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	Author	Mancini, Toni; Mari, Federico; Massini, Annalisa; Melatti, Igor; Merli, Fabio; Tronci, Enrico
	Title	System Level Formal Verification via Model Checking Driven Simulation			Type	Conference Article
	Year	2013	Publication	Proceedings of the 25th International Conference on Computer Aided Verification. July 13-19, 2013, Saint Petersburg, Russia	Abbreviated Journal	CAV 2013
	Volume		Issue		Pages	296-312
	Keywords
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	Springer - Verlag	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title	Lecture Notes in Computer Science	Abbreviated Series Title
	Series Volume	8044	Series Issue		Edition
	ISSN	0302-9743	ISBN	978-3-642-39798-1	Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @			Serial	113
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	Author	Intrigila, Benedetto; Salvo, Ivano; Sorgi, Stefano
	Title	A characterization of weakly Church-Rosser abstract reduction systems that are not Church-Rosser			Type	Journal Article
	Year	2001	Publication	Information and Computation	Abbreviated Journal
	Volume	171	Issue	2	Pages	137-155
	Keywords
	Abstract	Basic properties of rewriting systems can be stated in the framework of abstract reduction systems (ARS). Properties like confluence (or Church-Rosser, CR) and weak confluence (or weak Church-Rosser, WCR) and their relationships can be studied in this setting: as a matter of fact, well-known counterexamples to the implication WCR CR have been formulated as ARS. In this paper, starting from the observation that such counterexamples are structurally similar, we set out a graph-theoretic characterization of WCR ARS that is not CR in terms of a suitable class of reduction graphs, such that in every WCR not CR ARS, we can embed at least one element of this class. Moreover, we give a tighter characterization for a restricted class of ARS enjoying a suitable regularity condition. Finally, as a consequence of our approach, we prove some interesting results about ARS using the mathematical tools developed. In particular, we prove an extension of the NewmanÃ¢â‚¬â„¢s lemma and we find out conditions that, once assumed together with WCR property, ensure the unique normal form property. The Appendix treats two interesting examples, both generated by graph-rewriting rules, with specific combinatorial properties.
	Address
	Corporate Author				Thesis
	Publisher	Academic Press, Inc.	Place of Publication	Duluth, MN, USA	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0890-5401	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Intrigila-Salvo-Sorgi:01			Serial	68
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	Author	Della Penna, Giuseppe; Intrigila, Benedetto; Magazzeni, Daniele; Melatti, Igor; Tronci, Enrico
	Title	CGMurphi: Automatic synthesis of numerical controllers for nonlinear hybrid systems			Type	Journal Article
	Year	2013	Publication	European Journal of Control	Abbreviated Journal	European Journal of Control
	Volume	19	Issue	1	Pages	14-36
	Keywords
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	Elsevier North-Holland, Inc.	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0947-3580	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	Sapienza @ melatti @			Serial	114
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	Author	Bucciarelli, Antonio; Piperno, Adolfo; Salvo, Ivano
	Title	Intersection types and λ-definability			Type	Journal Article
	Year	2003	Publication	Mathematical Structures in Computer Science	Abbreviated Journal
	Volume	13	Issue	1	Pages	15-53
	Keywords
	Abstract	This paper presents a novel method for comparing computational properties of λ-terms that are typeable with intersection types, with respect to terms that are typeable with Curry types. We introduce a translation from intersection typing derivations to Curry typeable terms that is preserved by β-reduction: this allows the simulation of a computation starting from a term typeable in the intersection discipline by means of a computation starting from a simply typeable term. Our approach proves strong normalisation for the intersection system naturally by means of purely syntactical techniques. The paper extends the results presented in Bucciarelli et al. (1999) to the whole intersection type system of Barendregt, Coppo and Dezani, thus providing a complete proof of the conjecture, proposed in Leivant (1990), that all functions uniformly definable using intersection types are already definable using Curry types.
	Address
	Corporate Author				Thesis
	Publisher	Cambridge University Press	Place of Publication	New York, NY, USA	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0960-1295	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Bucciarelli-Piperno-Salvo:MSCS-03			Serial	69
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	Author	Mari, Federico; Melatti, Igor; Salvo, Ivano; Tronci, Enrico
	Title	Model Based Synthesis of Control Software from System Level Formal Specifications			Type	Journal Article
	Year	2014	Publication	ACM TRANSACTIONS ON SOFTWARE ENGINEERING AND METHODOLOGY	Abbreviated Journal	ACM TRANSACTIONS ON SOFTWARE ENGINEERING AND METHODOLOGY
	Volume	23	Issue	1	Pages	Article 6
	Keywords
	Abstract
	Address
	Corporate Author				Thesis
	Publisher	ACM	Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1049-331X	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	Sapienza @ melatti @			Serial	110
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	Author	Maggioli, F.; Mancini, T.; Tronci, E.
	Title	SBML2Modelica: Integrating biochemical models within open-standard simulation ecosystems			Type	Journal Article
	Year	2019	Publication	Bioinformatics	Abbreviated Journal
	Volume	36	Issue	7	Pages	2165â€“2172
	Keywords
	Abstract	SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard general-purpose simulation ecosystems. This hinders co-simulation and integration of SBML models within larger model networks, in order to, e.g., enable in-silico clinical trials of drugs, pharmacological protocols, or engineering artefacts such as biomedical devices against Virtual Physiological Human models.Modelica is one of the most popular existing open-standard general-purpose simulation languages, supported by many simulators. Modelica models are especially suited for the definition of complex networks of heterogeneous models from virtually all application domains. Models written in Modelica (and in 100+ other languages) can be readily exported into black-box Functional Mock-Up Units (FMUs), and seamlessly co-simulated and integrated into larger model networks within open-standard language-independent simulation ecosystems.In order to enable SBML model integration within heterogeneous model networks, we present SBML2Modelica, a software system translating SBML models into well-structured, user-intelligible, easily modifiable Modelica models. SBML2Modelica is SBML Level 3 Version 2 -compliant and succeeds on 96.47% of the SBML Test Suite Core (with a few rare, intricate, and easily avoidable combinations of constructs unsupported and cleanly signalled to the user). Our experimental campaign on 613 models from the BioModels database (with up to 5438 variables) shows that the major open-source (general-purpose) Modelica and FMU simulators achieve performance comparable to state-of-the-art specialised SBML simulators.SBML2Modelica is written in Java and is freely available for non-commercial use at https://bitbucket.org/mclab/sbml2modelica
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-4803	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	MCLab @ davi @ ref10.1093/bioinformatics/btz860			Serial	179
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	Author	Sinisi, S.; Alimguzhin, V.; Mancini, T.; Tronci, E.; Leeners, B.
	Title	Complete populations of virtual patients for in silico clinical trials			Type	Journal Article
	Year	2021	Publication	Bioinformatics	Abbreviated Journal
	Volume		Issue		Pages	1-8
	Keywords
	Abstract	Model-based approaches to safety and efficacy assessment of pharmacological drugs, treatment strategies, or medical devices (In Silico Clinical Trial, ISCT) aim to decrease time and cost for the needed experimentations, reduce animal and human testing, and enable precision medicine. Unfortunately, in presence of non-identifiable models (e.g., reaction networks), parameter estimation is not enough to generate complete populations of Virtual Patient (VPs), i.e., populations guaranteed to show the entire spectrum of model behaviours (phenotypes), thus ensuring representativeness of the trial.We present methods and software based on global search driven by statistical model checking that, starting from a (non-identifiable) quantitative model of the human physiology (plus drugs PK/PD) and suitable biological and medical knowledge elicited from experts, compute a population of VPs whose behaviours are representative of the whole spectrum of phenotypes entailed by the model (completeness) and pairwise distinguishable according to user-provided criteria. This enables full granularity control on the size of the population to employ in an ISCT, guaranteeing representativeness while avoiding over-representation of behaviours.We proved the effectiveness of our algorithm on a non-identifiable ODE-based model of the female Hypothalamic-Pituitary-Gonadal axis, by generating a population of 4 830 264 VPs stratified into 7 levels (at different granularity of behaviours), and assessed its representativeness against 86 retrospective health records from Pfizer, Hannover Medical School and University Hospital of Lausanne. The datasets are respectively covered by our VPs within Average Normalised Mean Absolute Error of 15%, 20%, and 35% (90% of the latter dataset is covered within 20% error).
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1367-4803	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	MCLab @ davi @ ref10.1093/bioinformatics/btaa1026			Serial	182
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	Author	Della Penna, Giuseppe; Intrigila, Benedetto; Melatti, Igor; Tronci, Enrico; Venturini Zilli, Marisa
	Title	Finite horizon analysis of Markov Chains with the Mur$\varphi$ verifier			Type	Journal Article
	Year	2006	Publication	Int. J. Softw. Tools Technol. Transf.	Abbreviated Journal
	Volume	8	Issue	4	Pages	397-409
	Keywords
	Abstract	In this paper we present an explicit disk-based verification algorithm for Probabilistic Systems defining discrete time/finite state Markov Chains. Given a Markov Chain and an integer k (horizon), our algorithm checks whether the probability of reaching an error state in at most k steps is below a given threshold. We present an implementation of our algorithm within a suitable extension of the Mur$\varphi$ verifier. We call the resulting probabilistic model checker FHP-Mur$\varphi$ (Finite Horizon Probabilistic Mur$\varphi$). We present experimental results comparing FHP-Mur$\varphi$ with (a finite horizon subset of) PRISM, a state-of-the-art symbolic model checker for Markov Chains. Our experimental results show that FHP-Mur$\varphi$ can handle systems that are out of reach for PRISM, namely those involving arithmetic operations on the state variables (e.g. hybrid systems).
	Address
	Corporate Author				Thesis
	Publisher	Springer-Verlag	Place of Publication	Berlin, Heidelberg	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1433-2779	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Dimtz06			Serial	78
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	Author	Melatti, Igor; Palmer, Robert; Sawaya, Geoffrey; Yang, Yu; Kirby, Robert Mike; Gopalakrishnan, Ganesh
	Title	Parallel and distributed model checking in Eddy			Type	Journal Article
	Year	2009	Publication	Int. J. Softw. Tools Technol. Transf.	Abbreviated Journal
	Volume	11	Issue	1	Pages	13-25
	Keywords
	Abstract	Model checking of safety properties can be scaled up by pooling the CPU and memory resources of multiple computers. As compute clusters containing 100s of nodes, with each node realized using multi-core (e.g., 2) CPUs will be widespread, a model checker based on the parallel (shared memory) and distributed (message passing) paradigms will more efficiently use the hardware resources. Such a model checker can be designed by having each node employ two shared memory threads that run on the (typically) two CPUs of a node, with one thread responsible for state generation, and the other for efficient communication, including (1) performing overlapped asynchronous message passing, and (2) aggregating the states to be sent into larger chunks in order to improve communication network utilization. We present the design details of such a novel model checking architecture called Eddy. We describe the design rationale, details of how the threads interact and yield control, exchange messages, as well as detect termination. We have realized an instance of this architecture for the Murphi modeling language. Called Eddy_Murphi, we report its performance over the number of nodes as well as communication parameters such as those controlling state aggregation. Nearly linear reduction of compute time with increasing number of nodes is observed. Our thread task partition is done in such a way that it is modular, easy to port across different modeling languages, and easy to tune across a variety of platforms.
	Address
	Corporate Author				Thesis
	Publisher	Springer-Verlag	Place of Publication	Berlin, Heidelberg	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1433-2779	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Mpsykg09			Serial	80
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	Author	Sinisi, S.; Alimguzhin, V.; Mancini, T.; Tronci, E.
	Title	Reconciling interoperability with efficient Verification and Validation within open source simulation environments			Type	Journal Article
	Year	2021	Publication	Simulation Modelling Practice and Theory	Abbreviated Journal
	Volume		Issue		Pages	102277
	Keywords	Simulation, Verification and Validation, Interoperability, FMI/FMU, Model Exchange, Cyber-Physical Systems
	Abstract	A Cyber-Physical System (CPS) comprises physical as well as software subsystems. Simulation-based approaches are typically used to support design and Verification and Validation (V&V) of CPSs in several domains such as: aerospace, defence, automotive, smart grid and healthcare. Accordingly, many simulation-based tools are available to support CPS design. This, on one side, enables designers to choose the toolchain that best suits their needs, on the other side poses huge interoperability challenges when one needs to simulate CPSs whose subsystems have been designed and modelled using different toolchains. To overcome such an interoperability problem, in 2010 the Functional Mock-up Interface (FMI) has been proposed as an open standard to support both Model Exchange (ME) and Co-Simulation (CS) of simulation models created with different toolchains. FMI has been adopted by several modelling and simulation environments. Models adhering to such a standard are called Functional Mock-up Units (FMUs). Indeed FMUs play an essential role in defining complex CPSs through, e.g., the System Structure and Parametrization (SSP) standard. Simulation-based V&V of CPSs typically requires exploring different simulation scenarios (i.e., exogenous input sequences to the CPS under design). Many such scenarios have a shared prefix. Accordingly, to avoid simulating many times such shared prefixes, the simulator state at the end of a shared prefix is saved and then restored and used as a start state for the simulation of the next scenario. In this context, an important FMI feature is the capability to save and restore the internal FMU state on demand. This is crucial to increase efficiency of simulation-based V&V. Unfortunately, the implementation of this feature is not mandatory and it is available only within some commercial software. As a result, the interoperability enabled by the FMI standard cannot be fully exploited for V&V when using open-source simulation environments. This motivates developing such a feature for open-source CPS simulation environments. Accordingly, in this paper, we focus on JModelica, an open-source modelling and simulation environment for CPSs based on an open standard modelling language, namely Modelica. We describe how we have endowed JModelica with our open-source implementation of the FMI 2.0 functions needed to save and restore internal states of FMUs for ME. Furthermore, we present experimental results evaluating, through 934 benchmark models, correctness and efficiency of our extended JModelica. Our experimental results show that simulation-based V&V is, on average, 22 times faster with our get/set functionality than without it.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1569-190x	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	MCLab @ davi @ Sinisi2021102277			Serial	186
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