Combining spectral sequencing and parallel simulated annealing for the MinLA problem

In this paper we present and analyze new sequential and parallel heuristics to approximate the Minimum Linear Arrangement problem (MinLA). The heuristics consist in obtaining a first global solution using Spectral Sequencing and improving it locally through Simulated Annealing. In order to accelerate the annealing process, we present a special neighborhood distribution that tends to favor moves with high probability to be accepted. We show how to make use of this neighborhood to parallelize the Metropolis stage on distributed memory machines by mapping partitions of the input graph to processors and performing moves concurrently. The paper reports the results obtained with this new heuristic when applied to a set of large graphs, including graphs arising from finite elements methods and graphs arising from VLSI applications. Compared to other heuristics, the measurements obtained show that the new heuristic improves the solution quality, decreases the running time and offers an excellent speedup when ran on a commodity network made of nine personal computers.Postprint (published version

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

The State-of-the-Art of Set Visualization

Sets comprise a generic data model that has been used in a variety of data analysis problems. Such problems involve analysing and visualizing set relations between multiple sets defined over the same collection of elements. However, visualizing sets is a non-trivial problem due to the large number of possible relations between them. We provide a systematic overview of state-of-the-art techniques for visualizing different kinds of set relations. We classify these techniques into six main categories according to the visual representations they use and the tasks they support. We compare the categories to provide guidance for choosing an appropriate technique for a given problem. Finally, we identify challenges in this area that need further research and propose possible directions to address these challenges. Further resources on set visualization are available at http://www.setviz.net

VLSI layouts and DNA physical mappings

We show that an important problem ($k$-ICG) in computational biology is equivalent to a colored version of a well-known graph layout problem ($k$-CVS).Comment: 7 page