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Ferdinanda Camporesi & Jérôme Feret.
Using alternative sums to express the occurrence number of extended patterns in site-graphs.

To appear in the PostProceedings of the 8th International Workshop on Static Analysis and Systems Biology (SASB 2017), New York, USA, August 29, 2017, J. Bachman & J. Yang (Eds).

Abstract: Site-graph rewriting languages as Kappa or BNGL supply a convenient way to describe models of signalling pathways. Unlike classical reaction networks, they emphasise on the biochemical structure of proteins. We use patterns to formalise properties about bio-molecular species. Intentionally, a pattern is a part of a species, but extensionally it denotes the multi-set of the species containing this pattern (with the multiplicity). Thus reasoning on patterns allows to handle symbolically arbitrarily big (if not infinite) multi-sets of species. This is a key point to design fast simulation algorithms or model reduction schemes. In this paper, we introduce the notion of extended patterns. Each extended pattern is made of a classical pattern and of a set of potential bonds between pairs of sites. Extended patterns have positive (when at least one of the potential bonds is realised) and negative (when none is realised) instances. They are important to express the consumption and the production of patterns by the rules that may break cycles in bio-molecular species by side-effects. We show that the number of positive (resp. negative) instances of extended patterns may be expressed as alternated sums of the number of occurrences of classical patterns.

@InProceedings{feret:SASB2017,
title = "Using alternated sums to express the occurrence number of extended patterns in site-graphs",
booktitle = "Eighteenth International Workshop on Static Analysis and Systems Biology (SASB'17)",
series = "ENTCS",
publisher = "elsevier",
note = "to appear",
author = "Ferdinanda Camporesi and J{\'e}r{\^o}me Feret"}