Biomedical named entity extraction: some issues of corpus compatibilities

BACKGROUND: Named Entity (NE) extraction is one of the most fundamental and important tasks in biomedical information extraction. It involves identification of certain entities from text and their classification into some predefined categories. In the biomedical community, there is yet no general consensus regarding named entity (NE) annotation; thus, it is very difficult to compare the existing systems due to corpus incompatibilities. Due to this problem we can not also exploit the advantages of using different corpora together. In our present work we address the issues of corpus compatibilities, and use a single objective optimization (SOO) based classifier ensemble technique that uses the search capability of genetic algorithm (GA) for NE extraction in biomedicine. We hypothesize that the reliability of predictions of each classifier differs among the various output classes. We use Conditional Random Field (CRF) and Support Vector Machine (SVM) frameworks to build a number of models depending upon the various representations of the set of features and/or feature templates. It is to be noted that we tried to extract the features without using any deep domain knowledge and/or resources. RESULTS: In order to assess the challenges of corpus compatibilities, we experiment with the different benchmark datasets and their various combinations. Comparison results with the existing approaches prove the efficacy of the used technique. GA based ensemble achieves around 2% performance improvements over the individual classifiers. Degradation in performance on the integrated corpus clearly shows the difficulties of the task. CONCLUSIONS: In summary, our used ensemble based approach attains the state-of-the-art performance levels for entity extraction in three different kinds of biomedical datasets. The possible reasons behind the better performance in our used approach are the (i). use of variety and rich features as described in Subsection “Features for named entity extraction”; (ii) use of GA based classifier ensemble technique to combine the outputs of multiple classifiers.