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2015 ; 55
(ä): 23-30
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Extracting drug-drug interactions from literature using a rich feature-based
linear kernel approach
#MMPMID25796456
Kim S
; Liu H
; Yeganova L
; Wilbur WJ
J Biomed Inform
2015[Jun]; 55
(ä): 23-30
PMID25796456
show ga
Identifying unknown drug interactions is of great benefit in the early detection
of adverse drug reactions. Despite existence of several resources for drug-drug
interaction (DDI) information, the wealth of such information is buried in a body
of unstructured medical text which is growing exponentially. This calls for
developing text mining techniques for identifying DDIs. The state-of-the-art DDI
extraction methods use Support Vector Machines (SVMs) with non-linear composite
kernels to explore diverse contexts in literature. While computationally less
expensive, linear kernel-based systems have not achieved a comparable performance
in DDI extraction tasks. In this work, we propose an efficient and scalable
system using a linear kernel to identify DDI information. The proposed approach
consists of two steps: identifying DDIs and assigning one of four different DDI
types to the predicted drug pairs. We demonstrate that when equipped with a rich
set of lexical and syntactic features, a linear SVM classifier is able to achieve
a competitive performance in detecting DDIs. In addition, the one-against-one
strategy proves vital for addressing an imbalance issue in DDI type
classification. Applied to the DDIExtraction 2013 corpus, our system achieves an
F1 score of 0.670, as compared to 0.651 and 0.609 reported by the top two
participating teams in the DDIExtraction 2013 challenge, both based on non-linear
kernel methods.