Knowledge-Based Biomedical Word Sense Disambiguation: An Evaluation and Application to Clinical Document Classification

Motivation: Word Sense Disambiguation (WSD) methods automatically assign an unambiguous concept to an ambiguous term based on context, and are important to many text processing tasks. In this study, we developed and evaluated a knowledge-based WSD method that uses semantic similarity measures derived from the Unified Medical Language System (UMLS), and we evaluated the contribution of WSD to clinical text classification. Results: We evaluated our system on biomedical WSD datasets; our system compares favorably to other knowledge-based methods. We evaluated the contribution of our WSD system to clinical document classification on the 2007 Computational Medicine Challenge corpus. Machine learning classifiers trained on disambiguated concepts significantly outperformed those trained using all concepts. Availability: We integrated our WSD system with MetaMap and cTAKES, two popular biomedical natural language processing systems. We released all code required to reproduce our results and all tools developed as part of this study as open source, available under http://code.google.com/p/ytex.