Basins of Attraction, Commitment Sets and Phenotypes of Boolean Networks

The attractors of Boolean networks and their basins have been shown to be highly relevant for model validation and predictive modelling, e.g., in systems biology. Yet there are currently very few tools available that are able to compute and visualise not only attractors but also their basins. In the realm of asynchronous, non-deterministic modeling not only is the repertoire of software even more limited, but also the formal notions for basins of attraction are often lacking. In this setting, the difficulty both for theory and computation arises from the fact that states may be ele- ments of several distinct basins. In this paper we address this topic by partitioning the state space into sets that are committed to the same attractors. These commitment sets can easily be generalised to sets that are equivalent w.r.t. the long-term behaviours of pre-selected nodes which leads us to the notions of markers and phenotypes which we illustrate in a case study on bladder tumorigenesis. For every concept we propose equivalent CTL model checking queries and an extension of the state of the art model checking software NuSMV is made available that is capa- ble of computing the respective sets. All notions are fully integrated as three new modules in our Python package PyBoolNet, including functions for visualising the basins, commitment sets and phenotypes as quotient graphs and pie charts

Structural Analysis of Boolean Equation Systems

We analyse the problem of solving Boolean equation systems through the use of structure graphs. The latter are obtained through an elegant set of Plotkin-style deduction rules. Our main contribution is that we show that equation systems with bisimilar structure graphs have the same solution. We show that our work conservatively extends earlier work, conducted by Keiren and Willemse, in which dependency graphs were used to analyse a subclass of Boolean equation systems, viz., equation systems in standard recursive form. We illustrate our approach by a small example, demonstrating the effect of simplifying an equation system through minimisation of its structure graph

Analysis of Boolean Equation Systems through Structure Graphs

We analyse the problem of solving Boolean equation systems through the use of structure graphs. The latter are obtained through an elegant set of Plotkin-style deduction rules. Our main contribution is that we show that equation systems with bisimilar structure graphs have the same solution. We show that our work conservatively extends earlier work, conducted by Keiren and Willemse, in which dependency graphs were used to analyse a subclass of Boolean equation systems, viz., equation systems in standard recursive form. We illustrate our approach by a small example, demonstrating the effect of simplifying an equation system through minimisation of its structure graph

Ackermann Encoding, Bisimulations, and OBDDs

We propose an alternative way to represent graphs via OBDDs based on the observation that a partition of the graph nodes allows sharing among the employed OBDDs. In the second part of the paper we present a method to compute at the same time the quotient w.r.t. the maximum bisimulation and the OBDD representation of a given graph. The proposed computation is based on an OBDD-rewriting of the notion of Ackermann encoding of hereditarily finite sets into natural numbers.Comment: To appear on 'Theory and Practice of Logic Programming

Model Checking Synchronized Products of Infinite Transition Systems

Formal verification using the model checking paradigm has to deal with two aspects: The system models are structured, often as products of components, and the specification logic has to be expressive enough to allow the formalization of reachability properties. The present paper is a study on what can be achieved for infinite transition systems under these premises. As models we consider products of infinite transition systems with different synchronization constraints. We introduce finitely synchronized transition systems, i.e. product systems which contain only finitely many (parameterized) synchronized transitions, and show that the decidability of FO(R), first-order logic extended by reachability predicates, of the product system can be reduced to the decidability of FO(R) of the components. This result is optimal in the following sense: (1) If we allow semifinite synchronization, i.e. just in one component infinitely many transitions are synchronized, the FO(R)-theory of the product system is in general undecidable. (2) We cannot extend the expressive power of the logic under consideration. Already a weak extension of first-order logic with transitive closure, where we restrict the transitive closure operators to arity one and nesting depth two, is undecidable for an asynchronous (and hence finitely synchronized) product, namely for the infinite grid.Comment: 18 page