Related papers: Combinatorial Algorithms for Control of Biological…
In the applications of Boolean networks to modeling biological systems, an important computational problem is the detection of the fixed points of these networks. This is an NP-complete problem in general. There have been various attempts…
In this survey paper, we will present a number of core algorithmic questions concerning several transitive reduction problems on network that have applications in network synthesis and analysis involving cellular processes. Our starting…
Control of complex processes is a major goal of network analyses. Most approaches to control nonlinearly coupled systems require the network topology and/or network dynamics. Unfortunately, neither the full set of participating nodes nor…
Direct cell reprogramming makes it feasible to reprogram abundant somatic cells into desired cells. It has great potential for regenerative medicine and tissue engineering. In this work, we study the control of biological networks, modelled…
We consider the Chance Constrained Model Predictive Control problem for polynomial systems subject to disturbances. In this problem, we aim at finding optimal control input for given disturbed dynamical system to minimize a given cost…
The links between optimal control of dynamical systems and neural networks have proved beneficial both from a theoretical and from a practical point of view. Several researchers have exploited these links to investigate the stability of…
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…
The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…
Boolean networks are special types of finite state time-discrete dynamical systems. A Boolean network can be described by a function from an n-dimensional vector space over the field of two elements to itself. A fundamental problem in…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Boolean networks may be viewed as idealizations of biological genetic networks, where each node is represented by an on-off switch which is a function of the binary output from some other nodes. We evolve connectivity in a single Boolean…
We introduce the problem of minimal actuator placement in a linear control system so that a bound on the minimum control effort for a given state transfer is satisfied while controllability is ensured. We first show that this is an NP-hard…
The description of gene interactions that constantly occur in the cellular environment is an extremely challenging task due to an immense number of degrees of freedom and incomplete knowledge about microscopic details. Hence, a…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
How to observe the state of a network from a limited number of measurements has become an important issue in complex networks, engineering, communication, epidemiology, etc. Under some scenarios, it is neither unfeasible nor unnecessary to…
This paper studies the minimum control node set problem for Boolean networks (BNs) with degree constraints. The main contribution is to derive the nontrivial lower and upper bounds on the size of the minimum control node set through…
We investigate to what extent the degree sequence of a directed network constrains the number of driver nodes. We develop a pair of algorithms that take a directed degree sequence as input and aim to output a network with the maximum or…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…
This paper studies the problem of controlling complex networks, that is, the joint problem of selecting a set of control nodes and of designing a control input to steer a network to a target state. For this problem (i) we propose a metric…
Boolean networks constitute relevant mathematical models to study the behaviours of genetic and signalling networks. These networks define regulatory influences between molecular nodes, each being associated to a Boolean variable and a…