Understanding the Polarity of Events in the Biomedical Literature: Deep Learning vs. Linguistically-informed Methods

AbstractAn important task in the machine reading of biochemical events expressed in biomedical texts is correctly reading the polarity, i.e., attributing whether the biochemical event is a promotion or an inhibition. Here we present a novel dataset for studying polarity attribution accuracy. We use this dataset to train and evaluate several deep learning models for polarity identification, and compare these to a linguistically-informed model. The best performing deep learning architecture achieves 0.968 average F1 performance in a five-fold cross-validation study, a considerable improvement over the linguistically informed model average F1 of 0.862.