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

Language in Our Time: An Empirical Analysis of Hashtags

Hashtags in online social networks have gained tremendous popularity during the past five years. The resulting large quantity of data has provided a new lens into modern society. Previously, researchers mainly rely on data collected from Twitter to study either a certain type of hashtags or a certain property of hashtags. In this paper, we perform the first large-scale empirical analysis of hashtags shared on Instagram, the major platform for hashtag-sharing. We study hashtags from three different dimensions including the temporal-spatial dimension, the semantic dimension, and the social dimension. Extensive experiments performed on three large-scale datasets with more than 7 million hashtags in total provide a series of interesting observations. First, we show that the temporal patterns of hashtags can be categorized into four different clusters, and people tend to share fewer hashtags at certain places and more hashtags at others. Second, we observe that a non-negligible proportion of hashtags exhibit large semantic displacement. We demonstrate hashtags that are more uniformly shared among users, as quantified by the proposed hashtag entropy, are less prone to semantic displacement. In the end, we propose a bipartite graph embedding model to summarize users' hashtag profiles, and rely on these profiles to perform friendship prediction. Evaluation results show that our approach achieves an effective prediction with AUC (area under the ROC curve) above 0.8 which demonstrates the strong social signals possessed in hashtags.Comment: WWW 201