Engineering Resilient Collective Adaptive Systems by Self-Stabilisation

Collective adaptive systems are an emerging class of networked computational systems, particularly suited in application domains such as smart cities, complex sensor networks, and the Internet of Things. These systems tend to feature large scale, heterogeneity of communication model (including opportunistic peer-to-peer wireless interaction), and require inherent self-adaptiveness properties to address unforeseen changes in operating conditions. In this context, it is extremely difficult (if not seemingly intractable) to engineer reusable pieces of distributed behaviour so as to make them provably correct and smoothly composable. Building on the field calculus, a computational model (and associated toolchain) capturing the notion of aggregate network-level computation, we address this problem with an engineering methodology coupling formal theory and computer simulation. On the one hand, functional properties are addressed by identifying the largest-to-date field calculus fragment generating self-stabilising behaviour, guaranteed to eventually attain a correct and stable final state despite any transient perturbation in state or topology, and including highly reusable building blocks for information spreading, aggregation, and time evolution. On the other hand, dynamical properties are addressed by simulation, empirically evaluating the different performances that can be obtained by switching between implementations of building blocks with provably equivalent functional properties. Overall, our methodology sheds light on how to identify core building blocks of collective behaviour, and how to select implementations that improve system performance while leaving overall system function and resiliency properties unchanged.Comment: To appear on ACM Transactions on Modeling and Computer Simulatio

Modelling and simulating in systems biology: an approach based on multi-agent systems

Systems Biology is an innovative way of doing biology recently raised in bio-informatics contexts, characterised by the study of biological systems as complex systems with a strong focus on the system level and on the interaction dimension. In other words, the objective is to understand biological systems as a whole, putting on the foreground not only the study of the individual parts as standalone parts, but also of their interaction and of the global properties that emerge at the system level by means of the interaction among the parts. This thesis focuses on the adoption of multi-agent systems (MAS) as a suitable paradigm for Systems Biology, for developing models and simulation of complex biological systems. Multi-agent system have been recently introduced in informatics context as a suitabe paradigm for modelling and engineering complex systems. Roughly speaking, a MAS can be conceived as a set of autonomous and interacting entities, called agents, situated in some kind of nvironment, where they fruitfully interact and coordinate so as to obtain a coherent global system behaviour. The claim of this work is that the general properties of MAS make them an effective approach for modelling and building simulations of complex biological systems, following the methodological principles identified by Systems Biology. In particular, the thesis focuses on cell populations as biological systems. In order to support the claim, the thesis introduces and describes (i) a MAS-based model conceived for modelling the dynamics of systems of cells interacting inside cell environment called niches. (ii) a computational tool, developed for implementing the models and executing the simulations. The tool is meant to work as a kind of virtual laboratory, on top of which kinds of virtual experiments can be performed, characterised by the definition and execution of specific models implemented as MASs, so as to support the validation, falsification and improvement of the models through the observation and analysis of the simulations. A hematopoietic stem cell system is taken as reference case study for formulating a specific model and executing virtual experiments

Setting the basis of best practices and standards for curation and annotation of logical models in biology

International audienceThe fast accumulation of biological data calls for their integration, analysis and exploitation through more systematic approaches. The generation of novel, relevant hypotheses from this enormous quantity of data remains challenging. Logical models have long been used to answer a variety of questions regarding the dynamical behaviours of regulatory networks. As the number of published logical models increases, there is a pressing need for systematic model annotation, referencing and curation in community-supported and standardised formats. This article summarises the key topics and future directions of a meeting entitled ‘Annotation and curation of computational models in biology’, organised as part of the 2019 [BC]2 conference. The purpose of the meeting was to develop and drive forward a plan towards the standardised annotation of logical models, review and connect various ongoing projects of experts from different communities involved in the modelling and annotation of molecular biological entities, interactions, pathways and models. This article defines a roadmap towards the annotation and curation of logical models, including milestones for best practices and minimum standard requirements

The Dynamics of Public Opinion in Complex Networks

This paper studies the problem of public opinion formation and concentrates on the interplays among three factors: individual attributes, environmental influences and information flow. We present a simple model to analyze the dynamics of four types of networks. Our simulations suggest that regular communities establish not only local consensus, but also global diversity in public opinions. However, when small world networks, random networks, or scale-free networks model social relationships, the results are sensitive to the elasticity coefficient of environmental influences and the average connectivity of the type of network. For example, a community with a higher average connectivity has a higher probability of consensus. Yet, it is misleading to predict results merely based on the characteristic path length of networks. In the process of changing environmental influences and average connectivity, sensitive areas are discovered in the system. By sensitive areas we mean that interior randomness emerges and we cannot predict unequivocally how many opinions will remain upon reaching equilibrium. We also investigate the role of authoritative individuals in information control. While enhancing average connectivity facilitates the diffusion of the authoritative opinion, it makes individuals subject to disturbance from non-authorities as well. Thus, a moderate average connectivity may be preferable because then the public will most likely form an opinion that is parallel with the authoritative one. In a community with a scale-free structure, the influence of authoritative individuals keeps constant with the change of the average connectivity. Provided that the influence of individuals is proportional to the number of their acquaintances, the smallest percentage of authorities is required for a controlled consensus in a scale free network. This study shows that the dynamics of public opinion varies from community to community due to the different degree of impressionability of people and the distinct social network structure of the community.Public Opinion, Complex Network, Consensus, Agent-Based Model

From distributed coordination to field calculus and aggregate computing

open6siThis work has been partially supported by: EU Horizon 2020 project HyVar (www.hyvar-project .eu), GA No. 644298; ICT COST Action IC1402 ARVI (www.cost -arvi .eu); Ateneo/CSP D16D15000360005 project RunVar (runvar-project.di.unito.it).Aggregate computing is an emerging approach to the engineering of complex coordination for distributed systems, based on viewing system interactions in terms of information propagating through collectives of devices, rather than in terms of individual devices and their interaction with their peers and environment. The foundation of this approach is the distillation of a number of prior approaches, both formal and pragmatic, proposed under the umbrella of field-based coordination, and culminating into the field calculus, a universal functional programming model for the specification and composition of collective behaviours with equivalent local and aggregate semantics. This foundation has been elaborated into a layered approach to engineering coordination of complex distributed systems, building up to pragmatic applications through intermediate layers encompassing reusable libraries of program components. Furthermore, some of these components are formally shown to satisfy formal properties like self-stabilisation, which transfer to whole application services by functional composition. In this survey, we trace the development and antecedents of field calculus, review the field calculus itself and the current state of aggregate computing theory and practice, and discuss a roadmap of current research directions with implications for the development of a broad range of distributed systems.embargoed_20210910Viroli, Mirko; Beal, Jacob; Damiani, Ferruccio; Audrito, Giorgio; Casadei, Roberto; Pianini, DaniloViroli, Mirko; Beal, Jacob; Damiani, Ferruccio; Audrito, Giorgio; Casadei, Roberto; Pianini, Danil