Corrado Priami - Academia.edu (original) (raw)

Papers by Corrado Priami

In this study we extend stochastic ß-calculus allowing general probabilistic distributions to occ... more In this study we extend stochastic ß-calculus allowing general probabilistic distributions to occur in its prefixes. We show that no additional information is needed in the labels of transitions or in the states of systems to derive an enabling relation between transitions. Enabling is ...

Briefings in Bioinformatics, 2008

We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX la... more We introduce the Beta Workbench (BWB), a scalable tool built on top of the newly defined BlenX language to model, simulate and analyse biological systems. We show the features and the incremental modelling process supported by the BWB on a running example based on the mitogen-activated kinase pathway. Finally, we provide a comparison with related approaches and some hints for future extensions.

314 L. Dematté, C. Priami, and A. Romanel represent a deadlock situation, where the process is un... more 314 L. Dematté, C. Priami, and A. Romanel represent a deadlock situation, where the process is unable to perform any sort of action or co-action, the nil operator is used. The behavior of a system is given by the ordered sequence of actions and reactions that a system can ...

This paper presents binders and operators, in the process calculi tradition, to reason about biol... more This paper presents binders and operators, in the process calculi tradition, to reason about biological interactions. Special binders are added to wrap a process just as membranes enclose some living matter and hence to mimick biological interfaces. A few operators are then added to the pi-calculus kernel to describe the dynamics of those interfaces.

Transactions on Computational Systems Biology, 2005

As a preliminary step in testing the expressiveness of Beta-binders against realistic case studie... more As a preliminary step in testing the expressiveness of Beta-binders against realistic case studies, we comment on a number of operational properties of the formalism and present a set of derived patterns that can be useful when modeling complex biosystems.

Briefings in Bioinformatics, 2004

The need for a more formal handling of biological information processing with stochastic and mobi... more The need for a more formal handling of biological information processing with stochastic and mobile process algebras is addressed. Biology can benefit this approach, yielding a better understanding of behavioural properties of cells, and computer science can benefit this approach, obtaining new computational models inspired by nature.

We introduce local environments for mobile processes, expressed in π-calculus. Each local name is... more We introduce local environments for mobile processes, expressed in π-calculus. Each local name is equipped with its relative address, i.e., with the information needed to point back to the process that generated it. Relative addresses are built upon the labels of the proved transition system of π-calculus. A router is specified that guarantees sound exportation of names.

Electronic Notes in Theoretical Computer Science, 2007

... 4.1 The biochemical stochastic π-calculus ... Since protein interactions directly affect cell... more ... 4.1 The biochemical stochastic π-calculus ... Since protein interactions directly affect cell function, these modifications are the main mechanism underlying many cellular functions ... Communication and channel transmission model chemical interaction and subsequent modifications. ...

We present a parametric tool for the analysis of distributed concurrent systems. Processes are in... more We present a parametric tool for the analysis of distributed concurrent systems. Processes are internally represented as proved transition systems. Actually, we use a fragment of them, in which only one transition exits from a node among those mutually concurrent. This permits to have compact representations that are linear in average with the number of actions in the term of the language that describes the system. Another important property of these compact transition systems is that they preserve truly concurrent bisimulations, that can be checked in average in polynomial time. Parametricity is achieved by resorting to the rich labelling of the transitions encoding the parallel structure of processes. These labels are then “observed” for retrieving the interleaving, causal and locational semantics.

We address the problem of message authentication using the -calculus, which has been given an ope... more We address the problem of message authentication using the -calculus, which has been given an operational semantics in [2] that provides each sequential process of a system with its own local space of names. We exploit here that semantics and its localized names to guarantee by construction that a message has been generated by a given entity. Therefore, our proposal can be seen as a reference for the analysis of "real" protocols. As an example, we study the way authentication is ensured by encrypting messages in the ×Ô -calculus .

Theoretical Computer Science, 2002

We consider two operational semantics for CCS deÿned in the literature: the ÿrst exploits proved ... more We consider two operational semantics for CCS deÿned in the literature: the ÿrst exploits proved transition systems (PTS) and the second rewriting logic (RL). We show that the interleaving interpretation of both semantics agree, in that they deÿne the same transitions and exhibit the same non-deterministic structure. In addition, we study causality in CCS computations. We recall its treatment via PTS, exhibiting the notion of causality presented in the literature, and we show how to recast it in the RL semantics via suitable axioms. Also in this case, the two semantics agree.

Mobile agents, i.e. pieces of programs that can be sent around networks of computers, are startin... more Mobile agents, i.e. pieces of programs that can be sent around networks of computers, are starting to appear on the Internet. Such programs may be seen as an enrichment of traditional distributed computing. Since mobile agents may carry communication links with them as they move across the network, they create very dynamic interconnection structures that can be extremely complex to analyse. In this paper we analyse a fragment of a system based on the mobile agent principle written in the Facile programming language. We propose a Structural Operational Semantics (SOS) for Facile, giving a proved transition system that records encodings of the derivation trees of transitions in their labels. This information allows us to easily recover non-interleaving semantics for Facile by looking only at the labels of transitions. We use the new Facile semantics to debug an agent based system. This example is a scaled down version of a system demonstrated at the European IT Conference Exhibition in Brussels, 1995.

Transactions of The Society for Modeling and Simulation International, 2004

This article presents a stochastic model of lymphocyte recruitment in inflamed brain microvessels... more This article presents a stochastic model of lymphocyte recruitment in inflamed brain microvessels. Recent studies about the inflammatory process of the brain that leads to multiple sclerosis have revealed that lymphocyte extravasation is a sequence of dynamical states, mediated by partially overlapped interactions of different adhesion molecules and activation factors. This study's model of lymphocyte recruitment is based on process algebras for mobile systems. The biochemical system is modelled as a set of concurrent processes of the biochemical stochastic π-calculus. Processes are driven by suitable probability distributions that quantitatively describe the rates and the times at which reactions to simulations occur. The results of the model reproduce, within the estimated experimental errors, the functional behavior of the data obtained from laboratory measurements.

IEEE Transactions on Software Engineering, 2001

AbstractWe use a structural operational semantics which drives us in inferring quantitative measu... more AbstractWe use a structural operational semantics which drives us in inferring quantitative measures on system evolution. The transitions of the system are labeled and we assign rates to them by only looking at these labels. The rates reflect the possibly distributed architecture on ...

ACM Computing Surveys, 2001

This article surveys the definition and application of an enhancement of structural operational s... more This article surveys the definition and application of an enhancement of structural operational semantics in the field of concurrent systems, and also addresses issues of distribution and mobility of code. The focus is on how enriching the labels of transitions with encodings of their ...

Theoretical Computer Science, 1999

This paper studies causality in the x-calculus. Our notion of causality combines the dependencies... more This paper studies causality in the x-calculus. Our notion of causality combines the dependencies given by the syntactic structure of processes with those originated by passing names. Our studies show that two transitions not causally related may however occur in a fixed ordering in any computation, i.e., the z-calculus may implicitly express a precedence between actions. The same partial order of transitions is associated with all the computations that are obtained by shuffling transitions that are concurrent (i.e. related neither by causality nor by precedence). Other non-interleaving semantics are investigated and compared. The presentation takes advantage of a parametric definition of process behaviour given in SOS style that permits us to take almost for free the interleaving theory and tools. Finally, we extend our approach to higherorder n-calculus, enriched with a spurn operation. @ 1999-Elsevier Science B.V. All rights rcscrvcd . 0304-3975/99/$ -see front matter @ 1999-Elsevier Science B.V. All rights reserved I'll: SO304-3975(97)00236-3

An incremental parametric model is presented that permits to recover different descriptions of co... more An incremental parametric model is presented that permits to recover different descriptions of concurrent systems. Given a calculus, its semantics is defined through a privileged transition system with transitions labelled by their proofs; then computations, i.e., paths in the transition system, are given a tree structure (proved trees). Different representation of the behaviour of a process are obtained by observing, via an observation function, the proved tree associated to the process. As an example, the paper shows how the interleaving, causal, and locational semantics are recovered, and shows how the corresponding bisimulations are compared, by a simple inspection of the used observation functions. Also, an algebra of proved trees is defined, and a generalized expansion law is exhibited. Through the appropriate observation function, this generalized law originates the analogous expansion law in the selected approach.

Electronic Notes in Theoretical Computer Science, 2006

This paper focuses on Beta-binders, a language of processes with typed interaction sites which ha... more This paper focuses on Beta-binders, a language of processes with typed interaction sites which has been recently introduced to represent biological entities. Here the syntax and semantics of Beta-binders are enriched to achieve a stochastic version of it, in order to obtain quantitative measures on biological phenomena. The relevance of quantitative reasoning is outlined running a biological example.

We study causality in the π-calculus. Our notion of causality combines the dependencies given by ... more We study causality in the π-calculus. Our notion of causality combines the dependencies given by the syntactic structure of processes with those originated by passing names. It turns out that two transitions not causally related may although occur in a fixed ordering in any computation, i.e., π-calculus may express implicitly a priority between actions. Our causality relation still induces the same partial order of transitions for all the computations that are obtained by shuffling transitions that are concurrent (= related neither by causality nor by priority). The presentation takes advantage from a parametric definition of process behaviour that highlights the essence of the topic. All the results on bisimulation based equivalences, congruences, axiomatizations and logics are taken (almost) for free from the interleaving theory.

Theoretical Computer Science, 2004

We use the -calculus to model the evolution of biochemical systems, taking advantage of their sim... more We use the -calculus to model the evolution of biochemical systems, taking advantage of their similarities with global computation applications. First, we present a reduction semantics for the -calculus from which causality and concurrency can be mechanically derived. We prove that our semantics agrees with the causal deÿnitions presented in the literature. We also extend our semantics to model biological compartments. Then, we show the applicability of our proposal on a couple of biological examples.