Brane Calculi Systems: A Static Preview of their Possible Behaviour

We improve the precision of a previous Control Flow Analysis for Brane Calculi, by adding information on the context and introducing causality information on the membranes. This allows us to prove some biological properties on the behaviour of systems specified in Brane Calculi.Comment: Presented at MeCBIC 201

A Constraint-based Language for Multiparty Interactions.

Abstract Multiparty interactions are common place in today's distributed systems. An agent usually communicates, in a single session, with other agents to accomplish a given task. Take for instance an online transaction including the vendor, the client, the credit card system and the bank. When specifying this kind of system, we probably observe a single transaction including several (binary) communications leading to changes in the state of all the involved agents. Multiway synchronization process calculi, that move from a binary to a multiparty synchronization discipline, have been proposed to formally study the behavior of those systems. However, adopting models such as Bodei, Brodo, and Bruni's Core Network Algebra (CNA), where the number of participants in an interaction is not fixed a priori, leads to an exponential blow-up in the number of states/behaviors that can be observed from the system. In this paper we explore mechanisms to tackle this problem. We extend CNA with constraints that declaratively allow the modeler to restrict the interaction that should actually happen. Our extended process algebra, called CCNA, finds application in balancing the interactions in a concurrent system, leading to a simple, deadlock-free and fair solution for the Dinning Philosopher problem. Our definition of constraints is general enough and it offers the possibility of accumulating costs in a multiparty negotiation. Hence, only computations respecting the thresholds imposed by the modeler are observed. We use this machinery to neatly model a Service Level Agreement protocol. We develop the theory of CCNA including its operational semantics and a behavioral equivalence that we prove to be a congruence. We also propose a prototypical implementation that allows us to verify, automatically, some of the systems explored in the paper

SOS Rules for Equivalences of Reaction Systems

Reaction Systems (RSs) are a successful computational framework inspired by biological systems. A RS pairs a set of entities with a set of reactions over them. Entities can be used to enable or inhibit each reaction, and are produced by reactions. Entities can also be provided by an external context. RS semantics is defined in terms of an (unlabelled) rewrite system: given the current set of entities, a rewrite step consists of the application of all and only the enabled reactions. In this paper we define, for the first time, a labelled transition system for RSs in the structural operational semantics (SOS) style. This is achieved by distilling a signature whose operators directly correspond to the ingredients of RSs and by defining some simple SOS inference rules for any such operator to define the behaviour of the RS in a compositional way. The rich information recorded in the labels allows us to define an assertion language to tailor behavioural equivalences on some specific properties or entities. The SOS approach is suited to drive additional enhancements of RSs along features such as quantitative measurements of entities and communication between RSs. The SOS rules have been also exploited to design a prototype implementation in logic programming.Comment: Part of WFLP 2020 pre-proceeding

Formal executable descriptions of biological systems

The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems

A Formal Approach to Open Multiparty Interactions

We present a process algebra aimed at describing interactions that are multiparty, i.e. that may involve more than two processes and that are open, i.e. the number of the processes they involve is not fixed or known a priori. Here we focus on the theory of a core version of a process calculus, without message passing, called Core Network Algebra (CNA). In CNA communication actions are given not in terms of channels but in terms of chains of links that record the source and the target ends of each hop of interactions. The operational semantics of our calculus mildly extends the one of CCS. The abstract semantics is given in the style of bisimulation but requires some ingenuity. Remarkably, the abstract semantics is a congruence for all operators of CNA and also with respect to substitutions, which is not the case for strong bisimilarity in CCS. As a motivating and running example, we illustrate the model of a simple software defined network infrastructure.Comment: 62 page

A flat process calculus for nested membrane interactions

The link-calculus has been recently proposed as a process calculus for representing interactions that are open (i.e. that the number of processes may vary), and multiparty (i.e. that may involve more than two processes). Here, we apply the link-calculus for expressing, possibly hierarchical and non dyadic, biological interactions. In particular, we provide a natural encoding of Cardelli's Brane calculus, a compartment-based calculus, introduced to model the behaviour of nested membranes. Notably, the link-calculus is at, but we can model membranes just as special processes taking part in the biological reaction. Moreover, we give evidence that the link-calculus allows one to directly model biological phenomena at the more appropriate level of abstraction

Statically detecting message confusions in a multi-protocol setting

In a multi-protocol setting, different protocols are concurrently executed, and each principal can participate in more than one. The possibilities of attacks therefore increase, often due to the presence of similar patterns in messages. Messages coming from one protocol can be confused with similar messages coming from another protocol. As a consequence, data of one type may be interpreted as data of another, and it is also possible that the type is the expected one, but the message is addressed to another protocol. In this paper, we shall present an extension of the LySa calculus [7, 4] that decorates encryption with tags including the protocol identifier, the protocol step identifier and the intended types of the encrypted terms. The additional information allows us to find the messages that can be confused and therefore to have hints to reconstruct the attack. We extend accordingly the standard static Control Flow Analysis for LySa, which over-approximates all the possible behaviour of the studied protocols, included the possible message confusions that may occur at run-time. Our analysis has been implemented and successfully applied to small sets of protocols. In particular, we discovered an undocumented family of attacks, that may arise when Bauer-Berson-Feiertag and the Woo-Lam authentication protocols are running in parallel. The implementation complexity of the analysis is low polynomial

On the quantitative estimation of short-term aging in human faces

Facial aging has been only partially studied in the past and mostly in a qualitative way. This paper presents a novel approach to the estimation of facial aging aimed to the quantitative evaluation of the changes in facial appearance over time. In particular, the changes both in face shape and texture, due to short-time aging, are considered. The developed framework exploits the concept of “distinctiveness” of facial features and the temporal evolution of such measure. The analysis is performed both at a global and local level to define the features which are more stable over time. Several experiments are performed on publicly available databases with image sequences densely sampled over a time span of several years. The reported results clearly show the potential of the methodology to a number of applications in biometric identification from human faces

A Global Occurrence Counting Analysis for Brane Calculi

We propose a polynomial static analysis for Brane Calculi, based on Abstract Interpretation 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 biological setting to investigate systems in which the information on the number of membranes occurring in the system plays a crucial role