Machine learning and genetic regulatory networks: a review and a roadmap

Abstract: Genetic regulatory networks (GRNs) are causal structures which can be represented as large directed graphs. Their inference is a central problem in bioinformatics. Because of the paucity of available data and high levels of associated noise, machine learning is essential in performing a good and tractable inference of the underlying causal structure.

This chapter serves as a review of the GRN field as a whole, as well as a roadmap for researchers new to the field. It describes the relevant theoretical and empirical biochemistry and the different types of GRN inference. It also describes the data that can be used to perform GRN inference. With this biologically-centred material as background, the chapter primarily focuses on previous applications of machine learning techniques and computational intelligence to GRN inference. It describes clustering, logical and mathematical formalisms, Bayesian approaches and their interaction. Each of these is shortly explained theoretically, and important examples of previous research using each are highlighted. Finally, the chapter analyses wider statistical problems in the field, and concludes with a summary of the main achievements of previous research as well as some open research questions in the field.

  author =    {Christopher Fogelberg and Vasile Palade},
  title =     {Genetic Regulatory Networks: A Review and a Roadmap},
  booktitle = {Foundations of Computational Intelligence},
  editor =    {Ajith Abraham and Aboul-Ella Hassanien and Athanasios Vasilakos and,Witold Pedrycz and
               Francisco Herrera and Patrick Siarry and Andre de Carvalho and Andries P Engelbrecht},
  publisher = {Springer Verlag},
  year =      2009,
  chapter =   {1:1},
  keywords =  {grn, grn inference, bayesian network, clustering, biclustering, fuzzy clustering,
               mutual information, sem}

Available here.