Related papers: Boolean constraint satisfaction problems for react…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
For dynamical systems arising from chemical reaction networks, persistence is the property that each species concentration remains positively bounded away from zero, as long as species concentrations were all positive in the beginning. We…
Complex diseases can be modeled as damage to intracellular networks that results in abnormal cell behaviors. Network-based dynamic models such as Boolean models have been employed to model a variety of biological systems including those…
Key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their…
How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemical reaction networks sample? We begin tackling these…
The science of complex networks is a new interdisciplinary branch of science which has arisen recently on the interface of physics, biology, social and computer sciences, and others. Its main goal is to discover general laws governing the…
We investigate the Constraint Satisfaction Problem (CSP) over templates with a group structure, and algorithms solving CSP that are equivariant, i.e. invariant under a natural group action induced by a template. Our main result is a method…
In this work, we focus on the Partial Constraint Satisfaction Problem (PCSP) over control-flow graphs (CFGs) of programs. PCSP serves as a generalization of the well-known Constraint Satisfaction Problem (CSP). In the CSP framework, we…
The Promise Constraint Satisfaction Problem (PCSP) is a recently introduced vast generalization of the Constraint Satisfaction Problem (CSP). We investigate the computational complexity of a class of PCSPs beyond the most studied cases -…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Chemical reaction networks (CRNs) model systems where molecules interact according to a finite set of reactions such as $A + B \to C$, representing that if a molecule of $A$ and $B$ collide, they disappear and a molecule of $C$ is produced.…
The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological…
A Boolean network (BN) with $n$ components is a discrete dynamical system described by the successive iterations of a function $f:\{0,1\}^n \to \{0,1\}^n$. This model finds applications in biology, where fixed points play a central role.…
Constraint satisfaction problems (CSPs) are about finding values of variables that satisfy the given constraints. We show that Transformer extended with recurrence is a viable approach to learning to solve CSPs in an end-to-end manner,…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is…
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. Motivated by…
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…
The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection…