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Passage extraction and result combination for genomics information retrieval

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Abstract

In this paper, we first propose algorithms for passage extraction to build indices for the purpose of generating more accurate passages as query answers. Second, we propose a basic result combination method and an improved result combination method to combine the retrieved results from different indices for the purpose of selecting and merging relevant passages as outputs. For passage extraction, three new algorithms are proposed, namely paragraphParsed, sentenceParsed and wordSentenceParsed. For result combination, a novel method is proposed, in which we use factor analysis to generate a better baseline result for combination by finding some hidden common factors that can be used to estimate the importance of keywords and keyword associations. Finally, we report the experimental results that confirm the effectiveness and superiority of the factor analysis based method for result combination. Our proposed approaches achieve excellent results on the TREC 2006 and 2007 Genomics data sets, which provide a promising avenue for constructing high performance information retrieval systems in biomedicine.

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Notes

  1. The “error” is a statistical term that means the amount by which an individual differs from what is average for the common factors.

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Acknowledgements

This research is supported in part by the research grant from the Natural Sciences & Engineering Research Council (NSERC) of Canada and the Early Researcher Award/Premier’s Research Excellence Award. We would like to thank Ming Zhong and Luo Si for their contributions at the early stage of this project. The authors are also grateful to the anonymous reviewers for their constructive comments, which have helped improve the quality of the paper.

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Authors and Affiliations

  1. Department of Computer Science & Engineering, York University, Toronto, Ontario, Canada

    Qinmin Hu

  2. School of Information Technology, York University, Toronto, Ontario, Canada

    Jimmy Xiangji Huang

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  1. Qinmin Hu
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  2. Jimmy Xiangji Huang
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Correspondence to Jimmy Xiangji Huang.

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Hu, Q., Huang, J.X. Passage extraction and result combination for genomics information retrieval. J Intell Inf Syst 34, 249–274 (2010). https://doi.org/10.1007/s10844-009-0097-4

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