Network alignment (NA) aims to find regions of similarities between molecular networks of different species. There exist two NA categories: local (LNA) or global (GNA). LNA finds small highly conserved network regions and produces a many-to-many node mapping. GNA finds large conserved regions and produces a one-to-one node mapping. Given the different outputs of LNA and GNA, when a new NA method is proposed, it is compared against existing methods from the same category. However, both NA categories have the same goal: to allow for transferring functional knowledge from well- to poorly-studied species between conserved network regions. So, which one to choose, LNA or GNA? To answer this, we introduce the first systematic evaluation of the two NA categories. We introduce new measures of alignment quality that allow for fair comparison of the different LNA and GNA outputs, as such measures do not exist. We provide user-friendly software for efficient alignment evaluation that implements the new and existing measures. We evaluate prominent LNA and GNA methods on synthetic and real-world biological networks. We study the effect on alignment quality of using different interaction types and confidence levels. We find that the superiority of one NA category over the other is context-dependent. Further, when we contrast LNA and GNA in the application of learning novel protein functional knowledge, the two produce very different predictions, indicating their complementarity. Our results and software provide guidelines for future NA method development and evaluation.
NA can also be categorized as or , based on how many networks it can align. See @cite_14 for a review of pairwise and multiple NA. Here, we focus on pairwise NA.
@cite_14
2119571791 2119593077 2391555403 2136266535
Complex networks exist in a wide range of real world systems, such as social networks, technological networks, and biological networks. During the last decades, many researchers have concentrated on exploring some common things contained in those large networks include the small-world property, power-law degree distributions, and network connectivity. In this paper, we will investigate another important issue, community discovery, in network analysis. We choose Nonnegative Matrix Factorization (NMF) as our tool to find the communities because of its powerful interpretability and close relationship between clustering methods. Targeting different types of networks (undirected, directed and compound), we propose three NMF techniques (Symmetric NMF, Asymmetric NMF and Joint NMF). The correctness and convergence properties of those algorithms are also studied. Finally the experiments on real world networks are presented to show the effectiveness of the proposed methods. We observe that (1) how a given named entity (NE) is translated (i.e., either semantically or phonetically) depends greatly on its associated entity type, and (2) entities within an aligned pair should share the same type. Also, (3) those initially detected NEs are anchors, whose information should be used to give certainty scores when selecting candidates. From this basis, an integrated model is thus proposed in this paper to jointly identify and align bilingual named entities between Chinese and English. It adopts a new mapping type ratio feature (which is the proportion of NE internal tokens that are semantically translated), enforces an entity type consistency constraint, and utilizes additional monolingual candidate certainty factors (based on those NE anchors). The experiments show that this novel approach has substantially raised the type-sensitive F-score of identified NE-pairs from 68.4 to 81.7 (42.1 F-score imperfection reduction) in our Chinese-English NE alignment task. Multiple networks naturally appear in numerous high-impact applications. Network alignment (i.e., finding the node correspondence across different networks) is often the very first step for many data mining tasks. Most, if not all, of the existing alignment methods are solely based on the topology of the underlying networks. Nonetheless, many real networks often have rich attribute information on nodes and or edges. In this paper, we propose a family of algorithms FINAL to align attributed networks. The key idea is to leverage the node edge attribute information to guide (topology-based) alignment process. We formulate this problem from an optimization perspective based on the alignment consistency principle, and develop effective and scalable algorithms to solve it. Our experiments on real networks show that (1) by leveraging the attribute information, our algorithms can significantly improve the alignment accuracy (i.e., up to a 30 improvement over the existing methods); (2) compared with the exact solution, our proposed fast alignment algorithm leads to a more than 10 times speed-up, while preserving a 95 accuracy; and (3) our on-query alignment method scales linearly, with an around 90 ranking accuracy compared with our exact full alignment method and a near real-time response time. 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.