Document-level medical relation extraction via edge-oriented graph neural network based on document structure and external knowledge

Abstract

Abstract Objective Relation extraction (RE) is a fundamental task of natural language processing, which always draws plenty of attention from researchers, especially RE at the document-level. We aim to explore an effective novel method for document-level medical relation extraction. Methods We propose a novel edge-oriented graph neural network based on document structure and external knowledge for document-level medical RE, called SKEoG. This network has the ability to take full advantage of document structure and external knowledge. Results We evaluate SKEoG on two public datasets, that is, Chemical-Disease Relation (CDR) dataset and Chemical Reactions dataset (CHR) dataset, by comparing it with other state-of-the-art methods. SKEoG achieves the highest F1-score of 70.7 on the CDR dataset and F1-score of 91.4 on the CHR dataset. Conclusion The proposed SKEoG method achieves new state-of-the-art performance. Both document structure and external knowledge can bring performance improvement in the EoG framework. Selecting proper methods for knowledge node representation is also very important.

Keywords

• Medical relation extraction
• Graph neural network
• Document structure
• External knowledge