Francesca Levi

Mobile safe ambients

Two forms of interferences are individuated in Cardelli and Gordons 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 resulting calculus is called Mobile Safe Ambients (SA).The modification also has computational significance. In the MA interaction rules, an ambient may enter, exit, or open another ambient. The second ambient undergoes the action; it has no control on when the action takes place. In SA this is rectified: any movement takes place only if both participants agree.Existing type systems for MA can be easily adapted to SA. The type systems for controlling mobility, however, appear to be more powerful in SA, in that (i) type systems for MA may give more precise information when transplanted onto SA , and (ii) new type systems may be defined. Two type systems are presented that remove all grave interferences.Other advantages of SA are: a useful algebraic theory; programs sometimes more robust (they require milder conditions for correctness) and/or simpler. All these points are illustrated in several examples.

Safe Ambients: Control Flow Analysis and Security

We present a Control Flow Analysis (CFA) for the Safe Ambients, a variant of the calculus of Mobile Ambients. The analysis refines and computes an approximation of the run-time topology of processes. We use the result of the analysis to establish a secrecy property.

Compilative Constructive Negation in Constraint Logic Programs

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 that it is a compilative technique, with the transformation and the associated normalization process being performed once and for all on the source program. We define several formal non-ground semantics, based either on the derivation rule or on the least fixpoint of an immediate consequence operator. All these semantics are proved to correctly model the observable behavior, from the viewpoint of answer constraints. We give some equivalence theorems and we show that all our denotations are the non-ground representation of a single partial interpretation, which is Φ P ↑ ω, where Φ P is the Fittings operator [12].

Probabilistic model checking of biological systems with uncertain kinetic rates

In this paper, we present a formalization of biological systems based on multiset rewriting and we investigate the use of abstract interpretation on its semantics. We consider a probabilistic semantics, which is well suited to represent the non-deterministic evolution of real biological systems. Abstract interpretation allows us to deal with systems in which the kinetic rates of the evolution rules are not precisely known. On the (abstract) systems, we perform probabilistic model checking obtaining lower and upper bounds for the probabilities of reaching states satisfying the given properties. We apply abstract probabilistic model checking to verify reachability properties in a model of tumor growth.

A new occurrence counting analysis for bioambients

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 information about the run-time behaviour of a system. The analysis is derived following the abstract interpretation approach and introduces two main novelties with respect to the analyses in literature [25,24,26,27]: (i) it records information about the number of occurrences of objects; (ii) it maintains more detailed information about the possible contents of ambients, at any time. In this way, the analysis gives substantially more precise results and captures both the quantitative and causal aspect which are really important for reasoning on the temporal and spatial structure of biological systems. The interest of the analysis is demonstrated by considering a few simple examples which point out the limitations of the existing analyses for BioAmbients.

An Abstract Interpretation Framework for Analysing Mobile Ambients

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.

On abstract interpretation of mobile ambients

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.

Abstract interpretation based verification of temporal properties for BioAmbients

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 to the analyses appearing in the literature: (i) it is able to address temporal properties which are more general than invariant properties; (ii) it supports, by means of a particular labeling discipline, the validation of systems where several copies of an ambient may appear. We also design new weaker and more efficient analyses by means of simple widening operators.

Maximally Parallel Probabilistic Semantics for Multiset Rewriting

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 tailored to describe, simulate and verify biological systems evolving with maximally parallel steps. Each step of the proposed semantics is parallel as each reaction can happen multiple times, and it is maximal as it leaves no enabled reaction i.e. as many reactions as possible are executed. We define a maximally parallel probabilistic semantics in terms of Discrete Time Markov Chain for systems described by stochastic multiset rewriting. We propose a simple, maximally parallel, model of Caenorhabditis elegans vulval development on which we show probabilistic simulations results.

An analysis for proving temporal properties of biological systems

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 respect to the analyses appearing in literature: (i) it is able to address temporal properties which are more general than invariant properties; (ii) it supports, by means of a particular labeling discipline, the validation of systems where several copies of an ambient may appear.