Classification of protein-protein interaction full-text documents using text and citation network features

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):400-11. doi: 10.1109/TCBB.2010.55.

Abstract

We participated (as Team 9) in the Article Classification Task of the Biocreative II.5 Challenge: binary classification of full-text documents relevant for protein-protein interaction. We used two distinct classifiers for the online and offline challenges: 1) the lightweight Variable Trigonometric Threshold (VTT) linear classifier we successfully introduced in BioCreative 2 for binary classification of abstracts and 2) a novel Naive Bayes classifier using features from the citation network of the relevant literature. We supplemented the supplied training data with full-text documents from the MIPS database. The lightweight VTT classifier was very competitive in this new full-text scenario: it was a top-performing submission in this task, taking into account the rank product of the Area Under the interpolated precision and recall Curve, Accuracy, Balanced F-Score, and Matthew's Correlation Coefficient performance measures. The novel citation network classifier for the biomedical text mining domain, while not a top performing classifier in the challenge, performed above the central tendency of all submissions, and therefore indicates a promising new avenue to investigate further in bibliome informatics.

MeSH terms

  • Abstracting and Indexing / classification*
  • Algorithms
  • Computational Biology / methods*
  • Data Mining / methods*
  • Databases, Bibliographic
  • Neural Networks, Computer
  • Periodicals as Topic
  • Protein Interaction Mapping / classification*