Prochain séminaire: Jeudi 14 Juin, 11h, salle 1D23– Jonathan Hayman (ENS Paris)

Bonjour

Le prochain séminaire PPS aura lieu jeudi prochain dans la salle 1D23
habituelle, à 11h.
Jonathan Hayman (ENS Paris et Cambridge Univ) nous parlera de causalité
dans un système de réécriture de graphes à sites pour la biologie des
systèmes.

Une collation avec café, thé et croissants sera servie dès 10.45 dans la
même salle.

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Graphs, rewriting and causality in rule-based models

The Kappa calculus defines how a graph, representing a system of linked
agents, can be modified by rules that specify which changes may occur at
places that match specific local patterns. Though the calculus has a
wide degree of applicability, it has emerged as a natural description of
protein-protein interaction systems and pathways in molecular biology.
This work describes and formalises an intuitive graph-based semantics
for Kappa that correctly handles subtle side-effects upon deletion of
elements of the graph. Central to the work is the use of spans of
morphisms to characterize rewriting in the style of single-pushout based
rewriting.
The sequential application of rules gives rise to trajectories, some of
which may lead to the production of particular patterns of interest. It
is then natural to seek to account for their production with a causal
history (a pathway). We introduce several notions of trajectory
compression, providing a foundation for techniques to reconstruct causal
histories at increasing levels of conciseness.
This is joint work with Vincent Danos, Jérôme Feret, Walter Fontana,
Russ Harmer, Jean Krivine, Chris Thompson-Walsh and Glynn Winskel.