Automatic Computational Discovery of Chemical Reaction Networks Using Genetic Programming

  • Authors:

  • John R. Koza;William Mydlowec;Guido Lanza;Jessen Yu;Martin A. Keane

  • Affiliations:

  • Biomedical Informatics, Department of Medicine, Department of Electrical Engineering, Stanford University, Stanford, California, USA;Genetic Programming Inc., Los Altos, California, USA;Genetic Programming Inc., Los Altos, California, USA;Genetic Programming Inc., Los Altos, California, USA;Econometrics Inc., Chicago, Illinois, USA

  • Venue:
  • Computational Discovery of Scientific Knowledge
  • Year:
  • 2007

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Abstract

The concentrations of substances participating in networks of chemical reactions are often modeled by non-linear continuous-time differential equations. Recent work has demonstrated that genetic programming is capable of automatically creating complex networks (such as analog electrical circuits and controllers) whose behavior is modeled by linear and non-linear continuous-time differential equations and whose behavior matches prespecified output values. This chapter demonstrates that it is possible to automatically induce (reverse engineer) a network of chemical reactions from observed time-domain data. Genetic programming starts with observed time-domain concentrations of substances and automatically creates both the topology of the network of chemical reactions and the rates of each reaction of a network such that the behavior of the automatically created network matches the observed time-domain data. Specifically, genetic programming automatically created a network of four chemical reactions that consume glycerol and fatty acid as input, use ATP as a cofactor, and produce diacyl-glycerol as the final product. The network was created from 270 data points. The topology and sizing of the entire network was automatically created using the time-domain concentration values of diacyl-glycerol (the final product). The automatically created network contains three key topological features, including an internal feedback loop, a bifurcation point where one substance is distributed to two different reactions, and an accumulation point where one substance is accumulated from two sources.