Dynamic hybrid clustering of bioinformatics by incorporating text mining and citation analysis

ABSTRACT

To unravel the concept structure and dynamics of the bioinformatics field, we analyze a set of 7401 publications from the Web of Science and MEDLINE databases, publication years 1981-2004. For delineating this complex, interdisciplinary field, a novel bibliometric retrieval strategy is used. Given that the performance of unsupervised clustering and classification of scientific publications is significantly improved by deeply merging textual contents with the structure of the citation graph, we proceed with a hybrid clustering method based on Fisher's inverse chi-square. The optimal number of clusters is determined by a compound semiautomatic strategy comprising a combination of distance-based and stability-based methods. We also investigate the relationship between number of Latent Semantic Indexing factors, number of clusters, and clustering performance. The HITS and PageRank algorithms are used to determine representative publications in each cluster. Next, we develop a methodology for dynamic hybrid clustering of evolving bibliographic data sets. The same clustering methodology is applied to consecutive periods defined by time windows on the set, and in a subsequent phase chains are formed by matching and tracking clusters through time. Term networks for the eleven resulting cluster chains present the cognitive structure of the field. Finally, we provide a view on how much attention the bioinformatics community has devoted to the different subfields through time.

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INDEX TERMS

Primary Classification:
  I. Computing Methodologies
  I.5 PATTERN RECOGNITION
      I.5.3 Clustering

Additional Classification:
  H. Information Systems
  H.2 DATABASE MANAGEMENT
      H.2.8 Database applications
          Subjects: Scientific databases; Data mining
  H.3 INFORMATION STORAGE AND RETRIEVAL
      H.3.1 Content Analysis and Indexing

General Terms:
Algorithms

Keywords:
cluster chains, fisher's inverse chi-square method