LATTE: Application Oriented Social Network Embedding

In recent years, many research works propose to embed the network structured data into a low-dimensional feature space, where each node is represented as a feature vector. However, due to the detachment of embedding process with external tasks, the learned embedding results by most existing embedding models can be ineffective for application tasks with specific objectives, e.g., community detection or information diffusion. In this paper, we propose study the application oriented heterogeneous social network embedding problem. Significantly different from the existing works, besides the network structure preservation, the problem should also incorporate the objectives of external applications in the objective function. To resolve the problem, in this paper, we propose a novel network embedding framework, namely the "appLicAtion orienTed neTwork Embedding" (Latte) model. In Latte, the heterogeneous network structure can be applied to compute the node "diffusive proximity" scores, which capture both local and global network structures. Based on these computed scores, Latte learns the network representation feature vectors by extending the autoencoder model model to the heterogeneous network scenario, which can also effectively unite the objectives of network embedding and external application tasks. Extensive experiments have been done on real-world heterogeneous social network datasets, and the experimental results have demonstrated the outstanding performance of Latte in learning the representation vectors for specific application tasks.Comment: 11 Pages, 12 Figures, 1 Tabl

Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network.

Traditional Chinese Medicine (TCM) has received increasing attention as a complementary approach or alternative to modern medicine. However, experimental methods for identifying novel targets of TCM herbs heavily relied on the current available herb-compound-target relationships. In this work, we present an Herb-Target Interaction Network (HTINet) approach, a novel network integration pipeline for herb-target prediction mainly relying on the symptom related associations. HTINet focuses on capturing the low-dimensional feature vectors for both herbs and proteins by network embedding, which incorporate the topological properties of nodes across multi-layered heterogeneous network, and then performs supervised learning based on these low-dimensional feature representations. HTINet obtains performance improvement over a well-established random walk based herb-target prediction method. Furthermore, we have manually validated several predicted herb-target interactions from independent literatures. These results indicate that HTINet can be used to integrate heterogeneous information to predict novel herb-target interactions

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