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Full Text Clustering and Relationship Network Analysis of Biomedical Publications

Author

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  • Renchu Guan
  • Chen Yang
  • Maurizio Marchese
  • Yanchun Liang
  • Xiaohu Shi

Abstract

Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP) to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers.

Suggested Citation

  • Renchu Guan & Chen Yang & Maurizio Marchese & Yanchun Liang & Xiaohu Shi, 2014. "Full Text Clustering and Relationship Network Analysis of Biomedical Publications," PLOS ONE, Public Library of Science, vol. 9(9), pages 1-9, September.
    • Handle: RePEc:plo:pone00:0108847
    DOI: 10.1371/journal.pone.0108847
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    References listed on IDEAS

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    1. Kevin W Boyack & David Newman & Russell J Duhon & Richard Klavans & Michael Patek & Joseph R Biberstine & Bob Schijvenaars & André Skupin & Nianli Ma & Katy Börner, 2011. "Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-11, March.
    2. Doug Howe & Maria Costanzo & Petra Fey & Takashi Gojobori & Linda Hannick & Winston Hide & David P. Hill & Renate Kania & Mary Schaeffer & Susan St Pierre & Simon Twigger & Owen White & Seung Yon Rhee, 2008. "The future of biocuration," Nature, Nature, vol. 455(7209), pages 47-50, September.
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