Integration of Reaction Kinetics Theory and Gene Expression Programming to Infer Reaction Mechanism
Mechanistic mathematical models of biomolecular systems have been used to describe biological phenomena in the hope that one day these models may be used to enhance our fundamental understanding of these phenomena, as well as to optimize and engineer biological systems. An evolutionary algorithm capable of formulating mass action kinetic models of biological systems from time series data sets was developed for a system of n-species. The strategy involved using a gene expression programming (GEP) based approach and heuristics based on chemical kinetic theory. The resulting algorithm was successfully validated by recapitulating a nonlinear model of viral dynamics using only a “noisy” set of time series data. While the system analyzed for this proof-of-principle study was relatively small, the approach presented here is easily parallelizable making it amenable for use with larger systems. Additionally, greater efficiencies may potentially be realized by further taking advantage of the problem domain along with future breakthroughs in computing power and algorithmic advances.
KeywordsEvolutionary algorithm Biochemical kinetics Mechanistic modeling Genetic programming Gene expression programming
This material is based upon work supported by the National Science Foundation under Grant No. 1137249 and 1517133.
Mathematica source code and instructions are available from http://www.rslabs.org under a BSD open source license.
- 2.Bonhoeffer, S., Coffin, J.M., Nowak, M.A.: Human immunodeficiency virus drug therapy and virus load. J. Virol. 71, 3275–3278 (1997)Google Scholar
- 13.Koza, J.: Genetic Programming, p. 819. MIT Press, Cambridge (1992)Google Scholar
- 18.Du, X., et al.: Convergence analysis of gener expression programming based on maintaining elitist. In: Proceedings og the first ACM/SIGEVO Summit on Genetic and Evolutionary Computation (GEC 2009), pp. 823–826. ACM, New York (2009)Google Scholar
- 20.Levenspiel, O.: Chemical Reaction Engineering, 2nd edn. Wiley, New York (1972)Google Scholar