An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

Maximum common subgraph isomorphism algorithms for the matching of chemical structures

The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks

Subgraph covers -- An information theoretic approach to motif analysis in networks

Many real world networks contain a statistically surprising number of certain subgraphs, called network motifs. In the prevalent approach to motif analysis, network motifs are detected by comparing subgraph frequencies in the original network with a statistical null model. In this paper we propose an alternative approach to motif analysis where network motifs are defined to be connectivity patterns that occur in a subgraph cover that represents the network using minimal total information. A subgraph cover is defined to be a set of subgraphs such that every edge of the graph is contained in at least one of the subgraphs in the cover. Some recently introduced random graph models that can incorporate significant densities of motifs have natural formulations in terms of subgraph covers and the presented approach can be used to match networks with such models. To prove the practical value of our approach we also present a heuristic for the resulting NP-hard optimization problem and give results for several real world networks.Comment: 10 pages, 7 tables, 1 Figur

Enhancing community detection using a network weighting strategy

A community within a network is a group of vertices densely connected to each other but less connected to the vertices outside. The problem of detecting communities in large networks plays a key role in a wide range of research areas, e.g. Computer Science, Biology and Sociology. Most of the existing algorithms to find communities count on the topological features of the network and often do not scale well on large, real-life instances. In this article we propose a strategy to enhance existing community detection algorithms by adding a pre-processing step in which edges are weighted according to their centrality w.r.t. the network topology. In our approach, the centrality of an edge reflects its contribute to making arbitrary graph tranversals, i.e., spreading messages over the network, as short as possible. Our strategy is able to effectively complements information about network topology and it can be used as an additional tool to enhance community detection. The computation of edge centralities is carried out by performing multiple random walks of bounded length on the network. Our method makes the computation of edge centralities feasible also on large-scale networks. It has been tested in conjunction with three state-of-the-art community detection algorithms, namely the Louvain method, COPRA and OSLOM. Experimental results show that our method raises the accuracy of existing algorithms both on synthetic and real-life datasets.Comment: 28 pages, 2 figure