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The use of mathematical models has helped to shed light on countless phenomena in chemistry and biology. Often, though, one finds that systems of interest in these fields are dauntingly complex. In this paper, we attempt to synthesize and…
Reaction networks are often used to model interacting species in fields such as biochemistry and ecology. When the counts of the species are sufficiently large, the dynamics of their concentrations are typically modeled via a system of…
Chemical algorithms are statistical algorithms described and represented as chemical reaction networks. They are particularly attractive for traffic shaping and general control of network dynamics; they are analytically tractable, they…
This paper proposes a model, the linear model, for randomly generating logic programs with low density of rules and investigates statistical properties of such random logic programs. It is mathematically shown that the average number of…
This work presents exact expressions for size distributions of weak/multilayer connected components in two generalisations of the configuration model: networks with directed edges and multiplex networks with arbitrary number of layers. The…
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…
We study the distribution of a fully connected neural network with random Gaussian weights and biases in which the hidden layer widths are proportional to a large constant $n$. Under mild assumptions on the non-linearity, we obtain…
In this paper we study a class of stochastic chemical reaction networks (CRNs) for which chemical species are created by a sequence of chain reactions. We prove that under some convenient conditions on the initial state, some of these…
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…
Can machine learning algorithms be implemented using chemistry? We demonstrate that this is possible in the case of support vector machines (SVMs). SVMs are powerful tools for data classification, leveraging Vapnik-Chervonenkis theory to…
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…
Chemically reacting flows are common in engineering, such as hypersonic flow, combustion, explosions, manufacturing processes and environmental assessments. For combustion, the number of reactions can be significant (over 100) and due to…
Chemical Reaction Neural Networks (CRNNs) have emerged as an interpretable machine learning framework for discovering reaction kinetics directly from data, while strictly adhering to the Arrhenius and mass action laws. However, standard…
We derive the Hessian geometric structure of nonequilibrium chemical reaction networks (CRN) on the flux and force spaces induced by the Legendre duality of convex dissipation functions and characterize their dynamics as a generalized flow.…
We develop a data-driven method to learn chemical reaction networks from trajectory data. Modeling the reaction system as a continuous-time Markov chain and assuming the system is fully observed, our method learns the propensity functions…
Generative adversarial networks constitute a powerful approach to generative modeling. While generated samples often are indistinguishable from real data, there is no guarantee that they will follow the true data distribution. For…
In many applications, for example when computing statistics of fast subsystems in a multiscale setting, we wish to find the stationary distributions of systems of continuous time Markov chains. Here we present a class of models that appears…
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 introduce a new type of graphical model called a "cumulative distribution network" (CDN), which expresses a joint cumulative distribution as a product of local functions. Each local function can be viewed as providing evidence about…
The trend to equilibrium for reaction-diffusion systems modelling chemical reaction networks is investigated, in the case when reaction processes happen on subsets of the domain. We prove the convergence to equilibrium by directly showing…