is then studied by aid of simulations, which show good results for a range of circumstances, for both algorithms. The graph-theoretic method gave better results than FCM for simulated signals. Also, when evaluating the methods on seven real-life data sets, the graph-theoretic method was the better method, in terms of closeness to the manual assessment by a neurophysiologist. However, there was some discrepancy between manual and automatic clustering and we suggest as an alternative method a human choice among a limited set of automatically obtained clusterings. Furthermore, we evaluate geometrically weighted feature extraction and conclude that it is useful as a supplementary dimension for clustering.

Algorithms↗

Graphical shape templates for automatic anatomy detection with applications to MRI brain scans.

A new method of model registration is proposed using graphical templates. A decomposable graph of landmarks is chosen in the template image. All possible candidates for these landmarks are found in the data image using robust relational local operators. A dynamic programming algorithm on the template graph finds the optimal match to a subset of the candidate points in polynomial time. This combination--local operators to describe points of interest/landmarks and a graph to describe their geometric arrangement in the plane--yields fast and precise matches of the model to the data with no initialization required. In addition, it provides a generic tool box for modeling shape in a variety of applications. This methodology is applied in the context of T2-weighted magnetic resonance (MR) axial and sagittal images of the brain to identify specific anatomies.

Algorithms↗

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

Algorithms↗

A tree-decomposition approach to protein structure prediction.

This paper proposes a tree decomposition of protein structures, which can be used to efficiently solve two key subproblems of protein structure prediction: protein threading for backbone prediction and protein side-chain prediction. To develop a unified tree-decomposition based approach to these two subproblems, we model them as a geometric neighborhood graph labeling problem. Theoretically, we can have a low-degree polynomial time algorithm to decompose a geometric neighborhood graph G = (V, E) into components with size O(|V|((2/3))log|V|). The computational complexity of the tree-decomposition based graph labeling algorithms is O(|V|Delta(tw+1)) where Delta is the average number of possible labels for each vertex and tw( = O(|V|((2/3))log|V|)) the tree width of G. Empirically, tw is very small and the tree-decomposition method can solve these two problems very efficiently. This paper also compares the computational efficiency of the tree-decomposition approach with the linear programming approach to these two problems and identifies the condition under which the tree-decomposition approach is more efficient than the linear programming approach. Experimental result indicates that the tree-decomposition approach is more efficient most of the time.

Algorithms↗

An efficient re-indexing algorithm for color-mapped images.

The efficiency of lossless compression algorithms for fixed-palette images (indexed images) may change if a different indexing scheme is adopted. Many lossless compression algorithms adopt a differential-predictive approach. Hence, if the spatial distribution of the indexes over the image is smooth, greater compression ratios may be obtained. Because of this, finding an indexing scheme that realizes such a smooth distribution is a relevant issue. Obtaining an optimal re-indexing scheme is suspected to be a hard problem and only approximate solutions have been provided in literature. In this paper, we restate the re-indexing problem as a graph optimization problem: an optimal re-indexing corresponds to the heaviest Hamiltonian path in a weighted graph. It follows that any algorithm which finds a good approximate solution to this graph-theoretical problem also provides a good re-indexing. We propose a simple and easy-to-implement approximation algorithm to find such a path. The proposed technique compares favorably with most of the algorithms proposed in literature, both in terms of computational complexity and of compression ratio.

Algorithms↗

Unsupervised contour closure algorithm for range image edge-based segmentation.

This paper presents an efficient technique for extracting closed contours from range images' edge points. Edge points are assumed to be given as input to the algorithm (i.e., previously computed by an edge-based range image segmentation technique). The proposed approach consists of three steps. Initially, a partially connected graph is generated from those input points. Then, the minimum spanning tree of that graph is computed. Finally, a postprocessing technique generates a single path through the regions' boundaries by removing noisy links and closing open contours. The novelty of the proposed approach lies in the fact that, by representing edge points as nodes of a partially connected graph, it reduces the contour closure problem to a minimum spanning tree partitioning problem plus a cost function minimization stage to generate closed contours. Experimental results with synthetic and real range images, together with comparisons with a previous technique, are presented.

Algorithms↗