Habilitation Thesis Defense
Static analysis and model reduction for site-graph rewriting
Jérôme Feret
Defended the 12th of December 2023
École normale supérieure
This thesis has been done at Département d'Informatique of the École Normale Supérieure (Paris)
President
Reviewers
- Franck Delaplace
- Roberto Giacobazzi
- Jean Goubault-Larrecq
Examiners
- Bernadette Charron-Bost
- Patrick Cousot
- Walter Fontana
- Marc Pouzet
- Xavier Rival
- Adelinde Uhrmacher
Software sciences have a role to play in the description, the organization, the execution, and the analysis of the molecular interaction systems such as biological signaling pathways. These systems involve a huge diversity of bio-molecular entities whereas their dynamics may be driven by races for shared resources, interactions at different time- and concentration-scales, and non-linear feedback loops. Understanding how the behavior of the populations of proteins orchestrates itself from their individual interactions, which is the holy grail on systems biology, requires dedicated languages offering adapted levels of abstraction and efficient analysis tools.
In this manuscript, we describe the design of formal tools for Kappa, a site-graph rewriting language inspired by bio-chemistry. In particular, we introduce a static analysis to compute some properties on the biological entities that may arise in models, so as to increase our confidence in them. We also present a model reduction approach based on a study of the flow of information between the different regions of the biological entities and the potential symmetries. This approach is applied both in the differential and in the stochastic semantics.A mobile system is a pool of agents that
may interact with each other.
Final version (in French) can be downloaded at:
https://theses.hal.science/tel-04326091
Slides of the 45mn presentation (in English) are available at:
https://www.di.ens.fr/~feret/hdr/talk_hdr.pdf