Artificial Intelligence Review

, Volume 42, Issue 3, pp 427–443 | Cite as

The Human Interactome Knowledge Base (HINT-KB): an integrative human protein interaction database enriched with predicted protein–protein interaction scores using a novel hybrid technique

  • Konstantinos Theofilatos
  • Christos Dimitrakopoulos
  • Spiros Likothanassis
  • Dimitrios Kleftogiannis
  • Charalampos Moschopoulos
  • Christos Alexakos
  • Stergios Papadimitriou
  • Seferina Mavroudi


Proteins are the functional components of many cellular processes and the identification of their physical protein–protein interactions (PPIs) is an area of mature academic research. Various databases have been developed containing information about experimentally and computationally detected human PPIs as well as their corresponding annotation data. However, these databases contain many false positive interactions, are partial and only a few of them incorporate data from various sources. To overcome these limitations, we have developed HINT-KB (, a knowledge base that integrates data from various sources, provides a user-friendly interface for their retrieval, calculates a set of features of interest and computes a confidence score for every candidate protein interaction. This confidence score is essential for filtering the false positive interactions which are present in existing databases, predicting new protein interactions and measuring the frequency of each true protein interaction. For this reason, a novel machine learning hybrid methodology, called (Evolutionary Kalman Mathematical Modelling—EvoKalMaModel), was used to achieve an accurate and interpretable scoring methodology. The experimental results indicated that the proposed scoring scheme outperforms existing computational methods for the prediction of PPIs.


Protein–protein interactions Human PPI scoring methods Genetic algorithms Kalman Filters Knowledge base 



This research has been co-financed by the European Union (European Social Fund—ESF) and Greek national funds through the Operational Program “Education and Lifelong Learning” of the National Strategic Reference Framework (NSRF)—Research Funding Program: Heracleitus II. Investing in knowledge society through the European Social Fund.


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Konstantinos Theofilatos
    • 1
  • Christos Dimitrakopoulos
    • 1
  • Spiros Likothanassis
    • 1
  • Dimitrios Kleftogiannis
    • 2
  • Charalampos Moschopoulos
    • 3
    • 4
  • Christos Alexakos
    • 1
  • Stergios Papadimitriou
    • 5
  • Seferina Mavroudi
    • 6
    • 1
  1. 1.Department of Computer Engineering and InformaticsUniversity of PatrasPatrasGreece
  2. 2.King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE)ThuwalSaudi Arabia
  3. 3.Department of Electrical Engineering-ESATSCD-SISTA, Katholieke Universiteit LeuvenHeverleeBelgium
  4. 4.iMinds Future Health DepartmentKatholieke Universiteit LeuvenHeverleeBelgium
  5. 5.Department of Computer Engineering and InformaticsTechnological Institute of KavalaKavalaGreece
  6. 6.Department of Social Work, School of Sciences of Health and CareTechnological Educational Institute of PatrasPatrasGreece

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