Learning Edge Representations via Low-Rank Asymmetric Projections

We propose a new method for embedding graphs while preserving directed edge information. Learning such continuous-space vector representations (or embeddings) of nodes in a graph is an important first step for using network information (from social networks, user-item graphs, knowledge bases, etc.) in many machine learning tasks. Unlike previous work, we (1) explicitly model an edge as a function of node embeddings, and we (2) propose a novel objective, the "graph likelihood", which contrasts information from sampled random walks with non-existent edges. Individually, both of these contributions improve the learned representations, especially when there are memory constraints on the total size of the embeddings. When combined, our contributions enable us to significantly improve the state-of-the-art by learning more concise representations that better preserve the graph structure. We evaluate our method on a variety of link-prediction task including social networks, collaboration networks, and protein interactions, showing that our proposed method learn representations with error reductions of up to 76% and 55%, on directed and undirected graphs. In addition, we show that the representations learned by our method are quite space efficient, producing embeddings which have higher structure-preserving accuracy but are 10 times smaller

SNE: Signed Network Embedding

Several network embedding models have been developed for unsigned networks. However, these models based on skip-gram cannot be applied to signed networks because they can only deal with one type of link. In this paper, we present our signed network embedding model called SNE. Our SNE adopts the log-bilinear model, uses node representations of all nodes along a given path, and further incorporates two signed-type vectors to capture the positive or negative relationship of each edge along the path. We conduct two experiments, node classification and link prediction, on both directed and undirected signed networks and compare with four baselines including a matrix factorization method and three state-of-the-art unsigned network embedding models. The experimental results demonstrate the effectiveness of our signed network embedding.Comment: To appear in PAKDD 201

Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs

Background: MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs. Here, we introduce a novel method based on a heterogeneous network that not only considers miRNAs but also the corresponding target genes in the network model. Results: Instead of constructing homogeneous miRNA networks, we built heterogeneous miRNA networks consisting of both miRNAs and their target genes, using databases of known miRNA-target gene interactions. In addition, as recent studies demonstrated reciprocal regulatory relations between miRNAs and their target genes, we considered these heterogeneous miRNA networks to be undirected, assuming mutual miRNA-target interactions. Next, we introduced a novel method (RWRMTN) operating on these mutual heterogeneous miRNA networks to rank candidate disease-related miRNAs using a random walk with restart (RWR) based algorithm. Using both known disease-associated miRNAs and their target genes as seed nodes, the method can identify additional miRNAs involved in the disease phenotype. Experiments indicated that RWRMTN outperformed two existing state-of-the-art methods: RWRMDA, a network-based method that also uses a RWR on homogeneous (rather than heterogeneous) miRNA networks, and RLSMDA, a machine learning-based method. Interestingly, we could relate this performance gain to the emergence of "disease modules" in the heterogeneous miRNA networks used as input for the algorithm. Moreover, we could demonstrate that RWRMTN is stable, performing well when using both experimentally validated and predicted miRNA-target gene interaction data for network construction. Finally, using RWRMTN, we identified 76 novel miRNAs associated with 23 disease phenotypes which were present in a recent database of known disease-miRNA associations. Conclusions: Summarizing, using random walks on mutual miRNA-target networks improves the prediction of novel disease-associated miRNAs because of the existence of "disease modules" in these networks

Quick Detection of High-degree Entities in Large Directed Networks

In this paper, we address the problem of quick detection of high-degree entities in large online social networks. Practical importance of this problem is attested by a large number of companies that continuously collect and update statistics about popular entities, usually using the degree of an entity as an approximation of its popularity. We suggest a simple, efficient, and easy to implement two-stage randomized algorithm that provides highly accurate solutions for this problem. For instance, our algorithm needs only one thousand API requests in order to find the top-100 most followed users in Twitter, a network with approximately a billion of registered users, with more than 90% precision. Our algorithm significantly outperforms existing methods and serves many different purposes, such as finding the most popular users or the most popular interest groups in social networks. An important contribution of this work is the analysis of the proposed algorithm using Extreme Value Theory -- a branch of probability that studies extreme events and properties of largest order statistics in random samples. Using this theory, we derive an accurate prediction for the algorithm's performance and show that the number of API requests for finding the top-k most popular entities is sublinear in the number of entities. Moreover, we formally show that the high variability among the entities, expressed through heavy-tailed distributions, is the reason for the algorithm's efficiency. We quantify this phenomenon in a rigorous mathematical way

Random walks in directed modular networks

Because diffusion typically involves symmetric interactions, scant attention has been focused on studying asymmetric cases. However, important networked systems underlain by diffusion (e.g. cortical networks and WWW) are inherently directed. In the case of undirected diffusion, it can be shown that the steady-state probability of the random walk dynamics is fully correlated with the degree, which no longer holds for directed networks. We investigate the relationship between such probability and the inward node degree, which we call efficiency, in modular networks. Our findings show that the efficiency of a given community depends mostly on the balance between its ingoing and outgoing connections. In addition, we derive analytical expressions to show that the internal degree of the nodes do not play a crucial role in their efficiency, when considering the Erd\H{o}s-R\'enyi and Barab\'asi-Albert models. The results are illustrated with respect to the macaque cortical network, providing subsidies for improving transportation and communication systems