Paolo Milazzo

Paolo Milazzo
Università di Pisa | UNIPI · Department of Computer Science

Ph.D.

About

124
Publications
13,402
Reads
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1,087
Citations
Additional affiliations
November 2016 - April 2017
Università di Pisa
Position
  • Professor (Associate)
December 2011 - present
Università di Pisa
Position
  • Professor (Assistant)
Education
January 2004 - June 2007
Università di Pisa
Field of study
  • Computer Science

Publications

Publications (124)
Chapter
Reaction Systems (RSs) are a successful natural computing framework inspired by chemical reaction networks. A RS consists of a set of entities and a set of reactions. Entities can enable or inhibit each reaction, and are produced by reactions or provided by the environment. In a previous paper, we defined an original labelled transition system (LTS...
Article
We present in silico modeling methods for the investigation of dynamical properties of biochemical pathways, that are chemical reaction networks underlying cell functioning. Since pathways are (complex) dynamical systems, in-silico models are often studied by applying numerical integration techniques for Ordinary Differential Equations (ODEs), or s...
Preprint
Full-text available
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that rarely can be solved in closed-form, but that can instead be used to reason on the system dynamics. In this context...
Preprint
Full-text available
Robustness is an observable property for which a chemical reaction network (CRN) can maintain its functionalities despite the influence of different perturbations. In general, to verify whether a network is robust, it is necessary to consider all the possible parameter configurations. This is a process that can entail a massive computational effort...
Chapter
Dynamical properties of biochemical pathways are often assessed by performing numerical (ODE-based) or stochastic simulations. These methods are often computationally very expensive and require reliable quantitative parameters, such as kinetic constants and initial concentrations, to be available. Biochemical pathways are often represented as graph...
Article
Gene regulatory networks represent the interactions among genes regulating the activation of specific cell functionalities and they have been successfully modeled using threshold Boolean networks. In this paper we propose a systematic translation of threshold Boolean networks into reaction systems. Our translation produces a non redundant set of ru...
Chapter
Full-text available
We propose a pipeline for the stochastic analysis of a SIR model for COVID-19 through the stochastic model checker PRISM. The pipeline consists in: (i) the definition of a modified SIR model, able to include governmental restriction and prevention measures through an additional time-dependent coefficient; (ii) parameter estimation based on real epi...
Article
Full-text available
In reaction systems, preimages and nth ancestors are sets of reactants leading to the production of a target set of products in either 1 or n steps, respectively. Many computational problems on preimages and ancestors, such as finding all minimum-cardinality nth ancestors, computing their size or counting them, are intractable. In this paper, we ch...
Article
Full-text available
Gene Regulatory Networks (GRNs) represent the interactions among genes regulating the activation of specific cell functionalities, such as reception of (chemical) signals or reaction to environmental changes. Studying and understanding these processes is crucial: they are the fundamental mechanism at the basis of cell functioning, and many diseases...
Chapter
Multitasking has become surprisingly present in our life. This is mostly due to the fact that nowadays most of our activities involve the interaction with one or more devices. In such a context the brain mechanism of selective attention plays a key role in determining the success of a human’s interaction with a device. Indeed, it is a resource to b...
Article
Gene regulatory networks represent the interactions among genes regulating the activation of specific cell functionalities. They have been successfully modelled using Boolean networks, where a set of Boolean variables model the activation state of each gene, and Boolean functions model positive and negative influences among genes. Moreover, when th...
Article
Full-text available
This paper follows an integrated approach of Internet-of-Things based sensing and Machine Learning for crop growth prediction in agriculture. A Dynamic Bayesian Network (DBN) relates crop growth associated measurement data to environmental control data via hidden states. The measurement data, having (non-linear) sigmoid-type dynamics, are instance...
Article
Full-text available
The paper presents an Internet-of-Things based agricultural decision support system for crop growth. A dynamic Bayesian network (DBN) relates indicative parameters of crop development to environmental control parameters via unobserved (hidden) Markov states. The expectation-maximization algorithm is used to track the states and to learn the paramet...
Article
The paper presents an Internet-of-Things based agricultural decision support system for crop growth. A dynamic Bayesian network (DBN) relates indicative parameters of crop development to environmental control parameters via unobserved (hidden) Markov states. The expectation-maximization algorithm is used to track the states and to learn the paramet...
Conference Paper
Full-text available
Biochemical pathways are often represented as graphs, in which nodes and edges give a qualitative description of the modeled reactions, while node and edge labels provide quantitative details such as kinetic and stoichiometric parameters. Dynamical properties of biochemical pathways are usually assessed by performing numerical (ODE-based) or stocha...
Article
Full-text available
When a person is concurrently interacting with different systems, the amount of cognitive resources required (cognitive load) could be too high and might prevent some tasks from being completed. When such human multitasking involves safety-critical tasks, such as in an airplane, a spacecraft, or a car, failure to devote sufficient attention to the...
Conference Paper
Full-text available
Gene Regulatory Networks represent the interactions among genes regulating the activation of speci�c cell functionalities and they have been successfully modeled using threshold Boolean networks. In this paper we propose a systematic translation of threshold Boolean networks into Reaction Systems. Our translation produces a non redundant set of rul...
Article
At the neurological level, the Dopamine System plays a key role in addiction processes. Mathematical models of the Dopamine System have been proposed to study addiction to nicotine, drugs, and gambling. In this paper, we propose a Hybrid Automata model of the Dopamine System, based on the mathematical model proposed by Gutkin et al.. Our model allo...
Chapter
The main goal of systems biology is to understand the dynamical properties of biological systems by investigating the interactions among the components of a biological system. In this work, we focus on the robustness property, a behaviour observed in several biological systems that allows them to preserve their functions despite external and intern...
Conference Paper
This paper presents on-going work developing a formal framework for the model-based analysis of human-machine interaction in multiple critical systems. The framework builds on classical results from applied psychology on selective attention and working memory. The framework is intended for developers of interactive critical systems to identify plau...
Conference Paper
Full-text available
The technological level of greenhouse cultivation, especially in the Mediterranean countries such as Italy, Turkey, Greece and Spain, is low, despite protected crops are of considerable importance both for extension and for the production of fresh foodstuffs and for exported ornamental plants. The project “HouseGarden High Tech” intends to increase...
Article
Full-text available
Reaction systems are a qualitative formalism for the modelling of systems of biochemical reactions. In their original formulation, a reaction system executes in an environment (or context) that can supply it with new objects at each evolution step. The context drives the behaviour of a reaction system: it can provide different inputs to the system...
Article
In this paper we investigate dynamic causalities in membrane systems by proposing the concept of “predictor”, originally defined in the context of the reaction systems by Brijder, Ehrenfeucht and Rozenberg. The goal is to characterise sufficient and necessary conditions for the presence of a multiset of molecules of interest in the configuration of...
Chapter
The brain mechanism of selective attention plays a key role in determining the success of a human’s interaction with a device. If the user has to perform concurrent tasks by interacting simultaneously with more than one device, her/his attention is directed at one of the devices at a time. Attention can therefore be seen as a shared resource, and t...
Chapter
Addiction is a complex phenomenon, stemming from environmental, biological and psychological causes. It is defined as a natural response of the body to external stimuli, such as drugs, alcohol, but also job, love and Internet technologies, that become compulsive needs, difficult to remove. At the neurological level, the Dopamine System plays a key...
Article
Among model checking tools, the behaviour of a system is often formalized as a transition system with atomic propositions associated with states (Kripke structure). In current modeling languages, transitions are usually specified as updates of the system’s variables to be performed when certain conditions are satisfied. However, such a low-level re...
Conference Paper
Full-text available
We describe two extensions of P systems for the modelling of populations and ecosystems. They are the Minimal Probabilistic P systems (MPP systems) and the Attributed Probabilistic P systems (APP systems). We describe also two case studies in which the two formalisms have been applied to the study of real ecological systems. The first case study de...
Article
Full-text available
Reaction systems are a qualitative formalism for modeling systems of biochemical reactions characterized by the non-permanency of the elements: molecules disappear if not produced by any enabled reaction. Reaction systems execute in an environment that provides new molecules at each step. Brijder, Ehrenfeucht and Rozemberg introduced the idea of pr...
Conference Paper
Among Model Checking tools, the behaviour of a system is often formalized as a transition system with atomic propositions associated with states (Kripke structure). In current modelling languages, transitions are usually specified as updates of the system’s variables to be performed when certain conditions are satisfied. However, such a low-level r...
Book
This book contains the thoroughly refereed technical papers presented in six workshops collocated with the International Conference on Software Technologies: Applications and Foundations, STAF 2016, held in Vienna, Austria, in July 2016. The six workshops whose papers are included in this volume are: DataMod, GCM, HOFM, MELO, SEMS, and VeryComp. T...
Article
Reaction systems are a qualitative formalism for modeling systems of biochemical reactions characterized by the non-permanency of the elements: molecules disappear if not produced by any enabled reaction. Moreover, reaction systems execute in an environment that provides new molecules at each step. Brijder, Ehrenfeucht and Rozenberg investigated dy...
Article
Full-text available
The most challenging task in colorectal cancer research nowadays is to understand the development of acquired resistance to anti-EGFR drugs. The key reason for this problem is the KRAS mutations appearence after the treatment with monoclonal antibodies (moAb). Here we present a mathematical model for the analysis of KRAS mutations behavior in color...
Article
In this paper we propose MPP systems as modelling notation for ecological systems, and we show how they can be used together with simulation and statistical model checking tools to study properties of such kind of systems. As a case study we consider the ecological problem of stability of European water frog populations. The paper shows that MPP sy...
Conference Paper
We propose probabilistic/statistical model checking as a tool for game design. Models of games under design can be used for the early evaluation of properties related with game duration, existence of different successful strategies, and balancing of the game core mechanics. To show the usefulness of model checking in game design we consider and dev...
Article
Biochemical pathways are abstract descriptions of the interactions among the molecular species involved in a cellular process. Different molecular species mentioned in a pathway often represent different states of the same biological entity, such as the unbound and bound states of a certain molecule. Hence, a pathway can be seen as a network of int...
Chapter
The most challenging task in colorectal cancer research nowadays is to understand the development of acquired resistance to anti-EGFR drugs. The key reason for this problem is the KRAS mutations produced after the treatment with monoclonal antibodies (mAb). KRAS screening tests done before the start of the treatment are not very sensitive to identi...
Conference Paper
We propose a variant of probabilistic P Systems, Attributed Probabilistic P systems (APP systems), in which objects are annotated with attributes. We use APP systems for modelling social behaviours of some species of primates. In this context attributes can represent position of the animals in the environment, age of the animal, dominance level, ag...
Conference Paper
Grid Systems is a formalism for modelling population and ecosystem dynamics that combines features of membrane computing, such as rewrite rules and maximal parallelism, with a representation of space similar to that of Cellular Automata. Moreover, Grid Systems include features for the description of environmental events and of events that can be as...
Chapter
Systolic automata are models of highly-concurrent language acceptors based on identical processors with one-way flow of information, amenable to efficient hardware implementation as multiprocessor chips. In this paper we investigate the relationship between Binary Systolic Tree Automata (BSTA), in which the underlying communication structure is an...
Article
Reaction systems are an abstract model of interactions among biochemical reactions, developed around two opposite mechanisms: facilitation and inhibition. The evolution of a Reaction System is driven by the external objects which are sent into the system by the environment at each step. In order to increase the modelling expressiveness of the calcu...
Article
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity, such as a protein, in all its states (free, bound, degraded, etc.). Component identification, which is made possible by the mass conservation principle, allows subpathways to be c...
Article
Full-text available
Background Some species of water frogs originated from hybridization between different species. Such hybrid populations have a particular reproduction system called hybridogenesis. In this paper we consider the two species Pelophylax ridibundus and Pelophylax lessonae, and their hybrids Pelophylax esculentus. P. lessonae and P. esculentus form stab...
Article
Spatial P systems are an extension of the P systems formalism in which objects and membranes are embedded into a two-dimensional discrete space. Spatial P systems are characterised by the distinction between ordinary objects and mutually exclusive objects, with the constraint that any position can accommodate any number of ordinary objects, and at...
Conference Paper
European water frog populations are mainly composed by two species: Pelophylax lessonae (pool frog) and Pelophylax esculentus (edible frog). These populations are called L-E complexes. Edible frogs are a hybrid form between P. lessonae and Pelophylax ridibundus (eastern lake frog) and they reproduce in a particular way, called hybridogenesis. These...
Conference Paper
A new formalism, Grid Systems, aimed at modelling population dynamics is presented. The formalism is inspired by concepts of Membrane Computing (P Systems) and spatiality dynamics of Cellular Automata. The semantics of Grid Systems describes how stochasticity is exploited for reaction duration as well as reaction selection. Grid Systems perform rea...
Article
Full-text available
Biochemical pathways are abstract descriptions of the interactions among the molecular species involved in a process. Different molecular species mentioned in a pathway often represent different states of the same biological entity (e.g. the unbound and bound states of a certain molecule). Hence, a pathway can be seen as a network of interactions b...
Article
Full-text available
Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In this paper we show the application of a component identification algorithm to a number of real-world models to...
Conference Paper
Reaction systems are an abstract model of interactions among biochemical reactions, developed around two opposite mechanisms: facilitation and inhibition. The evolution of a Reaction System is driven by the external objects which are sent into the system by the environment at each step. In this paper, we propose the Reaction Algebra, a calculus res...
Article
Full-text available
Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation that properties of interest often concern a rather small portion of the system. As a consequence, reduced models...
Article
Full-text available
Modular verification is a technique used to face the state explosion problem often encountered in the verification of properties of complex systems such as concurrent interactive systems. The modular approach is based on the observation that properties of interest often concern a rather small portion of the system. As a consequence, reduced models...
Article
Full-text available
Property preservation is investigated as an approach to modular verification, leading to reduction of the property verification time for formal models. For modelling purposes, formalisms with multi-way synchronisations are considered. For the modular verification technique to work, a specific type of synchronisation is required for which a sufficie...
Article
We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modeling of biological systems. In the usual semantics of process algebras for modeling biological systems actions are instantaneous. When different scale levels of biological systems are considered in a single model, one should take into account that ac...
Article
Full-text available
Carassius gibelio, a cyprinid fish from Eurasia, has the ability to reproduce both sexually and asexually. This fish is also known as an invasive species which colonized almost all continental Europe, most likely originating from Asia and Eastern Europe. Populations of both sexually and asexually reproducing individuals exist in sympatry. In this s...
Conference Paper
We present an abstraction of the probabilistic semantics of Multiset Rewriting to formally express systems of reactions with uncertain kinetic rates. This allows biological systems modelling when the exact rates are not known, but are supposed to lie in some intervals. On these (abstract) models we perform probabilistic model checking obtaining low...
Chapter
The Calculus of Looping Sequences (CLS) has been proposed as a formalism for representing and simulating biomolecular systems. CLS is based on a set of operators which allow to represent the structure of such systems. Systems evolution is described by means of rewrite rules. A stochastic extension of CLS has been defined in which rewite rules are e...
Article
Full-text available
In the evolution literature, sympatric speciation is the origin of two, or more, species from a single local population. Many models have been developed to study the role of ecological competition and sexual selection in sympatric speciation. In this paper we propose a methodology for systematically deriving efficient computational models to study...
Article
Full-text available
The aim of this paper is to give motivations for the development of operational semantics in membrane computing, and to survey existing proposals. In particular, the definitions are compared of three operational semantics available in the literature, namely a seman-tics proposed by Andrei, Ciobanu and Lucanu, another proposed by Busi, and another o...
Article
Full-text available
This paper presents Spatial CLS, an extension of the Calculus of Looping Sequences (CLS) with spatial features. Spatial CLS allows keeping track of the position of biological elements in a continuous space (2D or 3D) as time passes. The movement of elements in the space can be precisely described, and elements can interact when constraints on their...
Article
Full-text available
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...
Article
Full-text available
Delays in biological systems may be used to model events for which the underlying dynamics cannot be precisely observed. Mathematical modeling of biological systems with delays is usually based on Delay Differential Equations (DDEs), a kind of differential equations in which the derivative of the unknown function at a certain time is given in terms...
Article
Full-text available
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...
Article
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...