Pattern-based segmentation of digital documents: model and implementation

This thesis proposes a new document model, according to which any document can be segmented in some independent components and transformed in a pattern-based projection, that only uses a very small set of objects and composition rules. The point is that such a normalized document expresses the same fundamental information of the original one, in a simple, clear and unambiguous way. The central part of my work consists of discussing that model, investigating how a digital document can be segmented, and how a segmented version can be used to implement advanced tools of conversion. I present seven patterns which are versatile enough to capture the most relevant documents’ structures, and whose minimality and rigour make that implementation possible. The abstract model is then instantiated into an actual markup language, called IML. IML is a general and extensible language, which basically adopts an XHTML syntax, able to capture a posteriori the only content of a digital document. It is compared with other languages and proposals, in order to clarify its role and objectives. Finally, I present some systems built upon these ideas. These applications are evaluated in terms of users’ advantages, workflow improvements and impact over the overall quality of the output. In particular, they cover heterogeneous content management processes: from web editing to collaboration (IsaWiki and WikiFactory), from e-learning (IsaLearning) to professional printing (IsaPress).

Crashworthiness and composite materials: development of an experimental test method for the energy absorption determination and implementation of the relative numerical model

In this PhD thesis the crashworthiness topic is studied with the perspective of the development of a small-scale experimental test able to characterize a material in terms of energy absorption. The material properties obtained are then used to validate a nu- merical model of the experimental test itself. Consequently, the numerical model, calibrated on the specific ma- terial, can be extended to more complex structures and used to simulate their energy absorption behavior. The experimental activity started at University of Washington in Seattle, WA (USA) and continued at Second Faculty of Engi- neering, University of Bologna, Forl`ı (Italy), where the numerical model for the simulation of the experimental test was implemented and optimized.

Model and control of tendon actuated robots

The use of tendons for the transmission of the forces and the movements in robotic devices has been investigated from several researchers all over the world. The interest in this kind of actuation modality is based on the possibility of optimizing the position of the actuators with respect to the moving part of the robot, in the reduced weight, high reliability, simplicity in the mechanic design and, finally, in the reduced cost of the resulting kinematic chain. After a brief discussion about the benefits that the use of tendons can introduce in the motion control of a robotic device, the design and control aspects of the UB Hand 3 anthropomorphic robotic hand are presented. In particular, the tendon-sheaths transmission system adopted in the UB Hand 3 is analyzed and the problem of force control and friction compensation is taken into account. The implementation of a tendon based antagonistic actuated robotic arm is then investigated. With this kind of actuation modality, and by using transmission elements with nonlinear force/compression characteristic, it is possible to achieve simultaneous stiffness and position control, improving in this way the safety of the device during the operation in unknown environments and in the case of interaction with other robots or with humans. The problem of modeling and control of this type of robotic devices is then considered and the stability analysis of proposed controller is reported. At the end, some tools for the realtime simulation of dynamic systems are presented. This realtime simulation environment has been developed with the aim of improving the reliability of the realtime control applications both for rapid prototyping of controllers and as teaching tools for the automatic control courses.

Assimilation of Meteosat Second Generation (MSG) satellite data in a regional numerical weather prediction model using a one-dimensional variational approach

The quality of temperature and humidity retrievals from the infrared SEVIRI sensors on the geostationary Meteosat Second Generation (MSG) satellites is assessed by means of a one dimensional variational algorithm. The study is performed with the aim of improving the spatial and temporal resolution of available observations to feed analysis systems designed for high resolution regional scale numerical weather prediction (NWP) models. The non-hydrostatic forecast model COSMO (COnsortium for Small scale MOdelling) in the ARPA-SIM operational configuration is used to provide background fields. Only clear sky observations over sea are processed. An optimised 1D–VAR set-up comprising of the two water vapour and the three window channels is selected. It maximises the reduction of errors in the model backgrounds while ensuring ease of operational implementation through accurate bias correction procedures and correct radiative transfer simulations. The 1D–VAR retrieval quality is firstly quantified in relative terms employing statistics to estimate the reduction in the background model errors. Additionally the absolute retrieval accuracy is assessed comparing the analysis with independent radiosonde and satellite observations. The inclusion of satellite data brings a substantial reduction in the warm and dry biases present in the forecast model. Moreover it is shown that the retrieval profiles generated by the 1D–VAR are well correlated with the radiosonde measurements. Subsequently the 1D–VAR technique is applied to two three–dimensional case–studies: a false alarm case–study occurred in Friuli–Venezia–Giulia on the 8th of July 2004 and a heavy precipitation case occurred in Emilia–Romagna region between 9th and 12th of April 2005. The impact of satellite data for these two events is evaluated in terms of increments in the integrated water vapour and saturation water vapour over the column, in the 2 meters temperature and specific humidity and in the surface temperature. To improve the 1D–VAR technique a method to calculate flow–dependent model error covariance matrices is also assessed. The approach employs members from an ensemble forecast system generated by perturbing physical parameterisation schemes inside the model. The improved set–up applied to the case of 8th of July 2004 shows a substantial neutral impact.

Design and implementation of bioinformatics tools for large scale genome annotation

The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and cannot be accomplished only by in vitro analysis procedures resulting extremely expensive and time consuming when applied at a this large scale level. Thus, in silico methods need to be used to accomplish the task. The aim of this work was the implementation of predictive computational methods to allow a fast, reliable, and automated annotation of genomes and proteins starting from aminoacidic sequences. The first part of the work was focused on the implementation of a new machine learning based method for the prediction of the subcellular localization of soluble eukaryotic proteins. The method is called BaCelLo, and was developed in 2006. The main peculiarity of the method is to be independent from biases present in the training dataset, which causes the over‐prediction of the most represented examples in all the other available predictors developed so far. This important result was achieved by a modification, made by myself, to the standard Support Vector Machine (SVM) algorithm with the creation of the so called Balanced SVM. BaCelLo is able to predict the most important subcellular localizations in eukaryotic cells and three, kingdom‐specific, predictors were implemented. In two extensive comparisons, carried out in 2006 and 2008, BaCelLo reported to outperform all the currently available state‐of‐the‐art methods for this prediction task. BaCelLo was subsequently used to completely annotate 5 eukaryotic genomes, by integrating it in a pipeline of predictors developed at the Bologna Biocomputing group by Dr. Pier Luigi Martelli and Dr. Piero Fariselli. An online database, called eSLDB, was developed by integrating, for each aminoacidic sequence extracted from the genome, the predicted subcellular localization merged with experimental and similarity‐based annotations. In the second part of the work a new, machine learning based, method was implemented for the prediction of GPI‐anchored proteins. Basically the method is able to efficiently predict from the raw aminoacidic sequence both the presence of the GPI‐anchor (by means of an SVM), and the position in the sequence of the post‐translational modification event, the so called ω‐site (by means of an Hidden Markov Model (HMM)). The method is called GPIPE and reported to greatly enhance the prediction performances of GPI‐anchored proteins over all the previously developed methods. GPIPE was able to predict up to 88% of the experimentally annotated GPI‐anchored proteins by maintaining a rate of false positive prediction as low as 0.1%. GPIPE was used to completely annotate 81 eukaryotic genomes, and more than 15000 putative GPI‐anchored proteins were predicted, 561 of which are found in H. sapiens. In average 1% of a proteome is predicted as GPI‐anchored. A statistical analysis was performed onto the composition of the regions surrounding the ω‐site that allowed the definition of specific aminoacidic abundances in the different considered regions. Furthermore the hypothesis that compositional biases are present among the four major eukaryotic kingdoms, proposed in literature, was tested and rejected. All the developed predictors and databases are freely available at: BaCelLo http://gpcr.biocomp.unibo.it/bacello eSLDB http://gpcr.biocomp.unibo.it/esldb GPIPE http://gpcr.biocomp.unibo.it/gpipe

Interactions between normative systems and software cognitive agents. A formalization in temporal modal defeasible logic and its implementation

Sustainable computer systems require some flexibility to adapt to environmental unpredictable changes. A solution lies in autonomous software agents which can adapt autonomously to their environments. Though autonomy allows agents to decide which behavior to adopt, a disadvantage is a lack of control, and as a side effect even untrustworthiness: we want to keep some control over such autonomous agents. How to control autonomous agents while respecting their autonomy? A solution is to regulate agents’ behavior by norms. The normative paradigm makes it possible to control autonomous agents while respecting their autonomy, limiting untrustworthiness and augmenting system compliance. It can also facilitate the design of the system, for example, by regulating the coordination among agents. However, an autonomous agent will follow norms or violate them in some conditions. What are the conditions in which a norm is binding upon an agent? While autonomy is regarded as the driving force behind the normative paradigm, cognitive agents provide a basis for modeling the bindingness of norms. In order to cope with the complexity of the modeling of cognitive agents and normative bindingness, we adopt an intentional stance. Since agents are embedded into a dynamic environment, things may not pass at the same instant. Accordingly, our cognitive model is extended to account for some temporal aspects. Special attention is given to the temporal peculiarities of the legal domain such as, among others, the time in force and the time in efficacy of provisions. Some types of normative modifications are also discussed in the framework. It is noteworthy that our temporal account of legal reasoning is integrated to our commonsense temporal account of cognition. As our intention is to build sustainable reasoning systems running unpredictable environment, we adopt a declarative representation of knowledge. A declarative representation of norms will make it easier to update their system representation, thus facilitating system maintenance; and to improve system transparency, thus easing system governance. Since agents are bounded and are embedded into unpredictable environments, and since conflicts may appear amongst mental states and norms, agent reasoning has to be defeasible, i.e. new pieces of information can invalidate formerly derivable conclusions. In this dissertation, our model is formalized into a non-monotonic logic, namely into a temporal modal defeasible logic, in order to account for the interactions between normative systems and software cognitive agents.

A tuple space implementation for large-scale infrastructures

Coordinating activities in a distributed system is an open research topic. Several models have been proposed to achieve this purpose such as message passing, publish/subscribe, workflows or tuple spaces. We have focused on the latter model, trying to overcome some of its disadvantages. In particular we have applied spatial database techniques to tuple spaces in order to increase their performance when handling a large number of tuples. Moreover, we have studied how structured peer to peer approaches can be applied to better distribute tuples on large networks. Using some of these result, we have developed a tuple space implementation for the Globus Toolkit that can be used by Grid applications as a coordination service. The development of such a service has been quite challenging due to the limitations imposed by XML serialization that have heavily influenced its design. Nevertheless, we were able to complete its implementation and use it to implement two different types of test applications: a completely parallelizable one and a plasma simulation that is not completely parallelizable. Using this last application we have compared the performance of our service against MPI. Finally, we have developed and tested a simple workflow in order to show the versatility of our service.

A core calculus for the analysis and implementation of biologically inspired languages

The application of Concurrency Theory to Systems Biology is in its earliest stage of progress. The metaphor of cells as computing systems by Regev and Shapiro opened the employment of concurrent languages for the modelling of biological systems. Their peculiar characteristics led to the design of many bio-inspired formalisms which achieve higher faithfulness and specificity. In this thesis we present pi@, an extremely simple and conservative extension of the pi-calculus representing a keystone in this respect, thanks to its expressiveness capabilities. The pi@ calculus is obtained by the addition of polyadic synchronisation and priority to the pi-calculus, in order to achieve compartment semantics and atomicity of complex operations respectively. In its direct application to biological modelling, the stochastic variant of the calculus, Spi@, is shown able to model consistently several phenomena such as formation of molecular complexes, hierarchical subdivision of the system into compartments, inter-compartment reactions, dynamic reorganisation of compartment structure consistent with volume variation. The pivotal role of pi@ is evidenced by its capability of encoding in a compositional way several bio-inspired formalisms, so that it represents the optimal core of a framework for the analysis and implementation of bio-inspired languages. In this respect, the encodings of BioAmbients, Brane Calculi and a variant of P Systems in pi@ are formalised. The conciseness of their translation in pi@ allows their indirect comparison by means of their encodings. Furthermore it provides a ready-to-run implementation of minimal effort whose correctness is granted by the correctness of the respective encoding functions. Further important results of general validity are stated on the expressive power of priority. Several impossibility results are described, which clearly state the superior expressiveness of prioritised languages and the problems arising in the attempt of providing their parallel implementation. To this aim, a new setting in distributed computing (the last man standing problem) is singled out and exploited to prove the impossibility of providing a purely parallel implementation of priority by means of point-to-point or broadcast communication.

The assessment of change in rural landscape and the analysis of the driving forces. Proposal of a spatial model for the rural built environment

The presented study carried out an analysis on rural landscape changes. In particular the study focuses on the understanding of driving forces acting on the rural built environment using a statistical spatial model implemented through GIS techniques. It is well known that the study of landscape changes is essential for a conscious decision making in land planning. From a bibliography review results a general lack of studies dealing with the modeling of rural built environment and hence a theoretical modelling approach for such purpose is needed. The advancement in technology and modernity in building construction and agriculture have gradually changed the rural built environment. In addition, the phenomenon of urbanization of a determined the construction of new volumes that occurred beside abandoned or derelict rural buildings. Consequently there are two types of transformation dynamics affecting mainly the rural built environment that can be observed: the conversion of rural buildings and the increasing of building numbers. It is the specific aim of the presented study to propose a methodology for the development of a spatial model that allows the identification of driving forces that acted on the behaviours of the building allocation. In fact one of the most concerning dynamic nowadays is related to an irrational expansion of buildings sprawl across landscape. The proposed methodology is composed by some conceptual steps that cover different aspects related to the development of a spatial model: the selection of a response variable that better describe the phenomenon under study, the identification of possible driving forces, the sampling methodology concerning the collection of data, the most suitable algorithm to be adopted in relation to statistical theory and method used, the calibration process and evaluation of the model. A different combination of factors in various parts of the territory generated favourable or less favourable conditions for the building allocation and the existence of buildings represents the evidence of such optimum. Conversely the absence of buildings expresses a combination of agents which is not suitable for building allocation. Presence or absence of buildings can be adopted as indicators of such driving conditions, since they represent the expression of the action of driving forces in the land suitability sorting process. The existence of correlation between site selection and hypothetical driving forces, evaluated by means of modeling techniques, provides an evidence of which driving forces are involved in the allocation dynamic and an insight on their level of influence into the process. GIS software by means of spatial analysis tools allows to associate the concept of presence and absence with point futures generating a point process. Presence or absence of buildings at some site locations represent the expression of these driving factors interaction. In case of presences, points represent locations of real existing buildings, conversely absences represent locations were buildings are not existent and so they are generated by a stochastic mechanism. Possible driving forces are selected and the existence of a causal relationship with building allocations is assessed through a spatial model. The adoption of empirical statistical models provides a mechanism for the explanatory variable analysis and for the identification of key driving variables behind the site selection process for new building allocation. The model developed by following the methodology is applied to a case study to test the validity of the methodology. In particular the study area for the testing of the methodology is represented by the New District of Imola characterized by a prevailing agricultural production vocation and were transformation dynamic intensively occurred. The development of the model involved the identification of predictive variables (related to geomorphologic, socio-economic, structural and infrastructural systems of landscape) capable of representing the driving forces responsible for landscape changes.. The calibration of the model is carried out referring to spatial data regarding the periurban and rural area of the study area within the 1975-2005 time period by means of Generalised linear model. The resulting output from the model fit is continuous grid surface where cells assume values ranged from 0 to 1 of probability of building occurrences along the rural and periurban area of the study area. Hence the response variable assesses the changes in the rural built environment occurred in such time interval and is correlated to the selected explanatory variables by means of a generalized linear model using logistic regression. Comparing the probability map obtained from the model to the actual rural building distribution in 2005, the interpretation capability of the model can be evaluated. The proposed model can be also applied to the interpretation of trends which occurred in other study areas, and also referring to different time intervals, depending on the availability of data. The use of suitable data in terms of time, information, and spatial resolution and the costs related to data acquisition, pre-processing, and survey are among the most critical aspects of model implementation. Future in-depth studies can focus on using the proposed model to predict short/medium-range future scenarios for the rural built environment distribution in the study area. In order to predict future scenarios it is necessary to assume that the driving forces do not change and that their levels of influence within the model are not far from those assessed for the time interval used for the calibration.

Development of human visual system analysis for the implementation of a new instrument for flicker measurement

Flicker is a power quality phenomenon that applies to cycle instability of light intensity resulting from supply voltage fluctuation, which, in turn can be caused by disturbances introduced during power generation, transmission or distribution. The standard EN 61000-4-15 which has been recently adopted also by the IEEE as IEEE Standard 1453 relies on the analysis of the supply voltage which is processed according to a suitable model of the lamp – human eye – brain chain. As for the lamp, an incandescent 60 W, 230 V, 50 Hz source is assumed. As far as the human eye – brain model is concerned, it is represented by the so-called flicker curve. Such a curve was determined several years ago by statistically analyzing the results of tests where people were subjected to flicker with different combinations of magnitude and frequency. The limitations of this standard approach to flicker evaluation are essentially two. First, the provided index of annoyance Pst can be related to an actual tiredness of the human visual system only if such an incandescent lamp is used. Moreover, the implemented response to flicker is “subjective” given that it relies on the people answers about their feelings. In the last 15 years, many scientific contributions have tackled these issues by investigating the possibility to develop a novel model of the eye-brain response to flicker and overcome the strict dependence of the standard on the kind of the light source. In this light of fact, this thesis is aimed at presenting an important contribution for a new Flickermeter. An improved visual system model using a physiological parameter that is the mean value of the pupil diameter, has been presented, thus allowing to get a more “objective” representation of the response to flicker. The system used to both generate flicker and measure the pupil diameter has been illustrated along with all the results of several experiments performed on the volunteers. The intent has been to demonstrate that the measurement of that geometrical parameter can give reliable information about the feeling of the human visual system to light flicker.

Analysis and Implementation of Multiphase-Multilevel Inverter for Open-Winding Loads

Research work carried out in focusing a novel multiphase-multilevel ac motor drive system much suitable for low-voltage high-current power applications. In specific, six-phase asymmetrical induction motor with open-end stator winding configuration, fed from four standard two-level three-phase voltage source inverters (VSIs). Proposed synchronous reference frame control algorithm shares the total dc source power among the 4 VSIs in each switching cycle with three degree of freedom. Precisely, first degree of freedom concerns with the current sharing between two three-phase stator windings. Based on modified multilevel space vector pulse width modulation shares the voltage between each single VSIs of two three-phase stator windings with second and third degree of freedom, having proper multilevel output waveforms. Complete model of whole ac motor drive based on three-phase space vector decomposition approach was developed in PLECS - numerical simulation software working in MATLAB environment. Proposed synchronous reference control algorithm was framed in MATLAB with modified multilevel space vector pulse width modulator. The effectiveness of the entire ac motor drives system was tested. Simulation results are given in detail to show symmetrical and asymmetrical, power sharing conditions. Furthermore, the three degree of freedom are exploited to investigate fault tolerant capabilities in post-fault conditions. Complete set of simulation results are provided when one, two and three VSIs are faulty. Hardware prototype model of quad-inverter was implemented with two passive three-phase open-winding loads using two TMS320F2812 DSP controllers. Developed McBSP (multi-channel buffered serial port) communication algorithm able to control the four VSIs for PWM communication and synchronization. Open-loop control scheme based on inverse three-phase decomposition approach was developed to control entire quad-inverter configuration and tested with balanced and unbalanced operating conditions with simplified PWM techniques. Both simulation and experimental results are always in good agreement with theoretical developments.

Design and implementation of a novel multi-constellation FPGA-based dual frequency GNSS receiver for space applications

The PhD activity described in the document is part of the Microsatellite and Microsystem Laboratory of the II Faculty of Engineering, University of Bologna. The main objective is the design and development of a GNSS receiver for the orbit determination of microsatellites in low earth orbit. The development starts from the electronic design and goes up to the implementation of the navigation algorithms, covering all the aspects that are involved in this type of applications. The use of GPS receivers for orbit determination is a consolidated application used in many space missions, but the development of the new GNSS system within few years, such as the European Galileo, the Chinese COMPASS and the Russian modernized GLONASS, proposes new challenges and offers new opportunities to increase the orbit determination performances. The evaluation of improvements coming from the new systems together with the implementation of a receiver that is compatible with at least one of the new systems, are the main activities of the PhD. The activities can be divided in three section: receiver requirements definition and prototype implementation, design and analysis of the GNSS signal tracking algorithms, and design and analysis of the navigation algorithms. The receiver prototype is based on a Virtex FPGA by Xilinx, and includes a PowerPC processor. The architecture follows the software defined radio paradigm, so most of signal processing is performed in software while only what is strictly necessary is done in hardware. The tracking algorithms are implemented as a combination of Phase Locked Loop and Frequency Locked Loop for the carrier, and Delay Locked Loop with variable bandwidth for the code. The navigation algorithm is based on the extended Kalman filter and includes an accurate LEO orbit model.