text: Network alignment aims at inferring a set of anchor links matching the shared entities between different information networks, which has become a prerequisite step for effective fusion of multiple information networks. In this paper, we will study the network alignment problem to fuse online social networks specifically. Social network alignment is extremely challenging to address due to several reasons, i.e., lack of training data, network heterogeneity and one-to-one constraint. Existing network alignment works usually require a large number of training data, but such a demand can hardly be met in applications, as manual anchor link labeling is extremely expensive. Significantly different from other homogeneous network alignment works, information in online social networks is usually of heterogeneous categories, the incorporation of which in model building is not an easy task. Furthermore, the one-to-one cardinality constraint on anchor links renders their inference process intertwistingly correlated. To resolve these three challenges, a novel network alignment model, namely ActiveIter, is introduced in this paper. ActiveIter defines a set of inter-network meta diagrams for anchor link feature extraction, adopts active learning for effective label query and uses greedy link selection for anchor link cardinality filtering. Extensive experiments are conducted on real-world aligned networks datasets, and the experimental results have demonstrated the effectiveness of ActiveIter compared with other state-of-the-art baseline methods.
  @cite_30: A recent paper posed the question: "Graph Matching: What are we really talking about?". Far from providing a definite answer to that question, in this paper we will try to characterize the role that graphs play within the Pattern Recognition field. To this aim two taxonomies are presented and discussed. The first includes almost all the graph matching algorithms proposed from the late seventies, and describes the different classes of algorithms. The second taxonomy considers the types of common applications of graph-based techniques in the Pattern Recognition and Machine Vision field.
  @cite_4: 
  @cite_22: 
  @cite_7: Matching is an important combinatorial problem with a number of applications in areas such as community detection, sparse linear algebra, and network alignment. Since computing optimal matchings can be very time consuming, several fast approximation algorithms, both sequential and parallel, have been suggested. Common to the algorithms giving the best solutions is that they tend to be sequential by nature, while algorithms more suitable for parallel computation give solutions of lower quality. We present a new simple 1 2-approximation algorithm for the weighted matching problem. This algorithm is both faster than any other suggested sequential 1 2-approximation algorithm on almost all inputs and when parallelized also scales better than previous multithreaded algorithms. We further extend this to a general scalable multithreaded algorithm that computes matchings of weight comparable with the best sequential deterministic algorithms. The performance of the suggested algorithms is documented through extensive experiments on different multithreaded architectures.
  @cite_28: The recent proliferation of protein interaction networks has motivated research into network alignment: the cross-species comparison of conserved functional modules. Previous studies have laid the foundations for such comparisons and demonstrated their power on a select set of sparse interaction networks. Recently, however, new computational techniques have produced hundreds of predicted interaction networks with interconnection densities that push existing alignment algorithms to their limits. To find conserved functional modules in these new networks, we have developed Graemlin, the first algorithm capable of scalable multiple network alignment. Graemlin's explicit model of functional evolution allows both the generalization of existing alignment scoring schemes and the location of conserved network topologies other than protein complexes and metabolic pathways. To assess Graemlin's performance, we have developed the first quantitative benchmarks for network alignment, which allow comparisons of algorithms in terms of their ability to recapitulate the KEGG database of conserved functional modules. We find that Graemlin achieves substantial scalability gains over previous methods while improving sensitivity.
  @cite_1: We describe IsoBase, a database identifying functionally related proteins, across five major eukaryotic model organisms: Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus and Homo Sapiens. Nearly all existing algorithms for orthology detection are based on sequence comparison. Although these have been successful in orthology prediction to some extent, we seek to go beyond these methods by the integration of sequence data and protein–protein interaction (PPI) networks to help in identifying true functionally related proteins. With that motivation, we introduce IsoBase, the first publicly available ortholog database that focuses on functionally related proteins. The groupings were computed using the IsoRankN algorithm that uses spectral methods to combine sequence and PPI data and produce clusters of functionally related proteins. These clusters compare favorably with those from existing approaches: proteins within an IsoBase cluster are more likely to share similar Gene Ontology (GO) annotation. A total of 48 120 proteins were clustered into 12 693 functionally related groups. The IsoBase database may be browsed for functionally related proteins across two or more species and may also be queried by accession numbers, species-specific identifiers, gene name or keyword. The database is freely available for download at http: isobase.csail.mit.edu .
  @cite_32: To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein–protein interaction networks of Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. This comparison integrated protein interaction and sequence information to reveal 71 network regions that were conserved across all three species and many exclusive to the metazoans. We used this conservation, and found statistically significant support for 4,645 previously undescribed protein functions and 2,609 previously undescribed protein interactions. We tested 60 interaction predictions for yeast by two-hybrid analysis, confirming approximately half of these. Significantly, many of the predicted functions and interactions would not have been identified from sequence similarity alone, demonstrating that network comparisons provide essential biological information beyond what is gleaned from the genome.
  @cite_3: Matching elements of two data schemas or two data instances plays a key role in data warehousing, e-business, or even biochemical applications. In this paper we present a matching algorithm based on a fixpoint computation that is usable across different scenarios. The algorithm takes two graphs (schemas, catalogs, or other data structures) as input, and produces as output a mapping between corresponding nodes of the graphs. Depending on the matching goal, a subset of the mapping is chosen using filters. After our algorithm runs, we expect a human to check and if necessary adjust the results. As a matter of fact, we evaluate the 'accuracy' of the algorithm by counting the number of needed adjustments. We conducted a user study, in which our accuracy metric was used to estimate the labor savings that the users could obtain by utilizing our algorithm to obtain an initial matching. Finally, we illustrate how our matching algorithm is deployed as one of several high-level operators in an implemented testbed for managing information models and mappings.
  @cite_6: Motivation: With the increasing availability of large protein–protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across networks, and global alignment, which attempts to find a best mapping between all nodes of the two networks. In this article, our aim is to improve upon existing global alignment results. Better network alignment will enable, among other things, more accurate identification of functional orthologs across species. Results: We introduce IsoRankN (IsoRank-Nibble) a global multiplenetwork alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks. Being based on spectral methods, IsoRankN is both error tolerant and computationally efficient. Availability: Our software is available freely for non-commercial purposes on request from: http: isorank.csail.mit.edu
  @cite_24: This chapter studies ontology matching: the problem of finding the semantic mappings between two given ontologies. This problem lies at the heart of numerous information processing applications. Virtually any application that involves multiple ontologies must establish semantic mappings among them, to ensure interoperability. Examples of such applications arise in myriad domains, including e-commerce, knowledge management, e-learning, information extraction, bio-informatics, web services, and tourism (see Part D of this book on ontology applications).
  @cite_27: 
  @cite_5: Protein–protein interactions (PPIs) and their networks play a central role in all biological processes. Akin to the complete sequencing of genomes and their comparative analysis, complete descriptions of interactomes and their comparative analysis is fundamental to a deeper understanding of biological processes. A first step in such an analysis is to align two or more PPI networks. Here, we introduce an algorithm, IsoRank, for global alignment of multiple PPI networks. The guiding intuition here is that a protein in one PPI network is a good match for a protein in another network if their respective sequences and neighborhood topologies are a good match. We encode this intuition as an eigenvalue problem in a manner analogous to Google's PageRank method. Using IsoRank, we compute a global alignment of the Saccharomyces cerevisiae, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus, and Homo sapiens PPI networks. We demonstrate that incorporating PPI data in ortholog prediction results in improvements over existing sequence-only approaches and over predictions from local alignments of the yeast and fly networks. Previous methods have been effective at identifying conserved, localized network patterns across pairs of networks. This work takes the further step of performing a global alignment of multiple PPI networks. It simultaneously uses sequence similarity and network data and, unlike previous approaches, explicitly models the tradeoff inherent in combining them. We expect IsoRank—with its simultaneous handling of node similarity and network similarity—to be applicable across many scientific domains.
  @cite_20: 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.
  @cite_17: 
summary: Network alignment problem is an important research problem, which has been studied in various areas, e.g., protein-protein-interaction network alignment in bioinformatics @cite_20 @cite_4 @cite_27 , chemical compound matching in chemistry @cite_22 , data schemas matching data warehouse @cite_3 , ontology alignment web semantics @cite_24 , graph matching in combinatorial mathematics @cite_7 , and figure matching and merging in computer vision @cite_30 @cite_17 . Network alignment is an important problem for bioinformatics. By studying the cross-species variations of biological networks, network alignment problem can be applied to predict conserved functional modules @cite_32 and infer the functions of proteins @cite_1 . Graemlin @cite_28 conducts pairwise network alignment by maximizing an objective function based on a set of learned parameters. Some works have been done on aligning multiple network in bioinformatics. IsoRank proposed in @cite_5 can align multiple networks greedily based on the pairwise node similarity scores calculated with spectral graph theory. IsoRankN @cite_6 further extends IsoRank by exploiting a spectral clustering scheme.