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