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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	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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	Author	Pugliese, Rosario; Tronci, Enrico
	Title	Automatic Verification of a Hydroelectric Power Plant			Type	Conference Article
	Year	1996	Publication	Third International Symposium of Formal Methods Europe (FME), Co-Sponsored by IFIP WG 14.3	Abbreviated Journal
	Volume		Issue		Pages	425-444
	Keywords
	Abstract	We analyze the specification of a hydroelectric power plant by ENEL (the Italian Electric Company). Our goal is to show that for the specification of the plant (its control system in particular) some given properties hold. We were provided with an informal specification of the plant. From such informal specification we wrote a formal specification using the CCS/Meije process algebra formalism. We defined properties using μ-calculus. Automatic verification was carried out using model checking. This was done by translating our process algebra definitions (the model) and μ-calculus formulas into BDDs. In this paper we present the informal specification of the plant, its formal specification, some of the properties we verified and experimental results.
	Address
	Corporate Author				Thesis
	Publisher	Springer	Place of Publication	Oxford, UK	Editor	Gaudel, M.-C.; Woodcock, J.
	Language		Summary Language		Original Title
	Series Editor		Series Title	Lecture Notes in Computer Science	Abbreviated Series Title
	Series Volume	1051	Series Issue		Edition
	ISSN	3-540-60973-3	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ fme96			Serial	53
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	Author	Piperno, Adolfo; Tronci, Enrico
	Title	Regular Systems of Equations in λ-calculus			Type	Journal Article
	Year	1990	Publication	Int. J. Found. Comput. Sci.	Abbreviated Journal
	Volume	1	Issue	3	Pages	325-340
	Keywords
	Abstract	Many problems arising in equational theories like Lambda-calculus and Combinatory Logic can be expressed by combinatory equations or systems of equations. However, the solvability problem for an arbitrarily given class of systems is in general undecidable. In this paper we shall focus our attention on a decidable class of systems, which will be called regular systems, and we shall analyse some classical problems and well-known properties of Lambda-calculus that can be described and solved by means of regular systems. The significance of such class will be emphasized showing that for slight extensions of it the solvability problem turns out to be undecidable.
	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		ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ ijfcs90			Serial	60
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	Author	Piperno, Adolfo; Tronci, Enrico
	Title	Regular Systems of Equations in λ-calculus			Type	Conference Article
	Year	1989	Publication	Ictcs	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	Many problems arising in equational theories like Lambda-calculus and Combinatory Logic can be expressed by combinatory equations or systems of equations. However, the solvability problem for an arbitrarily given class of systems is in general undecidable. In this paper we shall focus our attention on a decidable class of systems, which will be called regular systems, and we shall analyse some classical problems and well-known properties of Lambda-calculus that can be described and solved by means of regular systems. The significance of such class will be emphasized showing that for slight extensions of it the solvability problem turns out to be undecidable.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Mantova - Italy	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN		ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ ictcs89			Serial	61
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	Author	Pappagallo, A.; Massini, A.; Tronci, E.
	Title	Monte Carlo Based Statistical Model Checking of Cyber-Physical Systems: A Review			Type	Journal Article
	Year	2020	Publication	Information	Abbreviated Journal
	Volume	11	Issue	558	Pages
	Keywords
	Abstract
	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		ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	no
	Call Number	MCLab @ davi @			Serial	181
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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	Melatti, Igor; Palmer, Robert; Sawaya, Geoffrey; Yang, Yu; Kirby, Robert Mike; Gopalakrishnan, Ganesh
	Title	Parallel and Distributed Model Checking in Eddy			Type	Conference Article
	Year	2006	Publication	Model Checking Software, 13th International SPIN Workshop, Vienna, Austria, March 30 – April 1, 2006, Proceedings	Abbreviated Journal
	Volume		Issue		Pages	108-125
	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 (i) performing overlapped asynchronous message passing, and (ii) 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		Editor	Valmari, A.
	Language		Summary Language		Original Title
	Series Editor		Series Title	Lecture Notes in Computer Science	Abbreviated Series Title
	Series Volume	3925	Series Issue		Edition
	ISSN	0302-9743	ISBN	978-3-540-33102-5	Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Mpsykg06			Serial	81
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	Author	Melatti, I.; Mari, F.; Mancini, T.; Prodanovic, M.; Tronci, E.
	Title	A Two-Layer Near-Optimal Strategy for Substation Constraint Management via Home Batteries			Type	Journal Article
	Year	2021	Publication	IEEE Transactions on Industrial Electronics	Abbreviated Journal
	Volume		Issue		Pages	1-1
	Keywords
	Abstract	Within electrical distribution networks, substation constraints management requires that aggregated power demand from residential users is kept within suitable bounds. Efficiency of substation constraints management can be measured as the reduction of constraints violations w.r.t. unmanaged demand. Home batteries hold the promise of enabling efficient and user-oblivious substation constraints management. Centralized control of home batteries would achieve optimal efficiency. However, it is hardly acceptable by users, since service providers (e.g., utilities or aggregators) would directly control batteries at user premises. Unfortunately, devising efficient hierarchical control strategies, thus overcoming the above problem, is far from easy. We present a novel two-layer control strategy for home batteries that avoids direct control of home devices by the service provider and at the same time yields near-optimal substation constraints management efficiency. Our simulation results on field data from 62 households in Denmark show that the substation constraints management efficiency achieved with our approach is at least 82% of the one obtained with a theoretical optimal centralized strategy.
	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		ISBN		Medium
	Area		Expedition		Conference
	Notes	To appear			Approved	no
	Call Number	MCLab @ davi @ ref9513535			Serial	190
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	Author	Mazzini, Silvia; Puri, Stefano; Mari, Federico; Melatti, Igor; Tronci, Enrico
	Title	Formal Verification at System Level			Type	Conference Article
	Year	2009	Publication	In: DAta Systems In Aerospace (DASIA), Org. EuroSpace, Canadian Space Agency, CNES, ESA, EUMETSAT. Instanbul, Turkey, EuroSpace	Abbreviated Journal
	Volume		Issue		Pages
	Keywords
	Abstract	System Level Analysis calls for a language comprehensible to experts with different background and yet precise enough to support meaningful analyses. SysML is emerging as an effective balance between such conflicting goals. In this paper we outline some the results obtained as for SysML based system level functional formal verification by an ESA/ESTEC study, with a collaboration among INTECS and La Sapienza University of Roma. The study focuses on SysML based system level functional requirements techniques.
	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		ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Dasia09			Serial	20
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