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56
MatrixExplorer: a DualRepresentation System to Explore Social Networks
 IEEE Transactions on Visualization and Computer Graphics
, 2006
"... Abstract — MatrixExplorer is a network visualization system that uses two representations: nodelink diagrams and matrices. Its design comes from a list of requirements formalized after several interviews and a participatory design session conducted with social science researchers. Although matrices ..."
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Cited by 92 (13 self)
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Abstract — MatrixExplorer is a network visualization system that uses two representations: nodelink diagrams and matrices. Its design comes from a list of requirements formalized after several interviews and a participatory design session conducted with social science researchers. Although matrices are commonly used in social networks analysis, very few systems support the matrixbased representations to visualize and analyze networks. MatrixExplorer provides several novel features to support the exploration of social networks with a matrixbased representation, in addition to the standard interactive filtering and clustering functions. It provides tools to reorder (layout) matrices, to annotate and compare findings across different layouts and find consensus among several clusterings. MatrixExplorer also supports Nodelink diagram views which are familiar to most users and remain a convenient way to publish or communicate exploration results. Matrix and nodelink representations are kept synchronized at all stages of the exploration process. Index Terms — social networks visualization, nodelink diagrams, matrixbased representations, exploratory process, matrix ordering, interactive clustering, consensus. Fig. 1. MatrixExplorer showing two synchronized representations of the same network: matrix on the left and nodelink on the right. 1
Graph edit distance from spectral seriation
 IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
, 2005
"... This paper is concerned with computing graph edit distance. One of the criticisms that can be leveled at existing methods for computing graph edit distance is that they lack some of the formality and rigor of the computation of string edit distance. Hence, our aim is to convert graphs to string seq ..."
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Cited by 40 (6 self)
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This paper is concerned with computing graph edit distance. One of the criticisms that can be leveled at existing methods for computing graph edit distance is that they lack some of the formality and rigor of the computation of string edit distance. Hence, our aim is to convert graphs to string sequences so that string matching techniques can be used. To do this, we use a graph spectral seriation method to convert the adjacency matrix into a string or sequence order. We show how the serial ordering can be established using the leading eigenvector of the graph adjacency matrix. We pose the problem of graphmatching as a maximum a posteriori probability (MAP) alignment of the seriation sequences for pairs of graphs. This treatment leads to an expression in which the edit cost is the negative logarithm of the a posteriori sequence alignment probability. We compute the edit distance by finding the sequence of string edit operations which minimizes the cost of the path traversing the edit lattice. The edit costs are determined by the components of the leading eigenvectors of the adjacency matrix and by the edge densities of the graphs being matched. We demonstrate the utility of the edit distance on a number of graph clustering problems.
A MultiScale Algorithm for the Linear Arrangement Problem
 Proc. 28th Inter. Workshop on GraphTheoretic Concepts in Computer Science (WG’02), LNCS 2573
, 2002
"... Finding a linear ordering of the vertices of a graph is a common problem arising in diverse applications. In this paper we present a lineartime algorithm for this problem, based on the multiscale paradigm. Experimental results are similar to those of the best known approaches, while the running ti ..."
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Cited by 31 (4 self)
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Finding a linear ordering of the vertices of a graph is a common problem arising in diverse applications. In this paper we present a lineartime algorithm for this problem, based on the multiscale paradigm. Experimental results are similar to those of the best known approaches, while the running time is significantly better, enabling it to deal with much larger graphs. The paper contains a general multiscale construction, which may be used for a broader range of ordering problems.
Geometric and Combinatorial Tiles in 01 Data
 In: Proceedings PKDD’04. Volume 3202 of LNAI
, 2004
"... In this paper we introduce a simple probabilistic model, hierarchical tiles, for 01 data. A basic tile (X,Y,p) specifies a subset X of the rows and a subset Y of the columns of the data, i.e., a rectangle, and gives a probability p for the occurrence of 1s in the cells of X x Y. A hierarchical tile ..."
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Cited by 22 (0 self)
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In this paper we introduce a simple probabilistic model, hierarchical tiles, for 01 data. A basic tile (X,Y,p) specifies a subset X of the rows and a subset Y of the columns of the data, i.e., a rectangle, and gives a probability p for the occurrence of 1s in the cells of X x Y. A hierarchical tile has additionally a set of exception tiles that specify the probabilities for subrectangles of the original rectangle. If the rows and columns are ordered and X and Y consist of consecutive elements in those orderings, then the tile is geometric; otherwise it is combinatorial. We give a simple randomized algorithm for finding good geometric tiles. Our main result shows that using spectral ordering techniques one can find good orderings that turn combinatorial tiles into geometric tiles. We give empirical results on the performance of the methods.
Experiments on the Minimum Linear Arrangement Problem
 Sistemes Informàtics, 2001. (Preliminary version in Alex ’98 — Building Bridges between Theory and Applications
, 2001
"... This paper deals with the Minimum Linear Arrangement problem from an experimental point of view. Using a testsuite of sparse graphs, we experimentally compare several algorithms to obtain upper and lower bounds for this problem. The algorithms considered include Successive Augmentation heuristics, ..."
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Cited by 21 (0 self)
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This paper deals with the Minimum Linear Arrangement problem from an experimental point of view. Using a testsuite of sparse graphs, we experimentally compare several algorithms to obtain upper and lower bounds for this problem. The algorithms considered include Successive Augmentation heuristics, Local Search heuristics and Spectral Sequencing. The testsuite is based on two random models and "real life" graphs. As a consequence of this study, two main conclusions can be drawn: On one hand, the best approximations are usually obtained using Simulated Annealing, which involves a large amount of computation time. However, solutions found with Spectral Sequencing are close to the ones found with Simulated Annealing and can be obtained in significantly less time. On the other hand, we notice that there exists a big gap between the best obtained upper bounds and the best obtained lower bounds. These two facts together show that, in practice, finding lower and upper bounds for the Minimum ...
Edit distance from graph spectra
 In Proc. 9th IEEE Int. Conf. Comp. Vis
, 2003
"... This paper is concerned with computing graph edit distance. One of the criticisms that can be leveled at existing methods for computing graph edit distance is that it lacks the formality and rigour of the computation of string edit distance. Hence, our aim is to convert graphs to string sequences so ..."
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Cited by 14 (2 self)
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This paper is concerned with computing graph edit distance. One of the criticisms that can be leveled at existing methods for computing graph edit distance is that it lacks the formality and rigour of the computation of string edit distance. Hence, our aim is to convert graphs to string sequences so that standard string edit distance techniques can be used. To do this we use graph spectral seriation method to convert the adjacency matrix into a string or sequence order. We pose the problem of graphmatching as maximum a posteriori probability alignment of the seriation sequences for pairs of graphs. This treatment leads to an expression for the edit costs. We compute the edit distance by finding the sequence of string edit operations which minimise the cost of the path traversing the edit lattice. The edit costs are defined in terms of the a posteriori probability of visiting a site on the lattice. We demonstrate the method with results on a dataset of Delaunay graphs. 1.
Reconstructing the temporal ordering of biological samples using microarray data
 Bioinformatics
, 2002
"... Motivation: Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multidimensional data, such as those resulting from DNA microarray experiments, in order to reconstru ..."
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Cited by 14 (0 self)
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Motivation: Accurate time series for biological processes are difficult to estimate due to problems of synchronization, temporal sampling and rate heterogeneity. Methods are needed that can utilize multidimensional data, such as those resulting from DNA microarray experiments, in order to reconstruct time series from unordered or poorly ordered sets of observations. Results: We present a set of algorithms for estimating temporal orderings from unordered sets of sample elements. The techniques we describe are based on modifications of a minimumspanning tree calculated from a weighted, undirected graph. We demonstrate the efficacy of our approach by applying these techniques to an artificial data set as well as several gene expression data sets derived from DNA microarray experiments. In addition to estimating orderings, the techniques we describe also provide useful heuristics for assessing relevant properties of sample datasets such as noise and sampling intensity, and we show how a data structure called a PQtree can be used to represent uncertainty in a reconstructed ordering. Availability: Academic implementations of the ordering algorithms are available as source code (in the programming language Python) on our web site, along with documentation on their use. The artificial ‘jelly roll ’ data set upon which the algorithm was tested is also available from this web site. The publicly available gene expression data may be found at
Graph Matching and Clustering Using Spectral Partitions
 Pattern Recognition
"... Although inexact graphmatching is a problem of potentially exponential complexity, the problem may be simplified by decomposing the graphs to be matched into smaller subgraphs. If this is done, then the process may cast into a hierarchical framework and hence rendered suitable for parallel computat ..."
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Cited by 14 (0 self)
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Although inexact graphmatching is a problem of potentially exponential complexity, the problem may be simplified by decomposing the graphs to be matched into smaller subgraphs. If this is done, then the process may cast into a hierarchical framework and hence rendered suitable for parallel computation. In this paper we describe a spectral method which can be used to partition graphs into nonoverlapping subgraphs. In particular, we demonstrate how the Fiedlervector of the Laplacian matrix can be used to decompose graphs into nonoverlapping neighbourhoods that can be used for the purposes of both matching and clustering.
Fragments of Order
, 2003
"... Highdimensional collections of 01 data occur in many applications. The attributes in such data sets are typically considered to be unordered. However, in many cases there is a natural total or partial order # underlying the variables of the data set. Examples of variables for which such orders exi ..."
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Cited by 13 (2 self)
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Highdimensional collections of 01 data occur in many applications. The attributes in such data sets are typically considered to be unordered. However, in many cases there is a natural total or partial order # underlying the variables of the data set. Examples of variables for which such orders exist include terms in documents, courses in enrollment data, and paleontological sites in fossil data collections. The observations in such applications are flat, unordered sets; however, the data sets respect the underlying ordering of the variables. By this we mean that if A # B # C are three variables respecting the underlying ordering #, and both of variables A and C appear in an observation, then, up to noise levels, variable B also appears in this observation. Similarly, if A1 # A2 # # A l1 # A l is a longer sequence of variables, we do not expect to see many observations for which there are indices i < j < k such that A i and Ak occur in the observation but A j does not.
Approximation and FixedParameter Algorithms for Consecutive Ones Submatrix Problems
 JOURNAL OF COMPUTER AND SYSTEM SCIENCES
"... We develop an algorithmically useful refinement of a forbidden submatrix characterization of 0/1matrices fulfilling the Consecutive Ones Property (C1P). This characterization finds applications in new polynomialtime approximation algorithms and fixedparameter tractability results for the NPhard ..."
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We develop an algorithmically useful refinement of a forbidden submatrix characterization of 0/1matrices fulfilling the Consecutive Ones Property (C1P). This characterization finds applications in new polynomialtime approximation algorithms and fixedparameter tractability results for the NPhard problem to delete a minimum number of rows or columns from a 0/1matrix such that the remaining submatrix has the C1P.