Related papers: Bigraphical Nets
Interaction nets are a graphical formalism inspired by Linear Logic proof-nets often used for studying higher order rewriting e.g. \Beta-reduction. Traditional presentations of interaction nets are based on graph theory and rely on…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
Draft translation to Russian of Chapter 7, Interaction-Based Models of Computation, from Models of Computation: An Introduction to Computability Theory by Maribel Fernandez. "In this chapter, we study interaction nets, a model of…
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…
Interaction nets are a form of restricted graph rewrite system that can serve as a graphical or textual programming language. As such, benefits include one-step confluence, ease of parallelism and explicit garbage collection. However, some…
We propose a method for encoding iterators (and recursion operators in general) using interaction nets (INs). There are two main applications for this: the method can be used to obtain a visual nota- tion for functional programs; and it can…
Gated networks are networks that contain gating connections, in which the outputs of at least two neurons are multiplied. Initially, gated networks were used to learn relationships between two input sources, such as pixels from two images.…
In this article, we extend several algebraic graph analysis methods to bipartite networks. In various areas of science, engineering and commerce, many types of information can be represented as networks, and thus the discipline of network…
As data structures and mathematical objects used for complex systems modeling, hypergraphs sit nicely poised between on the one hand the world of network models, and on the other that of higher-order mathematical abstractions from algebra,…
This paper revisits the bilinear attention networks in the visual question answering task from a graph perspective. The classical bilinear attention networks build a bilinear attention map to extract the joint representation of words in the…
The modern era always looks into advancements in technology. Design and topology of interconnection networks play a mutual role in development of technology. Analysing the topological properties and characteristics of an interconnection…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction…
Interaction nets constitute a visual programming language grounded in graph transformation. Owing to their distinctive properties, they inherently facilitate parallelism in the rewriting step. This paper showcases a simple and concise…
Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions…
Information Filtering Networks (IFNs) provide a powerful framework for modeling complex systems through globally sparse yet locally dense and interpretable structures that capture multivariate dependencies. This review offers a…
Graphical models are widely used to study biological networks. Interventions on network nodes are an important feature of many experimental designs for the study of biological networks. In this paper we put forward a causal variant of…
Motivation: Protein-protein interactions (PPIs) are usually modelled as networks. These networks have extensively been studied using graphlets, small induced subgraphs capturing the local wiring patterns around nodes in networks. They…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
Petri nets are an established graphical formalism for modeling and analyzing the behavior of systems. An important consideration of the value of Petri nets is their use in describing both the syntax and semantics of modeling formalisms.…