Extracting drug-drug interaction from the biomedical literature using a stacked generalization-based approach.

TitleExtracting drug-drug interaction from the biomedical literature using a stacked generalization-based approach.
Publication TypeJournal Article
Year of Publication2013
AuthorsHe L, Yang Z, Zhao Z, Lin H, Li Y
JournalPloS one
Volume8
Issue6
Paginatione65814
Date Published2013
Abstract

Drug-drug interaction (DDI) detection is particularly important for patient safety. However, the amount of biomedical literature regarding drug interactions is increasing rapidly. Therefore, there is a need to develop an effective approach for the automatic extraction of DDI information from the biomedical literature. In this paper, we present a Stacked Generalization-based approach for automatic DDI extraction. The approach combines the feature-based, graph and tree kernels and, therefore, reduces the risk of missing important features. In addition, it introduces some domain knowledge based features (the keyword, semantic type, and DrugBank features) into the feature-based kernel, which contribute to the performance improvement. More specifically, the approach applies Stacked generalization to automatically learn the weights from the training data and assign them to three individual kernels to achieve a much better performance than each individual kernel. The experimental results show that our approach can achieve a better performance of 69.24% in F-score compared with other systems in the DDI Extraction 2011 challenge task.

DOI10.3978/j.issn.2223-4292.2013.06.06
Alternate JournalPLoS ONE