Projects per year
Abstract
Computational analysis of the structure of intracellular molecular interaction networks can suggest novel therapeutic approaches for systemic diseases like cancer. Recent research in the area of network science has shown that network control theory can be a powerful tool in the understanding and manipulation of such biomedical networks. In 2011, Liu et al. developed a polynomial time optimization algorithm for computing the size of the minimal set of nodes controlling a given linear network. In 2014, Gao et al. generalized the problem for target structural control, where the objective is to optimize the size of the minimal set of nodes controlling a given target within a linear network. The working hypothesis in this case is that partial control might be “cheaper” (in the size of the controlling set) than the full control of a network. The authors developed a Greedy algorithm searching for the minimal solution of the structural target control problem, however, no suggestions were given over the actual complexity of the optimization problem. In here we prove that the structural target controllability problem is NPhard when looking to minimize the number of driven nodes within the network, i.e., the first set of nodes which need to be directly controlled in order to structurally control the target. We also show that the Greedy algorithm provided by Gao et al. in 2014 might in some special cases fail to pro vide a valid solution, and a subsequent validation step is required. Also, we improve their search algorithm using several heuristics, obtaining in the end up to a 10fold decrease in running time and also a significant decrease of the size of the minimal solution found by the algorithms.
Original language  Undefined/Unknown 

Title of host publication  Computational Methods in Systems Biology: 14th International Conference, CMSB 2016, Cambridge, UK, September 2123, 2016, Proceedings 
Editors  Bartocci, Ezio, Lio, Pietro, Paoletti, Nicola 
Publisher  Springer 
Pages  67–81 
ISBN (Electronic)  9783319451770 
ISBN (Print)  9783319451763 
DOIs  
Publication status  Published  2016 
MoE publication type  A4 Article in a conference publication 
Event  Computational Methods in Systems Biology  Computational Methods in Systems Biology: 14th International Conference, CMSB 2016 Duration: 1 Jan 2016 → … 
Conference
Conference  Computational Methods in Systems Biology 

Period  01/01/16 → … 
Projects
 1 Finished

NetPharma: Network pharmacology: drug repurposing and discovery of multidrug therapies by analytical approaches (Business Finland)
Czeizler, E.
01/06/16 → 31/12/18
Project: Research