Big Code Applications and Approaches

The availability of a huge amount of source code from code archives and open-source projects opens up the possibility to merge machine learning, programming languages, and software engineering research fields. This area is often referred to as Big Code where programming languages are treated instead of natural languages while different features and patterns of code can be exploited to perform many useful tasks and build supportive tools. Among all the possible applications which can be developed within the area of Big Code, the work presented in this research thesis mainly focuses on two particular tasks: the Programming Language Identification (PLI) and the Software Defect Prediction (SDP) for source codes. Programming language identification is commonly needed in program comprehension and it is usually performed directly by developers. However, when it comes at big scales, such as in widely used archives (GitHub, Software Heritage), automation of this task is desirable. To accomplish this aim, the problem is analyzed from different points of view (text and image-based learning approaches) and different models are created paying particular attention to their scalability. Software defect prediction is a fundamental step in software development for improving quality and assuring the reliability of software products. In the past, defects were searched by manual inspection or using automatic static and dynamic analyzers. Now, the automation of this task can be tackled using learning approaches that can speed up and improve related procedures. Here, two models have been built and analyzed to detect some of the commonest bugs and errors at different code granularity levels (file and method levels). Exploited data and models’ architectures are analyzed and described in detail. Quantitative and qualitative results are reported for both PLI and SDP tasks while differences and similarities concerning other related works are discussed.

Automatic code generation: from process algebraic architectural descriptions to multithreaded java programs

Process algebraic architectural description languages provide a formal means for modeling software systems and assessing their properties. In order to bridge the gap between system modeling and system im- plementation, in this thesis an approach is proposed for automatically generating multithreaded object-oriented code from process algebraic architectural descriptions, in a way that preserves – under certain assumptions – the properties proved at the architectural level. The approach is divided into three phases, which are illustrated by means of a running example based on an audio processing system. First, we develop an architecture-driven technique for thread coordination management, which is completely automated through a suitable package. Second, we address the translation of the algebraically-specified behavior of the individual software units into thread templates, which will have to be filled in by the software developer according to certain guidelines. Third, we discuss performance issues related to the suitability of synthesizing monitors rather than threads from software unit descriptions that satisfy specific constraints. In addition to the running example, we present two case studies about a video animation repainting system and the implementation of a leader election algorithm, in order to summarize the whole approach. The outcome of this thesis is the implementation of the proposed approach in a translator called PADL2Java and its integration in the architecture-centric verification tool TwoTowers.

Interactive theorem provers: issues faced as a user and tackled as a developer

Interactive theorem provers (ITP for short) are tools whose final aim is to certify proofs written by human beings. To reach that objective they have to fill the gap between the high level language used by humans for communicating and reasoning about mathematics and the lower level language that a machine is able to “understand” and process. The user perceives this gap in terms of missing features or inefficiencies. The developer tries to accommodate the user requests without increasing the already high complexity of these applications. We believe that satisfactory solutions can only come from a strong synergy between users and developers. We devoted most part of our PHD designing and developing the Matita interactive theorem prover. The software was born in the computer science department of the University of Bologna as the result of composing together all the technologies developed by the HELM team (to which we belong) for the MoWGLI project. The MoWGLI project aimed at giving accessibility through the web to the libraries of formalised mathematics of various interactive theorem provers, taking Coq as the main test case. The motivations for giving life to a new ITP are: • study the architecture of these tools, with the aim of understanding the source of their complexity • exploit such a knowledge to experiment new solutions that, for backward compatibility reasons, would be hard (if not impossible) to test on a widely used system like Coq. Matita is based on the Curry-Howard isomorphism, adopting the Calculus of Inductive Constructions (CIC) as its logical foundation. Proof objects are thus, at some extent, compatible with the ones produced with the Coq ITP, that is itself able to import and process the ones generated using Matita. Although the systems have a lot in common, they share no code at all, and even most of the algorithmic solutions are different. The thesis is composed of two parts where we respectively describe our experience as a user and a developer of interactive provers. In particular, the first part is based on two different formalisation experiences: • our internship in the Mathematical Components team (INRIA), that is formalising the finite group theory required to attack the Feit Thompson Theorem. To tackle this result, giving an effective classification of finite groups of odd order, the team adopts the SSReflect Coq extension, developed by Georges Gonthier for the proof of the four colours theorem. • our collaboration at the D.A.M.A. Project, whose goal is the formalisation of abstract measure theory in Matita leading to a constructive proof of Lebesgue’s Dominated Convergence Theorem. The most notable issues we faced, analysed in this part of the thesis, are the following: the difficulties arising when using “black box” automation in large formalisations; the impossibility for a user (especially a newcomer) to master the context of a library of already formalised results; the uncomfortable big step execution of proof commands historically adopted in ITPs; the difficult encoding of mathematical structures with a notion of inheritance in a type theory without subtyping like CIC. In the second part of the manuscript many of these issues will be analysed with the looking glasses of an ITP developer, describing the solutions we adopted in the implementation of Matita to solve these problems: integrated searching facilities to assist the user in handling large libraries of formalised results; a small step execution semantic for proof commands; a flexible implementation of coercive subtyping allowing multiple inheritance with shared substructures; automatic tactics, integrated with the searching facilities, that generates proof commands (and not only proof objects, usually kept hidden to the user) one of which specifically designed to be user driven.

Architectures and design patterns for functional design of logic control and diagnostics in industrial automation

Recently in most of the industrial automation process an ever increasing degree of automation has been observed. This increasing is motivated by the higher requirement of systems with great performance in terms of quality of products/services generated, productivity, efficiency and low costs in the design, realization and maintenance. This trend in the growth of complex automation systems is rapidly spreading over automated manufacturing systems (AMS), where the integration of the mechanical and electronic technology, typical of the Mechatronics, is merging with other technologies such as Informatics and the communication networks. An AMS is a very complex system that can be thought constituted by a set of flexible working stations, one or more transportation systems. To understand how this machine are important in our society let considerate that every day most of us use bottles of water or soda, buy product in box like food or cigarets and so on. Another important consideration from its complexity derive from the fact that the the consortium of machine producers has estimated around 350 types of manufacturing machine. A large number of manufacturing machine industry are presented in Italy and notably packaging machine industry,in particular a great concentration of this kind of industry is located in Bologna area; for this reason the Bologna area is called “packaging valley”. Usually, the various parts of the AMS interact among them in a concurrent and asynchronous way, and coordinate the parts of the machine to obtain a desiderated overall behaviour is an hard task. Often, this is the case in large scale systems, organized in a modular and distributed manner. Even if the success of a modern AMS from a functional and behavioural point of view is still to attribute to the design choices operated in the definition of the mechanical structure and electrical electronic architecture, the system that governs the control of the plant is becoming crucial, because of the large number of duties associated to it. Apart from the activity inherent to the automation of themachine cycles, the supervisory system is called to perform other main functions such as: emulating the behaviour of traditional mechanical members thus allowing a drastic constructive simplification of the machine and a crucial functional flexibility; dynamically adapting the control strategies according to the different productive needs and to the different operational scenarios; obtaining a high quality of the final product through the verification of the correctness of the processing; addressing the operator devoted to themachine to promptly and carefully take the actions devoted to establish or restore the optimal operating conditions; managing in real time information on diagnostics, as a support of the maintenance operations of the machine. The kind of facilities that designers can directly find on themarket, in terms of software component libraries provides in fact an adequate support as regard the implementation of either top-level or bottom-level functionalities, typically pertaining to the domains of user-friendly HMIs, closed-loop regulation and motion control, fieldbus-based interconnection of remote smart devices. What is still lacking is a reference framework comprising a comprehensive set of highly reusable logic control components that, focussing on the cross-cutting functionalities characterizing the automation domain, may help the designers in the process of modelling and structuring their applications according to the specific needs. Historically, the design and verification process for complex automated industrial systems is performed in empirical way, without a clear distinction between functional and technological-implementation concepts and without a systematic method to organically deal with the complete system. Traditionally, in the field of analog and digital control design and verification through formal and simulation tools have been adopted since a long time ago, at least for multivariable and/or nonlinear controllers for complex time-driven dynamics as in the fields of vehicles, aircrafts, robots, electric drives and complex power electronics equipments. Moving to the field of logic control, typical for industrial manufacturing automation, the design and verification process is approached in a completely different way, usually very “unstructured”. No clear distinction between functions and implementations, between functional architectures and technological architectures and platforms is considered. Probably this difference is due to the different “dynamical framework”of logic control with respect to analog/digital control. As a matter of facts, in logic control discrete-events dynamics replace time-driven dynamics; hence most of the formal and mathematical tools of analog/digital control cannot be directly migrated to logic control to enlighten the distinction between functions and implementations. In addition, in the common view of application technicians, logic control design is strictly connected to the adopted implementation technology (relays in the past, software nowadays), leading again to a deep confusion among functional view and technological view. In Industrial automation software engineering, concepts as modularity, encapsulation, composability and reusability are strongly emphasized and profitably realized in the so-calledobject-oriented methodologies. Industrial automation is receiving lately this approach, as testified by some IEC standards IEC 611313, IEC 61499 which have been considered in commercial products only recently. On the other hand, in the scientific and technical literature many contributions have been already proposed to establish a suitable modelling framework for industrial automation. During last years it was possible to note a considerable growth in the exploitation of innovative concepts and technologies from ICT world in industrial automation systems. For what concerns the logic control design, Model Based Design (MBD) is being imported in industrial automation from software engineering field. Another key-point in industrial automated systems is the growth of requirements in terms of availability, reliability and safety for technological systems. In other words, the control system should not only deal with the nominal behaviour, but should also deal with other important duties, such as diagnosis and faults isolations, recovery and safety management. Indeed, together with high performance, in complex systems fault occurrences increase. This is a consequence of the fact that, as it typically occurs in reliable mechatronic systems, in complex systems such as AMS, together with reliable mechanical elements, an increasing number of electronic devices are also present, that are more vulnerable by their own nature. The diagnosis problem and the faults isolation in a generic dynamical system consists in the design of an elaboration unit that, appropriately processing the inputs and outputs of the dynamical system, is also capable of detecting incipient faults on the plant devices, reconfiguring the control system so as to guarantee satisfactory performance. The designer should be able to formally verify the product, certifying that, in its final implementation, it will perform itsrequired function guarantying the desired level of reliability and safety; the next step is that of preventing faults and eventually reconfiguring the control system so that faults are tolerated. On this topic an important improvement to formal verification of logic control, fault diagnosis and fault tolerant control results derive from Discrete Event Systems theory. The aimof this work is to define a design pattern and a control architecture to help the designer of control logic in industrial automated systems. The work starts with a brief discussion on main characteristics and description of industrial automated systems on Chapter 1. In Chapter 2 a survey on the state of the software engineering paradigm applied to industrial automation is discussed. Chapter 3 presentes a architecture for industrial automated systems based on the new concept of Generalized Actuator showing its benefits, while in Chapter 4 this architecture is refined using a novel entity, the Generalized Device in order to have a better reusability and modularity of the control logic. In Chapter 5 a new approach will be present based on Discrete Event Systems for the problemof software formal verification and an active fault tolerant control architecture using online diagnostic. Finally conclusive remarks and some ideas on new directions to explore are given. In Appendix A are briefly reported some concepts and results about Discrete Event Systems which should help the reader in understanding some crucial points in chapter 5; while in Appendix B an overview on the experimental testbed of the Laboratory of Automation of University of Bologna, is reported to validated the approach presented in chapter 3, chapter 4 and chapter 5. In Appendix C some components model used in chapter 5 for formal verification are reported.

Sviluppo di un'applicazione bioinformatica per la gestione dei dati di antibiotico sensibilità di isolati clinici

Il problema dell'antibiotico-resistenza è un problema di sanità pubblica per affrontare il quale è necessario un sistema di sorveglianza basato sulla raccolta e l'analisi dei dati epidemiologici di laboratorio. Il progetto di dottorato è consistito nello sviluppo di una applicazione web per la gestione di tali dati di antibiotico sensibilità di isolati clinici utilizzabile a livello di ospedale. Si è creata una piattaforma web associata a un database relazionale per avere un’applicazione dinamica che potesse essere aggiornata facilmente inserendo nuovi dati senza dover manualmente modificare le pagine HTML che compongono l’applicazione stessa. E’ stato utilizzato il database open-source MySQL in quanto presenta numerosi vantaggi: estremamente stabile, elevate prestazioni, supportato da una grande comunità online ed inoltre gratuito. Il contenuto dinamico dell’applicazione web deve essere generato da un linguaggio di programmazione tipo “scripting” che automatizzi operazioni di inserimento, modifica, cancellazione, visualizzazione di larghe quantità di dati. E’ stato scelto il PHP, linguaggio open-source sviluppato appositamente per la realizzazione di pagine web dinamiche, perfettamente utilizzabile con il database MySQL. E’ stata definita l’architettura del database creando le tabelle contenenti i dati e le relazioni tra di esse: le anagrafiche, i dati relativi ai campioni, microrganismi isolati e agli antibiogrammi con le categorie interpretative relative al dato antibiotico. Definite tabelle e relazioni del database è stato scritto il codice associato alle funzioni principali: inserimento manuale di antibiogrammi, importazione di antibiogrammi multipli provenienti da file esportati da strumenti automatizzati, modifica/eliminazione degli antibiogrammi precedenti inseriti nel sistema, analisi dei dati presenti nel database con tendenze e andamenti relativi alla prevalenza di specie microbiche e alla chemioresistenza degli stessi, corredate da grafici. Lo sviluppo ha incluso continui test delle funzioni via via implementate usando reali dati clinici e sono stati introdotti appositi controlli e l’introduzione di una semplice e pulita veste grafica.

Analysis of optimal control problems for the incompressible MHD equations and implementation in a finite element multiphysics code

This thesis deals with the study of optimal control problems for the incompressible Magnetohydrodynamics (MHD) equations. Particular attention to these problems arises from several applications in science and engineering, such as fission nuclear reactors with liquid metal coolant and aluminum casting in metallurgy. In such applications it is of great interest to achieve the control on the fluid state variables through the action of the magnetic Lorentz force. In this thesis we investigate a class of boundary optimal control problems, in which the flow is controlled through the boundary conditions of the magnetic field. Due to their complexity, these problems present various challenges in the definition of an adequate solution approach, both from a theoretical and from a computational point of view. In this thesis we propose a new boundary control approach, based on lifting functions of the boundary conditions, which yields both theoretical and numerical advantages. With the introduction of lifting functions, boundary control problems can be formulated as extended distributed problems. We consider a systematic mathematical formulation of these problems in terms of the minimization of a cost functional constrained by the MHD equations. The existence of a solution to the flow equations and to the optimal control problem are shown. The Lagrange multiplier technique is used to derive an optimality system from which candidate solutions for the control problem can be obtained. In order to achieve the numerical solution of this system, a finite element approximation is considered for the discretization together with an appropriate gradient-type algorithm. A finite element object-oriented library has been developed to obtain a parallel and multigrid computational implementation of the optimality system based on a multiphysics approach. Numerical results of two- and three-dimensional computations show that a possible minimum for the control problem can be computed in a robust and accurate manner.

Genome characterization through a mathematical model of the genetic code: an analysis of the whole chromosome 1 of A. thaliana

The objective of this work is to characterize the genome of the chromosome 1 of A.thaliana, a small flowering plants used as a model organism in studies of biology and genetics, on the basis of a recent mathematical model of the genetic code. I analyze and compare different portions of the genome: genes, exons, coding sequences (CDS), introns, long introns, intergenes, untranslated regions (UTR) and regulatory sequences. In order to accomplish the task, I transformed nucleotide sequences into binary sequences based on the definition of the three different dichotomic classes. The descriptive analysis of binary strings indicate the presence of regularities in each portion of the genome considered. In particular, there are remarkable differences between coding sequences (CDS and exons) and non-coding sequences, suggesting that the frame is important only for coding sequences and that dichotomic classes can be useful to recognize them. Then, I assessed the existence of short-range dependence between binary sequences computed on the basis of the different dichotomic classes. I used three different measures of dependence: the well-known chi-squared test and two indices derived from the concept of entropy i.e. Mutual Information (MI) and Sρ, a normalized version of the “Bhattacharya Hellinger Matusita distance”. The results show that there is a significant short-range dependence structure only for the coding sequences whose existence is a clue of an underlying error detection and correction mechanism. No doubt, further studies are needed in order to assess how the information carried by dichotomic classes could discriminate between coding and noncoding sequence and, therefore, contribute to unveil the role of the mathematical structure in error detection and correction mechanisms. Still, I have shown the potential of the approach presented for understanding the management of genetic information.

Validation of the CFD code NEPTUNE for a full scale simulator for decay heat removal systems with in-pool heat exchangers

In the present work, a multi physics simulation of an innovative safety system for light water nuclear reactor is performed, with the aim to increase the reliability of its main decay heat removal system. The system studied, denoted by the acronym PERSEO (in Pool Energy Removal System for Emergency Operation) is able to remove the decay power from the primary side of the light water nuclear reactor through a heat suppression pool. The experimental facility, located at SIET laboratories (PIACENZA), is an evolution of the Thermal Valve concept where the triggering valve is installed liquid side, on a line connecting two pools at the bottom. During the normal operation, the valve is closed, while in emergency conditions it opens, the heat exchanger is flooded with consequent heat transfer from the primary side to the pool side. In order to verify the correct system behavior during long term accidental transient, two main experimental PERSEO tests are analyzed. For this purpose, a coupling between the mono dimensional system code CATHARE, which reproduces the system scale behavior, with a three-dimensional CFD code NEPTUNE CFD, allowing a full investigation of the pools and the injector, is implemented. The coupling between the two codes is realized through the boundary conditions. In a first analysis, the facility is simulated by the system code CATHARE V2.5 to validate the results with the experimental data. The comparison of the numerical results obtained shows a different void distribution during the boiling conditions inside the heat suppression pool for the two cases of single nodalization and three volume nodalization scheme of the pool. Finaly, to improve the investigation capability of the void distribution inside the pool and the temperature stratification phenomena below the injector, a two and three dimensional CFD models with a simplified geometry of the system are adopted.

Code synchronization and interference management techniques for satellite navigation and communications

This thesis collects the outcomes of a Ph.D. course in Telecommunications engineering and it is focused on enabling techniques for Spread Spectrum (SS) navigation and communication satellite systems. It provides innovations for both interference management and code synchronization techniques. These two aspects are critical for modern navigation and communication systems and constitute the common denominator of the work. The thesis is organized in two parts: the former deals with interference management. We have proposed a novel technique for the enhancement of the sensitivity level of an advanced interference detection and localization system operating in the Global Navigation Satellite System (GNSS) bands, which allows the identification of interfering signals received with power even lower than the GNSS signals. Moreover, we have introduced an effective cancellation technique for signals transmitted by jammers, exploiting their repetitive characteristics, which strongly reduces the interference level at the receiver. The second part, deals with code synchronization. More in detail, we have designed the code synchronization circuit for a Telemetry, Tracking and Control system operating during the Launch and Early Orbit Phase; the proposed solution allows to cope with the very large frequency uncertainty and dynamics characterizing this scenario, and performs the estimation of the code epoch, of the carrier frequency and of the carrier frequency variation rate. Furthermore, considering a generic pair of circuits performing code acquisition, we have proposed a comprehensive framework for the design and the analysis of the optimal cooperation procedure, which minimizes the time required to accomplish synchronization. The study results particularly interesting since it enables the reduction of the code acquisition time without increasing the computational complexity. Finally, considering a network of collaborating navigation receivers, we have proposed an innovative cooperative code acquisition scheme, which allows exploit the shared code epoch information between neighbor nodes, according to the Peer-to-Peer paradigm.