A graphbased algorithm for the multiobjective optimization of gene regulatory networks
Abstract
The evolution of gene regulatory networks in variable environments poses Multiobjective Optimization Problem (MOP), where the expression levels of genes must be tuned to meet the demands of each environment. When formalized in the context of monotone systems, this problem falls into a subclass of linear MOPs. Here, the constraints are partial orders and the objectives consist of either the minimization or maximization of single variables, but their number can be very large. To efficiently and exhaustively find Pareto optimal solutions, we introduce a mapping between coloured Hasse diagrams and polytopes associated with an ideal point. A dynamic program based on edge contractions yields an exact closedform description of the Pareto optimal set, in polynomial time of the number of objectives relative to the number of faces of the Pareto front. We additionnally discuss the special case of seriesparallel graphs with monochromatic connected components of bounded size, for which the running time and the representation of solutions can in principle be linear in the number of objectives.
 Publication:

arXiv eprints
 Pub Date:
 July 2016
 arXiv:
 arXiv:1607.00886
 Bibcode:
 2016arXiv160700886N
 Keywords:

 Mathematics  Optimization and Control