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	Author	Della Penna, Giuseppe; Intrigila, Benedetto; Tronci, Enrico; Venturini Zilli, Marisa
	Title	Exploiting Transition Locality in the Disk Based Mur$\varphi$ Verifier			Type	Conference Article
	Year	2002	Publication	4th International Conference on Formal Methods in Computer-Aided Design (FMCAD)	Abbreviated Journal
	Volume		Issue		Pages	202-219
	Keywords
	Abstract	The main obstruction to automatic verification of Finite State Systems is the huge amount of memory required to complete the verification task (state explosion). This motivates research on distributed as well as disk based verification algorithms. In this paper we present a disk based Breadth First Explicit State Space Exploration algorithm as well as an implementation of it within the Mur$\varphi$ verifier. Our algorithm exploits transition locality (i.e. the statistical fact that most transitions lead to unvisited states or to recently visited states) to decrease disk read accesses thus reducing the time overhead due to disk usage. A disk based verification algorithm for Mur$\varphi$ has been already proposed in the literature. To measure the time speed up due to locality exploitation we compared our algorithm with such previously proposed algorithm. Our experimental results show that our disk based verification algorithm is typically more than 10 times faster than such previously proposed disk based verification algorithm. To measure the time overhead due to disk usage we compared our algorithm with RAM based verification using the (standard) Mur$\varphi$ verifier with enough memory to complete the verification task. Our experimental results show that even when using 1/10 of the RAM needed to complete verification, our disk based algorithm is only between 1.4 and 5.3 times (3 times on average) slower than (RAM) Mur$\varphi$ with enough RAM memory to complete the verification task at hand. Using our disk based Mur$\varphi$ we were able to complete verification of a protocol with about $10^9$ reachable states. This would require more than 5 gigabytes of RAM using RAM based Mur$\varphi$.
	Address
	Corporate Author				Thesis
	Publisher	Springer	Place of Publication	Portland, OR, USA	Editor	Aagaard, M.; O'Leary, J.W.
	Language		Summary Language		Original Title
	Series Editor		Series Title	Lecture Notes in Computer Science	Abbreviated Series Title
	Series Volume	2517	Series Issue		Edition
	ISSN	3-540-00116-6	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ fmcad02			Serial	41
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	Author	Tronci, Enrico; Della Penna, Giuseppe; Intrigila, Benedetto; Venturini Zilli, Marisa
	Title	A Probabilistic Approach to Automatic Verification of Concurrent Systems			Type	Conference Article
	Year	2001	Publication	8th Asia-Pacific Software Engineering Conference (APSEC)	Abbreviated Journal
	Volume		Issue		Pages	317-324
	Keywords
	Abstract	The main barrier to automatic verification of concurrent systems is the huge amount of memory required to complete the verification task (state explosion). In this paper we present a probabilistic algorithm for automatic verification via model checking. Our algorithm trades space with time. In particular, when memory is full because of state explosion our algorithm does not give up verification. Instead it just proceeds at a lower speed and its results will only hold with some arbitrarily small error probability. Our preliminary experimental results show that by using our probabilistic algorithm we can typically save more than 30% of RAM with an average time penalty of about 100% w.r.t. a deterministic state space exploration with enough memory to complete the verification task. This is better than giving up the verification task because of lack of memory.
	Address
	Corporate Author				Thesis
	Publisher	IEEE Computer Society	Place of Publication	Macau, China	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0-7695-1408-1	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ apsec01			Serial	43
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	Author	Martinelli, Marco; Tronci, Enrico; Dipoppa, Giovanni; Balducelli, Claudio
	Title	Electric Power System Anomaly Detection Using Neural Networks			Type	Conference Article
	Year	2004	Publication	8th International Conference on: Knowledge-Based Intelligent Information and Engineering Systems (KES)	Abbreviated Journal
	Volume		Issue		Pages	1242-1248
	Keywords
	Abstract	The aim of this work is to propose an approach to monitor and protect Electric Power System by learning normal system behaviour at substations level, and raising an alarm signal when an abnormal status is detected; the problem is addressed by the use of autoassociative neural networks, reading substation measures. Experimental results show that, through the proposed approach, neural networks can be used to learn parameters underlaying system behaviour, and their output processed to detecting anomalies due to hijacking of measures, changes in the power network topology (i.e. transmission lines breaking) and unexpected power demand trend.
	Address
	Corporate Author				Thesis
	Publisher	Springer	Place of Publication	Wellington, New Zealand	Editor	Negoita, M.G.; Howlett, R.J.; Jain, L.C.
	Language		Summary Language		Original Title
	Series Editor		Series Title	Lecture Notes in Computer Science	Abbreviated Series Title
	Series Volume	3213	Series Issue		Edition
	ISSN	3-540-23318-0	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ kes04			Serial	35
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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	Della Penna, Giuseppe; Intrigila, Benedetto; Tronci, Enrico; Venturini Zilli, Marisa
	Title	Synchronized regular expressions			Type	Journal Article
	Year	2003	Publication	Acta Inf.	Abbreviated Journal
	Volume	39	Issue	1	Pages	31-70
	Keywords
	Abstract	Text manipulation is one of the most common tasks for everyone using a computer. The increasing number of textual information in electronic format that every computer user collects everyday also increases the need of more powerful tools to interact with texts. Indeed, much work has been done to provide simple and versatile tools that can be useful for the most common text manipulation tasks. Regular Expressions (RE), introduced by Kleene, are well known in the formal language theory. RE have been extended in various ways, depending on the application of interest. In almost all the implementations of RE search algorithms (e.g. the egrep [15] UNIX command, or the Perl [20] language pattern matching constructs) we find backreferences, i.e. expressions that make reference to the string matched by a previous subexpression. Generally speaking, it seems that all kinds of synchronizations between subexpressions in a RE can be very useful when interacting with texts. In this paper we introduce the Synchronized Regular Expressions (SRE) as an extension of the Regular Expressions. We use SRE to present a formal study of the already known backreferences extension, and of a new extension proposed by us, which we call the synchronized exponents. Moreover, since we are dealing with formalisms that should have a practical utility and be used in real applications, we have the problem of how to present SRE to the final users. Therefore, in this paper we also propose a user-friendly syntax for SRE to be used in implementations of SRE-powered search algorithms.
	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 @ actainf03			Serial	39
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	Author	Brizzolari, Francesco; Melatti, Igor; Tronci, Enrico; Della Penna, Giuseppe
	Title	Disk Based Software Verification via Bounded Model Checking			Type	Conference Article
	Year	2007	Publication	APSEC '07: Proceedings of the 14th Asia-Pacific Software Engineering Conference	Abbreviated Journal
	Volume		Issue		Pages	358-365
	Keywords
	Abstract	One of the most successful approach to automatic software verification is SAT based bounded model checking (BMC). One of the main factors limiting the size of programs that can be automatically verified via BMC is the huge number of clauses that the backend SAT solver has to process. In fact, because of this, the SAT solver may easily run out of RAM. We present two disk based algorithms that can considerably decrease the number of clauses that a BMC backend SAT solver has to process in RAM. Our experimental results show that using our disk based algorithms we can automatically verify programs that are out of reach for RAM based BMC.
	Address
	Corporate Author				Thesis
	Publisher	IEEE Computer Society	Place of Publication	Washington, DC, USA	Editor
	Language		Summary Language		Original Title
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0-7695-3057-5	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Bmtd07			Serial	76
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	Author	Bobbio, Andrea; Ciancamerla, Ester; Minichino, Michele; Tronci, Enrico
	Title	Functional analysis of a telecontrol system and stochastic measures of its GSM/GPRS connections			Type	Journal Article
	Year	2005	Publication	Archives of Transport – International Journal of Transport Problems	Abbreviated Journal
	Volume	17	Issue	3-4	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	yes
	Call Number	Sapienza @ mari @ jtp05			Serial	31
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	Author	Della Penna, Giuseppe; Intrigila, Benedetto; Melatti, Igor; Tronci, Enrico
	Title	Exploiting Hub States in Automatic Verification			Type	Conference Article
	Year	2005	Publication	Automated Technology for Verification and Analysis: Third International Symposium, ATVA 2005, Taipei, Taiwan, October 4-7, 2005, Proceedings	Abbreviated Journal
	Volume		Issue		Pages	54-68
	Keywords
	Abstract	In this paper we present a new algorithm to counteract state explosion when using Explicit State Space Exploration to verify protocol-like systems. We sketch the implementation of our algorithm within the Caching Mur$\varphi$ verifier and give experimental results showing its effectiveness. We show experimentally that, when memory is a scarce resource, our algorithm improves on the time performances of Caching Mur$\varphi$ verification algorithm, saving between 16% and 68% (45% on average) in computation time.
	Address
	Corporate Author				Thesis
	Publisher	Springer	Place of Publication		Editor	D.A. Peled; Y.-K. Tsay
	Language		Summary Language		Original Title
	Series Editor		Series Title	Lecture Notes in Computer Science	Abbreviated Series Title
	Series Volume	3707	Series Issue		Edition
	ISSN	3-540-29209-8	ISBN		Medium
	Area		Expedition		Conference
	Notes				Approved	yes
	Call Number	Sapienza @ mari @ Dimt04			Serial	83
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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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