Related papers: Combinatorial Algorithms for Control of Biological…
In this paper, we analyse large random Boolean networks in terms of a constraint satisfaction problem. We first develop an algorithmic scheme which allows to prune simple logical cascades and under-determined variables, returning thereby…
Given non-sequential snapshots from instances of a dynamical system, we design a compressed sensing based algorithm that reconstructs the dynamical system. On the theoretical side, we show that: (1) successful reconstruction is possible…
Network controllability is a powerful tool to study causal relationships in complex systems and identify the driver nodes for steering the network dynamics into desired states. However, due to ill-posed conditions, results become unreliable…
Gene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one…
Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive…
Many complex systems in biology, physics, and engineering include a large number of state-variables, and measuring the full state of the system is often impossible. Typically, a set of sensors is used to measure part of the state-variables.…
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into…
The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
Boolean networks (BNs) are discrete-time systems where nodes are inter-connected (here we call such connection rule among nodes as network structure), and the dynamics of each gene node is determined by logical functions. In this paper, we…
We consider networks of dynamical units that evolve in time according to different laws, and are coupled to each other in highly irregular ways. Studying how to steer the dynamics of such systems towards a desired evolution is of great…
Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…
Observing the internal state of the whole system using a small number of sensor nodes is important in analysis of complex networks. Here, we study the problem of determining the minimum number of sensor nodes to discriminate attractors…
The study of network structure has uncovered signatures of the organization of complex systems. However, there is also a need to understand how to control them; for example, identifying strategies to revert a diseased cell to a healthy…
We are interested in assigning a pre-specified number of nodes as leaders in order to minimize the mean-square deviation from consensus in stochastically forced networks. This problem arises in several applications including control of…
In this work, we investigate an indirect approach for the numerical solution of optimal control problems via neural networks. A customized neural network is constructed, where optimal state, co-state and control trajectories are…
Regulatory networks (RNs) are a well-accepted modelling formalism in computational systems biology. The control of RNs is currently receiving a lot of attention because it provides a computational basis for cell reprogramming -- an…
Networked discrete dynamical systems are often used to model the spread of contagions and decision-making by agents in coordination games. Fixed points of such dynamical systems represent configurations to which the system converges. In the…
Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical…
In this Letter we propose a method to control a set of arbitrary nodes in a directed network such that they follow a synchronous trajectory which is, in general, not shared by the other units of the network. The problem is inspired to those…