Development of advanced methods for the simulation of the reacting mixture formation in internal combustion engines with the use of machine learning algorithms

Besides increasing the share of electric and hybrid vehicles, in order to comply with more stringent environmental protection limitations, in the mid-term the auto industry must improve the efficiency of the internal combustion engine and the well to wheel efficiency of the employed fuel. To achieve this target, a deeper knowledge of the phenomena that influence the mixture formation and the chemical reactions involving new synthetic fuel components is mandatory, but complex and time intensive to perform purely by experimentation. Therefore, numerical simulations play an important role in this development process, but their use can be effective only if they can be considered accurate enough to capture these variations. The most relevant models necessary for the simulation of the reacting mixture formation and successive chemical reactions have been investigated in the present work, with a critical approach, in order to provide instruments to define the most suitable approaches also in the industrial context, which is limited by time constraints and budget evaluations. To overcome these limitations, new methodologies have been developed to conjugate detailed and simplified modelling techniques for the phenomena involving chemical reactions and mixture formation in non-traditional conditions (e.g. water injection, biofuels etc.). Thanks to the large use of machine learning and deep learning algorithms, several applications have been revised or implemented, with the target of reducing the computing time of some traditional tasks by orders of magnitude. Finally, a complete workflow leveraging these new models has been defined and used for evaluating the effects of different surrogate formulations of the same experimental fuel on a proof-of-concept GDI engine model.

Learning with Kernels on Graphs: DAG-based kernels, data streams and RNA function prediction.

In many application domains data can be naturally represented as graphs. When the application of analytical solutions for a given problem is unfeasible, machine learning techniques could be a viable way to solve the problem. Classical machine learning techniques are defined for data represented in a vectorial form. Recently some of them have been extended to deal directly with structured data. Among those techniques, kernel methods have shown promising results both from the computational complexity and the predictive performance point of view. Kernel methods allow to avoid an explicit mapping in a vectorial form relying on kernel functions, which informally are functions calculating a similarity measure between two entities. However, the definition of good kernels for graphs is a challenging problem because of the difficulty to find a good tradeoff between computational complexity and expressiveness. Another problem we face is learning on data streams, where a potentially unbounded sequence of data is generated by some sources. There are three main contributions in this thesis. The first contribution is the definition of a new family of kernels for graphs based on Directed Acyclic Graphs (DAGs). We analyzed two kernels from this family, achieving state-of-the-art results from both the computational and the classification point of view on real-world datasets. The second contribution consists in making the application of learning algorithms for streams of graphs feasible. Moreover,we defined a principled way for the memory management. The third contribution is the application of machine learning techniques for structured data to non-coding RNA function prediction. In this setting, the secondary structure is thought to carry relevant information. However, existing methods considering the secondary structure have prohibitively high computational complexity. We propose to apply kernel methods on this domain, obtaining state-of-the-art results.

Robotic Sensing and Manipulation of Deformable Linear Objects with Learning-based methods

Nowadays robotic applications are widespread and most of the manipulation tasks are efficiently solved. However, Deformable-Objects (DOs) still represent a huge limitation for robots. The main difficulty in DOs manipulation is dealing with the shape and dynamics uncertainties, which prevents the use of model-based approaches (since they are excessively computationally complex) and makes sensory data difficult to interpret. This thesis reports the research activities aimed to address some applications in robotic manipulation and sensing of Deformable-Linear-Objects (DLOs), with particular focus to electric wires. In all the works, a significant effort was made in the study of an effective strategy for analyzing sensory signals with various machine learning algorithms. In the former part of the document, the main focus concerns the wire terminals, i.e. detection, grasping, and insertion. First, a pipeline that integrates vision and tactile sensing is developed, then further improvements are proposed for each module. A novel procedure is proposed to gather and label massive amounts of training images for object detection with minimal human intervention. Together with this strategy, we extend a generic object detector based on Convolutional-Neural-Networks for orientation prediction. The insertion task is also extended by developing a closed-loop control capable to guide the insertion of a longer and curved segment of wire through a hole, where the contact forces are estimated by means of a Recurrent-Neural-Network. In the latter part of the thesis, the interest shifts to the DLO shape. Robotic reshaping of a DLO is addressed by means of a sequence of pick-and-place primitives, while a decision making process driven by visual data learns the optimal grasping locations exploiting Deep Q-learning and finds the best releasing point. The success of the solution leverages on a reliable interpretation of the DLO shape. For this reason, further developments are made on the visual segmentation.

Challenges and Opportunities of Machine Learning for Clinical and Omics Data

Clinical and omics data are a promising field of application for machine learning techniques even though these methods are not yet systematically adopted in healthcare institutions. Despite artificial intelligence has proved successful in terms of prediction of pathologies or identification of their causes, the systematic adoption of these techniques still presents challenging issues due to the peculiarities of the analysed data. The aim of this thesis is to apply machine learning algorithms to both clinical and omics data sets in order to predict a patient's state of health and get better insights on the possible causes of the analysed diseases. In doing so, many of the arising issues when working with medical data will be discussed while possible solutions will be proposed to make machine learning provide feasible results and possibly become an effective and reliable support tool for healthcare systems.

Automatic risk evaluation in elderly patients based on Autonomic Nervous System assessment

Dysfunction of Autonomic Nervous System (ANS) is a typical feature of chronic heart failure and other cardiovascular disease. As a simple non-invasive technology, heart rate variability (HRV) analysis provides reliable information on autonomic modulation of heart rate. The aim of this thesis was to research and develop automatic methods based on ANS assessment for evaluation of risk in cardiac patients. Several features selection and machine learning algorithms have been combined to achieve the goals. Automatic assessment of disease severity in Congestive Heart Failure (CHF) patients: a completely automatic method, based on long-term HRV was proposed in order to automatically assess the severity of CHF, achieving a sensitivity rate of 93% and a specificity rate of 64% in discriminating severe versus mild patients. Automatic identification of hypertensive patients at high risk of vascular events: a completely automatic system was proposed in order to identify hypertensive patients at higher risk to develop vascular events in the 12 months following the electrocardiographic recordings, achieving a sensitivity rate of 71% and a specificity rate of 86% in identifying high-risk subjects among hypertensive patients. Automatic identification of hypertensive patients with history of fall: it was explored whether an automatic identification of fallers among hypertensive patients based on HRV was feasible. The results obtained in this thesis could have implications both in clinical practice and in clinical research. The system has been designed and developed in order to be clinically feasible. Moreover, since 5-minute ECG recording is inexpensive, easy to assess, and non-invasive, future research will focus on the clinical applicability of the system as a screening tool in non-specialized ambulatories, in order to identify high-risk patients to be shortlisted for more complex investigations.

Embedded representations of social interactions

Social interactions have been the focus of social science research for a century, but their study has recently been revolutionized by novel data sources and by methods from computer science, network science, and complex systems science. The study of social interactions is crucial for understanding complex societal behaviours. Social interactions are naturally represented as networks, which have emerged as a unifying mathematical language to understand structural and dynamical aspects of socio-technical systems. Networks are, however, highly dimensional objects, especially when considering the scales of real-world systems and the need to model the temporal dimension. Hence the study of empirical data from social systems is challenging both from a conceptual and a computational standpoint. A possible approach to tackling such a challenge is to use dimensionality reduction techniques that represent network entities in a low-dimensional feature space, preserving some desired properties of the original data. Low-dimensional vector space representations, also known as network embeddings, have been extensively studied, also as a way to feed network data to machine learning algorithms. Network embeddings were initially developed for static networks and then extended to incorporate temporal network data. We focus on dimensionality reduction techniques for time-resolved social interaction data modelled as temporal networks. We introduce a novel embedding technique that models the temporal and structural similarities of events rather than nodes. Using empirical data on social interactions, we show that this representation captures information relevant for the study of dynamical processes unfolding over the network, such as epidemic spreading. We then turn to another large-scale dataset on social interactions: a popular Web-based crowdfunding platform. We show that tensor-based representations of the data and dimensionality reduction techniques such as tensor factorization allow us to uncover the structural and temporal aspects of the system and to relate them to geographic and temporal activity patterns.

Big data analytics for proactive and predictive maintenance in electric car battery packs

The idea behind the project is to develop a methodology for analyzing and developing techniques for the diagnosis and the prediction of the state of charge and health of lithium-ion batteries for automotive applications. For lithium-ion batteries, residual functionality is measured in terms of state of health; however, this value cannot be directly associated with a measurable value, so it must be estimated. The development of the algorithms is based on the identification of the causes of battery degradation, in order to model and predict the trend. Therefore, models have been developed that are able to predict the electrical, thermal and aging behavior. In addition to the model, it was necessary to develop algorithms capable of monitoring the state of the battery, online and offline. This was possible with the use of algorithms based on Kalman filters, which allow the estimation of the system status in real time. Through machine learning algorithms, which allow offline analysis of battery deterioration using a statistical approach, it is possible to analyze information from the entire fleet of vehicles. Both systems work in synergy in order to achieve the best performance. Validation was performed with laboratory tests on different batteries and under different conditions. The development of the model allowed to reduce the time of the experimental tests. Some specific phenomena were tested in the laboratory, and the other cases were artificially generated.

Data-stream driven Fuzzy-granular approaches for system maintenance

Intelligent systems are currently inherent to the society, supporting a synergistic human-machine collaboration. Beyond economical and climate factors, energy consumption is strongly affected by the performance of computing systems. The quality of software functioning may invalidate any improvement attempt. In addition, data-driven machine learning algorithms are the basis for human-centered applications, being their interpretability one of the most important features of computational systems. Software maintenance is a critical discipline to support automatic and life-long system operation. As most software registers its inner events by means of logs, log analysis is an approach to keep system operation. Logs are characterized as Big data assembled in large-flow streams, being unstructured, heterogeneous, imprecise, and uncertain. This thesis addresses fuzzy and neuro-granular methods to provide maintenance solutions applied to anomaly detection (AD) and log parsing (LP), dealing with data uncertainty, identifying ideal time periods for detailed software analyses. LP provides deeper semantics interpretation of the anomalous occurrences. The solutions evolve over time and are general-purpose, being highly applicable, scalable, and maintainable. Granular classification models, namely, Fuzzy set-Based evolving Model (FBeM), evolving Granular Neural Network (eGNN), and evolving Gaussian Fuzzy Classifier (eGFC), are compared considering the AD problem. The evolving Log Parsing (eLP) method is proposed to approach the automatic parsing applied to system logs. All the methods perform recursive mechanisms to create, update, merge, and delete information granules according with the data behavior. For the first time in the evolving intelligent systems literature, the proposed method, eLP, is able to process streams of words and sentences. Essentially, regarding to AD accuracy, FBeM achieved (85.64+-3.69)%; eGNN reached (96.17+-0.78)%; eGFC obtained (92.48+-1.21)%; and eLP reached (96.05+-1.04)%. Besides being competitive, eLP particularly generates a log grammar, and presents a higher level of model interpretability.

Technologies for urban and rural internet of things

Nowadays, application domains such as smart cities, agriculture or intelligent transportation, require communication technologies that combine long transmission ranges and energy efficiency to fulfill a set of capabilities and constraints to rely on. In addition, in recent years, the interest in Unmanned Aerial Vehicles (UAVs) providing wireless connectivity in such scenarios is substantially increased thanks to their flexible deployment. The first chapters of this thesis deal with LoRaWAN and Narrowband-IoT (NB-IoT), which recent trends identify as the most promising Low Power Wide Area Networks technologies. While LoRaWAN is an open protocol that has gained a lot of interest thanks to its simplicity and energy efficiency, NB-IoT has been introduced from 3GPP as a radio access technology for massive machine-type communications inheriting legacy LTE characteristics. This thesis offers an overview of the two, comparing them in terms of selected performance indicators. In particular, LoRaWAN technology is assessed both via simulations and experiments, considering different network architectures and solutions to improve its performance (e.g., a new Adaptive Data Rate algorithm). NB-IoT is then introduced to identify which technology is more suitable depending on the application considered. The second part of the thesis introduces the use of UAVs as flying Base Stations, denoted as Unmanned Aerial Base Stations, (UABSs), which are considered as one of the key pillars of 6G to offer service for a number of applications. To this end, the performance of an NB-IoT network are assessed considering a UABS following predefined trajectories. Then, machine learning algorithms based on reinforcement learning and meta-learning are considered to optimize the trajectory as well as the radio resource management techniques the UABS may rely on in order to provide service considering both static (IoT sensors) and dynamic (vehicles) users. Finally, some experimental projects based on the technologies mentioned so far are presented.

Anticancer drug discovery using artificial intelligence: an application in pharmacological activity prediction

Hematological cancers are a heterogeneous family of diseases that can be divided into leukemias, lymphomas, and myelomas, often called “liquid tumors”. Since they cannot be surgically removable, chemotherapy represents the mainstay of their treatment. However, it still faces several challenges like drug resistance and low response rate, and the need for new anticancer agents is compelling. The drug discovery process is long-term, costly, and prone to high failure rates. With the rapid expansion of biological and chemical "big data", some computational techniques such as machine learning tools have been increasingly employed to speed up and economize the whole process. Machine learning algorithms can create complex models with the aim to determine the biological activity of compounds against several targets, based on their chemical properties. These models are defined as multi-target Quantitative Structure-Activity Relationship (mt-QSAR) and can be used to virtually screen small and large chemical libraries for the identification of new molecules with anticancer activity. The aim of my Ph.D. project was to employ machine learning techniques to build an mt-QSAR classification model for the prediction of cytotoxic drugs simultaneously active against 43 hematological cancer cell lines. For this purpose, first, I constructed a large and diversified dataset of molecules extracted from the ChEMBL database. Then, I compared the performance of different ML classification algorithms, until Random Forest was identified as the one returning the best predictions. Finally, I used different approaches to maximize the performance of the model, which achieved an accuracy of 88% by correctly classifying 93% of inactive molecules and 72% of active molecules in a validation set. This model was further applied to the virtual screening of a small dataset of molecules tested in our laboratory, where it showed 100% accuracy in correctly classifying all molecules. This result is confirmed by our previous in vitro experiments.

Learning Methods and Algorithms for Semantic Text Classification across Multiple Domains

Information is nowadays a key resource: machine learning and data mining techniques have been developed to extract high-level information from great amounts of data. As most data comes in form of unstructured text in natural languages, research on text mining is currently very active and dealing with practical problems. Among these, text categorization deals with the automatic organization of large quantities of documents in priorly defined taxonomies of topic categories, possibly arranged in large hierarchies. In commonly proposed machine learning approaches, classifiers are automatically trained from pre-labeled documents: they can perform very accurate classification, but often require a consistent training set and notable computational effort. Methods for cross-domain text categorization have been proposed, allowing to leverage a set of labeled documents of one domain to classify those of another one. Most methods use advanced statistical techniques, usually involving tuning of parameters. A first contribution presented here is a method based on nearest centroid classification, where profiles of categories are generated from the known domain and then iteratively adapted to the unknown one. Despite being conceptually simple and having easily tuned parameters, this method achieves state-of-the-art accuracy in most benchmark datasets with fast running times. A second, deeper contribution involves the design of a domain-independent model to distinguish the degree and type of relatedness between arbitrary documents and topics, inferred from the different types of semantic relationships between respective representative words, identified by specific search algorithms. The application of this model is tested on both flat and hierarchical text categorization, where it potentially allows the efficient addition of new categories during classification. Results show that classification accuracy still requires improvements, but models generated from one domain are shown to be effectively able to be reused in a different one.

Metaheuristics for Search Problems in Genomics - New Algorithms and Applications

In this thesis we made the first steps towards the systematic application of a methodology for automatically building formal models of complex biological systems. Such a methodology could be useful also to design artificial systems possessing desirable properties such as robustness and evolvability. The approach we follow in this thesis is to manipulate formal models by means of adaptive search methods called metaheuristics. In the first part of the thesis we develop state-of-the-art hybrid metaheuristic algorithms to tackle two important problems in genomics, namely, the Haplotype Inference by parsimony and the Founder Sequence Reconstruction Problem. We compare our algorithms with other effective techniques in the literature, we show strength and limitations of our approaches to various problem formulations and, finally, we propose further enhancements that could possibly improve the performance of our algorithms and widen their applicability. In the second part, we concentrate on Boolean network (BN) models of gene regulatory networks (GRNs). We detail our automatic design methodology and apply it to four use cases which correspond to different design criteria and address some limitations of GRN modeling by BNs. Finally, we tackle the Density Classification Problem with the aim of showing the learning capabilities of BNs. Experimental evaluation of this methodology shows its efficacy in producing network that meet our design criteria. Our results, coherently to what has been found in other works, also suggest that networks manipulated by a search process exhibit a mixture of characteristics typical of different dynamical regimes.

Spectrum Sensing Algorithms for Cognitive Radio Applications

Future wireless communications systems are expected to be extremely dynamic, smart and capable to interact with the surrounding radio environment. To implement such advanced devices, cognitive radio (CR) is a promising paradigm, focusing on strategies for acquiring information and learning. The first task of a cognitive systems is spectrum sensing, that has been mainly studied in the context of opportunistic spectrum access, in which cognitive nodes must implement signal detection techniques to identify unused bands for transmission. In the present work, we study different spectrum sensing algorithms, focusing on their statistical description and evaluation of the detection performance. Moving from traditional sensing approaches we consider the presence of practical impairments, and analyze algorithm design. Far from the ambition of cover the broad spectrum of spectrum sensing, we aim at providing contributions to the main classes of sensing techniques. In particular, in the context of energy detection we studied the practical design of the test, considering the case in which the noise power is estimated at the receiver. This analysis allows to deepen the phenomenon of the SNR wall, providing the conditions for its existence and showing that presence of the SNR wall is determined by the accuracy of the noise power estimation process. In the context of the eigenvalue based detectors, that can be adopted by multiple sensors systems, we studied the practical situation in presence of unbalances in the noise power at the receivers. Then, we shift the focus from single band detectors to wideband sensing, proposing a new approach based on information theoretic criteria. This technique is blind and, requiring no threshold setting, can be adopted even if the statistical distribution of the observed data in not known exactly. In the last part of the thesis we analyze some simple cooperative localization techniques based on weighted centroid strategies.

Variational and learning models for image and time series inverse problems

Inverse problems are at the core of many challenging applications. Variational and learning models provide estimated solutions of inverse problems as the outcome of specific reconstruction maps. In the variational approach, the result of the reconstruction map is the solution of a regularized minimization problem encoding information on the acquisition process and prior knowledge on the solution. In the learning approach, the reconstruction map is a parametric function whose parameters are identified by solving a minimization problem depending on a large set of data. In this thesis, we go beyond this apparent dichotomy between variational and learning models and we show they can be harmoniously merged in unified hybrid frameworks preserving their main advantages. We develop several highly efficient methods based on both these model-driven and data-driven strategies, for which we provide a detailed convergence analysis. The arising algorithms are applied to solve inverse problems involving images and time series. For each task, we show the proposed schemes improve the performances of many other existing methods in terms of both computational burden and quality of the solution. In the first part, we focus on gradient-based regularized variational models which are shown to be effective for segmentation purposes and thermal and medical image enhancement. We consider gradient sparsity-promoting regularized models for which we develop different strategies to estimate the regularization strength. Furthermore, we introduce a novel gradient-based Plug-and-Play convergent scheme considering a deep learning based denoiser trained on the gradient domain. In the second part, we address the tasks of natural image deblurring, image and video super resolution microscopy and positioning time series prediction, through deep learning based methods. We boost the performances of supervised, such as trained convolutional and recurrent networks, and unsupervised deep learning strategies, such as Deep Image Prior, by penalizing the losses with handcrafted regularization terms.

Exploiting the environment for structural health monitoring: Strategies, algorithms, and technologies

A densely built environment is a complex system of infrastructure, nature, and people closely interconnected and interacting. Vehicles, public transport, weather action, and sports activities constitute a manifold set of excitation and degradation sources for civil structures. In this context, operators should consider different factors in a holistic approach for assessing the structural health state. Vibration-based structural health monitoring (SHM) has demonstrated great potential as a decision-supporting tool to schedule maintenance interventions. However, most excitation sources are considered an issue for practical SHM applications since traditional methods are typically based on strict assumptions on input stationarity. Last-generation low-cost sensors present limitations related to a modest sensitivity and high noise floor compared to traditional instrumentation. If these devices are used for SHM in urban scenarios, short vibration recordings collected during high-intensity events and vehicle passage may be the only available datasets with a sufficient signal-to-noise ratio. While researchers have spent efforts to mitigate the effects of short-term phenomena in vibration-based SHM, the ultimate goal of this thesis is to exploit them and obtain valuable information on the structural health state. First, this thesis proposes strategies and algorithms for smart sensors operating individually or in a distributed computing framework to identify damage-sensitive features based on instantaneous modal parameters and influence lines. Ordinary traffic and people activities become essential sources of excitation, while human-powered vehicles, instrumented with smartphones, take the role of roving sensors in crowdsourced monitoring strategies. The technical and computational apparatus is optimized using in-memory computing technologies. Moreover, identifying additional local features can be particularly useful to support the damage assessment of complex structures. Thereby, smart coatings are studied to enable the self-sensing properties of ordinary structural elements. In this context, a machine-learning-aided tomography method is proposed to interpret the data provided by a nanocomposite paint interrogated electrically.