Related papers: Robust Biomolecular Finite Automata
The Turing completeness of continuous chemical reaction networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…
Non-deterministic Finite Automata (NFA) represent regular languages concisely, increasing their appeal for applications such as word recognition. This paper proposes a new approach to generate NFA from an interaction language such as UML…
We study the composability of discrete chemical reaction networks (CRNs) that stably compute (i.e., with probability 0 of error) integer-valued functions $f:\mathbb{N}^d\to\mathbb{N}$. We consider output-oblivious CRNs in which the output…
Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…
The Turing completeness of continuous Chemical Reaction Networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…
We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modeling individual protein behaviors and systems-level…
The dynamics of a chemical reaction network (CRN) is often modelled under the assumption of mass action kinetics by a system of ordinary differential equations (ODEs) with polynomial right-hand sides that describe the time evolution of…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
Chemical reaction networks (CRNs) are foundational models for describing complex biochemical processes. We study noncompetitive CRNs, a class of networks whose static states are rate-independent, and that can implement ReLU neural networks.…
We investigate the internal representations that a recurrent neural network (RNN) uses while learning to recognize a regular formal language. Specifically, we train a RNN on positive and negative examples from a regular language, and ask if…
We present a formal and constructive simulation framework for nondeterministic finite automata (NFAs) using time-shared, depth-unrolled feedforward networks (TS-FFNs), i.e., acyclic unrolled computations with shared parameters that are…
The Gene Regulatory Network (GRN) of biological cells governs a number of key functionalities that enables them to adapt and survive through different environmental conditions. Close observation of the GRN shows that the structure and…
Chemical reaction networks, or CRNs, are known to stably compute semilinear Boolean-valued predicates and functions, provided that all reactions are irreversible. However, this property does not hold for wet-lab implementations, as all…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both…
We develop a representation suitable for the unconstrained recognition of words in natural images: the general case of no fixed lexicon and unknown length. To this end we propose a convolutional neural network (CNN) based architecture which…
Chemical reaction networks (CRNs) model systems where molecules interact according to a finite set of reactions such as $A + B \to C$, representing that if a molecule of $A$ and $B$ collide, they disappear and a molecule of $C$ is produced.…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
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. The original problem…
Chemical Reaction Networks (CRNs) provide a useful abstraction of molecular interaction networks in which molecular structures as well as mass conservation principles are abstracted away to focus on the main dynamical properties of the…