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

Gravity-Inspired Graph Autoencoders for Directed Link Prediction

Graph autoencoders (AE) and variational autoencoders (VAE) recently emerged as powerful node embedding methods. In particular, graph AE and VAE were successfully leveraged to tackle the challenging link prediction problem, aiming at figuring out whether some pairs of nodes from a graph are connected by unobserved edges. However, these models focus on undirected graphs and therefore ignore the potential direction of the link, which is limiting for numerous real-life applications. In this paper, we extend the graph AE and VAE frameworks to address link prediction in directed graphs. We present a new gravity-inspired decoder scheme that can effectively reconstruct directed graphs from a node embedding. We empirically evaluate our method on three different directed link prediction tasks, for which standard graph AE and VAE perform poorly. We achieve competitive results on three real-world graphs, outperforming several popular baselines.Comment: ACM International Conference on Information and Knowledge Management (CIKM 2019

Application of Support Vector Machine Modeling for the Rapid Seismic Hazard Safety Evaluation of Existing Buildings

The economic losses from earthquakes tend to hit the national economy considerably; therefore, models that are capable of estimating the vulnerability and losses of future earthquakes are highly consequential for emergency planners with the purpose of risk mitigation. This demands a mass prioritization filtering of structures to identify vulnerable buildings for retrofitting purposes. The application of advanced structural analysis on each building to study the earthquake response is impractical due to complex calculations, long computational time, and exorbitant cost. This exhibits the need for a fast, reliable, and rapid method, commonly known as Rapid Visual Screening (RVS). The method serves as a preliminary screening platform, using an optimum number of seismic parameters of the structure and predefined output damage states. In this study, the efficacy of the Machine Learning (ML) application in damage prediction through a Support Vector Machine (SVM) model as the damage classification technique has been investigated. The developed model was trained and examined based on damage data from the 1999 Düzce Earthquake in Turkey, where the building’s data consists of 22 performance modifiers that have been implemented with supervised machine learning