PT  - JOURNAL ARTICLE
AU  - Kiri Choi
AU  - Joesph Hellerstein
AU  - H. Steven Wiley
AU  - Herbert M. Sauro
TI  - Inferring Reaction Networks using Perturbation Data
AID  - 10.1101/351767
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 351767
4099  - http://biorxiv.org/content/early/2018/06/20/351767.short
4100  - http://biorxiv.org/content/early/2018/06/20/351767.full
AB  - In this paper we examine the use of perturbation data to infer the underlying mechanistic dynamic model. The approach uses an evolutionary strategy to evolve networks based on a fitness criterion that measures the difference between the experimentally determined set of perturbation data and proposed mechanistic models. At present we only deal with reaction networks that use mass-action kinetics employing uni-uni, bi-uni, uni-bi and bi-bi reactions. The key to our approach is to split the algorithm into two phases. The first phase focuses on evolving network topologies that are consistent with the perturbation data followed by a second phase that evolves the parameter values. This results in almost an exact match between the evolved network and the original network from which the perturbation data was generated from. We test the approach on four models that include linear chain, feed-forward loop, cyclic pathway and a branched pathway. Currently the algorithm is implemented using Python and libRoadRunner but could at a later date be rewritten in a compiled language to improve performance. Future studies will focus on the impact of noise in the perturbation data on convergence and variability in the evolved parameter values and topologies. In addition we will investigate the effect of nonlinear rate laws on generating unique solutions.