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Author Della Penna, Giuseppe; Intrigila, Benedetto; Tronci, Enrico; Venturini Zilli, Marisa pdf  doi
openurl 
  Title Exploiting Transition Locality in the Disk Based Mur$\varphi$ Verifier Type Conference Article
  Year 2002 Publication (up) 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 pdf  doi
openurl 
  Title A Probabilistic Approach to Automatic Verification of Concurrent Systems Type Conference Article
  Year 2001 Publication (up) 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 pdf  doi
openurl 
  Title Electric Power System Anomaly Detection Using Neural Networks Type Conference Article
  Year 2004 Publication (up) 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 pdf  url
doi  openurl
  Title Model Based Synthesis of Control Software from System Level Formal Specifications Type Journal Article
  Year 2014 Publication (up) 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 pdf  openurl
  Title Synchronized regular expressions Type Journal Article
  Year 2003 Publication (up) 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.  
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  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 pdf  doi
openurl 
  Title Disk Based Software Verification via Bounded Model Checking Type Conference Article
  Year 2007 Publication (up) 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 openurl 
  Title Functional analysis of a telecontrol system and stochastic measures of its GSM/GPRS connections Type Journal Article
  Year 2005 Publication (up) Archives of Transport – International Journal of Transport Problems Abbreviated Journal  
  Volume 17 Issue 3-4 Pages  
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  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 pdf  doi
openurl 
  Title Exploiting Hub States in Automatic Verification Type Conference Article
  Year 2005 Publication (up) 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. pdf  url
doi  openurl
  Title SBML2Modelica: Integrating biochemical models within open-standard simulation ecosystems Type Journal Article
  Year 2019 Publication (up) Bioinformatics Abbreviated Journal  
  Volume 36 Issue 7 Pages 2165â2172  
  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. pdf  url
doi  openurl
  Title Complete populations of virtual patients for in silico clinical trials Type Journal Article
  Year 2021 Publication (up) 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).  
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  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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