Topologically Ordered Graph Clustering via Deterministic Annealing

International audienceThis paper proposes an organized generalization of Newman and Girvan's modularity measure for graph clustering. Optimized via a deterministic annealing scheme, this measure produces topologically ordered graph partitions that lead to faithful and readable graph representations on a 2 dimensional SOM like planar grid

Optimizing an Organized Modularity Measure for Topographic Graph Clustering: a Deterministic Annealing Approach

This paper proposes an organized generalization of Newman and Girvan's modularity measure for graph clustering. Optimized via a deterministic annealing scheme, this measure produces topologically ordered graph clusterings that lead to faithful and readable graph representations based on clustering induced graphs. Topographic graph clustering provides an alternative to more classical solutions in which a standard graph clustering method is applied to build a simpler graph that is then represented with a graph layout algorithm. A comparative study on four real world graphs ranging from 34 to 1 133 vertices shows the interest of the proposed approach with respect to classical solutions and to self-organizing maps for graphs

Recherche et représentation de communautés dans des grands graphes

15 pagesNational audienceThis paper deals with the analysis and the visualization of large graphs. Our interest in such a subject-matter is related to the fact that graphs are convenient widespread data structures. Indeed, this type of data can be encountered in a growing number of concrete problems: Web, information retrieval, social networks, biological interaction networks... Furthermore, the size of these graphs becomes increasingly large as the progression of the means for data gathering and storage steadily strengthens. This calls for new methods in graph analysis and visualization which are now important and dynamic research fields at the interface of many disciplines such as mathematics, statistics, computer science and sociology. In this paper, we propose a method for graphs representation and visualization based on a prior clustering of the vertices. Newman and Girvan (2004) points out that “reducing [the] level of complexity [of a network] to one that can be interpreted readily by the human eye, will be invaluable in helping us to understand the large-scale structure of these new network data”: we rely on this assumption to use a priori a clustering of the vertices as a preliminary step for simplifying the representation of the graphs - as a whole. The clustering phase consists in optimizing a quality measure specifically suitable for the research of dense groups in graphs. This quality measure is the modularity and expresses the “distance” to a null model in which the graph edges do not depend on the clustering. The modularity has shown its relevance in solving the problem of uncovering dense groups in a graph. Optimization of the modularity is done through a stochastic simulated annealing algorithm. The visualization/representation phase, as such, is based on a force-directed algorithm described in Truong et al. (2007). After giving a short introduction to the problem and detailing the vertices clustering and representation algorithms, the paper will introduce and discuss two applications from the social network field

Contours in Visualization

This thesis studies the visualization of set collections either via or defines as the relations among contours. In the first part, dynamic Euler diagrams are used to communicate and improve semimanually the result of clustering methods which allow clusters to overlap arbitrarily. The contours of the Euler diagram are rendered as implicit surfaces called blobs in computer graphics. The interaction metaphor is the moving of items into or out of these blobs. The utility of the method is demonstrated on data arising from the analysis of gene expressions. The method works well for small datasets of up to one hundred items and few clusters. In the second part, these limitations are mitigated employing a GPU-based rendering of Euler diagrams and mixing textures and colors to resolve overlapping regions better. The GPU-based approach subdivides the screen into triangles on which it performs a contour interpolation, i.e. a fragment shader determines for each pixel which zones of an Euler diagram it belongs to. The rendering speed is thus increased to allow multiple hundred items. The method is applied to an example comparing different document clustering results. The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Adapting popular graph drawing approaches to the problem of contour tree drawing it is found that they are unable to convey this information. Five aesthetic criteria for drawing contour trees are proposed and a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria is presented. The implementation is fast and effective for contour tree sizes usually used in interactive systems and also produces readable pictures for larger trees. Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods to analyze these model\''s validity. The fourth part of the thesis focuses on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; they are huge and high dimensional. Their most salient features are described by their so-called barrier tree -- a contour tree for discrete observation spaces. The changing folding landscapes of a growing RNA chain are visualized as an animation of the corresponding barrier tree sequence. The animation is created as an adaption of the foresight layout with tolerance algorithm for dynamic graph layout. The adaptation requires changes to the concept of supergraph and it layout. The thesis finishes with some thoughts on how these approaches can be combined and how the task the application should support can help inform the choice of visualization modality

A survey of outlier detection methodologies

Outlier detection has been used for centuries to detect and, where appropriate, remove anomalous observations from data. Outliers arise due to mechanical faults, changes in system behaviour, fraudulent behaviour, human error, instrument error or simply through natural deviations in populations. Their detection can identify system faults and fraud before they escalate with potentially catastrophic consequences. It can identify errors and remove their contaminating effect on the data set and as such to purify the data for processing. The original outlier detection methods were arbitrary but now, principled and systematic techniques are used, drawn from the full gamut of Computer Science and Statistics. In this paper, we introduce a survey of contemporary techniques for outlier detection. We identify their respective motivations and distinguish their advantages and disadvantages in a comparative review

The influence of topology and information diffusion on networked game dynamics

This thesis studies the influence of topology and information diffusion on the strategic interactions of agents in a population. It shows that there exists a reciprocal relationship between the topology, information diffusion and the strategic interactions of a population of players. In order to evaluate the influence of topology and information flow on networked game dynamics, strategic games are simulated on populations of players where the players are distributed in a non-homogeneous spatial arrangement. The initial component of this research consists of a study of evolution of the coordination of strategic players, where the topology or the structure of the population is shown to be critical in defining the coordination among the players. Next, the effect of network topology on the evolutionary stability of strategies is studied in detail. Based on the results obtained, it is shown that network topology plays a key role in determining the evolutionary stability of a particular strategy in a population of players. Then, the effect of network topology on the optimum placement of strategies is studied. Using genetic optimisation, it is shown that the placement of strategies in a spatially distributed population of players is crucial in maximising the collective payoff of the population. Exploring further the effect of network topology and information diffusion on networked games, the non-optimal or bounded rationality of players is modelled using topological and directed information flow of the network. Based on the topologically distributed bounded rationality model, it is shown that the scale-free and small-world networks emerge in randomly connected populations of sub-optimal players. Thus, the topological and information theoretic interpretations of bounded rationality suggest the topology, information diffusion and the strategic interactions of socio-economical structures are cyclically interdependent

The influence of topology and information diffusion on networked game dynamics

This thesis studies the influence of topology and information diffusion on the strategic interactions of agents in a population. It shows that there exists a reciprocal relationship between the topology, information diffusion and the strategic interactions of a population of players. In order to evaluate the influence of topology and information flow on networked game dynamics, strategic games are simulated on populations of players where the players are distributed in a non-homogeneous spatial arrangement. The initial component of this research consists of a study of evolution of the coordination of strategic players, where the topology or the structure of the population is shown to be critical in defining the coordination among the players. Next, the effect of network topology on the evolutionary stability of strategies is studied in detail. Based on the results obtained, it is shown that network topology plays a key role in determining the evolutionary stability of a particular strategy in a population of players. Then, the effect of network topology on the optimum placement of strategies is studied. Using genetic optimisation, it is shown that the placement of strategies in a spatially distributed population of players is crucial in maximising the collective payoff of the population. Exploring further the effect of network topology and information diffusion on networked games, the non-optimal or bounded rationality of players is modelled using topological and directed information flow of the network. Based on the topologically distributed bounded rationality model, it is shown that the scale-free and small-world networks emerge in randomly connected populations of sub-optimal players. Thus, the topological and information theoretic interpretations of bounded rationality suggest the topology, information diffusion and the strategic interactions of socio-economical structures are cyclically interdependent

Coverage, Continuity and Visual Cortical Architecture

The primary visual cortex of many mammals contains a continuous representation of visual space, with a roughly repetitive aperiodic map of orientation preferences superimposed. It was recently found that orientation preference maps (OPMs) obey statistical laws which are apparently invariant among species widely separated in eutherian evolution. Here, we examine whether one of the most prominent models for the optimization of cortical maps, the elastic net (EN) model, can reproduce this common design. The EN model generates representations which optimally trade of stimulus space coverage and map continuity. While this model has been used in numerous studies, no analytical results about the precise layout of the predicted OPMs have been obtained so far. We present a mathematical approach to analytically calculate the cortical representations predicted by the EN model for the joint mapping of stimulus position and orientation. We find that in all previously studied regimes, predicted OPM layouts are perfectly periodic. An unbiased search through the EN parameter space identifies a novel regime of aperiodic OPMs with pinwheel densities lower than found in experiments. In an extreme limit, aperiodic OPMs quantitatively resembling experimental observations emerge. Stabilization of these layouts results from strong nonlocal interactions rather than from a coverage-continuity-compromise. Our results demonstrate that optimization models for stimulus representations dominated by nonlocal suppressive interactions are in principle capable of correctly predicting the common OPM design. They question that visual cortical feature representations can be explained by a coverage-continuity-compromise.Comment: 100 pages, including an Appendix, 21 + 7 figure

The Wiring Economy Principle: Connectivity Determines Anatomy in the Human Brain

Minimization of the wiring cost of white matter fibers in the human brain appears to be an organizational principle. We investigate this aspect in the human brain using whole brain connectivity networks extracted from high resolution diffusion MRI data of 14 normal volunteers. We specifically address the question of whether brain anatomy determines its connectivity or vice versa. Unlike previous studies we use weighted networks, where connections between cortical nodes are real-valued rather than binary off-on connections. In one set of analyses we found that the connectivity structure of the brain has near optimal wiring cost compared to random networks with the same number of edges, degree distribution and edge weight distribution. A specifically designed minimization routine could not find cheaper wiring without significantly degrading network performance. In another set of analyses we kept the observed brain network topology and connectivity but allowed nodes to freely move on a 3D manifold topologically identical to the brain. An efficient minimization routine was written to find the lowest wiring cost configuration. We found that beginning from any random configuration, the nodes invariably arrange themselves in a configuration with a striking resemblance to the brain. This confirms the widely held but poorly tested claim that wiring economy is a driving principle of the brain. Intriguingly, our results also suggest that the brain mainly optimizes for the most desirable network connectivity, and the observed brain anatomy is merely a result of this optimization