Integrating data from heterogeneous sources is often modeled as merging graphs. Given two or more 'compatible', but not-isomorphic graphs, the first step is to identify a graph alignment, where a potentially partial mapping of vertices between two graphs is computed. A significant portion of the literature on this problem only takes the global structure of the input graphs into account. Only more recent ones additionally use vertex and edge attributes to achieve a more accurate alignment. However, these methods are not designed to scale to map large graphs arising in many modern applications. We propose a new iterative graph aligner, gsaNA, that uses the global structure of the graphs to significantly reduce the problem size and align large graphs with a minimal loss of information. Concretely, we show that our proposed technique is highly flexible, can be used to achieve higher recall, and it is orders of magnitudes faster than the current state of the art techniques.
NetAlign @cite_31 formulates the network alignment problem as an integer quadratic programming problem to maximize the number of squares''. A near-optimal solution is obtained by finding the maximum a posteriori assignment using belief propagation heuristic and message-passing algorithms which yield near optimal results in practice. Another message passing network alignment algorithm on top of belief propagation is proposed by @cite_18 . @cite_8 propose to align two bipartite graphs with a fast projected gradient descent algorithm which exploits the structural properties of the graphs.
@cite_31 @cite_18 @cite_8
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We propose a new distributed algorithm for sparse variants of the network alignment problem, which occurs in a variety of data mining areas including systems biology, database matching, and computer vision. Our algorithm uses a belief propagation heuristic and provides near optimal solutions for this NP-hard combinatorial optimization problem. We show that our algorithm is faster and outperforms or ties existing algorithms on synthetic problems, a problem in bioinformatics, and a problem in ontology matching. We also provide a unified framework for studying and comparing all network alignment solvers. We consider the joint optimization of beamformers and linear receivers in a MIMO interference network. Each transmitter transmits a single beam corresponding to a rank-one precoder. When the number of users K is greater than the number of antennas at each terminal N, the maximum degrees of freedom is achieved via spatial interference alignment. Interference alignment is feasible for up to K = 2N−1 users, in which case there is a finite number of solutions to the alignment conditions. This number of solutions increases rapidly with N, and the solutions depend only on the cross-channel coefficients (i. e., they are independent of the direct channels). To maximize the achievable sum rate at high SNRs we therefore wish to select an aligned solution which is best matched to the direct channels. We evaluate the performance of this scheme for large K and N, assuming that the solution is the best out of a random subset of aligned solutions. We then compare numerically this performance with the performance of previously proposed numerical (e. g., forward-backward) techniques for optimizing beams, and a new technique which tracks the local optimum as the SNR is incrementally increased, similar to a homotopy method for improving convergence properties. We observe that the incremental technique typically achieves better performance than the previously proposed methods. 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. Results: We introduce the graph-based maximum structural matching formulation for pairwise global network alignment. We relate the formulation to previous work and prove NP-hardness of the problem. Based on the new formulation we build upon recent results in computational structural biology and present a novel Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments. The Lagrangian algorithm alone is a powerful heuristic method, which produces solutions that are often near-optimal and – unlike those computed by pure heuristics – come with a quality guarantee. Conclusion: Computational experiments on the alignment of protein-protein interaction networks and on the classification of metabolic subnetworks demonstrate that the new method is reasonably fast and has advantages over pure heuristics. Our software tool is freely available as part of the LISA library. Network alignment is the problem of matching the nodes of two graphs, maximizing the similarity of the matched nodes and the edges between them. This problem is encountered in a wide array of applications - from biological networks to social networks to ontologies - where multiple networked data sources need to be integrated. Due to the difficulty of the task, an accurate alignment can rarely be found without human assistance. Thus, it is of great practical importance to develop network alignment algorithms that can optimally leverage experts who are able to provide the correct alignment for a small number of nodes. Yet, only a handful of existing works address this active network alignment setting. The majority of the existing active methods focus on absolute queries ("are nodes @math and @math the same or not?"), whereas we argue that it is generally easier for a human expert to answer relative queries ("which node in the set @math is the most similar to node @math ?"). This paper introduces a novel relative-query strategy, TopMatchings, which can be applied on top of any network alignment method that constructs and solves a bipartite matching problem. Our method identifies the most informative nodes to query based on the top- @math matchings of a bipartite graph. We compare the proposed approach to several commonly-used query strategies and perform experiments on both synthetic and real-world datasets. Our matching-based strategy yields the highest overall performance, outperforming all the baseline methods by more than 15 percentage points in some cases.