Related papers: Robust Biomolecular Finite Automata
Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic…
Most chemical processes, such as distillation, absorption, extraction, and catalytic reactions, are extremely complex processes that are affected by multiple factors. The relationships between their input variables and output variables are…
Inferring chemical reaction networks (CRN) from concentration time series is a challenge encouragedby the growing availability of quantitative temporal data at the cellular level. This motivates thedesign of algorithms to infer the…
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…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
Grammatical inference consists in learning a language or a grammar from data. In this paper, we consider a number of models for inferring a non-deterministic finite automaton (NFA) with 3 sorts of states, that must accept some words, and…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
Chemical reactor networks (CRNs) enable simulations of combustion reactors with detailed chemical kinetics and strongly simplified flow structure. In this paper, the implementation of a reactor component with less idealized flow structure,…
An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics.
Biomolecular networks underpin emerging technologies in synthetic biology-from robust biomanufacturing and metabolic engineering to smart therapeutics and cell-based diagnostics-and also provide a mechanistic language for understanding…
In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an…
In this work, we introduce DeepDFA, a novel approach to identifying Deterministic Finite Automata (DFAs) from traces, harnessing a differentiable yet discrete model. Inspired by both the probabilistic relaxation of DFAs and Recurrent Neural…
We explore the range of probabilistic behaviours that can be engineered with Chemical Reaction Networks (CRNs). We show that at steady state CRNs are able to "program" any distribution with finite support in $\mathbb{N}^m$, with $m \geq 1$.…
The study of Chemical Reaction Networks (CRN's) is a very active field. Earlier well-known results \cite{Feinberg:def_01:87, Anderson:product_dist:10} identify a topological quantity called deficiency, for any CRN, which, when exactly equal…
In order to fully exploit the potential of molecular communication (MC) for intra-body communication, practically implementable cellular receivers are an important long-term goal. A variety of receiver architectures based on chemical…
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…
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…
This paper presents and analyzes an incremental algorithm for the construction of Acyclic Non-deterministic Finite-state Automata (NFA). Automata of this type are quite useful in computational linguistics, especially for storing lexicons.…
Chemical reaction networks (CRNs) are directed graphs with reactant or product complexes as vertices, and reactions as arcs. A CRN is weakly reversible if each of its connected components is strongly connected. Weakly reversible networks…
We give an unique string representation, up to isomorphism, for initially connected deterministic finite automata (ICDFAs) with n states over an alphabet of k symbols. We show how to generate all these strings for each n and k, and how its…