Strategic Graph Rewriting / Network Analysis / Visual Analytics Challenges and thoughts Bruno Pinaud University of Bordeaux Joint work with : Maribel Fernandez (King s College London, UK) Hélène Kirchner (Inria, France) Guy Melançon (University of Bordeaux) Oana Andrei (during her spare time as a post doc until 2014) Jason Vallet (U. Bordeaux, Phd defended Dec. 2017) Olivier Namet (King s College London, Phd defended in 2013) And many more... 1
Graph Rewriting in a nutshell Design of executable specifcations of complex systems Work ofcialy started (frst (small) grant) in 2009 on protein-protein network, interaction nets Very frst paper: protein-protein interaction network, 2011, 6th Int. Workshop on Computing with Terms and Graphs (TERMGRAPH) 2
Graph Rewriting in a nutshell Design of executable specifcations of complex systems Work ofcialy started (frst (small) grant) in 2009 on General aim protein-protein network, interaction nets Understand how the interaction behavior of Very frst paper: protein-protein network, the system at a global scale emerges from rules specifying how local modifcations operate. 2011, 6th Int. Workshop on Computing with Terms and Graphs (TERMGRAPH) 3
A Challenge Can we built a sort of universal data model to handle all operations of the system? 4
Main applications so far Social network : information propagation, build networks like in real life Phd defended Dec. 2017 (Jason Vallet) J. of Logical and Algebraic Method in Programming (JLAMP, 2018) Protein interaction network Other applications : capital markets, relational databases, interaction nets, graph theory 5
Two challenges: Provide a modelling framework for complex systems based on graph rewriting Complex Systems <State, Evolution Step, Control> <Graph, Set of Rules, Strategy> Strategic Graph Program Preserve all computations, start a computation from any existing state, provide interactive visualisation tools to help simulation, analysis and debugging. 6
Porgy in a minute Porgy is built with the Tulip Framework 7
All available rewrite rules Rewrite rule Porgy is built with the Tulip Framework 8
All available rewrite rules A state of the graph under rewriting Rewrite rule Porgy is built with the Tulip Framework 9
All available rewrite rules A state of the graph under rewriting Derivation tree Rewrite rule Strategy Program 10
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AND MUCH MORE... Shneiderman mantra is not far away 15
Another Question for the seminar Can we built a sort of universal data model to handle all operations of the system? Our (partial) answer : Labelled Port Graph : a formal structure for models, computation and visualisation Looks like multilayer graph Looking forward to Dagstuhl Seminar 19061, Visual Analytics of Multilayer Networks Across Disciplines Feb. 2019. Associated with project BLIZAAR - Hybrid Visualization of Dynamic Multilayer Graphs (collaboration with Luxembourg Institute of Science and Technology (LIST) with applications on Digital Cultural Heritage and bioinformatics (considering all -omics layer). PIs : Bruno Pinaud (Fr) / Mohammad Ghoniem (Lux) Every component of the rewriting system can be expressed as a labelled portgraph Makes computation and storing easier Labels can be colour, text, Boolean equation, code, predicates, 16
Problems with labelled portgraph 17
Problems with labelled portgraphs Need of a powerful and fexible graph framework Use of a graph hierarchy to handle backtracking and eliminates data duplication when making a new rewriting step Thanks to visualisation, the system is easy to use and intuitive (feedback from users) 18
Problems with labelled portgraphs Port graph not handled by default in many software Drawing nice layout for rules and graphs far from easy Bottleneck of the system: graph/subgraph isomorphism 19
Beyond port graph rules and graph framework Expression of higher order rule Use of a graph database (many works on graph/subgraph isomorphism) 20
Feel free to ask for a live demo of Tulip/Porgy (at your own risk)!!! 21