• Journal of KIISE
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• v.41 no.9
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• pp.652-665
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• 2014

Many important terminologies in biomedical text are expressed as abbreviations or acronyms. We newly suggest a semantic link topic model based on the concepts of topic and dependency link to disambiguate biomedical abbreviations and cluster long form variants of abbreviations which refer to the same senses. This model is a generative model inspired by the latent Dirichlet allocation (LDA) topic model, in which each document is viewed as a mixture of topics, with each topic characterized by a distribution over words. Thus, words of a document are generated from a hidden topic structure of a document and the topic structure is inferred from observable word sequences of document collections. In this study, we allow two distinct word generation to incorporate semantic dependencies between words, particularly between expansions (long forms) of abbreviations and their sentential co-occurring words. Besides topic information, the semantic dependency between words is defined as a link and a new random parameter for the link presence is assigned to each word. As a result, the most probable expansions with respect to abbreviations of a given abstract are decided by word-topic distribution, document-topic distribution, and word-link distribution estimated from document collection though the semantic dependency link topic model. The abstracts retrieved from the MEDLINE Entrez interface by the query relating 22 abbreviations and their 186 expansions were used as a data set. The link topic model correctly predicted expansions of abbreviations with the accuracy of 98.30%.