2,738 research outputs found
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
Quantified CTL: Expressiveness and Complexity
While it was defined long ago, the extension of CTL with quantification over
atomic propositions has never been studied extensively. Considering two
different semantics (depending whether propositional quantification refers to
the Kripke structure or to its unwinding tree), we study its expressiveness
(showing in particular that QCTL coincides with Monadic Second-Order Logic for
both semantics) and characterise the complexity of its model-checking and
satisfiability problems, depending on the number of nested propositional
quantifiers (showing that the structure semantics populates the polynomial
hierarchy while the tree semantics populates the exponential hierarchy)
Logics for Unranked Trees: An Overview
Labeled unranked trees are used as a model of XML documents, and logical
languages for them have been studied actively over the past several years. Such
logics have different purposes: some are better suited for extracting data,
some for expressing navigational properties, and some make it easy to relate
complex properties of trees to the existence of tree automata for those
properties. Furthermore, logics differ significantly in their model-checking
properties, their automata models, and their behavior on ordered and unordered
trees. In this paper we present a survey of logics for unranked trees
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