Parallel Calculations of Subgraph Census in Biological Networks

• Type: Article in International Conference Proceedings Book
• Date: 2010

Authors

Pedro Ribeiro (Author) FCUP; Fernando Silva (Author) FCUP; Luís Lopes (Author) FCUP

Conference proceedings International

Title: BIOINFORMATICS 2010 - Proceedings of the 1st International Conference on Bioinformatics

Pages: 56-65

1st International Conference on Bioinformatics, BIOINFORMATICS 2010

Valencia, Spain, 20 - 23 January, 2010

Indexing

COMPENDEX

Scientific classification

FOS: Natural sciences > Computer and information sciences

Other information

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

Notes: ISBN-13: 9789896740191; Main Heading: Bioinformatics; Controlled terms: Adaptive algorithms - Circuit theory - Parallel algorithms - Parallel architectures - Problem solving - Surveys.