Application of Approximate Pattern Matching in Two Dimensional Spaces to Grid Layout for Biochemical Network Maps

Jérémie Bourdon,Hideaki Yoshida,Hiroyuki Kurata,Shinichi Shimozono,Kentaro Inoue

doi:10.1371/journal.pone.0037739

Jérémie Bourdon, Hideaki Yoshida + Show 3 more

Open Access

https://doi.org/10.1371/journal.pone.0037739

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Abstract

BackgroundFor visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process.ResultsWe propose a hybrid grid layout algorithm that consists of a non-grid, fast layout (preprocessor) algorithm and an approximate pattern matching algorithm that distributes the resultant preprocessed nodes on square grid points. To demonstrate the feasibility of the hybrid layout algorithm, it is characterized in terms of the calculation time, numbers of edge-edge and node-edge crossings, relative edge lengths, and F-measures. The proposed algorithm achieves outstanding performances compared with other existing grid layouts.Conclusions Use of an approximate pattern matching algorithm quickly redistributes the laid-out nodes by fast, non-grid algorithms on the square grid points, while preserving the topological relationships among the nodes. The proposed algorithm is a novel use of the pattern matching, thereby providing a breakthrough for grid layout. This application program can be freely downloaded from http://www.cadlive.jp/hybridlayout/hybridlayout.html.

Highlights

Rapid advances in molecular biology have revealed a detailed map for gene regulatory networks, signal transduction pathways and metabolic circuits
LD, an improved version of grid layout algorithm (GL), calculated layouts faster than GL, but it was still slower than the hybrid layout algorithms
Comparison with a Non-Grid Layout Algorithm We focus on the grid layouts, while many scientists would be interested in the performance of fast, non-grid layout algorithms that avoid the overlapping of node labels

Summary

Introduction

Rapid advances in molecular biology have revealed a detailed map for gene regulatory networks, signal transduction pathways and metabolic circuits. Visual representations of such networks are critically important to help researchers gain insight into a largescale complex network [1], stimulating the interest in developing computational tools that support visualization of biochemical networks. For visualizing large-scale biochemical network maps, it is important to calculate the coordinates of molecular nodes quickly and to enhance the understanding or traceability of them. The grid layout is effective in drawing compact, orderly, balanced network maps with node label spaces, but existing grid layout algorithms often require a high computational cost because they have to consider complicated positional constraints through the entire optimization process

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