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LSAT: learning about alternative transcripts in MEDLINE

Item Type:Article
Title:LSAT: learning about alternative transcripts in MEDLINE
Creators Name:Shah, P.K. and Bork, P.
Abstract:Motivation: Generation of alternative transcripts from the same gene is an important biological event due to their contribution in creating functional diversity in eukaryotes. In this work, we choose the task of extracting information around this complex topic using a two-step procedure involving machine learning and information extraction. Results: In the first step, we trained a classifier that inductively learns to identify sentences about physiological transcript diversity from the MEDLINE abstracts. Using a large hand-built corpus, we compared the sentence classification performance of various text categorization methods. Support vector machines (SVMs) followed by the maximum entropy classifier outperformed other methods for the sentence classification task. The SVM with the radial basis function kernel and optimized parameters achieved F β-measure of 91% during the 4-fold cross validation and of 74% when applied to all sentences in more than 12 million abstracts of MEDLINE. In the second step, we identified eight frequently present semantic categories in the sentences and performed a limited amount of semantic role labeling. The role labeling step also achieved very high F β-measure for all eight categories.
Keywords:Benchmarking, Biological Models, Computational Biology, Database Management Systems, Information Storage and Retrieval, MEDLINE, User-Computer Interface
Publisher:Oxford University Press
Page Range:857-865
Date:1 April 2006
Official Publication:https://doi.org/10.1093/bioinformatics/btk044
PubMed:View item in PubMed

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