Structural characterization of decomposition in rate-insensitive stochastic Petri nets

This paper focuses on stochastic Petri nets that have an equilibrium distribution that is a product form over the number of tokens at the places. We formulate a decomposition result for the class of nets that have a product form solution irrespective of the values of the transition rates. These nets where algebraically characterized by Haddad et al.~as $S\Pi^2$ nets. By providing an intuitive interpretation of this algebraical characterization, and associating state machines to sets of $T$-invariants, we obtain a one-to-one correspondence between the marking of the original places and the places of the added state machines. This enables us to show that the subclass of stochastic Petri nets under study can be decomposed into subnets that are identified by sets of its $T$-invariants

Spin networks, quantum automata and link invariants

The spin network simulator model represents a bridge between (generalized) circuit schemes for standard quantum computation and approaches based on notions from Topological Quantum Field Theories (TQFT). More precisely, when working with purely discrete unitary gates, the simulator is naturally modelled as families of quantum automata which in turn represent discrete versions of topological quantum computation models. Such a quantum combinatorial scheme, which essentially encodes SU(2) Racah--Wigner algebra and its braided counterpart, is particularly suitable to address problems in topology and group theory and we discuss here a finite states--quantum automaton able to accept the language of braid group in view of applications to the problem of estimating link polynomials in Chern--Simons field theory.Comment: LateX,19 pages; to appear in the Proc. of "Constrained Dynamics and Quantum Gravity (QG05), Cala Gonone (Italy) September 12-16 200

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

Enaction-Based Artificial Intelligence: Toward Coevolution with Humans in the Loop

This article deals with the links between the enaction paradigm and artificial intelligence. Enaction is considered a metaphor for artificial intelligence, as a number of the notions which it deals with are deemed incompatible with the phenomenal field of the virtual. After explaining this stance, we shall review previous works regarding this issue in terms of artifical life and robotics. We shall focus on the lack of recognition of co-evolution at the heart of these approaches. We propose to explicitly integrate the evolution of the environment into our approach in order to refine the ontogenesis of the artificial system, and to compare it with the enaction paradigm. The growing complexity of the ontogenetic mechanisms to be activated can therefore be compensated by an interactive guidance system emanating from the environment. This proposition does not however resolve that of the relevance of the meaning created by the machine (sense-making). Such reflections lead us to integrate human interaction into this environment in order to construct relevant meaning in terms of participative artificial intelligence. This raises a number of questions with regards to setting up an enactive interaction. The article concludes by exploring a number of issues, thereby enabling us to associate current approaches with the principles of morphogenesis, guidance, the phenomenology of interactions and the use of minimal enactive interfaces in setting up experiments which will deal with the problem of artificial intelligence in a variety of enaction-based ways

On Verifying Complex Properties using Symbolic Shape Analysis

One of the main challenges in the verification of software systems is the analysis of unbounded data structures with dynamic memory allocation, such as linked data structures and arrays. We describe Bohne, a new analysis for verifying data structures. Bohne verifies data structure operations and shows that 1) the operations preserve data structure invariants and 2) the operations satisfy their specifications expressed in terms of changes to the set of objects stored in the data structure. During the analysis, Bohne infers loop invariants in the form of disjunctions of universally quantified Boolean combinations of formulas. To synthesize loop invariants of this form, Bohne uses a combination of decision procedures for Monadic Second-Order Logic over trees, SMT-LIB decision procedures (currently CVC Lite), and an automated reasoner within the Isabelle interactive theorem prover. This architecture shows that synthesized loop invariants can serve as a useful communication mechanism between different decision procedures. Using Bohne, we have verified operations on data structures such as linked lists with iterators and back pointers, trees with and without parent pointers, two-level skip lists, array data structures, and sorted lists. We have deployed Bohne in the Hob and Jahob data structure analysis systems, enabling us to combine Bohne with analyses of data structure clients and apply it in the context of larger programs. This report describes the Bohne algorithm as well as techniques that Bohne uses to reduce the ammount of annotations and the running time of the analysis

Symbolic Reachability Analysis of B through ProB and LTSmin

We present a symbolic reachability analysis approach for B that can provide a significant speedup over traditional explicit state model checking. The symbolic analysis is implemented by linking ProB to LTSmin, a high-performance language independent model checker. The link is achieved via LTSmin's PINS interface, allowing ProB to benefit from LTSmin's analysis algorithms, while only writing a few hundred lines of glue-code, along with a bridge between ProB and C using ZeroMQ. ProB supports model checking of several formal specification languages such as B, Event-B, Z and TLA. Our experiments are based on a wide variety of B-Method and Event-B models to demonstrate the efficiency of the new link. Among the tested categories are state space generation and deadlock detection; but action detection and invariant checking are also feasible in principle. In many cases we observe speedups of several orders of magnitude. We also compare the results with other approaches for improving model checking, such as partial order reduction or symmetry reduction. We thus provide a new scalable, symbolic analysis algorithm for the B-Method and Event-B, along with a platform to integrate other model checking improvements via LTSmin in the future