Integrative Neural Network Approach for Protein Interaction Prediction from Heterogeneous Data

  • Xue-wen Chen
  • Mei Liu
  • Yong Hu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5139)


Protein interactions are essential in discovery of protein functions and fundamental biological processes. In this paper, we aim to create a reliable computational model for protein interaction prediction by integrating information from complementary data sources. An integrative Artificial Neural Network (ANN) framework is developed to predict protein-protein interactions (PPIs) from heterogeneous data in Human. Performance of our proposed framework is empirically investigated by combining protein domain data, molecular function and biological process annotations in Gene Ontology. Experimental results demonstrate that our approach can predict PPIs with high sensitivity of 82.43% and specificity of 78.67%. The results suggest that combining multiple data sources can result in a 7% increase in sensitivity compared to using only domain information. We are able to construct a protein interaction network with proteins around mitotic spindle checkpoint of the human interactome map. Novel predictions are made and some are supported by evidences in literature.


Protein-Protein Interaction Interaction Network Prediction Heterogeneous Data Integration Integrative Neural Network 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Xue-wen Chen
    • 1
  • Mei Liu
    • 1
  • Yong Hu
    • 2
  1. 1.Bioinformatics and Computational Life-Sciences Laboratory, ITTC, Department of Electrical Engineering and Computer ScienceThe University of KansasLawrenceUSA
  2. 2.Department of Management Science, School of Business ManagementSun Yat-sen University, Guangdong University of Foreign Studies, GuangzhouGuangdongChina

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