BFL: a node and edge betweenness based fast layout algorithm for large scale networks.
BACKGROUND
Network visualization would serve as a useful first step for analysis. However, current graph layout algorithms for biological pathways are insensitive to biologically important information, e.g. subcellular localization, biological node and graph attributes, or/and not available for large scale networks, e.g. more than 10000 elements.


RESULTS
To overcome these problems, we propose the use of a biologically important graph metric, betweenness, a measure of network flow. This metric is highly correlated with many biological phenomena such as lethality and clusters. We devise a new fast parallel algorithm calculating betweenness to minimize the preprocessing cost. Using this metric, we also invent a node and edge betweenness based fast layout algorithm (BFL). BFL places the high-betweenness nodes to optimal positions and allows the low-betweenness nodes to reach suboptimal positions. Furthermore, BFL reduces the runtime by combining a sequential insertion algorim with betweenness. For a graph with n nodes, this approach reduces the expected runtime of the algorithm to O(n2) when considering edge crossings, and to O(n log n) when considering only density and edge lengths.


CONCLUSIONS
Our BFL algorithm is compared against fast graph layout algorithms and approaches requiring intensive optimizations. For gene networks, we show that our algorithm is faster than all layout algorithms tested while providing readability on par with intensive optimization algorithms. We achieve a 1.4 second runtime for a graph with 4000 nodes and 12000 edges on a standard desktop computer.
Hashimoto
Tatsunori B
TB
Harvard College, Adams House, Cambridge, Massachusetts, MA 02138, USA. thashim@fas.harvard.edu
Nagasaki
Masao
M
Kojima
Kaname
K
Miyano
Satoru
S
D000465:Algorithms; D003196:Computer Graphics; D053858:Metabolic Networks and Pathways; D010363:Pattern Recognition, Automated; D014584:User-Computer Interface