edge2vec: Representation learning using edge semantics for biomedical knowledge discovery

Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mostly focused on homogeneous graphs, an important current challenge is extending this methodology for richly heterogeneous graphs and knowledge domains. The biomedical sciences are such a domain, reflecting the complexity of biology, with entities such as genes, proteins, drugs, diseases, and phenotypes, and relationships such as gene co-expression, biochemical regulation, and biomolecular inhibition or activation. Therefore, the semantics of edges and nodes are critical for representation learning and knowledge discovery in real world biomedical problems. In this paper, we propose the edge2vec model, which represents graphs considering edge semantics. An edge-type transition matrix is trained by an Expectation-Maximization approach, and a stochastic gradient descent model is employed to learn node embedding on a heterogeneous graph via the trained transition matrix. edge2vec is validated on three biomedical domain tasks: biomedical entity classification, compound-gene bioactivity prediction, and biomedical information retrieval. Results show that by considering edge-types into node embedding learning in heterogeneous graphs, \textbf{edge2vec}\ significantly outperforms state-of-the-art models on all three tasks. We propose this method for its added value relative to existing graph analytical methodology, and in the real world context of biomedical knowledge discovery applicability.Comment: 10 page

Multilayer Networks

In most natural and engineered systems, a set of entities interact with each other in complicated patterns that can encompass multiple types of relationships, change in time, and include other types of complications. Such systems include multiple subsystems and layers of connectivity, and it is important to take such "multilayer" features into account to try to improve our understanding of complex systems. Consequently, it is necessary to generalize "traditional" network theory by developing (and validating) a framework and associated tools to study multilayer systems in a comprehensive fashion. The origins of such efforts date back several decades and arose in multiple disciplines, and now the study of multilayer networks has become one of the most important directions in network science. In this paper, we discuss the history of multilayer networks (and related concepts) and review the exploding body of work on such networks. To unify the disparate terminology in the large body of recent work, we discuss a general framework for multilayer networks, construct a dictionary of terminology to relate the numerous existing concepts to each other, and provide a thorough discussion that compares, contrasts, and translates between related notions such as multilayer networks, multiplex networks, interdependent networks, networks of networks, and many others. We also survey and discuss existing data sets that can be represented as multilayer networks. We review attempts to generalize single-layer-network diagnostics to multilayer networks. We also discuss the rapidly expanding research on multilayer-network models and notions like community structure, connected components, tensor decompositions, and various types of dynamical processes on multilayer networks. We conclude with a summary and an outlook.Comment: Working paper; 59 pages, 8 figure

Representation Learning for Attributed Multiplex Heterogeneous Network

Network embedding (or graph embedding) has been widely used in many real-world applications. However, existing methods mainly focus on networks with single-typed nodes/edges and cannot scale well to handle large networks. Many real-world networks consist of billions of nodes and edges of multiple types, and each node is associated with different attributes. In this paper, we formalize the problem of embedding learning for the Attributed Multiplex Heterogeneous Network and propose a unified framework to address this problem. The framework supports both transductive and inductive learning. We also give the theoretical analysis of the proposed framework, showing its connection with previous works and proving its better expressiveness. We conduct systematical evaluations for the proposed framework on four different genres of challenging datasets: Amazon, YouTube, Twitter, and Alibaba. Experimental results demonstrate that with the learned embeddings from the proposed framework, we can achieve statistically significant improvements (e.g., 5.99-28.23% lift by F1 scores; p<<0.01, t-test) over previous state-of-the-art methods for link prediction. The framework has also been successfully deployed on the recommendation system of a worldwide leading e-commerce company, Alibaba Group. Results of the offline A/B tests on product recommendation further confirm the effectiveness and efficiency of the framework in practice.Comment: Accepted to KDD 2019. Website: https://sites.google.com/view/gatn