Related papers: A Process Calculus for Molecular Interaction Maps
Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying…
Background: To understand protein function, it is important to study protein- protein interaction networks. These networks can be represented in network diagrams called protein interaction maps that can lead to better understanding by…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules…
We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and…
With the intervention of machine vision in our crucial day to day necessities including healthcare and automated power plants, attention has been drawn to the internal mechanisms of convolutional neural networks, and the reason why the…
The Shape Calculus is a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
ZX-Calculus is a versatile graphical language for quantum computation equipped with an equational theory. Getting inspiration from Geometry of Interaction, in this paper we propose a token-machine-based asynchronous model of both pure…
To study implementations and optimisations of interaction net systems we propose a calculus to allow us to reason about nets, a concrete data-structure that is in close correspondence with the calculus, and a low-level language to create…
As the request for deep learning solutions increases, the need for explainability is even more fundamental. In this setting, particular attention has been given to visualization techniques, that try to attribute the right relevance to each…
Interaction nets are a graphical model of computation, which has been used to define efficient evaluators for functional calculi, and specifically lambda calculi with patterns. However, the flat structure of interaction nets forces pattern…
Graph transformation approaches have been successfully used to analyse and design chemical and biological systems. Here we build on top of a DPO framework, in which molecules are modelled as typed attributed graphs and chemical reactions…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
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…
Machine learning continues to grow in popularity in academia, in industry, and is increasingly used in other fields. However, most of the common metrics used to evaluate even simple binary classification models have shortcomings that are…
In our understanding, a mind-map is an adaptive engine that basically works incrementally on the fundament of existing transactional streams. Generally, mind-maps consist of symbolic cells that are connected with each other and that become…