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.

Application of Deep Learning techniques in the search for BSM Higgs bosons in the $\mu\mu$ final state in CMS

The Standard Model (SM) of particle physics predicts the existence of a Higgs field responsible for the generation of particles' mass. However, some aspects of this theory remain unsolved, supposing the presence of new physics Beyond the Standard Model (BSM) with the production of new particles at a higher energy scale compared to the current experimental limits. The search for additional Higgs bosons is, in fact, predicted by theoretical extensions of the SM including the Minimal Supersymmetry Standard Model (MSSM). In the MSSM, the Higgs sector consists of two Higgs doublets, resulting in five physical Higgs particles: two charged bosons $H^{\pm}$, two neutral scalars $h$ and $H$, and one pseudoscalar $A$. The work presented in this thesis is dedicated to the search of neutral non-Standard Model Higgs bosons decaying to two muons in the model independent MSSM scenario. Proton-proton collision data recorded by the CMS experiment at the CERN LHC at a center-of-mass energy of 13 TeV are used, corresponding to an integrated luminosity of $35.9\ \text{fb}^{-1}$. Such search is sensitive to neutral Higgs bosons produced either via gluon fusion process or in association with a $\text{b}\bar{\text{b}}$ quark pair. The extensive usage of Machine and Deep Learning techniques is a fundamental element in the discrimination between signal and background simulated events. A new network structure called parameterised Neural Network (pNN) has been implemented, replacing a whole set of single neural networks trained at a specific mass hypothesis value with a single neural network able to generalise well and interpolate in the entire mass range considered. The results of the pNN signal/background discrimination are used to set a model independent 95\% confidence level expected upper limit on the production cross section times branching ratio, for a generic $\phi$ boson decaying into a muon pair in the 130 to 1000 GeV range.

The transformative potential of community engagement in higher education: an analysis of service-learning effects on students, communities, and institutions.

Service-learning in higher education is gaining attention as a reliable tool to support students’ learning and fulfil the mission of higher education institutions (HEIs). This dissertation addresses existing gaps in the literature by examining the effects and perspectives of service-learning in HEIs through three studies. The first study compares the effects of a voluntary semester-long service-learning course with traditional courses. A survey completed by 110 students before and after the lectures found no significant group differences in the psychosocial variables under inspection. Nevertheless, service-learning students showed higher scores concerning the quality of participation. Factors such as students’ perception of competence, duration of service-learning, and self-reported measures may have influenced the results. The second study explores the under-researched perspective of community partners in higher education and European settings. Twelve semi-structured interviews were conducted with community partners from various community organisations across Europe. The results highlight positive effects on community members and organisations, intrinsic motivations, organisational empowerment, different forms of reciprocity, the co-educational role of community partners, and the significant role of a sense of community and belonging. The third study focuses on faculty perspectives on service-learning in the European context. Twenty-two semi-structured interviews were conducted in 14 European countries. The findings confirm the transformative impact of service-learning on the community, students, teachers, and HEIs, emphasising the importance of motivation and institutionalisation processes in sustaining engaged scholarship. The study also identifies the relevance of the community experience, sense of community, and community responsibility with the service-learning experience; relatedness is proposed as the fifth pillar of service-learning. Overall, this dissertation provides new insights into the effects and perspectives of service-learning in higher education. It integrates the 4Rs model with the addition of relatedness, guiding the theoretical and practical implications of the findings. The dissertation also suggests limitations and areas for further research.

Development of unsupervised learning methods with applications to life sciences data

Machine Learning makes computers capable of performing tasks typically requiring human intelligence. A domain where it is having a considerable impact is the life sciences, allowing to devise new biological analysis protocols, develop patients’ treatments efficiently and faster, and reduce healthcare costs. This Thesis work presents new Machine Learning methods and pipelines for the life sciences focusing on the unsupervised field. At a methodological level, two methods are presented. The first is an “Ab Initio Local Principal Path” and it is a revised and improved version of a pre-existing algorithm in the manifold learning realm. The second contribution is an improvement over the Import Vector Domain Description (one-class learning) through the Kullback-Leibler divergence. It hybridizes kernel methods to Deep Learning obtaining a scalable solution, an improved probabilistic model, and state-of-the-art performances. Both methods are tested through several experiments, with a central focus on their relevance in life sciences. Results show that they improve the performances achieved by their previous versions. At the applicative level, two pipelines are presented. The first one is for the analysis of RNA-Seq datasets, both transcriptomic and single-cell data, and is aimed at identifying genes that may be involved in biological processes (e.g., the transition of tissues from normal to cancer). In this project, an R package is released on CRAN to make the pipeline accessible to the bioinformatic Community through high-level APIs. The second pipeline is in the drug discovery domain and is useful for identifying druggable pockets, namely regions of a protein with a high probability of accepting a small molecule (a drug). Both these pipelines achieve remarkable results. Lastly, a detour application is developed to identify the strengths/limitations of the “Principal Path” algorithm by analyzing Convolutional Neural Networks induced vector spaces. This application is conducted in the music and visual arts domains.

Development of machine learning methods for multi-modal biomarkers detection and integration

In medicine, innovation depends on a better knowledge of the human body mechanism, which represents a complex system of multi-scale constituents. Unraveling the complexity underneath diseases proves to be challenging. A deep understanding of the inner workings comes with dealing with many heterogeneous information. Exploring the molecular status and the organization of genes, proteins, metabolites provides insights on what is driving a disease, from aggressiveness to curability. Molecular constituents, however, are only the building blocks of the human body and cannot currently tell the whole story of diseases. This is why nowadays attention is growing towards the contemporary exploitation of multi-scale information. Holistic methods are then drawing interest to address the problem of integrating heterogeneous data. The heterogeneity may derive from the diversity across data types and from the diversity within diseases. Here, four studies conducted data integration using customly designed workflows that implement novel methods and views to tackle the heterogeneous characterization of diseases. The first study devoted to determine shared gene regulatory signatures for onco-hematology and it showed partial co-regulation across blood-related diseases. The second study focused on Acute Myeloid Leukemia and refined the unsupervised integration of genomic alterations, which turned out to better resemble clinical practice. In the third study, network integration for artherosclerosis demonstrated, as a proof of concept, the impact of network intelligibility when it comes to model heterogeneous data, which showed to accelerate the identification of new potential pharmaceutical targets. Lastly, the fourth study introduced a new method to integrate multiple data types in a unique latent heterogeneous-representation that facilitated the selection of important data types to predict the tumour stage of invasive ductal carcinoma. The results of these four studies laid the groundwork to ease the detection of new biomarkers ultimately beneficial to medical practice and to the ever-growing field of Personalized Medicine.

A Distributed Support based on Kubeflow to Ease MLOps of Federated Learning Algorithms

The main objective of my thesis work is to exploit the Google native and open-source platform Kubeflow, specifically using Kubeflow pipelines, to execute a Federated Learning scalable ML process in a 5G-like and simplified test architecture hosting a Kubernetes cluster and apply the largely adopted FedAVG algorithm and FedProx its optimization empowered by the ML platform ‘s abilities to ease the development and production cycle of this specific FL process. FL algorithms are more are and more promising and adopted both in Cloud application development and 5G communication enhancement through data coming from the monitoring of the underlying telco infrastructure and execution of training and data aggregation at edge nodes to optimize the global model of the algorithm ( that could be used for example for resource provisioning to reach an agreed QoS for the underlying network slice) and after a study and a research over the available papers and scientific articles related to FL with the help of the CTTC that suggests me to study and use Kubeflow to bear the algorithm we found out that this approach for the whole FL cycle deployment was not documented and may be interesting to investigate more in depth. This study may lead to prove the efficiency of the Kubeflow platform itself for this need of development of new FL algorithms that will support new Applications and especially test the FedAVG algorithm performances in a simulated client to cloud communication using a MNIST dataset for FL as benchmark.

Analysis of human posterior EEG alpha frequency as a function of implicit learning of probabilistic lateralized stimuli in a visual detection task

Alpha oscillatory activity has long been associated with perceptual and cognitive processes related to attention control. The aim of this study is to explore the task-dependent role of alpha frequency in a lateralized visuo-spatial detection task. Specifically, the thesis focuses on consolidating the scientific literature's knowledge about the role of alpha frequency in perceptual accuracy, and deepening the understanding of what determines trial-by-trial fluctuations of alpha parameters and how these fluctuations influence overall task performance. The hypotheses, confirmed empirically, were that different implicit strategies are put in place based on the task context, in order to maximize performance with optimal resource distribution (namely alpha frequency, associated positively with performance): “Lateralization” of the attentive resources towards one hemifield should be associated with higher alpha frequency difference between contralateral and ipsilateral hemisphere; “Distribution” of the attentive resources across hemifields should be associated with lower alpha frequency difference between hemispheres; These strategies, used by the participants according to their brain capabilities, have proven themselves adaptive or maladaptive depending on the different tasks to which they have been set: "Distribution" of the attentive resources seemed to be the best strategy when the distribution probability between hemifields was balanced: i.e. the neutral condition task. "Lateralization" of the attentive resources seemed to be more effective when the distribution probability between hemifields was biased towards one hemifield: i.e., the biased condition task.

Educational in a global environment: non-formal examples of learning practices at the international office

23rd SPACE AGM and Conference from 9 to 12 May 2012 Conference theme: The Role of Professional Higher Education: Responsibility and Reflection Venue: Mikkeli University of Applied Sciences, Mikkeli, Finland

Blended Learning project with Applied Optics. Case study

To show with the case of Applied Optics (AO), the adequacy of blended learning to the teaching/learning process in experimental Science and technology (S&T).

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Adaptive Learning in Games: Defining Profiles of Competitor Players

Artificial Intelligence has been applied to dynamic games for many years. The ultimate goal is creating responses in virtual entities that display human-like reasoning in the definition of their behaviors. However, virtual entities that can be mistaken for real persons are yet very far from being fully achieved. This paper presents an adaptive learning based methodology for the definition of players’ profiles, with the purpose of supporting decisions of virtual entities. The proposed methodology is based on reinforcement learning algorithms, which are responsible for choosing, along the time, with the gathering of experience, the most appropriate from a set of different learning approaches. These learning approaches have very distinct natures, from mathematical to artificial intelligence and data analysis methodologies, so that the methodology is prepared for very distinct situations. This way it is equipped with a variety of tools that individually can be useful for each encountered situation. The proposed methodology is tested firstly on two simpler computer versus human player games: the rock-paper-scissors game, and a penalty-shootout simulation. Finally, the methodology is applied to the definition of action profiles of electricity market players; players that compete in a dynamic game-wise environment, in which the main goal is the achievement of the highest possible profits in the market.

Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data

Propolis is a chemically complex biomass produced by honeybees (Apis mellifera) from plant resins added of salivary enzymes, beeswax, and pollen. The biological activities described for propolis were also identified for donor plants resin, but a big challenge for the standardization of the chemical composition and biological effects of propolis remains on a better understanding of the influence of seasonality on the chemical constituents of that raw material. Since propolis quality depends, among other variables, on the local flora which is strongly influenced by (a)biotic factors over the seasons, to unravel the harvest season effect on the propolis chemical profile is an issue of recognized importance. For that, fast, cheap, and robust analytical techniques seem to be the best choice for large scale quality control processes in the most demanding markets, e.g., human health applications. For that, UV-Visible (UV-Vis) scanning spectrophotometry of hydroalcoholic extracts (HE) of seventy-three propolis samples, collected over the seasons in 2014 (summer, spring, autumn, and winter) and 2015 (summer and autumn) in Southern Brazil was adopted. Further machine learning and chemometrics techniques were applied to the UV-Vis dataset aiming to gain insights as to the seasonality effect on the claimed chemical heterogeneity of propolis samples determined by changes in the flora of the geographic region under study. Descriptive and classification models were built following a chemometric approach, i.e. principal component analysis (PCA) and hierarchical clustering analysis (HCA) supported by scripts written in the R language. The UV-Vis profiles associated with chemometric analysis allowed identifying a typical pattern in propolis samples collected in the summer. Importantly, the discrimination based on PCA could be improved by using the dataset of the fingerprint region of phenolic compounds ( = 280-400m), suggesting that besides the biological activities of those secondary metabolites, they also play a relevant role for the discrimination and classification of that complex matrix through bioinformatics tools. Finally, a series of machine learning approaches, e.g., partial least square-discriminant analysis (PLS-DA), k-Nearest Neighbors (kNN), and Decision Trees showed to be complementary to PCA and HCA, allowing to obtain relevant information as to the sample discrimination.

Analysis, modelling and classification of geospatial data using machine learning

The research considers the problem of spatial data classification using machine learning algorithms: probabilistic neural networks (PNN) and support vector machines (SVM). As a benchmark model simple k-nearest neighbor algorithm is considered. PNN is a neural network reformulation of well known nonparametric principles of probability density modeling using kernel density estimator and Bayesian optimal or maximum a posteriori decision rules. PNN is well suited to problems where not only predictions but also quantification of accuracy and integration of prior information are necessary. An important property of PNN is that they can be easily used in decision support systems dealing with problems of automatic classification. Support vector machine is an implementation of the principles of statistical learning theory for the classification tasks. Recently they were successfully applied for different environmental topics: classification of soil types and hydro-geological units, optimization of monitoring networks, susceptibility mapping of natural hazards. In the present paper both simulated and real data case studies (low and high dimensional) are considered. The main attention is paid to the detection and learning of spatial patterns by the algorithms applied.

Reinforcement learning utilizes proxemics: an avatar learns to manipulate the position of people in immersive virtual reality

A reinforcement learning (RL) method was used to train a virtual character to move participants to a specified location. The virtual environment depicted an alleyway displayed through a wide field-of-view head-tracked stereo head-mounted display. Based on proxemics theory, we predicted that when the character approached within a personal or intimate distance to the participants, they would be inclined to move backwards out of the way. We carried out a between-groups experiment with 30 female participants, with 10 assigned arbitrarily to each of the following three groups: In the Intimate condition the character could approach within 0.38m and in the Social condition no nearer than 1.2m. In the Random condition the actions of the virtual character were chosen randomly from among the same set as in the RL method, and the virtual character could approach within 0.38m. The experiment continued in each case until the participant either reached the target or 7 minutes had elapsed. The distributions of the times taken to reach the target showed significant differences between the three groups, with 9 out of 10 in the Intimate condition reaching the target significantly faster than the 6 out of 10 who reached the target in the Social condition. Only 1 out of 10 in the Random condition reached the target. The experiment is an example of applied presence theory: we rely on the many findings that people tend to respond realistically in immersive virtual environments, and use this to get people to achieve a task of which they had been unaware. This method opens up the door for many such applications where the virtual environment adapts to the responses of the human participants with the aim of achieving particular goals.

Reinforcement learning utilizes proxemics: an avatar learns to manipulate the position of people in immersive virtual reality

A reinforcement learning (RL) method was used to train a virtual character to move participants to a specified location. The virtual environment depicted an alleyway displayed through a wide field-of-view head-tracked stereo head-mounted display. Based on proxemics theory, we predicted that when the character approached within a personal or intimate distance to the participants, they would be inclined to move backwards out of the way. We carried out a between-groups experiment with 30 female participants, with 10 assigned arbitrarily to each of the following three groups: In the Intimate condition the character could approach within 0.38m and in the Social condition no nearer than 1.2m. In the Random condition the actions of the virtual character were chosen randomly from among the same set as in the RL method, and the virtual character could approach within 0.38m. The experiment continued in each case until the participant either reached the target or 7 minutes had elapsed. The distributions of the times taken to reach the target showed significant differences between the three groups, with 9 out of 10 in the Intimate condition reaching the target significantly faster than the 6 out of 10 who reached the target in the Social condition. Only 1 out of 10 in the Random condition reached the target. The experiment is an example of applied presence theory: we rely on the many findings that people tend to respond realistically in immersive virtual environments, and use this to get people to achieve a task of which they had been unaware. This method opens up the door for many such applications where the virtual environment adapts to the responses of the human participants with the aim of achieving particular goals.