Quantification of reachable attractors in asynchronous discrete dynamics

Abstract

Motivation: Models of discrete concurrent systems often lead to huge and complex state transition graphs that represent their dynamics. This makes difficult to analyse dynamical properties. In particular, for logical models of biological regulatory networks, it is of real interest to study attractors and their reachability from specific initial conditions, i.e. to assess the potential asymptotical behaviours of the system. Beyond the identification of the reachable attractors, we propose to quantify this reachability. Results: Relying on the structure of the state transition graph, we estimate the probability of each attractor reachable from a given initial condition or from a portion of the state space. First, we present a quasi-exact solution with an original algorithm called Firefront, based on the exhaustive exploration of the reachable state space. Then, we introduce an adapted version of Monte Carlo simulation algorithm, termed Avatar, better suited to larger models. Firefront and Avatar methods are validated and compared to other related approaches, using as test cases logical models of synthetic and biological networks. Availability: Both algorithms are implemented as Perl scripts that can be freely downloaded from http://compbio.igc.gulbenkian.pt/nmd/node/59 along with Supplementary Material.Comment: 19 pages, 2 figures, 2 algorithms and 2 table