Model Checking Markov Chains with Actions and State Labels

In the past, logics of several kinds have been proposed for reasoning about discrete- or continuous-time Markov chains. Most of these logics rely on either state labels (atomic propositions) or on transition labels (actions). However, in several applications it is useful to reason about both state-properties and action-sequences. For this purpose, we introduce the logic asCSL which provides powerful means to characterize execution paths of Markov chains with actions and state labels. asCSL can be regarded as an extension of the purely state-based logic asCSL (continuous stochastic logic). \ud In asCSL, path properties are characterized by regular expressions over actions and state-formulas. Thus, the truth value of path-formulas does not only depend on the available actions in a given time interval, but also on the validity of certain state formulas in intermediate states.\ud We compare the expressive power of CSL and asCSL and show that even the state-based fragment of asCSL is strictly more expressive than CSL if time intervals starting at zero are employed. Using an automaton-based technique, an asCSL formula and a Markov chain with actions and state labels are combined into a product Markov chain. For time intervals starting at zero we establish a reduction of the model checking problem for asCSL to CSL model checking on this product Markov chain. The usefulness of our approach is illustrated by through an elaborate model of a scalable cellular communication system for which several properties are formalized by means of asCSL-formulas, and checked using the new procedure

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

Generalization Strategies for the Verification of Infinite State Systems

We present a method for the automated verification of temporal properties of infinite state systems. Our verification method is based on the specialization of constraint logic programs (CLP) and works in two phases: (1) in the first phase, a CLP specification of an infinite state system is specialized with respect to the initial state of the system and the temporal property to be verified, and (2) in the second phase, the specialized program is evaluated by using a bottom-up strategy. The effectiveness of the method strongly depends on the generalization strategy which is applied during the program specialization phase. We consider several generalization strategies obtained by combining techniques already known in the field of program analysis and program transformation, and we also introduce some new strategies. Then, through many verification experiments, we evaluate the effectiveness of the generalization strategies we have considered. Finally, we compare the implementation of our specialization-based verification method to other constraint-based model checking tools. The experimental results show that our method is competitive with the methods used by those other tools. To appear in Theory and Practice of Logic Programming (TPLP).Comment: 24 pages, 2 figures, 5 table

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

Reachability Analysis of Communicating Pushdown Systems

The reachability analysis of recursive programs that communicate asynchronously over reliable FIFO channels calls for restrictions to ensure decidability. Our first result characterizes communication topologies with a decidable reachability problem restricted to eager runs (i.e., runs where messages are either received immediately after being sent, or never received). The problem is EXPTIME-complete in the decidable case. The second result is a doubly exponential time algorithm for bounded context analysis in this setting, together with a matching lower bound. Both results extend and improve previous work from La Torre et al

SPDL Model Checking via Property-Driven State Space Generation

In this report we describe how both, memory and time requirements for stochastic model checking of SPDL (stochastic propositional dynamic logic) formulae can significantly be reduced. SPDL is the stochastic extension of the multi-modal program logic PDL.\ud SPDL provides means to specify path-based properties with or without timing restrictions. Paths can be characterised by so-called programs, essentially regular expressions, where the executability can be made dependent on the validity of test formulae. For model-checking SPDL path formulae it is necessary to build a product transition system (PTS)\ud between the system model and the program automaton belonging to the path formula that is to be verified.\ud In many cases, this PTS can be drastically reduced during the model checking procedure, as the program restricts the number of potentially satisfying paths. Therefore, we propose an approach that directly generates the reduced PTS from a given SPA specification and an SPDL path formula.\ud The feasibility of this approach is shown through a selection of case studies, which show enormous state space reductions, at no increase in generation time.\u

Deriving Petri nets from finite transition systems

This paper presents a novel method to derive a Petri net from any specification model that can be mapped into a state-based representation with arcs labeled with symbols from an alphabet of events (a Transition System, TS). The method is based on the theory of regions for Elementary Transition Systems (ETS). Previous work has shown that, for any ETS, there exists a Petri Net with minimum transition count (one transition for each label) with a reachability graph isomorphic to the original Transition System. Our method extends and implements that theory by using the following three mechanisms that provide a framework for synthesis of safe Petri nets from arbitrary TSs. First, the requirement of isomorphism is relaxed to bisimulation of TSs, thus extending the class of synthesizable TSs to a new class called Excitation-Closed Transition Systems (ECTS). Second, for the first time, we propose a method of PN synthesis for an arbitrary TS based on mapping a TS event into a set of transition labels in a PN. Third, the notion of irredundant region set is exploited, to minimize the number of places in the net without affecting its behavior. The synthesis method can derive different classes of place-irredundant Petri Nets (e.g., pure, free choice, unique choice) from the same TS, depending on the constraints imposed on the synthesis algorithm. This method has been implemented and applied in different frameworks. The results obtained from the experiments have demonstrated the wide applicability of the method.Peer ReviewedPostprint (published version

A Monte Carlo model checker for probabilistic LTL with numerical constraints

We define the syntax and semantics of a new temporal logic called probabilistic LTL with numerical constraints (PLTLc). We introduce an efficient model checker for PLTLc properties. The efficiency of the model checker is through approximation using Monte Carlo sampling of finite paths through the model’s state space (simulation outputs) and parallel model checking of the paths. Our model checking method can be applied to any model producing quantitative output – continuous or stochastic, including those with complex dynamics and those with an infinite state space. Furthermore, our offline approach allows the analysis of observed (real-life) behaviour traces. We find in this paper that PLTLc properties with constraints over free variables can replace full model checking experiments, resulting in a significant gain in efficiency. This overcomes one disadvantage of model checking experiments which is that the complexity depends on system granularity and number of variables, and quickly becomes infeasible. We focus on models of biochemical networks, and specifically in this paper on intracellular signalling pathways; however our method can be applied to a wide range of biological as well as technical systems and their models. Our work contributes to the emerging field of synthetic biology by proposing a rigourous approach for the structured formal engineering of biological systems