Related papers: Output-Oblivious Stochastic Chemical Reaction Netw…
Most current image super-resolution (SR) methods based on convolutional neural networks (CNNs) use residual learning in network structural design, which favors to effective back propagation and hence improves SR performance by increasing…
Neural approaches to sequence labeling often use a Conditional Random Field (CRF) to model their output dependencies, while Recurrent Neural Networks (RNN) are used for the same purpose in other tasks. We set out to establish RNNs as an…
Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in…
We address a fundamental question: under which conditions do the dynamics and thermodynamics of open chemical reaction networks (CRNs), grounded on the notion of idealized chemostats that exchange selected species, emerge from underlying…
Existing Collaborative Filtering (CF) methods are mostly designed based on the idea of matching, i.e., by learning user and item embeddings from data using shallow or deep models, they try to capture the associative relevance patterns in…
We investigate a broad family of chemical reaction networks (CRNs) assigned with mass action kinetics, called complex-balanced-produced-CRNs (CBP-CRNs), which are generated by any given complex balanced mass action system (MAS) and whose…
Much of the theory on chemical-reaction networks (CRNs) has been developed in the ideal-solution limit, where interactions between the solutes are negligible. However, there is a large variety of phenomena in biological cells and…
We establish a generalized work theorem for stochastic chemical reaction networks (CRNs). By using a compensated Poisson jump process, we identify a martingale structure in a generalized entropy defined relative to an auxiliary backward…
Neural-network-based controllers (NNCs) can represent complex, highly nonlinear control laws, but verifying the closed-loop stability of dynamical systems using them remains challenging. This work presents contributions to a…
Continuous time recurrent neural networks (CTRNN) are systems of coupled ordinary differential equations that are simple enough to be insightful for describing learning and computation, from both biological and machine learning viewpoints.…
Autocatalysis is an important feature of metabolic networks, contributing crucially to the self-maintenance of organisms. Autocatalytic subsystems of chemical reaction networks (CRNs) are characterized in terms of algebraic conditions on…
The ability of a chemical reaction network to generate itself by catalyzed reactions from constantly present environmental food sources is considered a fundamental property in origin-of-life research. Based on Kaufmann's autocatalytic sets,…
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
A reaction system exhibits "absolute concentration robustness" (ACR) in some species if the positive steady-state value of that species does not depend on initial conditions. Mathematically, this means that the positive part of the variety…
Reservoir computing - information processing based on untrained recurrent neural networks with random connections - is expected to depend on the nonlinear properties of the neurons and the resulting oscillatory, chaotic, or fixpoint…
Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…
Disjunctive finitary programs are a class of logic programs admitting function symbols and hence infinite domains. They have very good computational properties, for example ground queries are decidable while in the general case the stable…
Most differential equations found in chemical reaction networks (CRNs) have the form $dx/dt=f(x)= Sv(x)$, where $x$ lies in the nonnegative orthant, where $S$ is a real matrix (the stoichiometric matrix) and $v$ is a column vector…
Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the…
Stochastic reaction networks (SRNs) provide models of many real-world networks. Examples include networks in epidemiology, pharmacology, genetics, ecology, chemistry, and social sciences. Here, we model stochastic reaction networks by…