相关论文: Reachability Problems for Continuous Chemical Reac…
The study of the dynamics of chemical reactions, and in particular phenomena such as oscillating reactions, has led to the recognition that many dynamical properties of a chemical reaction can be predicted from graph theoretical properties…
The Chemical Reaction Networks (CRN) interpreted through the differential semantics, even when restricted to elementary reactions with mass action law kinetics, form a Turing-complete language. This means that any computable real function…
Metal energy carriers recently gained growing interest in research as a promising storage and transport material for renewable electricity. Within the development of a metal-fueled circular energy economy, research involves a model…
In this essay, we investigate some relations between Chemical Reaction Networks (CRN) and Mathematical Epidemiology (ME) and report on several pleasant surprises which we had simply by putting these two topics together. Firstly, we propose…
We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations. Forward CRN bisimulation identifies a partition where each equivalence class…
Our paper reviews some key concepts in chemical reaction network theory and mathematical epidemiology, and examines their intersection, with three goals. The first is to make the case that mathematical epidemiology (ME), and also related…
Reaction networks have become a major modelling framework in the biological sciences from epidemiology and population biology to genetics and cellular biology. In recent years, much progress has been made on stochastic reaction networks…
Prediction of complete step-by-step chemical reaction mechanisms (CRMs) remains a major challenge. Whereas the traditional approaches in CRM tasks rely on expert-driven experiments or costly quantum chemical computations, contemporary deep…
Molecule representation learning (MRL) methods aim to embed molecules into a real vector space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or GNN-based (Graph Neural Networks) MRL methods either take…
We identify the thermodynamic conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics. We also characterize the thermodynamic efficiency of growth by…
We analyze the solutions, on single network instances, of a recently introduced class of constraint-satisfaction problems (CSPs), describing feasible steady states of chemical reaction networks. First, we show that the CSPs generalize the…
Neural networks (NNs) have been shown to learn complex control laws successfully, often with performance advantages or decreased computational cost compared to alternative methods. Neural network controllers (NNCs) are, however, highly…
Neural networks achieve outstanding accuracy in classification and regression tasks. However, understanding their behavior still remains an open challenge that requires questions to be addressed on the robustness, explainability and…
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…
The Turing completeness result for continuous chemical reaction networks (CRN) shows that any computable function over the real numbers can be computed by a CRN over a finite set of formal molecular species using at most bimolecular…
Power law dynamics is used to describe the stability behavior in metabolic networks such as chemical reaction networks (CRN's). These systems allow multiple steady states within a single stoichiometric class. On the other side thermodynamic…
We propose a direct optimization framework for learning reduced and sparse chemical reaction networks (CRNs) from time-series trajectory data. In contrast to widely used indirect methods-such as those based on sparse identification of…
Well-mixed chemical reaction networks (CRNs) contain many distinct chemical species with copy numbers that fluctuate in correlated ways. While those correlations are typically monitored via Monte Carlo sampling of stochastic trajectories,…
Regular model checking is a well-established technique for the verification of regular transition systems (RTS): transition systems whose initial configurations and transition relation can be effectively encoded as regular languages. In…
Reachability queries ask whether there exists a path from the source vertex to the target vertex on a graph. Recently, several powerful reachability queries, such as Label-Constrained Reachability (LCR) queries and Regular Path Queries…