2,098 research outputs found
Symbolic Algorithms for Language Equivalence and Kleene Algebra with Tests
We first propose algorithms for checking language equivalence of finite
automata over a large alphabet. We use symbolic automata, where the transition
function is compactly represented using a (multi-terminal) binary decision
diagrams (BDD). The key idea consists in computing a bisimulation by exploring
reachable pairs symbolically, so as to avoid redundancies. This idea can be
combined with already existing optimisations, and we show in particular a nice
integration with the disjoint sets forest data-structure from Hopcroft and
Karp's standard algorithm. Then we consider Kleene algebra with tests (KAT), an
algebraic theory that can be used for verification in various domains ranging
from compiler optimisation to network programming analysis. This theory is
decidable by reduction to language equivalence of automata on guarded strings,
a particular kind of automata that have exponentially large alphabets. We
propose several methods allowing to construct symbolic automata out of KAT
expressions, based either on Brzozowski's derivatives or standard automata
constructions. All in all, this results in efficient algorithms for deciding
equivalence of KAT expressions
Under-approximating Cut Sets for Reachability in Large Scale Automata Networks
In the scope of discrete finite-state models of interacting components, we
present a novel algorithm for identifying sets of local states of components
whose activity is necessary for the reachability of a given local state. If all
the local states from such a set are disabled in the model, the concerned
reachability is impossible. Those sets are referred to as cut sets and are
computed from a particular abstract causality structure, so-called Graph of
Local Causality, inspired from previous work and generalised here to finite
automata networks. The extracted sets of local states form an
under-approximation of the complete minimal cut sets of the dynamics: there may
exist smaller or additional cut sets for the given reachability. Applied to
qualitative models of biological systems, such cut sets provide potential
therapeutic targets that are proven to prevent molecules of interest to become
active, up to the correctness of the model. Our new method makes tractable the
formal analysis of very large scale networks, as illustrated by the computation
of cut sets within a Boolean model of biological pathways interactions
gathering more than 9000 components
Organising metabolic networks: cycles in flux distributions
Metabolic networks are among the most widely studied biological systems. The topology and interconnections of metabolic reactions have been well described for many species, but are not sufficient to understand how their activity is regulated in living organisms. The principles directing the dynamic organisation of reaction fluxes remain poorly understood. Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment. In this work, we investigate the role of fluxes of matter cycling in metabolic networks. First, we introduce a methodology for the computation of cyclic and acyclic fluxes in metabolic networks, adapted from an algorithm initially developed to study cyclic fluxes in trophic networks. Subsequently, we apply this methodology to the analysis of three metabolic systems, including the central metabolism of wild type and a deletion mutant of Escherichia coli, erythrocyte metabolism and the central metabolism of the bacterium Methylobacterium extorquens. The role of cycles in driving and maintaining the performance of metabolic functions upon perturbations is unveiled through these examples. This methodology may be used to further investigate the role of cycles in living organisms, their pro-activity and organisational invariance, leading to a better understanding of biological entailment and information processing
Splitting Proofs for Interpolation
We study interpolant extraction from local first-order refutations. We
present a new theoretical perspective on interpolation based on clearly
separating the condition on logical strength of the formula from the
requirement on the com- mon signature. This allows us to highlight the space of
all interpolants that can be extracted from a refutation as a space of simple
choices on how to split the refuta- tion into two parts. We use this new
insight to develop an algorithm for extracting interpolants which are linear in
the size of the input refutation and can be further optimized using metrics
such as number of non-logical symbols or quantifiers. We implemented the new
algorithm in first-order theorem prover VAMPIRE and evaluated it on a large
number of examples coming from the first-order proving community. Our
experiments give practical evidence that our work improves the state-of-the-art
in first-order interpolation.Comment: 26th Conference on Automated Deduction, 201
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