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

Similarity Learning via Kernel Preserving Embedding

Data similarity is a key concept in many data-driven applications. Many algorithms are sensitive to similarity measures. To tackle this fundamental problem, automatically learning of similarity information from data via self-expression has been developed and successfully applied in various models, such as low-rank representation, sparse subspace learning, semi-supervised learning. However, it just tries to reconstruct the original data and some valuable information, e.g., the manifold structure, is largely ignored. In this paper, we argue that it is beneficial to preserve the overall relations when we extract similarity information. Specifically, we propose a novel similarity learning framework by minimizing the reconstruction error of kernel matrices, rather than the reconstruction error of original data adopted by existing work. Taking the clustering task as an example to evaluate our method, we observe considerable improvements compared to other state-of-the-art methods. More importantly, our proposed framework is very general and provides a novel and fundamental building block for many other similarity-based tasks. Besides, our proposed kernel preserving opens up a large number of possibilities to embed high-dimensional data into low-dimensional space.Comment: Published in AAAI 201