Selection of GO-Based Semantic Similarity Measures through AMDE for Predicting Protein-Protein Interactions

  • Anirban Mukhopadhyay
  • Moumita De
  • Ujjwal Maulik
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7077)


Protein-protein interactions (PPI) form the core part of the entire interatomic system for all the living elements. In this article, the role of different Gene Ontology(GO)-based semantic similarity measures in predicting PPIs have been explored. To find out a relevant subset of semantic similarity measures, a feature selection approach is developed with Angle Modulated Differential Evolution(AMDE), an improved binary differential evolution technique. In this feature selection approach, SVM classifier is used as a wrapper where different metrics like sensitivity, specificity accuracy and Area Under Curve (AUC) are measured to find the best performing feature subset. Results have been demonstrated for real-life PPI data of yeast.


Protein-Protein Interaction GO-based protein similarity Angle Modulated Differential Evolution (AMDE) feature selection 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Ashburner, M., Ball, C., Blake, J., Botstein, D., Butler, H., Cherry, J., Davis, A., Dolinski, K., Dwight, S., Eppig, J., et al.: Gene ontology: tool for the unification of biology. the gene ontology consortium. Nature Genetics 25, 25–29 (2000)CrossRefGoogle Scholar
  2. 2.
    Benabderrahmane, S., Smail-Tabbone, M., Poch, O., Napoli, A., Devignes, M.-D.: Intelligo: a new vector-based semantic similarity measure including annotation origin. BMC Bioinformatics 11(588), 1471–2105 (2010)Google Scholar
  3. 3.
    Couto, F.M., Silva, M.J., Coutinho, P.M.: Measuring semantic similarity between gene ontology terms. Data and Knowledge Engineering 61(10), 137–152 (2007)CrossRefGoogle Scholar
  4. 4.
    Jiang, J.J., Conrath, D.W.: Semantic similarity based on corpus statistics and lexical taxonomy. In: Proc. International Conference Research on Computational Linguistics, Taiwan (1997)Google Scholar
  5. 5.
    Lin, D.: An information-theoretic definition of similarity. In: Proc. 15th International Conference on Machine Learning, San Francisco, CA, pp. 296–304 (1998)Google Scholar
  6. 6.
    Mukhopadhyay, A., Maulik, U., Bandyopadhyay, S., Brors, B.: Goga: Go-driven genetic algorithm-based fuzzy clustering of gene expression data. In: Proc. Int. Conf. Systems in Medicine and Biology (ICSMB 2010), pp. 349–353 (2010)Google Scholar
  7. 7.
    Ovaska, K., Laakso, M., Hautaniemi, S.: Fast gene ontology based clustering for microarray experiments. BioData Mining 1(11) (2008)Google Scholar
  8. 8.
    Pampar, G., Engelbrecht, A., Franken, N.: Binary differential evolution. In: Proc. IEEE Congress on Evolutionary Computation, pp. 16–21 (2006)Google Scholar
  9. 9.
    Resnik, P.: Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. Journal of Artificial Intelligence Research 11, 95–130 (1999)zbMATHGoogle Scholar
  10. 10.
    Setubal, J., Meidanis, J.: Introduction to Computational Molecular Biology. PWS Publishing Company, MA (1997)Google Scholar
  11. 11.
    Storn, R., Price, K.: Differential evolution - a simple and efficient heuristic for global optimization over continuous spaces. Journal of Global Optimization 11(4), 341–359 (1997)MathSciNetCrossRefzbMATHGoogle Scholar
  12. 12.
    Vapnik, V.: The Nature of Statistical Learning Theory. Springer, Heidelberg (1995)CrossRefzbMATHGoogle Scholar
  13. 13.
    Wang, J.Z., Du, Z., Payattakool, R., Yu, P.S., Chen, C.-F.: A new method to measure the semantic similarity of go terms. BMC Bioinformatics 23(10), 1274–1281 (2007)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Anirban Mukhopadhyay
    • 1
  • Moumita De
    • 1
  • Ujjwal Maulik
    • 2
  1. 1.Department of Computer Science and EngineeringUniversity of KalyaniKalyaniIndia
  2. 2.Department of Computer Science and EngineeringJadavpur UniversityKolkataIndia

Personalised recommendations