相关论文: A semi-quantitative equivalence for abstracting fr…

In the presence of multiscale dynamics in a reaction network, direct simulation methods become inefficient as they can only advance the system on the smallest scale. This work presents stochastic averaging techniques to accelerate…

The standard two-step model of homogeneous-catalyzed reactions had been theoretically analyzed at various levels of approximations from time to time. The primary aim was to check the validity of the quasi-steady-state approximation, and…

Answer Set Programming (ASP) is a prominent rule-based language for knowledge representation and reasoning with roots in logic programming and non-monotonic reasoning. The aim to capture the essence of removing (ir)relevant details in ASP…

Concurrent constraint programming (ccp) is a well-established model for concurrency that singles out the fundamental aspects of asynchronous systems whose agents (or processes) evolve by posting and querying (partial) information in a…

The analysis of concurrent and reactive systems is based to a large degree on various notions of process equivalence, ranging, on the so-called linear-time/branching-time spectrum, from fine-grained equivalences such as strong bisimilarity…

Automata representing game-semantic models of programs are meant to operate in environments whose input-output behaviour is constrained by the rules of a game. This can lead to a notion of equivalence between states which is weaker than the…

The statistical thermodynamics of binary mixtures of polyatomic species was developed on a generalization in the spirit of the lattice-gas model and the quasi-chemical approximation (QCA). The new theoretical framework is obtained by…

The probability distribution describing the state of a Stochastic Reaction Network evolves according to the Chemical Master Equation (CME). It is common to estimated its solution using Monte Carlo methods such as the Stochastic Simulation…

We consider principled alternatives to unsupervised learning in data mining by situating the learning task in the context of the subsequent analysis task. Specifically, we consider a query-answering (hypothesis-testing) task: In the…

For a long time biologists have used visual representations of biochemical networks to gain a quick overview of important structural properties. Recently SBGN, the Systems Biology Graphical Notation, has been developed to standardise the…

The quasi-steady-state assumption (QSSA) is an approximation that is widely used in chemistry and chemical engineering to simplify reaction mechanisms. The key step in the method requires a solution by radicals of a system of multivariate…

We introduce a general categorical framework for the definition of weak behavioural equivalences, building on and extending recent results in the field. This framework is based on parametrized saturation categories, i.e. categories whose…

A relation giving a minimum for the irreversible work in quasi-equilibrium processes was derived by Sekimoto et al. (K. Sekimoto and S. Sasa, J. Phys. Soc. Jpn. {\bf 66} (1997), 3326) in the framework of stochastic energetics. This relation…

We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian…

In this paper, we study the asymptotic behavior of a semi-linear slow-fast stochastic partial differential equation with singular coefficients. Using the Poisson equation in Hilbert space, we first establish the strong convergence in the…

Linear response theory is a well-established method in physics and chemistry for exploring excitations of many-body systems. In particular, the quasiparticle random-phase approximation (QRPA) provides a powerful microscopic framework by…

The relationship between components of biochemical network and the resulting dynamics of the overall system is a key focus of computational biology. However, as these networks and resulting mathematical models are inherently complex and…

One of the basic sanity properties of a behavioural semantics is that it constitutes a congruence with respect to standard process operators. This issue has been traditionally addressed by the development of rule formats for transition…

Pomset automata are an operational model of weak bi-Kleene algebra, which describes programs that can fork an execution into parallel threads, upon completion of which execution can join to resume as a single thread. We characterize a…

Semisupervised methods inevitably invoke some assumption that links the marginal distribution of the features to the regression function of the label. Most commonly, the cluster or manifold assumptions are used which imply that the…