On the cost of simulating a parallel Boolean automata network by a block-sequential one
Florian Bridoux, Pierre Guillon, K\'evin Perrot, Sylvain Sen\'e,, Guillaume Theyssier

TL;DR
This paper investigates the minimal additional automata needed to simulate a parallel Boolean automata network with a block-sequential schedule, introducing a graph-based approach to bound this cost.
Contribution
It introduces the NECC graph and relates its chromatic number to the simulation cost, providing bounds and conjectures for the minimal automata needed.
Findings
Bounds the simulation cost between n/2 and 2n/3+2
Shows the clique number of NECC graphs is at most n/2
For bijective BANs, the cost is at most n/2+1
Abstract
In this article we study the minimum number of additional automata that a Boolean automata network (BAN) associated with a given block-sequential update schedule needs in order to simulate a given BAN with a parallel update schedule. We introduce a graph that we call graph built from the BAN and the update schedule. We show the relation between and the chromatic number of the graph. Thanks to this graph, we bound in the worst case between and ( being the size of the BAN simulated) and we conjecture that this number equals . We support this conjecture with two results: the clique number of a graph is always less than or equal to and, for the subclass of bijective BANs, is always less than or equal to .
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Taxonomy
TopicsFormal Methods in Verification · Gene Regulatory Network Analysis · DNA and Biological Computing
