5,107 research outputs found
Automated Synthesis of Distributed Self-Stabilizing Protocols
In this paper, we introduce an SMT-based method that automatically
synthesizes a distributed self-stabilizing protocol from a given high-level
specification and network topology. Unlike existing approaches, where synthesis
algorithms require the explicit description of the set of legitimate states,
our technique only needs the temporal behavior of the protocol. We extend our
approach to synthesize ideal-stabilizing protocols, where every state is
legitimate. We also extend our technique to synthesize monotonic-stabilizing
protocols, where during recovery, each process can execute an most once one
action. Our proposed methods are fully implemented and we report successful
synthesis of well-known protocols such as Dijkstra's token ring, a
self-stabilizing version of Raymond's mutual exclusion algorithm,
ideal-stabilizing leader election and local mutual exclusion, as well as
monotonic-stabilizing maximal independent set and distributed Grundy coloring
Boolean Delay Equations: A simple way of looking at complex systems
Boolean Delay Equations (BDEs) are semi-discrete dynamical models with
Boolean-valued variables that evolve in continuous time. Systems of BDEs can be
classified into conservative or dissipative, in a manner that parallels the
classification of ordinary or partial differential equations. Solutions to
certain conservative BDEs exhibit growth of complexity in time. They represent
therewith metaphors for biological evolution or human history. Dissipative BDEs
are structurally stable and exhibit multiple equilibria and limit cycles, as
well as more complex, fractal solution sets, such as Devil's staircases and
``fractal sunbursts``. All known solutions of dissipative BDEs have stationary
variance. BDE systems of this type, both free and forced, have been used as
highly idealized models of climate change on interannual, interdecadal and
paleoclimatic time scales. BDEs are also being used as flexible, highly
efficient models of colliding cascades in earthquake modeling and prediction,
as well as in genetics. In this paper we review the theory of systems of BDEs
and illustrate their applications to climatic and solid earth problems. The
former have used small systems of BDEs, while the latter have used large
networks of BDEs. We moreover introduce BDEs with an infinite number of
variables distributed in space (``partial BDEs``) and discuss connections with
other types of dynamical systems, including cellular automata and Boolean
networks. This research-and-review paper concludes with a set of open
questions.Comment: Latex, 67 pages with 15 eps figures. Revised version, in particular
the discussion on partial BDEs is updated and enlarge
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra
Background: Many biological systems are modeled qualitatively with discrete
models, such as probabilistic Boolean networks, logical models, Petri nets, and
agent-based models, with the goal to gain a better understanding of the system.
The computational complexity to analyze the complete dynamics of these models
grows exponentially in the number of variables, which impedes working with
complex models. Although there exist sophisticated algorithms to determine the
dynamics of discrete models, their implementations usually require
labor-intensive formatting of the model formulation, and they are oftentimes
not accessible to users without programming skills. Efficient analysis methods
are needed that are accessible to modelers and easy to use. Method: By
converting discrete models into algebraic models, tools from computational
algebra can be used to analyze their dynamics. Specifically, we propose a
method to identify attractors of a discrete model that is equivalent to solving
a system of polynomial equations, a long-studied problem in computer algebra.
Results: A method for efficiently identifying attractors, and the web-based
tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other
analysis methods for discrete models. ADAM converts several discrete model
types automatically into polynomial dynamical systems and analyzes their
dynamics using tools from computer algebra. Based on extensive experimentation
with both discrete models arising in systems biology and randomly generated
networks, we found that the algebraic algorithms presented in this manuscript
are fast for systems with the structure maintained by most biological systems,
namely sparseness, i.e., while the number of nodes in a biological network may
be quite large, each node is affected only by a small number of other nodes,
and robustness, i.e., small number of attractors
Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming
A fundamental question in systems biology is the construction and training to
data of mathematical models. Logic formalisms have become very popular to model
signaling networks because their simplicity allows us to model large systems
encompassing hundreds of proteins. An approach to train (Boolean) logic models
to high-throughput phospho-proteomics data was recently introduced and solved
using optimization heuristics based on stochastic methods. Here we demonstrate
how this problem can be solved using Answer Set Programming (ASP), a
declarative problem solving paradigm, in which a problem is encoded as a
logical program such that its answer sets represent solutions to the problem.
ASP has significant improvements over heuristic methods in terms of efficiency
and scalability, it guarantees global optimality of solutions as well as
provides a complete set of solutions. We illustrate the application of ASP with
in silico cases based on realistic networks and data
Fundamentals of Large Sensor Networks: Connectivity, Capacity, Clocks and Computation
Sensor networks potentially feature large numbers of nodes that can sense
their environment over time, communicate with each other over a wireless
network, and process information. They differ from data networks in that the
network as a whole may be designed for a specific application. We study the
theoretical foundations of such large scale sensor networks, addressing four
fundamental issues- connectivity, capacity, clocks and function computation.
To begin with, a sensor network must be connected so that information can
indeed be exchanged between nodes. The connectivity graph of an ad-hoc network
is modeled as a random graph and the critical range for asymptotic connectivity
is determined, as well as the critical number of neighbors that a node needs to
connect to. Next, given connectivity, we address the issue of how much data can
be transported over the sensor network. We present fundamental bounds on
capacity under several models, as well as architectural implications for how
wireless communication should be organized.
Temporal information is important both for the applications of sensor
networks as well as their operation.We present fundamental bounds on the
synchronizability of clocks in networks, and also present and analyze
algorithms for clock synchronization. Finally we turn to the issue of gathering
relevant information, that sensor networks are designed to do. One needs to
study optimal strategies for in-network aggregation of data, in order to
reliably compute a composite function of sensor measurements, as well as the
complexity of doing so. We address the issue of how such computation can be
performed efficiently in a sensor network and the algorithms for doing so, for
some classes of functions.Comment: 10 pages, 3 figures, Submitted to the Proceedings of the IEE
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