PARALLEL CALCULATION OF SUBGRAPH CENSUS IN BIOLOGICAL NETWORKS

Pedro Ribeiro, Fernando Silva, Luís Lopes

2010

Abstract

Mining meaningful data from complex biological networks is a critical task in many areas of research. One important example is calculating the frequency of all subgraphs of a certain size, also known as the subgraph census problem. This can provide a very comprehensive structural characterization of a network and is also used as an intermediate step in the computation of network motifs, an important basic building block of networks, that try to bridge the gap between structure and function. The subgraph census problem is computationally hard and here we present several parallel strategies to solve this problem. Our initial strategies were refined towards achieving an efficient and scalable adaptive parallel algorithm. This algorithm achieves almost linear speedups up to 128 cores when applied to a representative set of biological networks from different domains and makes the calculation of census for larger subgraph sizes feasible.

Paper Citation

in Harvard Style

Ribeiro P., Silva F. and Lopes L. (2010). PARALLEL CALCULATION OF SUBGRAPH CENSUS IN BIOLOGICAL NETWORKS . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 56-65. DOI: 10.5220/0002749600560065

in Bibtex Style

@conference{bioinformatics10,
author={Pedro Ribeiro and Fernando Silva and Luís Lopes},
title={PARALLEL CALCULATION OF SUBGRAPH CENSUS IN BIOLOGICAL NETWORKS},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={56-65},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002749600560065},
isbn={978-989-674-019-1},
}

in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - PARALLEL CALCULATION OF SUBGRAPH CENSUS IN BIOLOGICAL NETWORKS
SN - 978-989-674-019-1
AU - Ribeiro P.
AU - Silva F.
AU - Lopes L.
PY - 2010
SP - 56
EP - 65
DO - 10.5220/0002749600560065