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

Deep Multi-view Learning to Rank

We study the problem of learning to rank from multiple information sources. Though multi-view learning and learning to rank have been studied extensively leading to a wide range of applications, multi-view learning to rank as a synergy of both topics has received little attention. The aim of the paper is to propose a composite ranking method while keeping a close correlation with the individual rankings simultaneously. We present a generic framework for multi-view subspace learning to rank (MvSL2R), and two novel solutions are introduced under the framework. The first solution captures information of feature mappings from within each view as well as across views using autoencoder-like networks. Novel feature embedding methods are formulated in the optimization of multi-view unsupervised and discriminant autoencoders. Moreover, we introduce an end-to-end solution to learning towards both the joint ranking objective and the individual rankings. The proposed solution enhances the joint ranking with minimum view-specific ranking loss, so that it can achieve the maximum global view agreements in a single optimization process. The proposed method is evaluated on three different ranking problems, i.e. university ranking, multi-view lingual text ranking and image data ranking, providing superior results compared to related methods.Comment: Published at IEEE TKD