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This article is part of the supplement: Machine Learning for Biomedical Literature Analysis and Text Retrieval

Open Access Research

Machine learning with naturally labeled data for identifying abbreviation definitions

Lana Yeganova*, Donald C Comeau and W John Wilbur

Author Affiliations

National Center for Biotechnology Information, NLM, NIH, Bethesda, MD, USA

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BMC Bioinformatics 2011, 12(Suppl 3):S6  doi:10.1186/1471-2105-12-S3-S6

Published: 9 June 2011

Abstract

Background

The rapid growth of biomedical literature requires accurate text analysis and text processing tools. Detecting abbreviations and identifying their definitions is an important component of such tools. Most existing approaches for the abbreviation definition identification task employ rule-based methods. While achieving high precision, rule-based methods are limited to the rules defined and fail to capture many uncommon definition patterns. Supervised learning techniques, which offer more flexibility in detecting abbreviation definitions, have also been applied to the problem. However, they require manually labeled training data.

Methods

In this work, we develop a machine learning algorithm for abbreviation definition identification in text which makes use of what we term naturally labeled data. Positive training examples are naturally occurring potential abbreviation-definition pairs in text. Negative training examples are generated by randomly mixing potential abbreviations with unrelated potential definitions. The machine learner is trained to distinguish between these two sets of examples. Then, the learned feature weights are used to identify the abbreviation full form. This approach does not require manually labeled training data.

Results

We evaluate the performance of our algorithm on the Ab3P, BIOADI and Medstract corpora. Our system demonstrated results that compare favourably to the existing Ab3P and BIOADI systems. We achieve an F-measure of 91.36% on Ab3P corpus, and an F-measure of 87.13% on BIOADI corpus which are superior to the results reported by Ab3P and BIOADI systems. Moreover, we outperform these systems in terms of recall, which is one of our goals.