Graph rewriting systems are natural verification and validation tools: they provide visual, intuitive representations of complex systems while specifying the dynamic behaviour of the system in a formal way. In this talk we will describe the use of strategic port graph rewriting as a basis for the implementation of a visual modelling tool: PORGY. We will present attributed hierarchical port graphs (AHP) and a notion of strategic AHP-rewriting as a mechanism to model the behaviour of dynamic systems. The system modelled is represented by an initial graph and a collection of graph rewrite rules, together with a user-defined strategy to control the application of rules. The traditional operators found in strategy languages for term rewriting have been adapted to deal with the more general setting of graph rewriting, and some new constructs have been included in the strategy language to deal with graph traversal and management of rewriting positions in the graph. In the second part of the talk, we describe PORGY and give examples of application in the areas of biochemistry, social networks and finance.

This is joint work with members of the PORGY team at Bordeaux and King’s College London.

YouTube live recording of the seminar

Any computational method in chemistry must choose some level of precision in the modeling. One choice is made in the methods of quantum chemistry based on quantum field theory. While highly accurate, the methods are computationally very demanding, which restricts their practical use to single reactions of molecules of moderate size even when run on supercomputers. At the same time, most existing computational methods for systems chemistry and biology are formulated at the other abstraction extreme, in which the structure of molecules is represented either not at all or in a very rudimentary fashion that does not permit the tracking of individual atoms across a series of reactions.

In this talk, we present our on-going work on creating a practical modelling framework for chemistry based on Double Pushout graph transformation, and how it can be applied to analyse chemical systems. We will address important technical design decisions as well as the importance of methods inspired from Algorithm Engineering in order to reach the required efficiency of our implementation. We will present chemically relevant features that our framework provides (e.g. automatic atom tracing) as well as a set of chemical systems we investigated are currently investigating. If time allows we will discuss variations of graph transformation rule compositions and their chemical validity.

video recording of the seminar on YouTube

We review the integration of (first-order) logic respectively nested conditions into graph transformation. Conditions can serve various purposes: they can constrain graph rewriting, symbolically specify sets of graphs, be used in query languages and in verification (for instance in Hoare logic and for behavioural equivalence checking).

In the graph transformation community the formalism of nested graph conditions has emerged, that is, conditions which are equivalent to first-order logic, but directly integrate graphs and graph morphisms, in order to express constraints more succinctly.

In this talk we also explain how the notion of nested conditions can be lifted from graph transformation systems to the setting of reactive systems as defined by Leifer and Milner. It turns out that some constructions for graph transformation systems (such as computing weakest preconditions and strongest postconditions and showing local confluence by means of critical pair analysis) can be done quite elegantly in the more general setting.

video recording of the seminar on YouTube