3,879 research outputs found
Unified Analysis of Collapsible and Ordered Pushdown Automata via Term Rewriting
We model collapsible and ordered pushdown systems with term rewriting, by
encoding higher-order stacks and multiple stacks into trees. We show a uniform
inverse preservation of recognizability result for the resulting class of term
rewriting systems, which is obtained by extending the classic saturation-based
approach. This result subsumes and unifies similar analyses on collapsible and
ordered pushdown systems. Despite the rich literature on inverse preservation
of recognizability for term rewrite systems, our result does not seem to follow
from any previous study.Comment: in Proc. of FRE
Applying Formal Methods to Networking: Theory, Techniques and Applications
Despite its great importance, modern network infrastructure is remarkable for
the lack of rigor in its engineering. The Internet which began as a research
experiment was never designed to handle the users and applications it hosts
today. The lack of formalization of the Internet architecture meant limited
abstractions and modularity, especially for the control and management planes,
thus requiring for every new need a new protocol built from scratch. This led
to an unwieldy ossified Internet architecture resistant to any attempts at
formal verification, and an Internet culture where expediency and pragmatism
are favored over formal correctness. Fortunately, recent work in the space of
clean slate Internet design---especially, the software defined networking (SDN)
paradigm---offers the Internet community another chance to develop the right
kind of architecture and abstractions. This has also led to a great resurgence
in interest of applying formal methods to specification, verification, and
synthesis of networking protocols and applications. In this paper, we present a
self-contained tutorial of the formidable amount of work that has been done in
formal methods, and present a survey of its applications to networking.Comment: 30 pages, submitted to IEEE Communications Surveys and Tutorial
Model Checking Linear Logic Specifications
The overall goal of this paper is to investigate the theoretical foundations
of algorithmic verification techniques for first order linear logic
specifications. The fragment of linear logic we consider in this paper is based
on the linear logic programming language called LO enriched with universally
quantified goal formulas. Although LO was originally introduced as a
theoretical foundation for extensions of logic programming languages, it can
also be viewed as a very general language to specify a wide range of
infinite-state concurrent systems.
Our approach is based on the relation between backward reachability and
provability highlighted in our previous work on propositional LO programs.
Following this line of research, we define here a general framework for the
bottom-up evaluation of first order linear logic specifications. The evaluation
procedure is based on an effective fixpoint operator working on a symbolic
representation of infinite collections of first order linear logic formulas.
The theory of well quasi-orderings can be used to provide sufficient conditions
for the termination of the evaluation of non trivial fragments of first order
linear logic.Comment: 53 pages, 12 figures "Under consideration for publication in Theory
and Practice of Logic Programming
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
Petri nets for systems and synthetic biology
We give a description of a Petri net-based framework for
modelling and analysing biochemical pathways, which uni¯es the qualita-
tive, stochastic and continuous paradigms. Each perspective adds its con-
tribution to the understanding of the system, thus the three approaches
do not compete, but complement each other. We illustrate our approach
by applying it to an extended model of the three stage cascade, which
forms the core of the ERK signal transduction pathway. Consequently
our focus is on transient behaviour analysis. We demonstrate how quali-
tative descriptions are abstractions over stochastic or continuous descrip-
tions, and show that the stochastic and continuous models approximate
each other. Although our framework is based on Petri nets, it can be
applied more widely to other formalisms which are used to model and
analyse biochemical networks
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