The computational prediction of drug-disease interactions using the dual-network L 2,1-CMF method

BMC Bioinformatics. 2019 Jan 5;20(1):5. doi: 10.1186/s12859-018-2575-6.

Abstract

Background: Predicting drug-disease interactions (DDIs) is time-consuming and expensive. Improving the accuracy of prediction results is necessary, and it is crucial to develop a novel computing technology to predict new DDIs. The existing methods mostly use the construction of heterogeneous networks to predict new DDIs. However, the number of known interacting drug-disease pairs is small, so there will be many errors in this heterogeneous network that will interfere with the final results.

Results: A novel method, known as the dual-network L2,1-collaborative matrix factorization, is proposed to predict novel DDIs. The Gaussian interaction profile kernels and L2,1-norm are introduced in our method to achieve better results than other advanced methods. The network similarities of drugs and diseases with their chemical and semantic similarities are combined in this method.

Conclusions: Cross validation is used to evaluate our method, and simulation experiments are used to predict new interactions using two different datasets. Finally, our prediction accuracy is better than other existing methods. This proves that our method is feasible and effective.

Keywords: Drug-disease interactions; Gaussian interaction profile; L2,1-norm; Matrix factorization.

MeSH terms

  • Algorithms*
  • Area Under Curve
  • Computational Biology / methods*
  • Databases as Topic
  • Disease*
  • Drug Interactions*
  • Humans
  • Reproducibility of Results
  • Semantics