Francesca Levi

University of Pisa | UNIPI

Background. RNA secondary structure comparison is important for RNA classification, RNA structure prediction and for the study of evolution. Comparison can be done efficiently only for pseudoknot-free structures, while alignment of pseudoknots is more computationally challenging. Results. In this work, we start from the already introduced idea of...

Reaction systems (RSs) are a successful natural computing framework inspired by chemical reaction networks. A RS consists of a set of entities and a set of reactions. Entities can enable or inhibit each reaction and are produced by reactions or provided by the environment. In this paper, we define two quantitative variants of RSs: the first one is...

Reaction Systems (RSs) are a successful natural computing framework inspired by chemical reaction networks. A RS consists of a set of entities and a set of reactions. Entities can enable or inhibit each reaction, and are produced by reactions or provided by the environment. In a previous paper, we defined an original labelled transition system (LTS...

Gene regulatory networks represent the interactions among genes regulating the activation of specific cell functionalities and they have been successfully modeled using threshold Boolean networks. In this paper we propose a systematic translation of threshold Boolean networks into reaction systems. Our translation produces a non redundant set of ru...

Gene Regulatory Networks represent the interactions among genes regulating the activation of speci�c cell functionalities and they have been successfully modeled using threshold Boolean networks. In this paper we propose a systematic translation of threshold Boolean networks into Reaction Systems. Our translation produces a non redundant set of rul...

Reaction systems are a qualitative formalism for the modelling of systems of biochemical reactions. In their original formulation, a reaction system executes in an environment (or context) that can supply it with new objects at each evolution step. The context drives the behaviour of a reaction system: it can provide different inputs to the system...

In this paper we propose a static analysis for Brane Calculi , based on Abstract Interpretation techniques. Our analysis statically approximates the dynamic behaviour of Brane systems, by providing a description of the possible hierarchical structure of membranes and of the processes possibly associated to each membrane, together with global occurr...

Reaction systems are a qualitative formalism for modeling systems of biochemical reactions characterized by the non-permanency of the elements: molecules disappear if not produced by any enabled reaction. Reaction systems execute in an environment that provides new molecules at each step. Brijder, Ehrenfeucht and Rozemberg introduced the idea of pr...

Reaction systems are a qualitative formalism for modeling systems of biochemical reactions characterized by the non-permanency of the elements: molecules disappear if not produced by any enabled reaction. Moreover, reaction systems execute in an environment that provides new molecules at each step. Brijder, Ehrenfeucht and Rozenberg investigated dy...

We propose a polynomial static analysis for Brane Calculi [6], based on Abstract Interpretation [8] techniques. The analysis provides a description of the possible hierarchical structure of membranes and of the processes possibly associated to each membrane, together with global occurrence counting information. Our analysis can be applied in the bi...

We present here a static analysis, based on Abstract Interpretation [8], obtained by defining an abstract version of the causal semantics for the Mate/Bud/Drip (MBD) version of Brane Calculi [7], proposed by Busi [6]. Our analysis statically approximates the dynamic behaviour of MBD systems. More precisely, the analysis is able to describe the esse...

We present here an analysis, based on Abstract Interpretation [P. Cousot and R. Cousot. Abstract Interpretation: A Unified Lattice Model for Static Analysis of Programs by Construction or Approximation of Fixpoints. In Proc. Fourth ACM Symp. Principles of Programming Languages (POPLʼ77), pp. 238–252, 1977.], obtained by defining a finite computable...

In this paper we apply the abstract interpretation approach for approximating the behavior of biological systems, modeled specifically using the Chemical Ground Form calculus, a simple stochastic calculus rich enough to model the dynamics of biochemical reactions.The analysis is based on the idea of representing a set of experiments, which differ o...

We present an abstraction of the probabilistic semantics of Multiset Rewriting to formally express systems of reactions with uncertain kinetic rates. This allows biological systems modelling when the exact rates are not known, but are supposed to lie in some intervals. On these (abstract) models we perform probabilistic model checking obtaining low...

Maximally parallel semantics have been proposed for many formalisms as an alternative to the standard interleaving semantics for some modelling scenarios. Nevertheless, in the probabilistic setting an affirmed interpretation of maximal parallelism still lacks. We define a synchronous maximally parallel probabilistic semantics for multiset rewriting...

This paper concerns the application of formal methods to biological systems, modeled specifically in BioAmbients, a variant of the Mobile Ambients calculus. Following the semantic-based approach of abstract interpretation, we define a new static analysis that computes an abstract transition system. Our analysis has two main advantages with respect...

In a previous paper the authors applied the Abstract Interpretation approach for approximating the probabilistic semantics of biological systems, modeled specifically using the Chemical Ground Form calculus. The methodology is based on the idea of representing a set of experiments, which differ only for the initial concentrations, by abstracting th...

In this paper we apply the Abstract Interpretation approach [P. Cousot and R. Cousot. Abstract Interpretation: A Unified Lattice Model for Static Analysis of Programs by Construction or Approximation of Fixpoints. Proc. of POPL'77, 238–252, 1977; P. Cousot and R. Cousot. Systematic Design of Program Analysis Frameworks. Proc. of POPL'79, 269–282, 1...

This paper concerns the application of formal methods to biological systems, modeled specifically in BioAmbients [34], a variant of the Mobile Ambients [4] calculus. Following the semantic-based approach of abstract interpretation, we define a new static analysis that computes an abstract transition system. Our analysis has two main advantages with...

We present: (i) an encoding of Boxed Ambients into a variant of Safe Ambients; and (ii) a new type system for multi-level security of Safe Ambients in the style of Cardelli et al. (Information and Computation 177(2), 160–194 (2002)) and Dezani-Ciancaglini and Salvo (Security types for mobile safe ambients. In: Proceedings of ASIAN '00, LNCS 1961, p...

This paper concerns the application of formal methods to biological systems, modelled specifically in BioAmbients [30]. BioAmbients [30] is a variant of the Mobile Ambients (MA) [7] calculus, designed precisely for more faithfully capturing basic biological concepts. We propose a new static analysis for BioAmbients which computes approximate inform...

We present two main contributions: (i) an encoding of Boxed Ambients into a variant of Safe Ambients; (ii) a new Control Flow Analysis for Safe Ambients. Then, we show that the analysis, when applied to the encoded processes, permits to accurately verify Mandatory Access Control policies of the source processes.

We introduce an abstract interpretation framework for Mobile Ambients, based on a new semantics called normal semantics. Then, we derive within this setting two analyses computing a safe approximation of the run-time topological structure of processes. Such a static information can be successfully used to establish interesting security properties.

We extend the evolving types of X. Guan, Y. Yang and J. You [Inf. Process. Lett. 80, 265-270 (2001; Zbl 1003.68093)] to full Safe Ambients following the lines of the single-threaded types of F. Levi and D. Sangiorgi [“Controlling interference in ambients”, in: Proc. POPL’00. ACM Press, 352-364 (2000)] for communication. Then, we introduce more flex...

Two forms of interferences are individuated in Cardelli and Gordon's Mobile Ambients (MA): plain interferences, which are similar to the interferences one finds in CCS and π-calculus; and grave interferences, which are more dangerous and may be regarded as programming errors. To control interferences, the MA movement primitives are modified; the re...

In this paper we propose a process language JSP which abstractly models timed statecharts with minimal and maximal delays associated to transitions. Statecharts processes are equipped with a labelled transition system semantics that combines the basic principles of the semantics of Pnueli and Shalev with discrete time. Furthermore, we propose a com...

We introduce an abstract interpretation framework for Mobile Ambients, based on a new fixed-point semantics. Then, we derive within this setting two analyses computing a safe approximation of a property about the run-time topological structure of processes which is relevant to security.

. We present a Control Flow Analysis (CFA) for the Safe Ambients, a variant of the calculus of Mobile Ambients. The analysis renes [12] and computes an approximation of the run-time topology of processes. We use the result of the analysis to establish a secrecy property. 1 Introduction Mobile Ambients (MA [6]) has recently emerged as a core program...

In this paper we present a symbolic semantics of value-passing concurrent processes where classical branching is replaced by separate relations of non-deterministic branch and alternative choice. The obtained symbolic graph is finite for regular processes and can suitably be interpreted over abstract values to effectively compute a safe abstract mo...

cted ambient n has no control on when the action takes place. Safe Ambients (SA [5]) extends MA, by allowing a movement to take place only when the involved ambient agrees, oering the corresponding coaction: in n; out n; open n. This variation does not change the expressiveness of MA, yet reduces the space of possible computations. Security is a ce...

Introduction. Mobile Ambients (MA [4]) has recently emerged as a core programming language for the Web and, at the same time, as a model for reasoning about properties of mobile processes. It is based on the notion of movement of ambients, i.e. named locations, that can be nested and can move according to three basic capabilities: inn and out n all...

In this paper we propose a quite general process language called script capital L sign℘, which can be suitably instantiated to model the synchronous language statecharts. The main novelty of the language is an operator of process refinement for representing statecharts hierarchy. Moreover, we define a compositional proof system for checking μ-calcu...

In this paper we define a new compilative version of constructive negation (intensional negation) in CLP and we prove its (non-ground) correctness and completeness wrt the 3-valued completion. We show that intensional negation is essentially equivalent to constructive negation and that it is indeed more efficient, as one would expect from the fact...

In this paper we define a new compilative version of constructive negation (intensional negation) in CLP and we prove its (non-ground) correctness and completeness wrt the 3-valued completion. We show that intensional negation is essentially equivalent to constructive negation and that it is indeed more efficient, as one would expect from the fact...

We present a finite symbolic semantics of value-passing concurrent processes, that can be suitably interpreted over abstract values to compute a lower approximate semantics of full μ calculus. The main feature of the semantics is that classical branching is replaced by explicit relations of non-deterministic and alternative choices among transition...

This thesis is concerned with the formal verification of statecharts. Statecharts are a synchronous formalism for the specification of reactive systems that is obtained by introducing in classical state-transition diagrams notions of hierarchy, parallelism and communication. Propositional µ-calculus is a very convenient formalism for expressing the...

. We propose a compositional proof system for the verification of a dicrete timed process language T SP with minimal and maximal delays associated to actions. For expressing real-time properties we consider a discrete extension of ¯-calculus with freeze quantification over clocks and clock constraints. The language T SP is parametric in the set of...

. We define a compositional labelled transition system semantics for statecharts via a translation into a new process language called SP. The main novelty of the language is an operator of process refinement, which reflects the statecharts hierarchical structure. The translation agrees with Pnueli and Shalev semantics of statecharts. However, since...

We present a compositional approach for the verification of temporal and real-time properties of statecharts. Statecharts is a synchronous language that is obtained by extending classical state-transition diagrams with notions of parallelism, broadcast communication and hierarchy. These features have been shown to permit very elegant and modular sp...

Two forms of interferences are individuated in Cardelli and Gordon's Mobile Ambients (MA): plain interferences, which are similar to the interferences one finds in CCS and pi-calculus; and grave interferences, which are more dangerous and may be regarded as programming errors. To control interferences, the MA movement primitives are modified. On th...