A Knowledge Graph based Bidirectional Recurrent Neural Network Method for Literature-based Discovery

Abstract

In this paper, we present a model which incorporates biomedical knowledge graph, graph embedding and deep learning methods for literature-based discovery. Firstly, the relations between entities are extracted from biomedical abstracts and then a knowledge graph is constructed by using these obtained relations. Secondly, the graph embedding technologies are applied to convert the entities and relations in the knowledge graph into a low-dimensional vector space. Thirdly, a bidirectional Long Short-Term Memory network is trained based on the entity associations represented by the pre-trained graph embeddings. Finally, the learned model is used for open and closed literature-based discovery tasks. The experimental results show that our method could not only effectively discover hidden associations between entities, but also reveal the corresponding mechanism of interactions. It suggests that incorporating knowledge graph and deep learning methods is an effective way for capturing the underlying complex associations between entities hidden in the literature.