Balanced undersampling: a novel sentence-based undersampling method to improve recognition of named entities in chemical and biomedical text

The class imbalance problem is a key factor that affects the performance of many classification tasks when using machine learning methods. This mainly refers to the problem where the number of samples in certain classes is much greater than in others. Such imbalance considerably affects the performance of classifiers in which the majority class or classes are often favored, thus resulting in high-precision/low-recall classifiers. Named entity recognition in free text suffers from this problem to a large extent because in any given free text, many samples do not belong to a specific entity. Furthermore, the data used in this specific type of classification is in sequenced mode and is different than that used in other common classification tasks such as image classification, spam detection, and text classification in which no semantic or syntactic relation exists between samples. In this study, we propose an undersampling approach for sequenced data that preserves existing correlations between sequenced samples that comprise sentences and thus improve the performance of classifiers. We call this method balanced undersampling (BUS). Considering the recent increased interest in the use of NER in the chemical and biomedical domains, the proposed method is developed and tested on four recent state-of-the-art corpora in these domains, including BioCreative IV ChemDNER, Bio-entity Recognition Challenge of JNLPBA (JNLPBA), SemEval2013 DDI DrugBank, and SemEval2013 DDI Medline datasets. The performance of the proposed method is evaluated against two other common undersampling methods: random undersampling and stop-word filtering. Our method is shown to outperform both methods with respect to F-score for all datasets used.