相关论文: Determining the Equivalence of Small Zero-one Reac…
Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology,…
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…
A natural condition on the structure of the underlying chemical reaction network, namely weak reversibility, is shown to guarantee the existence of an equilibrium (steady state) in each positive stoichiometric compatibility class for the…
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…
While the analytical solution for the marginal distribution of a stochastic chemical reaction network has been extensively studied, its joint distribution, i.e. the solution of a high-dimensional chemical master equation, has received much…
We consider stochastic reaction networks modeled by continuous-time Markov chains. Such reaction networks often contain many reactions, potentially occurring at different time scales, and have unknown parameters (kinetic rates, total…
Heterogeneous graph neural networks (GNNs) achieve strong performance on node classification tasks in a semi-supervised learning setting. However, as in the simpler homogeneous GNN case, message-passing-based heterogeneous GNNs may struggle…
We study two specific measures of quality of chemical reaction networks, Precision and Sensitivity. The two measures arise in the study of sensory adaptation, in which the reaction network is viewed as an input-output system. Given a step…
The connectivity of individual neurons of large neural networks determine both the steady state activity of the network and its answer to external stimulus. Highly diluted random networks have zero activity. We show that increasing the…
In this article, we revisit and expand our prior work on graph similarity. As with our earlier work, we focus on a view of similarity which does not require node correspondence between graphs under comparison. Our work is suited to the…
Motivated by problems from Chemical Reaction Network Theory, we investigate whether steady state ideals of reversible reaction networks are generated by binomials. We take an algebraic approach considering, besides concentrations of…
In Refs.[1] and [2], calculation of effective resistances on distance-regular networks was investigated, where in the first paper, the calculation was based on the stratification of the network and Stieltjes function associated with the…
A multistationarity region is the part of a reaction network's parameter space that gives rise to multiple steady states. Mathematically, this region consists of the positive parameters for which a parametrized family of polynomial…
Analogous to biological sequence comparison, comparing cellular networks is an important problem that could provide insight into biological understanding and therapeutics. For technical reasons, comparing large networks is computationally…
Dynamical system models of complex biochemical reaction networks are usually high-dimensional, nonlinear, and contain many unknown parameters. In some cases the reaction network structure dictates that positive equilibria must be unique for…
Chemical reaction networks (CRNs) are directed graphs with reactant or product complexes as vertices, and reactions as arcs. A CRN is weakly reversible if each of its connected components is strongly connected. Weakly reversible networks…
Reaction networks are a general formalism for describing collections of classical entities interacting in a random way. While reaction networks are mainly studied by chemists, they are equivalent to Petri nets, which are used for similar…
For three typical sets of small reaction networks (networks with two reactions, one irreversible and one reversible reaction, or two reversible-reaction pairs), we completely answer the challenging question: what is the smallest subset of…
The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…
We present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks.…