Email updates

Keep up to date with the latest news and content from BMC Systems Biology and BioMed Central.

This article is part of the supplement: Selected articles from the Third International Symposium on Optimization and Systems Biology

Open Access Open Badges Proceedings

Comparing biological networks via graph compression

Morihiro Hayashida and Tatsuya Akutsu

Author Affiliations

Bioinformatics Center, Institute for Chemical Research, Kyoto University,Gokasho, Uji, Kyoto, 611-0011, Japan

BMC Systems Biology 2010, 4(Suppl 2):S13  doi:10.1186/1752-0509-4-S2-S13

Published: 13 September 2010



Comparison of various kinds of biological data is one of the main problems in bioinformatics and systems biology. Data compression methods have been applied to comparison of large sequence data and protein structure data. Since it is still difficult to compare global structures of large biological networks, it is reasonable to try to apply data compression methods to comparison of biological networks. In existing compression methods, the uniqueness of compression results is not guaranteed because there is some ambiguity in selection of overlapping edges.


This paper proposes novel efficient methods, CompressEdge and CompressVertices, for comparing large biological networks. In the proposed methods, an original network structure is compressed by iteratively contracting identical edges and sets of connected edges. Then, the similarity of two networks is measured by a compression ratio of the concatenated networks. The proposed methods are applied to comparison of metabolic networks of several organisms, H. sapiens, M. musculus, A. thaliana, D. melanogaster, C. elegans, E. coli, S. cerevisiae, and B. subtilis, and are compared with an existing method. These results suggest that our methods can efficiently measure the similarities between metabolic networks.


Our proposed algorithms, which compress node-labeled networks, are useful for measuring the similarity of large biological networks.