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Author |
Sinisi, S.; Alimguzhin, V.; Mancini, T.; Tronci, E.; Mari, F.; Leeners, B. |
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Title |
Optimal Personalised Treatment Computation through In Silico Clinical Trials on Patient Digital Twins |
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Journal Article |
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Year |
2020 |
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Abbreviated Journal |
Fundamenta Informaticae |
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Volume |
174 |
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Pages |
283-310 |
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Keywords |
Artificial Intelligence; Virtual Physiological Human; In Silico Clinical Trials; Simulation; Personalised Medicine; In Silico Treatment Optimisation |
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Abstract |
In Silico Clinical Trials (ISCT), i.e. clinical experimental campaigns carried out by means of computer simulations, hold the promise to decrease time and cost for the safety and efficacy assessment of pharmacological treatments, reduce the need for animal and human testing, and enable precision medicine. In this paper we present methods and an algorithm that, by means of extensive computer simulation-based experimental campaigns (ISCT) guided by intelligent search, optimise a pharmacological treatment for an individual patient (precision medicine ). We show the effectiveness of our approach on a case study involving a real pharmacological treatment, namely the downregulation phase of a complex clinical protocol for assisted reproduction in humans. |
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IOS Press |
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1875-8681 |
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MCLab @ davi @ |
Serial |
187 |
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Author |
Chen, Q.M.; Finzi, A.; Mancini, T.; Melatti, I.; Tronci, E. |
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Title |
MILP, Pseudo-Boolean, and OMT Solvers for Optimal Fault-Tolerant Placements of Relay Nodes in Mission Critical Wireless Networks |
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Journal Article |
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Year |
2020 |
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Abbreviated Journal |
Fundamenta Informaticae |
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Volume |
174 |
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Pages |
229-258 |
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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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Author |
Mancini, T.; Melatti, I.; Tronci, E. |
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Title |
Any-horizon uniform random sampling and enumeration of constrained scenarios for simulation-based formal verification |
Type |
Journal Article |
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Year |
2021 |
Publication |
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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ISSN |
1939-3520 |
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To appear |
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Call Number |
MCLab @ davi @ ref9527998 |
Serial |
191 |
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Author |
Mari, Federico; Melatti, Igor; Salvo, Ivano; Tronci, Enrico |
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Title |
Synthesizing Control Software from Boolean Relations |
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Journal Article |
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Year |
2012 |
Publication |
International Journal on Advances in Software |
Abbreviated Journal |
Intern. Journal on Advances in SW |
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Volume |
vol. 5, nr 3&4 |
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Pages |
212-223 |
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Keywords |
Control Software Synthesis; Embedded Systems; Model Checking |
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Abstract |
Many software as well digital hardware automatic
synthesis methods define the set of
implementations meeting the given system
specifications with a boolean relation K. In
such a context a fundamental step in the software
(hardware) synthesis process is finding effective
solutions to the functional equation defined by
K. This entails finding a (set of) boolean
function(s) F (typically represented using
OBDDs, Ordered Binary Decision Diagrams)
such that: 1) for all x for which K is
satisfiable, K(x, F(x)) = 1 holds; 2) the
implementation of F is efficient with respect
to given implementation parameters such as code
size or execution time. While this problem has
been widely studied in digital hardware synthesis,
little has been done in a software synthesis
context. Unfortunately, the approaches developed
for hardware synthesis cannot be directly used in
a software context. This motivates investigation
of effective methods to solve the above problem
when F has to be implemented with software. In
this paper, we present an algorithm that, from an
OBDD representation for K, generates a C code
implementation for F that has the same size as
the OBDD for F and a worst case execution time
linear in nr, being n = |x| the number of
input arguments for functions in F and r the
number of functions in F. Moreover, a formal
proof of the proposed algorithm correctness is
also shown. Finally, we present experimental
results showing effectiveness of the proposed
algorithm. |
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Publisher |
IARIA |
Place of Publication |
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Editor |
Luigi Lavazza |
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ISSN |
1942-2628 |
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Approved |
yes |
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Call Number |
Sapienza @ melatti @ |
Serial |
108 |
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Author |
Mari, Federico; Melatti, Igor; Salvo, Ivano; Tronci, Enrico |
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Title |
Linear Constraints and Guarded Predicates as a Modeling Language for Discrete Time Hybrid Systems |
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Journal Article |
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Year |
2013 |
Publication |
International Journal on Advances in Software |
Abbreviated Journal |
Intern. Journal on Advances in SW |
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Volume |
vol. 6, nr 1&2 |
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155-169 |
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Keywords |
Model-based software design; Linear predicates; Hybrid systems |
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Abstract |
Model based design is particularly appealing in
software based control systems (e.g., embedded
software) design, since in such a case system
level specifications are much easier to define
than the control software behavior itself. In
turn, model based design of embedded systems
requires modeling both continuous subsystems
(typically, the plant) as well as discrete
subsystems (the controller). This is typically
done using hybrid systems. Mixed Integer Linear
Programming (MILP) based abstraction techniques
have been successfully applied to automatically
synthesize correct-by-construction control
software for discrete time linear hybrid systems,
where plant dynamics is modeled as a linear
predicate over state, input, and next state
variables. Unfortunately, MILP solvers require
such linear predicates to be conjunctions of
linear constraints, which is not a natural way of
modeling hybrid systems. In this paper we show
that, under the hypothesis that each variable
ranges over a bounded interval, any linear
predicate built upon conjunction and disjunction
of linear constraints can be automatically
translated into an equivalent conjunctive
predicate. Since variable bounds play a key role
in this translation, our algorithm includes a
procedure to compute all implicit variable bounds
of the given linear predicate. Furthermore, we
show that a particular form of linear predicates,
namely guarded predicates, are a natural and
powerful language to succinctly model discrete
time linear hybrid systems dynamics. Finally, we
experimentally show the feasibility of our
approach on an important and challenging case
study taken from the literature, namely the
multi-input Buck DC-DC Converter. As an example,
the guarded predicate that models (with 57
constraints) a 6-inputs Buck DC-DC Converter is
translated in a conjunctive predicate (with 102
linear constraints) in about 40 minutes. |
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Publisher |
IARIA |
Place of Publication |
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Editor |
Luigi Lavazza |
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ISSN |
1942-2628 |
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Approved |
yes |
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Call Number |
Sapienza @ melatti @ |
Serial |
115 |
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Author |
Mancini, T.; Mari, F.; Massini, A.; Melatti, I.; Tronci, E. |
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Title |
On Checking Equivalence of Simulation Scripts |
Type |
Journal Article |
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Year |
2021 |
Publication |
Journal of Logical and Algebraic Methods in Programming |
Abbreviated Journal |
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Issue |
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Pages |
100640 |
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Keywords |
Formal verification, Simulation based formal verification, Formal Verification of cyber-physical systems, System-level formal verification |
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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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2352-2208 |
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no |
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Call Number |
MCLab @ davi @ Mancini2021100640 |
Serial |
183 |
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Author |
Della Penna, Giuseppe; Intrigila, Benedetto; Tronci, Enrico; Venturini Zilli, Marisa |
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Title |
Exploiting Transition Locality in the Disk Based Mur$\varphi$ Verifier |
Type |
Conference Article |
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Year |
2002 |
Publication |
4th International Conference on Formal Methods in Computer-Aided Design (FMCAD) |
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Pages |
202-219 |
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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$\varphi$. |
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Springer |
Place of Publication |
Portland, OR, USA |
Editor |
Aagaard, M.; O'Leary, J.W. |
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Lecture Notes in Computer Science |
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Series Volume |
2517 |
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ISSN |
3-540-00116-6 |
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yes |
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Call Number |
Sapienza @ mari @ fmcad02 |
Serial |
41 |
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Author |
Della Penna, Giuseppe; Intrigila, Benedetto; Melatti, Igor; Minichino, Michele; Ciancamerla, Ester; Parisse, Andrea; Tronci, Enrico; Venturini Zilli, Marisa |
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Title |
Automatic Verification of a Turbogas Control System with the Mur$\varphi$ Verifier |
Type |
Conference Article |
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Year |
2003 |
Publication |
Hybrid Systems: Computation and Control, 6th International Workshop, HSCC 2003 Prague, Czech Republic, April 3-5, 2003, Proceedings |
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Pages |
141-155 |
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Automatic analysis of Hybrid Systems poses formidable challenges both from a modeling as well as from a verification point of view. We present a case study on automatic verification of a Turbogas Control System (TCS) using an extended version of the Mur$\varphi$ verifier. TCS is the heart of ICARO, a 2MW Co-generative Electric Power Plant. For large hybrid systems, as TCS is, the modeling effort accounts for a significant part of the whole verification activity. In order to ease our modeling effort we extended the Mur$\varphi$ verifier by importing the C language long double type (finite precision real numbers) into it. We give experimental results on running our extended Mur$\varphi$ on our TCS model. For example using Mur$\varphi$ we were able to compute an admissible range of values for the variation speed of the user demand of electric power to the turbogas. |
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Springer |
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Editor |
Maler, O.; Pnueli, A. |
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Lecture Notes in Computer Science |
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Series Volume |
2623 |
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3-540-00913-2 |
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yes |
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Call Number |
Sapienza @ mari @ Dimmcptz03 |
Serial |
88 |
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Author |
Della Penna, Giuseppe; Intrigila, Benedetto; Melatti, Igor; Tronci, Enrico; Venturini Zilli, Marisa |
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Title |
Finite Horizon Analysis of Stochastic Systems with the Mur$\varphi$ Verifier |
Type |
Conference Article |
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Year |
2003 |
Publication |
Theoretical Computer Science, 8th Italian Conference, ICTCS 2003, Bertinoro, Italy, October 13-15, 2003, Proceedings |
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58-71 |
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Many reactive systems are actually Stochastic Processes. Automatic analysis of such systems is usually very difficult thus typically one simplifies the analysis task by using simulation or by working on a simplified model (e.g. a Markov Chain). We present a Finite Horizon Probabilistic Model Checking approach which essentially can handle the same class of stochastic processes of a typical simulator. This yields easy modeling of the system to be analyzed together with formal verification capabilities. Our approach is based on a suitable disk based extension of the Mur$\varphi$ verifier. Moreover we present experimental results showing effectiveness of our approach. |
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Springer |
Place of Publication |
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Editor |
Blundo, C.; Laneve, C. |
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Series Editor |
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Series Title |
Lecture Notes in Computer Science |
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Series Volume |
2841 |
Series Issue |
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Edition |
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ISSN |
3-540-20216-1 |
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Approved |
yes |
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Call Number |
Sapienza @ mari @ DIMTZ03c |
Serial |
90 |
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Author |
Della Penna, Giuseppe; Intrigila, Benedetto; Melatti, Igor; Tronci, Enrico; Venturini Zilli, Marisa |
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Title |
Finite Horizon Analysis of Markov Chains with the Mur$\varphi$ Verifier |
Type |
Conference Article |
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Year |
2003 |
Publication |
Correct Hardware Design and Verification Methods, 12th IFIP WG 10.5 Advanced Research Working Conference, CHARME 2003, L'Aquila, Italy, October 21-24, 2003, Proceedings |
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394-409 |
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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 FHP-Mur$\varphi$ (Finite Horizon Probabilistic Mur$\varphi$). We present experimental results comparing FHP-Mur$\varphi$ with (a finite horizon subset of) PRISM, a state-of-the-art symbolic model checker for Markov Chains. Our experimental results show that FHP-Mur$\varphi$ can handle systems that are out of reach for PRISM, namely those involving arithmetic operations on the state variables (e.g. hybrid systems). |
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Springer |
Place of Publication |
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Editor |
Geist, D.; Tronci, E. |
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Lecture Notes in Computer Science |
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Series Volume |
2860 |
Series Issue |
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ISSN |
3-540-20363-X |
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Approved |
yes |
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Call Number |
Sapienza @ mari @ Dimtz03 |
Serial |
84 |
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