17,167 research outputs found
Information visualization for DNA microarray data analysis: A critical review
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
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
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
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
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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