| Records |
| 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 |
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| Volume |
36 |
Issue |
7 |
Pages |
2165–2172 |
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| 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 |
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1367-4803 |
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MCLab @ davi @ ref10.1093/bioinformatics/btz860 |
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179 |
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| Author |
Chen, Q.M.; Finzi, A.; Mancini, T.; Melatti, I.; Tronci, E. |
| Title |
MILP, Pseudo-Boolean, and OMT Solvers for Optimal Fault-Tolerant Placements of Relay Nodes in Mission Critical Wireless Networks |
Type |
Journal Article |
| Year |
2020 |
Publication |
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Abbreviated Journal |
Fundamenta Informaticae |
| Volume |
174 |
Issue |
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Pages |
229-258 |
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| Abstract |
In critical infrastructures like airports, much care has to be devoted in protecting radio communication networks from external electromagnetic interference. Protection of such mission-critical radio communication networks is usually tackled by exploiting radiogoniometers: at least three suitably deployed radiogoniometers, and a gateway gathering information from them, permit to monitor and localise sources of electromagnetic emissions that are not supposed to be present in the monitored area. Typically, radiogoniometers are connected to the gateway through relay nodes . As a result, some degree of fault-tolerance for the network of relay nodes is essential in order to offer a reliable monitoring. On the other hand, deployment of relay nodes is typically quite expensive. As a result, we have two conflicting requirements: minimise costs while guaranteeing a given fault-tolerance. In this paper, we address the problem of computing a deployment for relay nodes that minimises the overall cost while at the same time guaranteeing proper working of the network even when some of the relay nodes (up to a given maximum number) become faulty (fault-tolerance ). We show that, by means of a computation-intensive pre-processing on a HPC infrastructure, the above optimisation problem can be encoded as a 0/1 Linear Program, becoming suitable to be approached with standard Artificial Intelligence reasoners like MILP, PB-SAT, and SMT/OMT solvers. Our problem formulation enables us to present experimental results comparing the performance of these three solving technologies on a real case study of a relay node network deployment in areas of the Leonardo da Vinci Airport in Rome, Italy. |
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IOS Press |
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1875-8681 |
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MCLab @ davi @ |
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188 |
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Fischer, S.; Ehrig, R.; Schaefer, S.; Tronci, E.; Mancini, T.; Egli, M.; Ille, F.; Krueger, T.H.C.; Leeners, B.; Roeblitz, S. |
| Title |
Mathematical Modeling and Simulation Provides Evidence for New Strategies of Ovarian Stimulation |
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Journal Article |
| Year |
2021 |
Publication |
Frontiers in Endocrinology |
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12 |
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117 |
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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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1664-2392 |
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MCLab @ davi @ ref10.3389/fendo.2021.613048 |
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189 |
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| Author |
Alimguzhin, V.; Mari, F.; Melatti, I.; Salvo, I.; Tronci, E. |
| Title |
Linearising Discrete Time Hybrid Systems |
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Journal Article |
| Year |
2017 |
Publication |
IEEE Transactions on Automatic Control |
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62 |
Issue |
10 |
Pages |
5357-5364 |
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Model Based Design approaches for embedded systems aim at generating correct-by-construction control software, guaranteeing that the closed loop system (controller and plant) meets given system level formal specifications. This technical note addresses control synthesis for safety and reachability properties of possibly non-linear discrete time hybrid systems. By means of syntactical transformations that require non-linear terms to be Lipschitz continuous functions, we over-approximate non-linear dynamics with a linear system whose controllers are guaranteed to be controllers of the original system. We evaluate performance of our approach on meaningful control synthesis benchmarks, also comparing it to a state-of-the-art tool. |
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0018-9286 |
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Sapienza @ mari @ ref7902199 |
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164 |
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Melatti, I.; Mari, F.; Mancini, T.; Prodanovic, M.; Tronci, E. |
| Title |
A Two-Layer Near-Optimal Strategy for Substation Constraint Management via Home Batteries |
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Journal Article |
| Year |
2021 |
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IEEE Transactions on Industrial Electronics |
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1-1 |
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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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To appear |
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MCLab @ davi @ ref9513535 |
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190 |
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Mancini, T.; Melatti, I.; Tronci, E. |
| Title |
Any-horizon uniform random sampling and enumeration of constrained scenarios for simulation-based formal verification |
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Journal Article |
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2021 |
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IEEE Transactions on Software Engineering |
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1-1 |
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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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1939-3520 |
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To appear |
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MCLab @ davi @ ref9527998 |
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191 |
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Mancini, T.; Tronci, E.; Scialanca, A.; Lanciotti, F.; Finzi, A.; Guarneri, R.; Di Pompeo, S. |
| Title |
Optimal Fault-Tolerant Placement of Relay Nodes in a Mission Critical Wireless Network |
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Conference Article |
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2018 |
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25th RCRA International Workshop on “Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion” (RCRA 2018) |
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MCLab @ davi @ |
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174 |
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Mancini, T.; Mari, F.; Massini, A.; Melatti, I.; Salvo, I.; Sinisi, S.; Tronci, E.; Ehrig, R.; Röblitz, S.; Leeners, B. |
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Computing Personalised Treatments through In Silico Clinical Trials. A Case Study on Downregulation in Assisted Reproduction |
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2018 |
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25th RCRA International Workshop on “Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion” (RCRA 2018) |
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MCLab @ davi @ |
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175 |
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Driouich, Y.; Parente, M.; Tronci, E. |
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Model Checking Cyber-Physical Energy Systems |
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2018 |
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Proceedings of 2017 International Renewable and Sustainable Energy Conference, IRSEC 2017 |
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Institute of Electrical and Electronics Engineers Inc. |
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MCLab @ davi @ Driouich2018 |
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177 |
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Mancini, T.; Mari, F.; Melatti, I.; Salvo, I.; Tronci, E.; Gruber, J.; Hayes, B.; Prodanovic, M.; Elmegaard, L. |
| Title |
Parallel Statistical Model Checking for Safety Verification in Smart Grids |
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Conference Article |
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2018 |
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2018 IEEE International Conference on Communications, Control, and Computing Technologies for Smart Grids (SmartGridComm) |
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1-6 |
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MCLab @ davi @ mancini-etal:2018:smartgridcomm |
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