Related papers: Regulated Multiset Rewriting Systems
Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…
Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain…
What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic…
We propose a mechanism for the vertical refinement of bigraphical reactive systems, based upon a mechanism for limiting observations and utilising the underlying categorical structure of bigraphs. We present a motivating example to…
This work aims to produce translations that convey source language content at a formality level that is appropriate for a particular audience. Framing this problem as a neural sequence-to-sequence task ideally requires training triplets…
We propose a formalism to model and reason about multi-agent systems. We allow agents to interact and communicate in different modes so that they can pursue joint tasks; agents may dynamically synchronize, exchange data, adapt their…
In this paper we examine a number of term rewriting system for integer number representations, building further upon the datatype defining systems described in [2]. In particular, we look at automated methods for proving confluence and…
Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…
Building on our recent work on {\em neuromimetic control theory}, new results on resilience and neuro-inspired quantization are reported. The term neuromimetic refers to the models having features that are characteristic of the neurobiology…
With the needs of science and business, data sharing and re-use has become an intensive activity for various areas. In many cases, governance imposes rules concerning data use, but there is no existing computational technique to help…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
Graph-Rewriting Automata (GRA) are an extension of Cellular Automata to a dynamic structure using local graph-rewriting rules. This work introduces linear algebra based tools that allow for a practical investigation of their behavior in…
Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Formal methods refer to rigorous, mathematical approaches to system development and have played a key role in establishing the correctness of safety-critical systems. The main building blocks of formal methods are models and specifications,…
Reactive synthesis aims at automatic construction of systems from their behavioural specifications. The research mostly focuses on synthesis of systems dealing with Boolean signals. But real-life systems are often described using…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…
In this paper we present a minimal object oriented core calculus for modelling the biological notion of type that arises from biological ontologies in formalisms based on term rewriting. This calculus implements encapsulation, method…
This paper proposes a new view to algorithms, Algorithms as defining dynamic systems. This view extends the traditional, deterministic view that an algorithm is a step by step procedure with nondeterminism. As a dynamic system can be…