PARALLEL CALCULATION OF SUBGRAPH CENSUS IN BIOLOGICAL NETWORKS

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

Authors

Ribeiro, P (Author) Other; Silva, F (Author) FCUP; Lopes, L (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, 20 January 2010 through 23 January 2010

Indexing

ISI Web of Knowledge - 5 Citations

Scopus - 8 Citations

Other information

Authenticus ID: P-007-VDF

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 sub graph 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 com-putationally 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

No. of pages: 10