Related papers: Learning chemical reaction networks from trajector…

We examine reaction networks (CRNs) through their associated continuous-time Markov processes. Studying the dynamics of such networks is in general hard, both analytically and by simulation. In particular, stationary distributions of…

We propose a novel Markov chain Monte-Carlo (MCMC) method for reverse engineering the topological structure of stochastic reaction networks, a notoriously challenging problem that is relevant in many modern areas of research, like…

We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…

Trajectory mutual information is frequently used to quantify information transfer in biochemical systems. Tractable solutions of the trajectory mutual information can be obtained via the widely used Linear-Noise Approximation (LNA) using…

For the application of MPC design in on-line regulation or tracking control problems, several studies have attempted to develop an accurate model, and realize adequate uncertainty description of linear or non-linear plants of the processes.…

We propose a numerical technique for parameter inference in Markov models of biological processes. Based on time-series data of a process we estimate the kinetic rate constants by maximizing the likelihood of the data. The computation of…

Constructing an accurate system model for formal model verification can be both resource demanding and time-consuming. To alleviate this shortcoming, algorithms have been proposed for automatically learning system models based on observed…

In this paper, we propose a data-driven method to discover multiscale chemical reactions governed by the law of mass action. First, we use a single matrix to represent the stoichiometric coefficients for both the reactants and products in a…

Continuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to…

We address a fundamental problem in chemistry known as chemical reaction product prediction. Our main insight is that the input reactant and reagent molecules can be jointly represented as a graph, and the process of generating product…

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…

Mechanistic understanding of organic reactions can facilitate reaction development, impurity prediction, and in principle, reaction discovery. While several machine learning models have sought to address the task of predicting reaction…

The main motivation of this work is to assess the validity of a LWR traffic flow model to model measurements obtained from trajectory data, and propose extensions of this model to improve it. A formulation for a discrete dynamical system is…

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…

We present a data-driven verification approach that determines whether or not a given chemical reaction network (CRN) satisfies a given property, expressed as a formula in a modal logic. Our approach consists of three phases, integrating…

Stochastic reaction network models arise in intracellular chemical reactions, epidemiological models and other population process models, and are a class of continuous time Markov chains which have the nonnegative integer lattice as state…

The development of chemical reaction models aids understanding and prediction in areas ranging from biology to electrochemistry and combustion. A systematic approach to building reaction network models uses observational data not only to…

Reduction of detailed chemical reaction mechanisms is one of the key methods for mitigating the computational cost of reactive flow simulations. Exploitation of species and elementary reaction sparsity ensures the compactness of the reduced…

We consider the problem of learning the dynamics of autonomous linear systems (i.e., systems that are not affected by external control inputs) from observations of multiple trajectories of those systems, with finite sample guarantees.…

Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…