Graph Transformation Theory and Applications

I love graph rewriting—the study of ways to change one graph into another by changing one small part at a time. My student Daniel Cicala did his thesis on this! So I’m happy to hear about the new virtual seminar series GReTA: Graph TRansformation Theory and Applications.

It aims to serve as a platform for the international graph rewriting community, promote recent developments and trends in the field, and encourage regular networking and interaction between members of this community.

Seminars are held twice a month in the form of Zoom sessions (some of which will be live-streamed to YouTube). Go to the link if you want to join on Zoom.

You can get regular updates on the GReTA seminars in several ways:

• Subscribe to the GReTA YouTube channel.

• Subscribe to the GReTA Google Calendar (or alternatively import it in iCal format).

• Subscribe to the GReTA mailing list.

Here are the two talks so far. Any subject that can promote talks on both logic and chemistry must be good! Thinking of chemistry and logic as two aspects of the same thing is bound to trigger new ideas. (Just as a sequence of chemical reactions converts reactants into products, a proof converts assumptions into conclusions.)

Speaker: Barbara König
Title: Graph transformation meets logic

Abstract. 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.

Speakers: Daniel Merkle and Jakob Lykke Andersen
Title: Chemical graph transformation and applications

Abstract: 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.

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