A Survey of Cellular Automata: Types, Dynamics, Non-uniformity and Applications

Cellular automata (CAs) are dynamical systems which exhibit complex global behavior from simple local interaction and computation. Since the inception of cellular automaton (CA) by von Neumann in 1950s, it has attracted the attention of several researchers over various backgrounds and fields for modelling different physical, natural as well as real-life phenomena. Classically, CAs are uniform. However, non-uniformity has also been introduced in update pattern, lattice structure, neighborhood dependency and local rule. In this survey, we tour to the various types of CAs introduced till date, the different characterization tools, the global behaviors of CAs, like universality, reversibility, dynamics etc. Special attention is given to non-uniformity in CAs and especially to non-uniform elementary CAs, which have been very useful in solving several real-life problems.Comment: 43 pages; Under review in Natural Computin

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

Parallel symbolic state-space exploration is difficult, but what is the alternative?

State-space exploration is an essential step in many modeling and analysis problems. Its goal is to find the states reachable from the initial state of a discrete-state model described. The state space can used to answer important questions, e.g., "Is there a dead state?" and "Can N become negative?", or as a starting point for sophisticated investigations expressed in temporal logic. Unfortunately, the state space is often so large that ordinary explicit data structures and sequential algorithms cannot cope, prompting the exploration of (1) parallel approaches using multiple processors, from simple workstation networks to shared-memory supercomputers, to satisfy large memory and runtime requirements and (2) symbolic approaches using decision diagrams to encode the large structured sets and relations manipulated during state-space generation. Both approaches have merits and limitations. Parallel explicit state-space generation is challenging, but almost linear speedup can be achieved; however, the analysis is ultimately limited by the memory and processors available. Symbolic methods are a heuristic that can efficiently encode many, but not all, functions over a structured and exponentially large domain; here the pitfalls are subtler: their performance varies widely depending on the class of decision diagram chosen, the state variable order, and obscure algorithmic parameters. As symbolic approaches are often much more efficient than explicit ones for many practical models, we argue for the need to parallelize symbolic state-space generation algorithms, so that we can realize the advantage of both approaches. This is a challenging endeavor, as the most efficient symbolic algorithm, Saturation, is inherently sequential. We conclude by discussing challenges, efforts, and promising directions toward this goal

Computing Nash Equilibrium in Wireless Ad Hoc Networks: A Simulation-Based Approach

This paper studies the problem of computing Nash equilibrium in wireless networks modeled by Weighted Timed Automata. Such formalism comes together with a logic that can be used to describe complex features such as timed energy constraints. Our contribution is a method for solving this problem using Statistical Model Checking. The method has been implemented in UPPAAL model checker and has been applied to the analysis of Aloha CSMA/CD and IEEE 802.15.4 CSMA/CA protocols.Comment: In Proceedings IWIGP 2012, arXiv:1202.422

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

Dynamic Protocol Reverse Engineering a Grammatical Inference Approach

Round trip engineering of software from source code and reverse engineering of software from binary files have both been extensively studied and the state-of-practice have documented tools and techniques. Forward engineering of protocols has also been extensively studied and there are firmly established techniques for generating correct protocols. While observation of protocol behavior for performance testing has been studied and techniques established, reverse engineering of protocol control flow from observations of protocol behavior has not received the same level of attention. State-of-practice in reverse engineering the control flow of computer network protocols is comprised of mostly ad hoc approaches. We examine state-of-practice tools and techniques used in three open source projects: Pidgin, Samba, and rdesktop . We examine techniques proposed by computational learning researchers for grammatical inference. We propose to extend the state-of-art by inferring protocol control flow using grammatical inference inspired techniques to reverse engineer automata representations from captured data flows. We present evidence that grammatical inference is applicable to the problem domain under consideration

On the connection of probabilistic model checking, planning, and learning for system verification

This thesis presents approaches using techniques from the model checking, planning, and learning community to make systems more reliable and perspicuous. First, two heuristic search and dynamic programming algorithms are adapted to be able to check extremal reachability probabilities, expected accumulated rewards, and their bounded versions, on general Markov decision processes (MDPs). Thereby, the problem space originally solvable by these algorithms is enlarged considerably. Correctness and optimality proofs for the adapted algorithms are given, and in a comprehensive case study on established benchmarks it is shown that the implementation, called Modysh, is competitive with state-of-the-art model checkers and even outperforms them on very large state spaces. Second, Deep Statistical Model Checking (DSMC) is introduced, usable for quality assessment and learning pipeline analysis of systems incorporating trained decision-making agents, like neural networks (NNs). The idea of DSMC is to use statistical model checking to assess NNs resolving nondeterminism in systems modeled as MDPs. The versatility of DSMC is exemplified in a number of case studies on Racetrack, an MDP benchmark designed for this purpose, flexibly modeling the autonomous driving challenge. In a comprehensive scalability study it is demonstrated that DSMC is a lightweight technique tackling the complexity of NN analysis in combination with the state space explosion problem.Diese Arbeit präsentiert Ansätze, die Techniken aus dem Model Checking, Planning und Learning Bereich verwenden, um Systeme verlässlicher und klarer verständlich zu machen. Zuerst werden zwei Algorithmen für heuristische Suche und dynamisches Programmieren angepasst, um Extremwerte für Erreichbarkeitswahrscheinlichkeiten, Erwartungswerte für Kosten und beschränkte Varianten davon, auf generellen Markov Entscheidungsprozessen (MDPs) zu untersuchen. Damit wird der Problemraum, der ursprünglich mit diesen Algorithmen gelöst wurde, deutlich erweitert. Korrektheits- und Optimalitätsbeweise für die angepassten Algorithmen werden gegeben und in einer umfassenden Fallstudie wird gezeigt, dass die Implementierung, namens Modysh, konkurrenzfähig mit den modernsten Model Checkern ist und deren Leistung auf sehr großen Zustandsräumen sogar übertrifft. Als Zweites wird Deep Statistical Model Checking (DSMC) für die Qualitätsbewertung und Lernanalyse von Systemen mit integrierten trainierten Entscheidungsgenten, wie z.B. neuronalen Netzen (NN), eingeführt. Die Idee von DSMC ist es, statistisches Model Checking zur Bewertung von NNs zu nutzen, die Nichtdeterminismus in Systemen, die als MDPs modelliert sind, auflösen. Die Vielseitigkeit des Ansatzes wird in mehreren Fallbeispielen auf Racetrack gezeigt, einer MDP Benchmark, die zu diesem Zweck entwickelt wurde und die Herausforderung des autonomen Fahrens flexibel modelliert. In einer umfassenden Skalierbarkeitsstudie wird demonstriert, dass DSMC eine leichtgewichtige Technik ist, die die Komplexität der NN-Analyse in Kombination mit dem State Space Explosion Problem bewältigt

Algorithmic Verification of Asynchronous Programs

Asynchronous programming is a ubiquitous systems programming idiom to manage concurrent interactions with the environment. In this style, instead of waiting for time-consuming operations to complete, the programmer makes a non-blocking call to the operation and posts a callback task to a task buffer that is executed later when the time-consuming operation completes. A co-operative scheduler mediates the interaction by picking and executing callback tasks from the task buffer to completion (and these callbacks can post further callbacks to be executed later). Writing correct asynchronous programs is hard because the use of callbacks, while efficient, obscures program control flow. We provide a formal model underlying asynchronous programs and study verification problems for this model. We show that the safety verification problem for finite-data asynchronous programs is expspace-complete. We show that liveness verification for finite-data asynchronous programs is decidable and polynomial-time equivalent to Petri Net reachability. Decidability is not obvious, since even if the data is finite-state, asynchronous programs constitute infinite-state transition systems: both the program stack and the task buffer of pending asynchronous calls can be potentially unbounded. Our main technical construction is a polynomial-time semantics-preserving reduction from asynchronous programs to Petri Nets and conversely. The reduction allows the use of algorithmic techniques on Petri Nets to the verification of asynchronous programs. We also study several extensions to the basic models of asynchronous programs that are inspired by additional capabilities provided by implementations of asynchronous libraries, and classify the decidability and undecidability of verification questions on these extensions.Comment: 46 pages, 9 figure