Functional Annotation of Genes Using Hierarchical Text Categorization

This paper addresses the task of functional annotation of genes from biomedical literature. We view this task as a hierarchical text categorization problem with Gene Ontology as a class hierarchy. We present a novel global hierarchical learning approach that takes into account the semantics of a class hierarchy. This algorithm with AdaBoost as the underlying learning procedure significantly outperforms the corresponding “flat” approach, i.e. the approach that does not consider any hierarchical information. In addition, we propose a novel hierarchical evaluation measure that gives credit to partially correct classification and discriminates errors by both distance and depth in a class hierarchy.