Fast and Accurate Alignment of Multiple Protein Networks

Abstract

Abstract. Comparative analysis of protein networks has proven to be a powerful approach for elucidating network structure and predicting protein function and interaction. A fundamental challenge for the successful application of this approach is to devise an efficient multiple network alignment algorithm. Here we present a novel framework for the problem. At the heart of the framework is a novel representation of multiple networks that is only linear in their size as opposed to current exponential representations. Our alignment algorithm is very efficient, being capable of aligning 10 networks with tens of thousands of proteins each in minutes. We show that our algorithm outperforms a previous strategy for the problem that is based on progressive alignment, and produces results that are more in line with current biological knowledge.

Meta-path-based link prediction in schema-rich heterogeneous information network

“…And kinds of data mining tasks for HIN are realized recently. These research developments include similarity measure [12,24], clustering [25,26], classification [9,11], link prediction [2,22], ranking [14,34], recommendation [8,18], information fusion [10,19]. But these tasks just work on simple HINs with simple schema.…”

A Survey on Evolutionary Analysis in PPI Networks

“…Recently, a supervised, automated parameter learner was proposed to lessen the burden of parameter tuning (Flannick et al, 2009). Another phylogeny-guided local network alignment was proposed by Kalaev et al (2008). Although the method uses the same probabilistic scoring for conserved complex as Network-BLAST, it avoids its exponential scalability by redefining the alignment model such that it does not construct the merged representation of aligned networks but represents them as separate layers interconnected via orthologous mapping.…”

NetMatchStar: an enhanced Cytoscape network querying app

“…Several different methods have been developed for this purpose: (i) Network Motif fiding [3][4][5][6][7][8][9][10][11][12] , network querying [13][14][15] and network alignment [16][17][18][19][20][21] algorithms.…”