
Giuseppe Della Penna, Benedetto Intrigila, Igor Melatti, Enrico Tronci, and Marisa Venturini Zilli. "Finite horizon analysis of Markov Chains with the Mur$\varphi$ verifier." Int. J. Softw. Tools Technol. Transf. 8, no. 4 (2006): 397–409. SpringerVerlag. ISSN: 14332779. DOI: 10.1007/s1000900502167.
Abstract: In this paper we present an explicit diskbased 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 FHPMur$\varphi$ (Finite Horizon Probabilistic Mur$\varphi$). We present experimental results comparing FHPMur$\varphi$ with (a finite horizon subset of) PRISM, a stateoftheart symbolic model checker for Markov Chains. Our experimental results show that FHPMur$\varphi$ can handle systems that are out of reach for PRISM, namely those involving arithmetic operations on the state variables (e.g. hybrid systems).



Giuseppe Della Penna, Daniele Magazzeni, Alberto Tofani, Benedetto Intrigila, Igor Melatti, and Enrico Tronci. "Automated Generation of Optimal Controllers through Model Checking Techniques." In IcincoIcso, edited by J. AndradeCetto, J.  L. Ferrier, J. M. C. D. Pereira and J. Filipe, 26–33. INSTICC Press, 2006. ISSN: 9728865597. DOI: 10.1007/9783540791423.
Abstract: We present a methodology for the synthesis of controllers, which exploits (explicit) model checking techniques. That is, we can cope with the systematic exploration of a very large state space. This methodology can be applied to systems where other approaches fail. In particular, we can consider systems with an highly nonlinear dynamics and lacking a uniform mathematical description (model). We can also consider situations where the required control action cannot be specified as a local action, and rather a kind of planning is required. Our methodology individuates first a raw optimal controller, then extends it to obtain a more robust one. A case study is presented which considers the well known trucktrailer obstacle avoidance parking problem, in a parking lot with obstacles on it. The complex nonlinear dynamics of the trucktrailer system, within the presence of obstacles, makes the parking problem extremely hard. We show how, by our methodology, we can obtain optimal controllers with different degrees of robustness.



Igor Melatti, Robert Palmer, Geoffrey Sawaya, Yu Yang, Robert Mike Kirby, and Ganesh Gopalakrishnan. "Parallel and distributed model checking in Eddy." Int. J. Softw. Tools Technol. Transf. 11, no. 1 (2009): 13–25. SpringerVerlag. ISSN: 14332779. DOI: 10.1007/s100090080094x.
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 multicore (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.



Igor Melatti, Robert Palmer, Geoffrey Sawaya, Yu Yang, Robert Mike Kirby, and Ganesh Gopalakrishnan. "Parallel and Distributed Model Checking in Eddy." In Model Checking Software, 13th International SPIN Workshop, Vienna, Austria, March 30 – April 1, 2006, Proceedings, edited by A. Valmari, 108–125. Lecture Notes in Computer Science 3925. Springer  Verlag, 2006. ISSN: 03029743. ISBN: 9783540331025. DOI: 10.1007/11691617_7.
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 multicore (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.



Benedetto Intrigila, Igor Melatti, Alberto Tofani, and Guido Macchiarelli. "Computational models of myocardial endomysial collagen arrangement." Computer Methods and Programs in Biomedicine 86, no. 3 (2007): 232–244. Elsevier NorthHolland, Inc.. ISSN: 01692607. DOI: 10.1016/j.cmpb.2007.03.004.
Abstract: Collagen extracellular matrix is one of the factors related to high passive stiffness of cardiac muscle. However, the architecture and the mechanical aspects of the cardiac collagen matrix are not completely known. In particular, endomysial collagen contribution to the passive mechanics of cardiac muscle as well as its micro anatomical arrangement is still a matter of debate. In order to investigate mechanical and structural properties of endomysial collagen, we consider two alternative computational models of some specific aspects of the cardiac muscle. These two models represent two different views of endomysial collagen distribution: (1) the traditional view and (2) a new view suggested by the data obtained from scanning electron microscopy (SEM) in NaOH macerated samples (a method for isolating collagen from the other tissue). We model the myocardial tissue as a net of spring elements representing the cardiomyocytes together with the endomysial collagen distribution. Each element is a viscous elastic spring, characterized by an elastic and a viscous constant. We connect these springs to imitate the interconnections between collagen fibers. Then we apply to the net of springs some external forces of suitable magnitude and direction, obtaining an extension of the net itself. In our setting, the ratio forces magnitude /net extension is intended to model the stress /strain ratio of a microscopical portion of the myocardial tissue. To solve the problem of the correct identification of the values of the different parameters involved, we use an artificial neural network approach. In particular, we use this technique to learn, given a distribution of external forces, the elastic constants of the springs needed to obtain a desired extension as an equilibrium position. Our experimental findings show that, in the model of collagen distribution structured according to the new view, a given stress /strain ratio (of the net of springs, in the sense specified above) is obtained with much smaller (w.r.t. the other model, corresponding to the traditional view) elasticity constants of the springs. This seems to indicate that by an appropriate structure, a given stiffness of the myocardial tissue can be obtained with endomysial collagen fibers of much smaller size.



Giuseppe Della Penna, Benedetto Intrigila, Igor Melatti, and Enrico Tronci. "Exploiting Hub States in Automatic Verification." In Automated Technology for Verification and Analysis: Third International Symposium, ATVA 2005, Taipei, Taiwan, October 47, 2005, Proceedings, edited by D.A. Peled and Y.K. Tsay, 54–68. Lecture Notes in Computer Science 3707. Springer, 2005. ISSN: 3540292098. DOI: 10.1007/11562948_7.
Abstract: In this paper we present a new algorithm to counteract state explosion when using Explicit State Space Exploration to verify protocollike 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.



Giuseppe Della Penna, Benedetto Intrigila, Igor Melatti, Enrico Tronci, and Marisa Venturini Zilli. "Finite Horizon Analysis of Markov Chains with the Mur$\varphi$ Verifier." In Correct Hardware Design and Verification Methods, 12th IFIP WG 10.5 Advanced Research Working Conference, CHARME 2003, L'Aquila, Italy, October 2124, 2003, Proceedings, edited by D. Geist and E. Tronci, 394–409. Lecture Notes in Computer Science 2860. Springer, 2003. ISSN: 354020363X. DOI: 10.1007/9783540397243_34.
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 FHPMur$\varphi$ (Finite Horizon Probabilistic Mur$\varphi$). We present experimental results comparing FHPMur$\varphi$ with (a finite horizon subset of) PRISM, a stateoftheart symbolic model checker for Markov Chains. Our experimental results show that FHPMur$\varphi$ can handle systems that are out of reach for PRISM, namely those involving arithmetic operations on the state variables (e.g. hybrid systems).



Giuseppe Della Penna, Benedetto Intrigila, Igor Melatti, Enrico Tronci, and Marisa Venturini Zilli. "Integrating RAM and Disk Based Verification within the Mur$\varphi$ Verifier." In Correct Hardware Design and Verification Methods, 12th IFIP WG 10.5 Advanced Research Working Conference, CHARME 2003, L'Aquila, Italy, October 2124, 2003, Proceedings, edited by D. Geist and E. Tronci, 277–282. Lecture Notes in Computer Science 2860. Springer, 2003. ISSN: 354020363X. DOI: 10.1007/9783540397243_25.
Abstract: We present a verification algorithm that can automatically switch from RAM based verification to disk based verification without discarding the work done during the RAM based verification phase. This avoids having to choose beforehand the proper verification algorithm. Our experimental results show that typically our integrated algorithm is as fast as (sometime faster than) the fastest of the two base (i.e. RAM based and disk based) verification algorithms.



Giuseppe Della Penna, Antinisca Di Marco, Benedetto Intrigila, Igor Melatti, and Alfonso Pierantonio. "Xere: Towards a Natural Interoperability between XML and ER Diagrams." In Fundamental Approaches to Software Engineering, 6th International Conference, FASE 2003, Held as Part of the Joint European Conferences on Theory and Practice of Software, ETAPS 2003, Warsaw, Poland, April 711, 2003, Proceedings, edited by M. PezzÃ¨, 356–371. Lecture Notes in Computer Science 2621. Springer, 2003. ISSN: 3540008993. DOI: 10.1007/3540365788_25.
Abstract: XML (eXtensible Markup Language) is becoming the standard format for documents on Internet and is widely used to exchange data. Often, the relevant information contained in XML documents needs to be also stored in legacy databases (DB) in order to integrate the new data with the preexisting ones. In this paper, we introduce a technique for the automatic XMLDB integration, which we call Xere. In particular we present, as the first step of Xere, the mapping algorithm which allows the translation of XML Schemas into EntityRelationship diagrams.



Giuseppe Della Penna, Benedetto Intrigila, Igor Melatti, Enrico Tronci, and Marisa Venturini Zilli. "Bounded Probabilistic Model Checking with the Mur$\varphi$ Verifier." In Formal Methods in ComputerAided Design, 5th International Conference, FMCAD 2004, Austin, Texas, USA, November 1517, 2004, Proceedings, edited by A. J. Hu and A. K. Martin, 214–229. Lecture Notes in Computer Science 3312. Springer, 2004. ISSN: 3540237380. DOI: 10.1007/9783540304944_16.
Abstract: In this paper we present an explicit verification algorithm for Probabilistic Systems defining discrete time/finite state Markov Chains. We restrict ourselves to verification of Bounded PCTL formulas (BPCTL), that is, PCTL formulas in which all Until operators are bounded, possibly with different bounds. This means that we consider only paths (system runs) of bounded length. Given a Markov Chain $\cal M$ and a BPCTL formula Φ, our algorithm checks if Φ is satisfied in $\cal M$. This allows to verify important properties, such as reliability in Discrete Time Hybrid Systems. We present an implementation of our algorithm within a suitable extension of the Mur$\varphi$ verifier. We call FHPMur$\varphi$ (Finite Horizon Probabilistic Mur$\varphi$) such extension of the Mur$\varphi$ verifier. We give experimental results comparing FHPMur$\varphi$ with (a finite horizon subset of) PRISM, a stateoftheart symbolic model checker for Markov Chains. Our experimental results show that FHPMur$\varphi$ can effectively handle verification of BPCTL formulas for systems that are out of reach for PRISM, namely those involving arithmetic operations on the state variables (e.g. hybrid systems).

