Quantification of reachable attractors in asynchronous discrete dynamics

Motivation: Models of discrete concurrent systems often lead to huge and complex state transition graphs that represent their dynamics. This makes difficult to analyse dynamical properties. In particular, for logical models of biological regulatory networks, it is of real interest to study attractors and their reachability from specific initial conditions, i.e. to assess the potential asymptotical behaviours of the system. Beyond the identification of the reachable attractors, we propose to quantify this reachability. Results: Relying on the structure of the state transition graph, we estimate the probability of each attractor reachable from a given initial condition or from a portion of the state space. First, we present a quasi-exact solution with an original algorithm called Firefront, based on the exhaustive exploration of the reachable state space. Then, we introduce an adapted version of Monte Carlo simulation algorithm, termed Avatar, better suited to larger models. Firefront and Avatar methods are validated and compared to other related approaches, using as test cases logical models of synthetic and biological networks. Availability: Both algorithms are implemented as Perl scripts that can be freely downloaded from http://compbio.igc.gulbenkian.pt/nmd/node/59 along with Supplementary Material.Comment: 19 pages, 2 figures, 2 algorithms and 2 table

Faster Algorithms for Weighted Recursive State Machines

Pushdown systems (PDSs) and recursive state machines (RSMs), which are linearly equivalent, are standard models for interprocedural analysis. Yet RSMs are more convenient as they (a) explicitly model function calls and returns, and (b) specify many natural parameters for algorithmic analysis, e.g., the number of entries and exits. We consider a general framework where RSM transitions are labeled from a semiring and path properties are algebraic with semiring operations, which can model, e.g., interprocedural reachability and dataflow analysis problems. Our main contributions are new algorithms for several fundamental problems. As compared to a direct translation of RSMs to PDSs and the best-known existing bounds of PDSs, our analysis algorithm improves the complexity for finite-height semirings (that subsumes reachability and standard dataflow properties). We further consider the problem of extracting distance values from the representation structures computed by our algorithm, and give efficient algorithms that distinguish the complexity of a one-time preprocessing from the complexity of each individual query. Another advantage of our algorithm is that our improvements carry over to the concurrent setting, where we improve the best-known complexity for the context-bounded analysis of concurrent RSMs. Finally, we provide a prototype implementation that gives a significant speed-up on several benchmarks from the SLAM/SDV project

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

Using decision diagrams to compactly represent the state space for explicit model checking

pre-printThe enormous number of states reachable during explicit model checking is the main bottleneck for scalability. This paper presents approaches of using decision diagrams to represent very large state space compactly and efficiently. This is possible for asynchronous systems as two system states connected by a transition often share many same local portions. Using decision diagrams can significantly reduce memory demand by not using memory to store the redundant information among different states. This paper considers multi-value decision diagrams for this purpose. Additionally, a technique to reduce the runtime overhead of using these diagrams is also described. Experimental results and comparison with the state compression method as implemented in the model checker SPIN show that the approaches presented in this paper are memory efficient for storing large state space with acceptable runtime overhead

Rapid Recovery for Systems with Scarce Faults

Our goal is to achieve a high degree of fault tolerance through the control of a safety critical systems. This reduces to solving a game between a malicious environment that injects failures and a controller who tries to establish a correct behavior. We suggest a new control objective for such systems that offers a better balance between complexity and precision: we seek systems that are k-resilient. In order to be k-resilient, a system needs to be able to rapidly recover from a small number, up to k, of local faults infinitely many times, provided that blocks of up to k faults are separated by short recovery periods in which no fault occurs. k-resilience is a simple but powerful abstraction from the precise distribution of local faults, but much more refined than the traditional objective to maximize the number of local faults. We argue why we believe this to be the right level of abstraction for safety critical systems when local faults are few and far between. We show that the computational complexity of constructing optimal control with respect to resilience is low and demonstrate the feasibility through an implementation and experimental results.Comment: In Proceedings GandALF 2012, arXiv:1210.202

Separating computation from communication: a design approach for concurrent program verification

We describe an approach to design static analysis and verification tools for concurrent programs that separates intra-thread computation from inter-thread communication by means of a shared memory abstraction (SMA). We formally characterize the concept of thread-asynchronous transition systems that underpins our approach and that allows us to design tools as two independent components, the intra-thread analysis, which can be optimized separately, and the implementation of the SMA itself, which can be exchanged easily (e.g., from the SC to the TSO memory model). We describe the SMA’s API and show that several concurrent verification techniques from the literature can easily be recast in our setting and thus be extended to weak memory models. We give SMA implementations for the SC, TSO, and PSO memory models that are based on the idea of individual memory unwindings. We instantiate our approach by developing a new, efficient BMC-based bug finding tool for multi-threaded C programs under SC, TSO, or PSO based on these SMAs, and show experimentally that it is competitive to existing tools

Modeling and Analyzing Cyber-Physical Systems Using Hybrid Predicate Transition Nets

Cyber-Physical Systems (CPSs) are software controlled physical devices that are being used everywhere from utility features in household devices to safety-critical features in cars, trains, aircraft, robots, smart healthcare devices. CPSs have complex hybrid behaviors combining discrete states and continuous states capturing physical laws. Developing reliable CPSs are extremely difficult. Formal modeling methods are especially useful for abstracting and understanding complex systems and detecting and preventing early system design problems. To ensure the dependability of formal models, various analysis techniques, including simulation and reachability analysis, have been proposed in recent decades. This thesis aims to provide a unified formal modeling and analysis methodology for studying CPSs. Firstly, this thesis contributes to the modeling and analysis of discrete, continuous, and hybrid systems. This work enhances modeling of discrete systems using predicate transition nets (PrTNs) by fully realizing the underlying specification through incorporating the first-order logic with set theory, improving the type system, and providing incremental model composition. This work enhances the technique of analyzing discrete systems using PrTN by improving the simulation algorithm and its efficient implementation. This work also improves the analysis of discrete systems using SPIN by providing a more accurate and complete translation method. Secondly, this work contributes to the modeling and analysis of hybrid systems by proposing an extension of PrTNs, hybrid predicate transition nets (HPrTNs). The proposed method incorporates a novel concept of token evolution, which nicely addresses the continuous state evolution and the conflicts present in other related works. This work presents a powerful simulation capability that can handle linear, non-linear dynamics, transcendental functions through differential equations. This work also provides a complementary technique for reachability analysis through the translation of HPrTN models for analysis using SpaceEx

Embedding weak memory models within eager sequentialization

Sequentialization is one of the most promising approaches for the symbolic analysis of concurrent programs. However, existing sequentializations assume sequential consistency, which modern hardware architectures no longer guarantee. In this paper we describe an approach to embed weak memory models within eager sequentializations (a la Lal/Reps). Our approach is based on the separation of intra-thread computations from inter-thread communications by means of a shared memory abstraction (SMA). We give details of SMA implementations for the SC, TSO, and PSO memory models that are based on the idea of individual memory unwindings, and sketch an extension to the Power memory model. We use our approach to implement a new, efficient BMC-based bug finding tool for multi-threaded C programs under SC, TSO, or PSO based on these SMAs, and show experimentally that it is competitive to existing tools