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

Towards Exploiting Implicit Human Feedback for Improving RDF2vec Embeddings

RDF2vec is a technique for creating vector space embeddings from an RDF knowledge graph, i.e., representing each entity in the graph as a vector. It first creates sequences of nodes by performing random walks on the graph. In a second step, those sequences are processed by the word2vec algorithm for creating the actual embeddings. In this paper, we explore the use of external edge weights for guiding the random walks. As edge weights, transition probabilities between pages in Wikipedia are used as a proxy for the human feedback for the importance of an edge. We show that in some scenarios, RDF2vec utilizing those transition probabilities can outperform both RDF2vec based on random walks as well as the usage of graph internal edge weights.Comment: Workshop paper accepted at Deep Learning for Knowledge Graphs Workshop 202

More is not Always Better: The Negative Impact of A-box Materialization on RDF2vec Knowledge Graph Embeddings

RDF2vec is an embedding technique for representing knowledge graph entities in a continuous vector space. In this paper, we investigate the effect of materializing implicit A-box axioms induced by subproperties, as well as symmetric and transitive properties. While it might be a reasonable assumption that such a materialization before computing embeddings might lead to better embeddings, we conduct a set of experiments on DBpedia which demonstrate that the materialization actually has a negative effect on the performance of RDF2vec. In our analysis, we argue that despite the huge body of work devoted on completing missing information in knowledge graphs, such missing implicit information is actually a signal, not a defect, and we show examples illustrating that assumption.Comment: Accepted at the Workshop on Combining Symbolic and Sub-symbolic methods and their Applications (CSSA 2020

I am all EARS: Using open data and knowledge graph embeddings for music recommendations

Music streaming platforms offer music listeners an overwhelming choice of music. Therefore, users of streaming platforms need the support of music recommendation systems to find music that suits their personal taste. Currently, a new class of recommender systems based on knowledge graph embeddings promises to improve the quality of recommendations, in particular to provide diverse and novel recommendations. This paper investigates how knowledge graph embeddings can improve music recommendations. First, it is shown how a collaborative knowledge graph can be derived from open music data sources. Based on this knowledge graph, the music recommender system EARS (knowledge graph Embedding-based Artist Recommender System) is presented in detail, with particular emphasis on recommendation diversity and explainability. Finally, a comprehensive evaluation with real-world data is conducted, comparing of different embeddings and investigating the influence of different types of knowledge