Reversible Sesqui-Pushout Rewriting

The paper proposes a variant of sesqui-pushout rewriting (SqPO) that allows one to develop the theory of nested application conditions (NACs) for arbitrary rule spans; this is a considerable generalisation compared with existing results for NACs, which only hold for linear rules (w.r.t. a suitable class of monos). Besides this main contribution, namely an adapted shifting construction for NACs, the paper presents a uniform commutativity result for a revised notion of independence that applies to arbitrary rules; these theorems hold in any category with (enough) stable pushouts and a class of monos rendering it weak adhesive HLR. To illustrate results and concepts, we use simple graphs, i.e. the category of binary endorelations and relation preserving functions, as it is a paradigmatic example of a category with stable pushouts; moreover, using regular monos to give semantics to NACs, we can shift NACs over arbitrary rule spans

Deduction as Reduction

Deduction systems and graph rewriting systems are compared within a common categorical framework. This leads to an improved deduction method in diagrammatic logics

On the definition of parallel independence in the algebraic approaches to graph transformation

Parallel independence between transformation steps is a basic and well-understood notion of the algebraic approaches to graph transformation, and typically guarantees that the two steps can be applied in any order obtaining the same resulting graph, up to isomorphism. The concept has been redefined for several algebraic approaches as variations of a classical “algebraic” condition, requiring that each matching morphism factorizes through the context graphs of the other transformation step. However, looking at some classical papers on the double-pushout approach, one finds that the original definition of parallel independence was formulated in set-theoretical terms, requiring that the intersection of the images of the two left-hand sides in the host graph is contained in the intersection of the two interface graphs. The relationship between this definition and the standard algebraic one is discussed in this position paper, both in the case of left-linear and non-left-linear rules

On the essence of parallel independence for the double-pushout and sesqui-pushout approaches

Parallel independence between transformation steps is a basic notion in the algebraic approaches to graph transformation, which is at the core of some static analysis techniques like Critical Pair Analysis. We propose a new categorical condition of parallel independence and show its equivalence with two other conditions proposed in the literature, for both left-linear and non-left-linear rules. Next we present some preliminary experimental results aimed at comparing the three conditions with respect to computational efficiency. To this aim, we implemented the three conditions, for left-linear rules only, in the Verigraph system, and used them to check parallel independence of pairs of overlapping redexes generated from some sample graph transformation systems over categories of typed graphs

Parallelism in AGREE transformations

The AGREE approach to graph transformation allows to specify rules that clone items of the host graph, controlling in a finegrained way how to deal with the edges that are incident, but not matched, to the rewritten part of the graph. Here, we investigate in which ways cloning (with controlled embedding) may affect the dependencies between two rules applied to the same graph. We extend to AGREE the classical notion of parallel independence between the matches of two rules to the same graph, identifying sufficient conditions that guarantee that two rules can be applied in any order leading to the same result

Rate Equations for Graphs

In this paper, we combine ideas from two different scientific traditions: 1) graph transformation systems (GTSs) stemming from the theory of formal languages and concurrency, and 2) mean field approximations (MFAs), a collection of approximation techniques ubiquitous in the study of complex dynamics. Using existing tools from algebraic graph rewriting, as well as new ones, we build a framework which generates rate equations for stochastic GTSs and from which one can derive MFAs of any order (no longer limited to the humanly computable). The procedure for deriving rate equations and their approximations can be automated. An implementation and example models are available online at https://rhz.github.io/fragger. We apply our techniques and tools to derive an expression for the mean velocity of a two-legged walker protein on DNA.Comment: to be presented at the 18th International Conference on Computational Methods in Systems Biology (CMSB 2020

Convolution Products on Double Categories and Categorification of Rule Algebras

Motivated by compositional categorical rewriting theory, we introduce a convolution product over presheaves of double categories which generalizes the usual Day tensor product of presheaves of monoidal categories. One interesting aspect of the construction is that this convolution product is in general only oplax associative. For that reason, we identify several classes of double categories for which the convolution product is not just oplax associative, but fully associative. This includes in particular framed bicategories on the one hand, and double categories of compositional rewriting theories on the other. For the latter, we establish a formula which justifies the view that the convolution product categorifies the rule algebra product

Rate Equations for Graphs

International audienceIn this paper, we combine ideas from two different scientifictraditions: 1) graph transformation systems (GTSs) stemming from thetheory of formal languages and concurrency, and 2) mean field approx-imations (MFAs), a collection of approximation techniques ubiquitousin the study of complex dynamics. Using existing tools from algebraicgraph rewriting, as well as new ones, we build a framework which gener-ates rate equations for stochastic GTSs and from which one can deriveMFAs of any order (no longer limited to the humanly computable). Theprocedure for deriving rate equations and their approximations can beautomated. An implementation and example models are available onlineat https://rhz.github.io/fragger. We apply our techniques and tools toderive an expression for the mean velocity of a two-legged walker proteinon DNA

Graph Transformations for the Resource Description Framework

The Resource Description Framework (RDF) is a standard developed by the World Wide Web Consortium (W3C) to facilitate the representation and exchange of structured (meta-)data in the "SemanticWeb". While there is a large body of work dealing with inference on RDF, a concept for transformation and manipulation is still missing. Since RDF uses graphs as a formal basis, this paper proposes the use of algebraic graph transformations with their wealth of well-known constructions and results for this purpose. It turns out that RDF graphs are an interesting application area for graph transformation methods, where some significant differences to classical graphs yield practically relevant solutions for features like attribution, typing and globally unique nodes