Repotting the Geraniums: On Nested Graph Transformation Rules

We propose a scheme for rule amalgamation based on nested graph predicates. Essentially, we extend all the graphs in such a predicate with right hand sides. Whenever such an enriched nested predicate matches (i.e., is satisfied by) a given host graph, this results in many individual match morphisms, and thus many “small” rule applications. The total effect is described by the amalgamated rule. This makes for a smooth, uniform and very powerful amalgamation scheme, which we demonstrate on a number of examples. Among the examples is the following, which we believe to be inexpressible in very few other parallel rule formalism proposed in the literature: repot all flowering geraniums whose pots have cracked.\u

Modeling and Reasoning over Distributed Systems using Aspect-Oriented Graph Grammars

Aspect-orientation is a relatively new paradigm that introduces abstractions to modularize the implementation of system-wide policies. It is based on a composition operation, called aspect weaving, that implicitly modifies a base system by performing related changes within the system modules. Aspect-oriented graph grammars (AOGG) extend the classic graph grammar formalism by defining aspects as sets of rule-based modifications over a base graph grammar. Despite the advantages of aspect-oriented concepts regarding modularity, the implicit nature of the aspect weaving operation may also introduce issues when reasoning about the system behavior. Since in AOGGs aspect weaving is characterized by means of rule-based rewriting, we can overcome these problems by using known analysis techniques from the graph transformation literature to study aspect composition. In this paper, we present a case study of a distributed client-server system with global policies, modeled as an aspect-oriented graph grammar, and discuss how to use the AGG tool to identify potential conflicts in aspect weaving

Canonical Derivations with Negative Application Conditions

Using graph transformations to specify the dynamics of distributed systems and networks, we require a precise understanding of concurrency. Negative application conditions (NACs) are an essential means for controlling the application of rules, extending our ability to model complex systems. A classical notion of concurrency in graph transformation is based on shift equivalence and its representation by canonical derivations, i.e., normal forms of the shift operation anticipating independent steps. These concepts are lifted to graph transformation systems with NACs and it is shown that canonical derivations exist for so-called incremental NACs

Concurrent Computing: from Petri Nets to Graph Grammars

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A Graph-based Semantics For Object-oriented Programming Constructs

AbstractThis paper presents a graph-based formalism for object-oriented class structure specifications. The formalism combines labelled graphs with partial orders, to adequately model the (single) inheritance relation among objects and the overriding relation between methods within derived classes. The semantics of system extension by inheritance and aggregation is then defined as colimits in a suitable category of object-oriented system specifications and their morphisms

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

Algebraic transformation of unary partial algebras II: Single-pushout approach

AbstractThe single-pushout approach to graph transformation is extended to the algebraic transformation of partial many-sorted unary algebras. Such a generalization has been motivated by the need to model the transformation of structures which are richer and more complex than graphs and hypergraphs.The main result presented in this article is an algebraic characterization of the single-pushout transformation in the categories of all conformisms, all closed quomorphisms, and all closed-domain closed quomorphisms of unary partial algebras over a given signature, together with a corresponding operational characterization that may serve as a basis for implementation.Moreover, all three categories are shown to satisfy all of the HLR (high-level replacement) conditions for parallelism, taking as occurrences the total morphisms in each category. Another important result presented in this article is the definition of HLR conditions for amalgamation, which are also satisfied by the categories of partial homomorphisms considered here, taking again the corresponding total morphisms as occurrences

Analysis of Generative Chemistries

For the modelling of chemistry we use undirected, labelled graphs as explicit models of molecules and graph transformation rules for modelling generalised chemical reactions. This is used to define artificial chemistries on the level of individual bonds and atoms, where formal graph grammars implicitly represent large spaces of chemical compounds. We use a graph rewriting formalism, rooted in category theory, called the Double Pushout approach, which directly expresses the transition state of chemical reactions. Using concurrency theory for transformation rules, we define algorithms for the composition of rewrite rules in a chemically intuitive manner that enable automatic abstraction of the level of detail in chemical pathways. Based on this rule composition we define an algorithmic framework for generation of vast reaction networks for specific spaces of a given chemistry, while still maintaining the level of detail of the model down to the atomic level. The framework also allows for computation with graphs and graph grammars, which is utilised to model non-trivial chemical systems. The graph generation relies on graph isomorphism testing, and we review the general individualisation-refinement paradigm used in the state-of-the-art algorithms for graph canonicalisation, isomorphism testing, and automorphism discovery. We present a model for chemical pathways based on a generalisation of network flows from ordinary directed graphs to directed hypergraphs. The model allows for reasoning about the flow of individual molecules in general pathways, and the introduction of chemically motivated routing constraints. It further provides the foundation for defining specialised pathway motifs, which is illustrated by defining necessary topological constraints for both catalytic and autocatalytic pathways. We also prove that central types of pathway questions are NP-complete, even for restricted classes of reaction networks. The complete pathway model, including constraints for catalytic and autocatalytic pathways, is implemented using integer linear programming. This implementation is used in a tree search method to enumerate both optimal and near-optimal pathway solutions. The formal methods are applied to multiple chemical systems: the enzyme catalysed beta-lactamase reaction, variations of the glycolysis pathway, and the formose process. In each of these systems we use rule composition to abstract pathways and calculate traces for isotope labelled carbon atoms. The pathway model is used to automatically enumerate alternative non-oxidative glycolysis pathways, and enumerate thousands of candidates for autocatalytic pathways in the formose process

Matrix Graph Grammars

This book objective is to develop an algebraization of graph grammars. Equivalently, we study graph dynamics. From the point of view of a computer scientist, graph grammars are a natural generalization of Chomsky grammars for which a purely algebraic approach does not exist up to now. A Chomsky (or string) grammar is, roughly speaking, a precise description of a formal language (which in essence is a set of strings). On a more discrete mathematical style, it can be said that graph grammars -- Matrix Graph Grammars in particular -- study dynamics of graphs. Ideally, this algebraization would enforce our understanding of grammars in general, providing new analysis techniques and generalizations of concepts, problems and results known so far.Comment: 321 pages, 75 figures. This book has is publisehd by VDM verlag, ISBN 978-363921255