17,167 research outputs found

    Information visualization for DNA microarray data analysis: A critical review

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    Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work

    A parent-centered radial layout algorithm for interactive graph visualization and animation

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    We have developed (1) a graph visualization system that allows users to explore graphs by viewing them as a succession of spanning trees selected interactively, (2) a radial graph layout algorithm, and (3) an animation algorithm that generates meaningful visualizations and smooth transitions between graphs while minimizing edge crossings during transitions and in static layouts. Our system is similar to the radial layout system of Yee et al. (2001), but differs primarily in that each node is positioned on a coordinate system centered on its own parent rather than on a single coordinate system for all nodes. Our system is thus easy to define recursively and lends itself to parallelization. It also guarantees that layouts have many nice properties, such as: it guarantees certain edges never cross during an animation. We compared the layouts and transitions produced by our algorithms to those produced by Yee et al. Results from several experiments indicate that our system produces fewer edge crossings during transitions between graph drawings, and that the transitions more often involve changes in local scaling rather than structure. These findings suggest the system has promise as an interactive graph exploration tool in a variety of settings

    Improving the Asymmetric TSP by Considering Graph Structure

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    Recent works on cost based relaxations have improved Constraint Programming (CP) models for the Traveling Salesman Problem (TSP). We provide a short survey over solving asymmetric TSP with CP. Then, we suggest new implied propagators based on general graph properties. We experimentally show that such implied propagators bring robustness to pathological instances and highlight the fact that graph structure can significantly improve search heuristics behavior. Finally, we show that our approach outperforms current state of the art results.Comment: Technical repor

    Persistent Homology Guided Force-Directed Graph Layouts

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    Graphs are commonly used to encode relationships among entities, yet their abstractness makes them difficult to analyze. Node-link diagrams are popular for drawing graphs, and force-directed layouts provide a flexible method for node arrangements that use local relationships in an attempt to reveal the global shape of the graph. However, clutter and overlap of unrelated structures can lead to confusing graph visualizations. This paper leverages the persistent homology features of an undirected graph as derived information for interactive manipulation of force-directed layouts. We first discuss how to efficiently extract 0-dimensional persistent homology features from both weighted and unweighted undirected graphs. We then introduce the interactive persistence barcode used to manipulate the force-directed graph layout. In particular, the user adds and removes contracting and repulsing forces generated by the persistent homology features, eventually selecting the set of persistent homology features that most improve the layout. Finally, we demonstrate the utility of our approach across a variety of synthetic and real datasets

    Static consensus in passifiable linear networks

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    Sufficient conditions of consensus (synchronization) in networks described by digraphs and consisting of identical determenistic SIMO systems are derived. Identical and nonidentical control gains (positive arc weights) are considered. Connection between admissible digraphs and nonsmooth hypersurfaces (sufficient gain boundary) is established. Necessary and sufficient conditions for static consensus by output feedback in networks consisting of certain class of double integrators are rediscovered. Scalability for circle digraph in terms of gain magnitudes is studied. Examples and results of numerical simulations are presented.Comment: 13 pages, 5 figure
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