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Querying Complex Networks in Vector Space

William L. Hamilton, Payal Bajaj, Marinka Zitnik, Dan Jurafsky, Jure Leskovec

posted on 08 June 2018

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Learning vector embeddings of complex networks is a powerful approach used to predict missing or unobserved edges in network data. However, an open challenge in this area is developing techniques that can reason about $\textit{subgraphs}$ in network data, which can involve the logical conjunction of several edge relationships. Here we introduce a framework to make predictions about conjunctive logical queries---i.e., subgraph relationships---on heterogeneous network data. In our approach, we embed network nodes in a low-dimensional space and represent logical operators as learned geometric operations (e.g., translation, rotation) in this embedding space. We prove that a small set of geometric operations are sufficient to represent conjunctive logical queries on a network, and we introduce a series of increasingly strong implementations of these operators. We demonstrate the utility of this framework in two application studies on networks with millions of edges: predicting unobserved subgraphs in a network of drug-gene-disease interactions and in a network of social interactions derived from a popular web forum. These experiments demonstrate how our framework can efficiently make logical predictions such as "what drugs are likely to target proteins involved with both diseases X and Y?" Together our results highlight how imposing logical structure can make network embeddings more useful for large-scale knowledge discovery.