Self-training in significance space of support vectors for imbalanced biomedical event data

Background: Pairwise relationships extracted from biomedical literature are insufficient in formulating biomolecular interactions. Extraction of complex relations (namely, biomedical events) has become the main focus of the text-mining community. However, there are two critical issues that are seldom dealt with by existing systems. First, an annotated corpus for training a prediction model is highly imbalanced. Second, supervised models trained on only a single annotated corpus can limit system performance. Fortunately, there is a large pool of unlabeled data containing much of the domain background that one can exploit. Results: In this study, we develop a new semi-supervised learning method to address the issues outlined above. The proposed algorithm efficiently exploits the unlabeled data to leverage system performance. We furthermore extend our algorithm to a two-phase learning framework. The first phase balances the training data for initial model induction. The second phase incorporates domain knowledge into the event extraction model. The effectiveness of our method is evaluated on the Genia event extraction corpus and a PubMed document pool. Our method can identify a small subset of the majority class, which is sufficient for building a well-generalized prediction model. It outperforms the traditional self-training algorithm in terms of f measure. Our model, based on the training data and the unlabeled data pool, achieves comparable performance to the state-of-the-art systems that are trained on a larger annotated set consisting of training and evaluation data.