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Leveraging prior knowledge for protein–protein interaction extraction with memory network

Automatically extracting protein–protein interactions (PPIs) from biomedical literature provides additional support for precision medicine efforts. This paper proposes a novel memory network-based model (MNM) for PPI extraction, which leverages prior knowledge about protein–protein pairs with memory...

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Detalles Bibliográficos
Autores principales: Zhou, Huiwei, Liu, Zhuang, Ning, Shixian, Yang, Yunlong, Lang, Chengkun, Lin, Yingyu, Ma, Kun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047414/
https://www.ncbi.nlm.nih.gov/pubmed/30010731
http://dx.doi.org/10.1093/database/bay071
Descripción
Sumario:Automatically extracting protein–protein interactions (PPIs) from biomedical literature provides additional support for precision medicine efforts. This paper proposes a novel memory network-based model (MNM) for PPI extraction, which leverages prior knowledge about protein–protein pairs with memory networks. The proposed MNM captures important context clues related to knowledge representations learned from knowledge bases. Both entity embeddings and relation embeddings of prior knowledge are effective in improving the PPI extraction model, leading to a new state-of-the-art performance on the BioCreative VI PPI dataset. The paper also shows that multiple computational layers over an external memory are superior to long short-term memory networks with the local memories. Database URL: http://www.biocreative.org/tasks/biocreative-vi/track-4/