Luca Tesei

University of Camerino | UNICAM · Scuola di Scienze e Tecnologie

Current methods for comparing RNA secondary structures are based on tree representations and exploit edit distance or alignment algorithms. Most of them can only process structures without pseudoknots. To overcome this limitation we introduce ASPRAlign, a Java tool that aligns particular algebraic tree representations of RNA. These trees neglect th...

Complex systems are ubiquitous. Their components, agents, live in an environment perceiving its changes and reacting with appropriate actions; they also interact with each other causing changes in the environment itself. Modelling an environment that shows this feedback loop with agents is still a big issue because the model must take into account...

In this paper we introduce a new data-driven run-time monitoring system for analysing the behaviour of time evolving complex systems. The monitor controls the evolution of the whole system but it is mined from the data produced by its single interacting components. Relevant behavioural changes happening at the component level and that are responsib...

Background RNA secondary structure comparison is a fundamental task for several studies, among which are RNA structure prediction and evolution. The comparison can currently be done efficiently only for pseudoknot-free structures due to their inherent tree representation. Results In this work, we introduce an algebraic language to represent RNA se...

Transforming the latent value of big data into real value requires the great human intelligence and application of human-data scientists. Data scientists are expected to have a wide range of technical skills alongside being passionate self-directed people who are able to work easily with others and deliver high quality outputs under pressure. There...

Objective: An innovative method based on topological data analysis is introduced for classifying EEG recordings of patients affected by epilepsy. We construct a topological space from a collection of EEGs signals using Persistent Homology; then, we analyse the space by Persistent entropy, a global topological feature, in order to classify healthy...

The methods proposed in the literature for RNA comparison focus mainly on pseudoknot free structures. The comparison of pseudoknotted structures is still a challenge. In this work, we propose a new algebraic representation of RNA secondary structures based on relations among hairpins in terms of nesting, crossing, and concatenation. Such algebraic...

The methods proposed in the literature for RNA comparison focus mainly on pseudoknot free structures. The comparison of pseudoknotted structures is still a challenge. In this work, we propose a new algebraic representation of RNA secondary structures based on relations among hairpins in terms of nesting, crossing, and concatenation. Such algebraic...

Many biological phenomena are inherently multiscale (MS) - i.e. they are characterised by interactions involving simultaneously different spatial and temporal scales. The needs of describing systems in a MS fashion and, more in general, MS problems across multiple scientific disciplines require a common modelling approach being able to (i) unify th...

We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour resembles the one of a self-adaptive system. Each RNA configuration is a graph and the evolution o...

We present a formal model for modelling Event-Condition-Action Rules by partitioning a state space and evolution function taking into account the fea- tures that are typical of Intelligent Environments. This model allows for a precise definition of formal requirements and for their efficient verification.

Several deterministically/stochastically timed process calculi have been proposed in the literature that, apart from their synchronization mechanism, mainly differ for the way in which actions and delays are represented. In particular, a distinction is made between integrated-time calculi, in which actions are durational, and orthogonal-time calcul...

Topological data analysis has been recently used to extract meaningful information frombiomolecules. Here we introduce the application of persistent homology, a topological data analysis tool, for computing persistent features (loops) of the RNA folding space. The scaffold of the RNA folding space is a complex graph from which the global features a...

In this paper we introduce a shape language for representing RNA secondary structures in a non-standard, non-linear way. The main motivation is to propose a new interpretation of RNA folding as a self-adaptability process, within the S[B] paradigm, towards a minimum free energy configuration. An RNA secondary structure is decomposed first by disti...

In this paper, we propose a methodology for deriving a model of a complex system by exploiting the information extracted from topological data analysis. Central to our approach is the S[B] paradigm in which a complex system is represented by a two-level model. One level, the structural S one, is derived using the newly-introduced quantitative conce...

In this paper we propose a methodology for deriving a model of a complex system by exploiting the information extracted from Topological Data Analysis. Central to our approach is the S[B] paradigm in which a complex system is represented by a two-level model. One level, the structural S one, is derived using the newly introduced quantitative concep...

A hierarchical approach for modelling the adaptability features of complex systems is introduced. It is based on a structural level S, describing the adaptation dynamics of the system, and a behavioural level B accounting for the description of the admissible dynamics of the system. Moreover, a unified system, called , is defined by coupling S and...

The fish stock of the common sole in the Adriatic Sea has been analysed by agent-based modelling and simulation techniques as an integration of other classical stock assessment models. In this work we start investigating also about the formal probabilistic modelling of our case study in order to extract valuable biological information from availabl...

DISPAS is an agent-based simulator for fish stock assessment developed as a decision making support for the sustainable management of fishery. In this work we enlarge the underlying model of DISPAS allowing it to model and simulate a multi-scale scenario. We retain the currently available spatial scale, able to represent a limited average region of...

Persistent Organic Pollutants represent a global ecological concern due to their ability to accumulate in organisms and to spread species-by-species via feeding connections. In this work we focus on the estimation and simulation of the bioaccumulation dynamics of persistent pollutants in the marine ecosystem, and we apply the approach for reconstru...

A hierarchical model for multi-level adaptive systems is built on two basic levels: a lower behavioural level B accounting for the actual behaviour of the system and an upper structural level S describing the adaptation dynamics of the system. The behavioural level is modelled as a state machine and the structural level as a higher-order system who...

We introduce DISPAS, Demersal fIsh Stock Probabilistic Agent-based Simulator, with the aim of helping to investigate and understand sustainability in the exploitation of fishery resources. The simulator has capabilities for exploring different fishing scenarios, focusing on the case study of the common sole (Solea solea) stock in the Northern Adria...

A hierarchical model for multi-level adaptive systems is built on two basic levels: a lower behavioural level B accounting for the actual behaviour of the system and an upper structural level S describing the adaptation dynamics of the system. The behavioural level is modelled as a state machine and the structural level as a higher-order system who...

Several timed process calculi have been proposed in the literature, which mainly differ for the way in which delays are represented. In particular, a distinction is made between integrated-time calculi, in which actions are durational, and orthogonal-time calculi, in which actions are instantaneous and delays are expressed separately. To reconcile...

We provide a unifying view of timed models such as timed automata, probabilistic timed automata, and Markov automata. The timed models and their bisimulation semantics are encoded in the framework of uniform labeled transition systems. In this unifying framework, we show that the timed bisimilarities present in the literature can be re-obtained and...

Software agents are particularly suitable for engineering models and simulations of cellular systems. In a very natural and intuitive manner, individual software components are therein delegated to reproduce "in silico" the behavior of individual components of alive systems at a given level of resolution. Individuals' actions and interactions among...

This work introduces a general multi-level model for self-adaptive systems. A self-adaptive system is seen as composed by two levels: the lower level describing the actual behaviour of the system and the upper level accounting for the dynamically changing environmental constraints on the system. In order to keep our description as general as possib...

micro-scale (microorganisms) on the macro-scale (food-web), up to the top of the food chain where humans are placed. Due to their high persistence, lipophilicity, long-range transport and other chemical and physical properties, Polychronated Biphenyls (PCBs) are subject to the phenomena of bio-accumulation and bio-magnification. Considering that PC...

Background / Purpose: The application of formal methods in computational biology and biomedicine is quite an established field and, recently, these techniques have been extended in order to consider Euclidean spatial aspects of biological systems such as the position, an interaction radius or a physical shape. We define a formal language that can...

Background / Purpose: The marine environment is a sink of contaminants that, if persistent, sooner or later will be reintroduced into the ecosystem. This is a hazard for both humans and wildlife, which are exposed to the ingestion of contaminated fish. Microbial ecology can clarify how the bioremediation potential of microorganisms can influence,...

This work introduces a general multi-level model for self-adaptive systems. A self-adaptive system is seen as composed by two levels: the lower level describing the actual behaviour of the system and the upper level accounting for the dynamically changing environmental constraints on the system. In order to keep our description as general as possib...

The Shape Calculus is a bio-inspired timed and spatial calculus for describing 3D geometrical shapes moving in a space. Shapes, combined with a behaviour, form 3D processes, i.e., individual entities able to bind with other processes on compatible spatial channels and to split over previously established bonds. Due to geometrical space, timed behav...

Existing approaches in multiscale (MS) science and engineering have evolved from a range of ideas and solutions that are reflective of their original problem domains. As a result, research in MS science has followed widely diverse and disjoint paths, which present a barrier to cross pollination of ideas and application of methods outside their appl...

Testing equivalence was originally defined by De Nicola and Hennessy in a process algebraic setting (CCS) with the aim of defining an equivalence relation between processes being less discriminating than bisimulation and with a natural interpretation in the practice of system development. Finite characterizations of the defined preorders and relati...

Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different spatial and temporal scales. Although several ways to provide "multilayer" models have been proposed, only Com...

The simulation and visualization of biological system models are becoming more and more important, in both clinical and research activities. Many tools help biologists and bioengineers to analyse and to study complex biological phenomena, such as disease spreading, tissue development and neurological reactivity. We present ongoing work on BioShape...

We present Spatial P systems, a variant of P systems which embodies the concept of space and position inside a membrane. Objects in membranes are associated with positions. Rules specify, in the usual way, the objects which are consumed and the ones which are produced; in addition, they can specify the positions of the produced objects. Objects bel...

Many biological phenomena are inherently multiscale, i.e. they are characterised by interactions involving different scales at the same time. This is the case of bone remodelling, where macroscopic behaviour (at organ and tissue scale) and microstructure (at cell scale) strongly influence each other. Consequently, several approaches have been defin...

The Shape Calculus is a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel that models naturally binding sites on the surface of shapes. In this paper, the full formal timed operational s...

The Shape Calculus is a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel that models naturally binding sites on the surface of shapes. Processes can represent molecules or other mobile...

Many biological phenomena are inherently multiscale, i.e. they are characterized by interactions involving different spatial and temporal scales simultaneously. Though several approaches have been proposed to provide "multilayer" models, only Complex Automata, derived from Cellular Automata, naturally embed spatial information and realize multiscal...

We define an individual-based probabilistic model of a sole (Solea solea) behaviour. The individual model is given in terms of an Extended Probabilistic Discrete Timed Automaton (EPDTA), a new formalism that is introduced in the paper and that is shown to be interpretable as a Markov decision process. A given EPDTA model can be probabilistically mo...

The Java virtual machine embodies a verifier that performs a set of checks on Java bytecode programs before their execution. The verifier carries out an efficient data-flow analysis applied to a type-level abstract interpretation of the code. The implementations of the bytecode verifier presented a significant problem with programs compiled with th...

The simulation and visualization of biological system models is becoming more and more important both in clinical use and in basic research. Since many systems are characterized by interactions involving different scales at the same time, several approaches have been defined to handle such complex systems at different spatial and temporal scale. In...

We define a subclass of timed automata, called oscillator timed automata, suitable to model biological oscillators. Coupled biological oscillators may synchronise, as emerging behaviour, after a period of time in which they interact through physical or chemical means. We introduce a parametric semantics for their interaction that is general enough...

We present a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel to naturally model binding sites on the surface of shapes. The calculus embeds collision detection and response, binding of...

We define a subclass of timed automata, called oscillator timed automata, suitable to model biological oscillators. The semantics of their interactions, parametric w.r.t. a model of synchronization, is introduced. We apply it to the Kuramoto model. Then, we introduce a logic, Kuramoto Synchronization Logic (KSL), and a model checking algorithm in o...

To study systems whose dynamics changes with time, an extension of timed P systems is introduced in which evolution rules may vary with time. The proposed model is a timed automaton with a discrete time domain and in which each state is a timed P system. A result on expressive power and on features of the formalism sufficient for full expressivenes...

La responsabilità dei contenuti dei Rapporti Tecnici depositati in archivio è esclusivamente dell'autore, che solleva il Dipartimento di Matematica e Informatica e i gestori dell'archivio da ogni responsabilità nei confronti di terze parti, la violazione dei cui diritti ricade espressamente sull'autore. Il contenuto delle singole opere riflette le...

We introduce the main concepts of a bio-inspired calculus for describing 3D shapes moving in a space. Each shape contains a timed CCS-like process specifying an internal behaviour based on shape-dependent channels and splitting actions. Interactions among such enti-ties, called 3D processes, are collision-driven, i.e. collisions are detected and re...

To study systems whose dynamics changes with time, an extension of timed P systems is introduced in which evolution rules may vary with time. The proposed model is a timed automaton with a discrete time domain and in which each state is a timed P system. A result on expressive power and on features of the formalism sufficient for full expressivenes...

In a service-oriented architecture, systems communicate by exchanging messages. In this work, we propose a formal model based on OCL-constrained UML Class diagrams and a methodology based on Alloy Analyzer respectively for describing and verifying any first-order constrained client-server conversations. This framework allows us to verify conversati...

Digital services can be thought as internet based applications that fulfil users' needs and their quality represents a basic element during the delivery process. In such a context, usability is one the main quality parameters and it refers to the ease of benefiting from the functionalities and the information the service provides. We propose a list...

In this paper we investigate the use of abstract interpretation techniques for statically preventing race conditions. To this purpose we enrich the concurrent object calculus concζ by annotating terms with the set of "locks" owned at any time. We use an abstract form of the object calculus to check the absence of race conditions. We show that abstr...

We propose an extension to the formalism of timed automata by allowing urgent transitions. An urgent transition is a transition which must be taken within a fixed time interval from its enabling time and it has higher priority than other non-urgent transitions enabled in the same state. We give a set of rules formally describing the behavior of urg...