2009
DOI: 10.1186/1471-2105-10-s1-s59
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A new graph-based method for pairwise global network alignment

Abstract: Background: In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to NPhard problems. Most previous algorithmic work on network alignments is heuristic in nature.

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Cited by 180 publications
(119 citation statements)
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“…Network alignment problem has also been studied by many works in recent years, which has many applications bioinformatics [11,19]. Bayati et.…”
Section: Related Workmentioning
confidence: 99%
“…Network alignment problem has also been studied by many works in recent years, which has many applications bioinformatics [11,19]. Bayati et.…”
Section: Related Workmentioning
confidence: 99%
“…This corresponds to a QAP instance with a symmetric and sparse weight matrix. We improve upon an existing Lagrangian relaxation approach presented in previous work [7] to obtain strong upper and lower bounds for the problem. We exploit the closeness to QAP and generalize a dual descent method for updating the Lagrangian multipliers to the generalized problem.…”
Section: Contributionmentioning
confidence: 99%
“…The IsoRank algorithm by Singh et al [6] formulates the global alignment problem as an eigenvalue problem, which preferentially matches nodes with similar neighborhood. Klau [7] presented Natalie, the predecessor of Natalie 2.0, which is described in detail in this paper. The methods are based on an integer linear programming approach solved by Lagrangian relaxation.…”
mentioning
confidence: 99%
“…For instance Zaslavskiy et al (2009) redefined the problem of global alignment as a standard graph matching problem and investigated methods using ideas and approaches from state-of-the-art graph matching techniques. (Klau, 2009) formalized global network alignment as an integer linear programming problem, where a near-optimal solution with a quality guarantee is found by solving a Lagrangian relaxation of the original optimization formulation. Recently, Chindelevitch et al (2010) proposed a method where the global alignment is encoded as bipartite matching and applied a very efficient local optimization heuristic used for the well-known Travelling Salesman Problem.…”
Section: Global Pairwise Network Alignmentmentioning
confidence: 99%