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Author Pappagallo, A.; Massini, A.; Tronci, E. pdf  doi
openurl 
  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  
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  Publisher (up) Place of Publication Editor  
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  ISSN ISBN Medium  
  Area Expedition Conference  
  Notes Approved no  
  Call Number MCLab @ davi @ Serial 181  
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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 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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  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 Mancini, T.; Mari, F.; Massini, A.; Melatti, I.; Tronci, E. pdf  url
doi  openurl
  Title On Checking Equivalence of Simulation Scripts Type Journal Article
  Year 2021 Publication Journal of Logical and Algebraic Methods in Programming Abbreviated Journal  
  Volume Issue Pages 100640  
  Keywords Formal verification, Simulation based formal verification, Formal Verification of cyber-physical systems, System-level formal verification  
  Abstract To support Model Based Design of Cyber-Physical Systems (CPSs) many simulation based approaches to System Level Formal Verification (SLFV) have been devised. Basically, these are Bounded Model Checking approaches (since simulation horizon is of course bounded) relying on simulators to compute the system dynamics and thereby verify the given system properties. The main obstacle to simulation based SLFV is the large number of simulation scenarios to be considered and thus the huge amount of simulation time needed to complete the verification task. To save on computation time, simulation based SLFV approaches exploit the capability of simulators to save and restore simulation states. Essentially, such a time saving is obtained by optimising the simulation script defining the simulation activity needed to carry out the verification task. Although such approaches aim to (bounded) formal verification, as a matter of fact, the proof of correctness of the methods to optimise simulation scripts basically relies on an intuitive semantics for simulation scripting languages. This hampers the possibility of formally showing that the optimisations introduced to speed up the simulation activity do not actually omit checking of relevant behaviours for the system under verification. The aim of this paper is to fill the above gap by presenting an operational semantics for simulation scripting languages and by proving soundness and completeness properties for it. This, in turn, enables formal proofs of equivalence between unoptimised and optimised simulation scripts.  
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  Publisher (up) Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 2352-2208 ISBN Medium  
  Area Expedition Conference  
  Notes Approved no  
  Call Number MCLab @ davi @ Mancini2021100640 Serial 183  
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Author Leeners, B.; Krueger, T.; Geraedts, K.; Tronci, E.; Mancini, T.; Ille, F.; Egli, M.; Roeblitz, S.; Wunder, D.; Saleh, L.; Schippert, C.; Hengartner, M.P. pdf  url
doi  openurl
  Title Cognitive function in association with high estradiol levels resulting from fertility treatment Type Journal Article
  Year 2021 Publication Hormones and Behavior Abbreviated Journal  
  Volume 130 Issue Pages 104951  
  Keywords Cognition, Estrogen, Estradiol, Fertility treatment, Attention, Cognitive bias  
  Abstract The putative association between hormones and cognitive performance is controversial. While there is evidence that estradiol plays a neuroprotective role, hormone treatment has not been shown to improve cognitive performance. Current research is flawed by the evaluation of combined hormonal effects throughout the menstrual cycle or in the menopausal transition. The stimulation phase of a fertility treatment offers a unique model to study the effect of estradiol on cognitive function. This quasi-experimental observational study is based on data from 44 women receiving IVF in Zurich, Switzerland. We assessed visuospatial working memory, attention, cognitive bias, and hormone levels at the beginning and at the end of the stimulation phase of ovarian superstimulation as part of a fertility treatment. In addition to inter-individual differences, we examined intra-individual change over time (within-subject effects). The substantial increases in estradiol levels resulting from fertility treatment did not relate to any considerable change in cognitive functioning. As the tests applied represent a broad variety of cognitive functions on different levels of complexity and with various brain regions involved, we can conclude that estradiol does not show a significant short-term effect on cognitive function.  
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  Corporate Author Thesis  
  Publisher (up) Place of Publication Editor  
  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0018-506x ISBN Medium  
  Area Expedition Conference  
  Notes Approved no  
  Call Number MCLab @ davi @ Leeners2021104951 Serial 185  
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Author Sinisi, S.; Alimguzhin, V.; Mancini, T.; Tronci, E. pdf  url
doi  openurl
  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.  
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  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 Fischer, S.; Ehrig, R.; Schaefer, S.; Tronci, E.; Mancini, T.; Egli, M.; Ille, F.; Krueger, T.H.C.; Leeners, B.; Roeblitz, S. pdf  url
doi  openurl
  Title Mathematical Modeling and Simulation Provides Evidence for New Strategies of Ovarian Stimulation Type Journal Article
  Year 2021 Publication Frontiers in Endocrinology Abbreviated Journal  
  Volume 12 Issue Pages 117  
  Keywords  
  Abstract New approaches to ovarian stimulation protocols, such as luteal start, random start or double stimulation, allow for flexibility in ovarian stimulation at different phases of the menstrual cycle. It has been proposed that the success of these methods is based on the continuous growth of multiple cohorts (“waves”) of follicles throughout the menstrual cycle which leads to the availability of ovarian follicles for ovarian controlled stimulation at several time points. Though several preliminary studies have been published, their scientific evidence has not been considered as being strong enough to integrate these results into routine clinical practice. This work aims at adding further scientific evidence about the efficiency of variable-start protocols and underpinning the theory of follicular waves by using mathematical modeling and numerical simulations. For this purpose, we have modified and coupled two previously published models, one describing the time course of hormones and one describing competitive follicular growth in a normal menstrual cycle. The coupled model is used to test ovarian stimulation protocols in silico. Simulation results show the occurrence of follicles in a wave-like manner during a normal menstrual cycle and qualitatively predict the outcome of ovarian stimulation initiated at different time points of the menstrual cycle.  
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  ISSN 1664-2392 ISBN Medium  
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  Notes Approved no  
  Call Number MCLab @ davi @ ref10.3389/fendo.2021.613048 Serial 189  
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Author Melatti, I.; Mari, F.; Mancini, T.; Prodanovic, M.; Tronci, E. pdf  doi
openurl 
  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.  
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  Notes To appear Approved no  
  Call Number MCLab @ davi @ ref9513535 Serial 190  
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Author Mancini, T.; Melatti, I.; Tronci, E. pdf  doi
openurl 
  Title Any-horizon uniform random sampling and enumeration of constrained scenarios for simulation-based formal verification Type Journal Article
  Year 2021 Publication IEEE Transactions on Software Engineering Abbreviated Journal  
  Volume Issue Pages 1-1  
  Keywords  
  Abstract Model-based approaches to the verification of non-terminating Cyber-Physical Systems (CPSs) usually rely on numerical simulation of the System Under Verification (SUV) model under input scenarios of possibly varying duration, chosen among those satisfying given constraints. Such constraints typically stem from requirements (or assumptions) on the SUV inputs and its operational environment as well as from the enforcement of additional conditions aiming at, e.g., prioritising the (often extremely long) verification activity, by, e.g., focusing on scenarios explicitly exercising selected requirements, or avoiding </i>vacuity</i> in their satisfaction. In this setting, the possibility to efficiently sample at random (with a known distribution, e.g., uniformly) within, or to efficiently enumerate (possibly in a uniformly random order) scenarios among those satisfying all the given constraints is a key enabler for the practical viability of the verification process, e.g., via simulation-based statistical model checking. Unfortunately, in case of non-trivial combinations of constraints, iterative approaches like Markovian random walks in the space of sequences of inputs in general fail in extracting scenarios according to a given distribution (e.g., uniformly), and can be very inefficient to produce at all scenarios that are both legal (with respect to SUV assumptions) and of interest (with respect to the additional constraints). For example, in our case studies, up to 91% of the scenarios generated using such iterative approaches would need to be neglected. In this article, we show how, given a set of constraints on the input scenarios succinctly defined by multiple finite memory monitors, a data structure (scenario generator) can be synthesised, from which any-horizon scenarios satisfying the input constraints can be efficiently extracted by (possibly uniform) random sampling or (randomised) enumeration. Our approach enables seamless support to virtually all simulation-based approaches to CPS verification, ranging from simple random testing to statistical model checking and formal (i.e., exhaustive) verification, when a suitable bound on the horizon or an iterative horizon enlargement strategy is defined, as in the spirit of bounded model checking.  
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  Language Summary Language Original Title  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1939-3520 ISBN Medium  
  Area Expedition Conference  
  Notes To appear Approved no  
  Call Number MCLab @ davi @ ref9527998 Serial 191  
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Author Intrigila, Benedetto; Salvo, Ivano; Sorgi, Stefano pdf  doi
openurl 
  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 Newmanââ¬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.  
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  Corporate Author Thesis  
  Publisher (up) 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 Chierichetti, Flavio; Lattanzi, Silvio; Mari, Federico; Panconesi, Alessandro pdf  doi
openurl 
  Title On Placing Skips Optimally in Expectation Type Conference Article
  Year 2008 Publication Web Search and Web Data Mining (WSDM 2008) Abbreviated Journal  
  Volume Issue Pages 15-24  
  Keywords Information Retrieval  
  Abstract We study the problem of optimal skip placement in an inverted list. Assuming the query distribution to be known in advance, we formally prove that an optimal skip placement can be computed quite efficiently. Our best algorithm runs in time O(n log n), n being the length of the list. The placement is optimal in the sense that it minimizes the expected time to process a query. Our theoretical results are matched by experiments with a real corpus, showing that substantial savings can be obtained with respect to the tra- ditional skip placement strategy, that of placing consecutive skips, each spanning sqrt(n) many locations.  
  Address  
  Corporate Author Thesis  
  Publisher (up) Acm Place of Publication Editor Najork, M.; Broder, A.Z.; Chakrabarti, S.  
  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 @ ChiLatMar08 Serial 94  
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