BioCreative II Gene Mention Tagging System at IBM Watson

This paper describes our system developed for the BioCreative II gene mention tagging task. The goal of this task is to annotate mentions of genes or gene products in the given Medline sentences. Our focus was to experiment with a semi-supervised learning method, Alternating Structure Optimization (ASO)(1), by which we exploited a large amount of unlabeled datain addition to the labeled training data provided by the organizer. The system is also equipped with automatic induction of high-order features, gene name lexicon lookup, classifier combination, and simple post- processing. Our system appears to be competitive. All of our three official runs belong to the Quartile 1.