Related papers: Boolean constraint satisfaction problems for react…
The model of Dynamic Meta-Constraints has special activity constraints which can activate other constraints. It also has meta-constraints which range over other constraints. An algorithm is presented in which constraints can be assigned one…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
We show that several important resource allocation problems in wireless networks fit within the common framework of Constraint Satisfaction Problems (CSPs). Inspired by the requirements of these applications, where variables are located at…
Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…
We initiate the study of constraint satisfaction problems (CSPs) in the presence of counting quantifiers, which may be seen as variants of CSPs in the mould of quantified CSPs (QCSPs). We show that a single counting quantifier strictly…
The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables,…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
The Constraint Satisfaction Problem (CSP) framework offers a simple and sound basis for representing and solving simple decision problems, without uncertainty. This paper is devoted to an extension of the CSP framework enabling us to deal…
Stochastic reaction networks is a powerful class of models for the representation a wide variety of population models including biochemistry. The control of such networks has been recently considered due to their important implications for…
The constraint satisfaction problem (CSP) involves deciding, given a set of variables and a set of constraints on the variables, whether or not there is an assignment to the variables satisfying all of the constraints. One formulation of…
This paper studies the mathematical properties of collectively canalizing Boolean functions, a class of functions that has arisen from applications in systems biology. Boolean networks are an increasingly popular modeling framework for…
The study of phase transition phenomenon of NP complete problems plays an important role in understanding the nature of hard problems. In this paper, we follow this line of research by considering the problem of counting solutions of…
The stochastic kinetics of BRN are described by a chemical master equation (CME) and the underlying laws of mass action. The CME must be usually solved numerically by generating enough traces of random reaction events. The resulting…
We investigate rules which allow variable elimination in binary CSP (constraint satisfaction problem) instances while conserving satisfiability. We study variable-elimination rules based on the language of forbidden patterns enriched with…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
In the last two decades the study of random instances of constraint satisfaction problems (CSPs) has flourished across several disciplines, including computer science, mathematics and physics. The diversity of the developed methods, on the…
In this paper, we study the possibility of designing non-trivial random CSP models by exploiting the intrinsic connection between structures and typical-case hardness. We show that constraint consistency, a notion that has been developed to…
Promise Constraint Satisfaction Problems (PCSP) were proposed recently by Brakensiek and Guruswami arXiv:1704.01937 as a framework to study approximations for Constraint Satisfaction Problems (CSP). Informally a PCSP asks to distinguish…
A Boolean constraint satisfaction instance is a conjunction of constraint applications, where the allowed constraints are drawn from a fixed set B of Boolean functions. We consider the problem of determining whether two given constraint…
A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe) is constructed solely on the basis of the known biochemical interaction topology. Simulating the model in the computer, faithfully…