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Title: REFBSS: Reference Based Similarity Search in Biological Network Databases
Authors: Söylev, Arda
Abul, Osman
Keywords: Biological networks
biological database
network querying
network alignment
reference based indexing
network clustering
highest degree node
Issue Date: 2015
Publisher: IEEE
Source: Soylev, A., & Abul, O. (2015, August). Refbss: Reference based similarity search in biological network databases. In 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (pp. 1-8). IEEE.
Abstract: Biological networks, mostly abstracted as graphs, are key to many important activities inside the cell. Similarity-based analysis is one of the techniques for understanding the role of a query network. In that context, a database consisting of biological networks is aligned with a query network and the networks having a similarity score higher and lower than a predefined cutoff value are separated. Because of the NP-complete sub-graph isomorphism problem, nontrivial similarity score calculation is computationally too expensive. To this end, several methods are proposed in the literature for an acceptable solution. Reference-based indexing methods are one of the popular solutions which indexes the network database by extracting small sized networks as references to be aligned with the query network. Based on this strategy, we propose a novel model that has methodological and heuristic improvements for fast approximate similarity search, which all turn out to be fast and accurate. We also have a high-performance implementation on Hadoop that achieved 11.42 speedup on a Hadoop cluster with 18 cores on a sample KEGG network database.
Description: IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology CIBCB (2015 : Honolulu, HI)
ISBN: 978-1-4799-6926-5
Appears in Collections:Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

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