Related papers: Practical Modelling with Bigraphs
A graphical model is a statistical model that is associated to a graph whose nodes correspond to variables of interest. The edges of the graph reflect allowed conditional dependencies among the variables. Graphical models admit…
Multi-population evolutionary algorithms are, by nature, highly complex and difficult to describe. Even two populations working in concert (or opposition) present a myriad of potential configurations that are often difficult to relate using…
Process theories combine a graphical language for compositional reasoning with an underlying categorical semantics. They have been successfully applied to fields such as quantum computation, natural language processing, linear dynamical…
Ontologies are built on systems that conceptually evolve over time. In addition, techniques and languages for building ontologies evolve too. This has led to numerous studies in the field of ontology versioning and ontology evolution. This…
Motivated by questions from program transformations, eight notions of isomorphisms between term rewriting systems are defined, analysed, and classified. The notions include global isomorphisms, where the renaming of variables and function…
The use of rewriting-based visual formalisms is on the rise. In the formal methods community, this is due also to the introduction of adhesive categories, where most properties of classical approaches to graph transformation, such as those…
Probabilistic programming is becoming increasingly popular thanks to its ability to specify problems with a certain degree of uncertainty. In this work, we focus on term rewriting, a well-known computational formalism. In particular, we…
We describe a tool to create, edit, visualise and compute with interaction nets - a form of graph rewriting systems. The editor, called GraphPaper, allows users to create and edit graphs and their transformation rules using an intuitive…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
This paper investigates the use of graph rewriting systems as a modelling tool, and advocates the embedding of such systems in an interactive environment. One important application domain is the modelling of biochemical systems, where…
A biform theory is a combination of an axiomatic theory and an algorithmic theory that supports the integration of reasoning and computation. These are ideal for formalizing algorithms that manipulate mathematical expressions. A theory…
Probabilistic model checking is an approach to the formal modelling and analysis of stochastic systems. Over the past twenty five years, the number of different formalisms and techniques developed in this field has grown considerably, as…
Probabilistic graphical models combine the graph theory and probability theory to give a multivariate statistical modeling. They provide a unified description of uncertainty using probability and complexity using the graphical model.…
We present a new and powerful algebraic framework for graph rewriting, based on drags, a class of graphs enjoying a novel composition operator. Graphs are embellished with roots and sprouts, which can be wired together to form edges. Drags…
We develop a novel method to analyze the dynamics of stochastic rewriting systems evolving over finitary adhesive, extensive categories. Our formalism is based on the so-called rule algebra framework and exhibits an intimate relationship…
Graphs are widespread data structures used to model a wide variety of problems. The sheer amount of data to be processed has prompted the creation of a myriad of systems that help us cope with massive scale graphs. The pressure to deliver…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
String diagrams are a powerful tool for reasoning about physical processes, logic circuits, tensor networks, and many other compositional structures. Dixon, Duncan and Kissinger introduced string graphs, which are a combinatoric…
The basic principle of graph rewriting is the stepwise replacement of subgraphs inside a host graph. A challenge in such replacement steps is the treatment of the patch graph, consisting of those edges of the host graph that touch the…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…