A novel feature-based approach to extract drug-drug interactions from biomedical text

Motivation: Knowledge of drug-drug interactions (DDIs) is crucial for healthcare professionals in order to avoid adverse effects when co-administering drugs to patients. Since most newly discovered DDIs are made available through scientific publications, automatic DDI extraction is highly relevant.

Results: We propose a novel feature-based approach to extract DDIs from text. Our approach consists of three steps. First, we apply text preprocessing to convert input sentences from a given dataset into structured representations. Second, we map each candidate DDI pair from that dataset into a suitable syntactic structure. Based on that, a novel set of features is used to generate feature vectors for these candidate DDI pairs. Third, the obtained feature vectors are used to train a support vector machine (SVM) classifier. When evaluated on two DDI extraction challenge test datasets from 2011 and 2013, our system achieves F-scores of 71.1% and 83.5%, respectively, outperforming any state-of-the-art DDI extraction system.

Availability: The source code is available for academic use at http://www.biosemantics.org/uploads/DDI.zip