Related papers: Boolean constraint satisfaction problems for react…
This paper investigates the reconfiguration variant of the Constraint Satisfaction Problem (CSP), referred to as the Reconfiguration CSP (RCSP). Given a CSP instance and two of its solutions, RCSP asks whether one solution can be…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…
Constraint satisfaction problem (CSP) is a well-studied combinatorial search problem, in which we are asked to find an assignment of values to given variables so as to satisfy all of given constraints. We study a reconfiguration variant of…
Schaefer's theorem is a complexity classification result for so-called Boolean constraint satisfaction problems: it states that every Boolean constraint satisfaction problem is either contained in one out of six classes and can be solved in…
LECTURE GIVEN AT TH2002. Given a set of Boolean variables, and some constraints between them, is it possible to find a configuration of the variables which satisfies all constraints? This problem, which is at the heart of combinatorial…
A classic result due to Schaefer (1978) classifies all constraint satisfaction problems (CSPs) over the Boolean domain as being either in $\mathsf{P}$ or $\mathsf{NP}$-hard. This paper considers a promise-problem variant of CSPs called…
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…
The determination and classification of fixed points of large Boolean networks is addressed in terms of constraint satisfaction problem. We develop a general simplification scheme that, removing all those variables and functions belonging…
Autocatalytic chemical networks play a predominant role in a large number of natural systems such as in metabolic pathways and in ecological networks. Despite recent efforts, the precise impact of thermodynamic constraints on these networks…
We investigate how classifiers for Boolean networks (BNs) can be constructed and modified under constraints. A typical constraint is to observe only states in attractors or even more specifically steady states of BNs. Steady states of BNs…
Constraint satisfaction problems (CSPs) consist of a set of variables taking values from some finite domain and a set of local constraints on these variables. The objective is to find an assignment to the variables that maximizes the…
For Boolean satisfiability problems, the structure of the solution space is characterized by the solution graph, where the vertices are the solutions, and two solutions are connected iff they differ in exactly one variable. For this…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…
A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
Many biological systems, such as metabolic pathways, exhibit bistability behavior: these biological systems exhibit two distinct stable states with switching between the two stable states controlled by certain conditions. Since…
A counting constraint satisfaction problem (#CSP) asks for the number of ways to satisfy a given list of constraints, drawn from a fixed constraint language \Gamma. We study how hard it is to evaluate this number approximately. There is an…
The constraint satisfaction problem (CSP) on a relational structure B is to decide, given a set of constraints on variables where the relations come from B, whether or not there is a assignment to the variables satisfying all of the…