Drug-drug interaction extraction from biomedical texts using long short-term memory network.
Journal:
Journal of biomedical informatics
Published Date:
Aug 21, 2018
Abstract
The simultaneous administration of multiple drugs increases the probability of interaction among them, as one drug may affect the activities of others. This interaction among drugs may have a positive or negative impact on the therapeutic outcomes. Thus, identification of unknown drug-drug interactions (DDIs) is of significant concern for improving the safety and efficacy of drug consumption. Although multiple DDI resources exist, it is becoming infeasible to maintain these up-to-date manually with the number of biomedical texts growing at a fast pace. Most existing methods model DDI extraction as a classification problem and rely mainly on handcrafted features, and certain features further depend on domain-specific tools. Recently, neural network models using latent features have been demonstrated to yield similar or superior performance compared to existing models. In this study, we present three long short-term memory (LSTM) network models, namely B-LSTM, AB-LSTM, and Joint AB-LSTM. All three models use word and position embedding as latent features; thus, they do not rely on explicit feature engineering. Furthermore, the use of a bidirectional LSTM (Bi-LSTM) network allows for extraction of implicit features from an entire sentence. The two models AB-LSTM and Joint AB-LSTM also apply attentive pooling in the Bi-LSTM layer output in order to assign weights to features. Our experimental results on the SemEval-2013 DDI extraction dataset indicate that the Joint AB-LSTM model produces reasonable performance (F-score: 69.39%) even with the simple architecture.