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Indexed by:Journal Papers

Date of Publication:2019-11-01

Journal:IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

Included Journals:SCIE

Volume:16

Issue:6

Page Number:1879-1889

ISSN No.:1545-5963

Key Words:CDR extraction; attention mechanism; knowledge representations; context representations

Abstract:Automatically extracting the relationships between chemicals and diseases is significantly important to various areas of biomedical research and health care. Biomedical experts have built many large-scale knowledge bases (KBs) to advance the development of biomedical research. KBs contain huge amounts of structured information about entities and relationships, therefore plays a pivotal role in chemical-disease relation (CDR) extraction. However, previous researches pay less attention to the prior knowledge existing in KBs. This paper proposes a neural network-based attention model (NAM) for CDR extraction, which makes full use of context information in documents and prior knowledge in KBs. For a pair of entities in a document, an attention mechanism is employed to select important context words with respect to the relation representations learned from KBs. Experiments on the BioCreative V CDR dataset show that combining context and knowledge representations through the attention mechanism, could significantly improve the CDR extraction performance while achieve comparable results with state-of-the-art systems.