Data-driven and data-oriented methods for materials science and technologies

The discovery of new materials and their functions has always been a fundamental component of technological progress. Nowadays, the quest for new materials is stronger than ever: sustainability, medicine, robotics and electronics are all key assets which depend on the ability to create specifically tailored materials. However, designing materials with desired properties is a difficult task, and the complexity of the discipline makes it difficult to identify general criteria. While scientists developed a set of best practices (often based on experience and expertise), this is still a trial-and-error process. This becomes even more complex when dealing with advanced functional materials. Their properties depend on structural and morphological features, which in turn depend on fabrication procedures and environment, and subtle alterations leads to dramatically different results. Because of this, materials modeling and design is one of the most prolific research fields. Many techniques and instruments are continuously developed to enable new possibilities, both in the experimental and computational realms. Scientists strive to enforce cutting-edge technologies in order to make progress. However, the field is strongly affected by unorganized file management, proliferation of custom data formats and storage procedures, both in experimental and computational research. Results are difficult to find, interpret and re-use, and a huge amount of time is spent interpreting and re-organizing data. This also strongly limit the application of data-driven and machine learning techniques. This work introduces possible solutions to the problems described above. Specifically, it talks about developing features for specific classes of advanced materials and use them to train machine learning models and accelerate computational predictions for molecular compounds; developing method for organizing non homogeneous materials data; automate the process of using devices simulations to train machine learning models; dealing with scattered experimental data and use them to discover new patterns.

Data driven regularization models of non-linear ill-posed inverse problems in imaging

Imaging technologies are widely used in application fields such as natural sciences, engineering, medicine, and life sciences. A broad class of imaging problems reduces to solve ill-posed inverse problems (IPs). Traditional strategies to solve these ill-posed IPs rely on variational regularization methods, which are based on minimization of suitable energies, and make use of knowledge about the image formation model (forward operator) and prior knowledge on the solution, but lack in incorporating knowledge directly from data. On the other hand, the more recent learned approaches can easily learn the intricate statistics of images depending on a large set of data, but do not have a systematic method for incorporating prior knowledge about the image formation model. The main purpose of this thesis is to discuss data-driven image reconstruction methods which combine the benefits of these two different reconstruction strategies for the solution of highly nonlinear ill-posed inverse problems. Mathematical formulation and numerical approaches for image IPs, including linear as well as strongly nonlinear problems are described. More specifically we address the Electrical impedance Tomography (EIT) reconstruction problem by unrolling the regularized Gauss-Newton method and integrating the regularization learned by a data-adaptive neural network. Furthermore we investigate the solution of non-linear ill-posed IPs introducing a deep-PnP framework that integrates the graph convolutional denoiser into the proximal Gauss-Newton method with a practical application to the EIT, a recently introduced promising imaging technique. Efficient algorithms are then applied to the solution of the limited electrods problem in EIT, combining compressive sensing techniques and deep learning strategies. Finally, a transformer-based neural network architecture is adapted to restore the noisy solution of the Computed Tomography problem recovered using the filtered back-projection method.

Data-driven multivariate flood hazard modeling

The present Dissertation shows how recent statistical analysis tools and open datasets can be exploited to improve modelling accuracy in two distinct yet interconnected domains of flood hazard (FH) assessment. In the first Part, unsupervised artificial neural networks are employed as regional models for sub-daily rainfall extremes. The models aim to learn a robust relation to estimate locally the parameters of Gumbel distributions of extreme rainfall depths for any sub-daily duration (1-24h). The predictions depend on twenty morphoclimatic descriptors. A large study area in north-central Italy is adopted, where 2238 annual maximum series are available. Validation is performed over an independent set of 100 gauges. Our results show that multivariate ANNs may remarkably improve the estimation of percentiles relative to the benchmark approach from the literature, where Gumbel parameters depend on mean annual precipitation. Finally, we show that the very nature of the proposed ANN models makes them suitable for interpolating predicted sub-daily rainfall quantiles across space and time-aggregation intervals. In the second Part, decision trees are used to combine a selected blend of input geomorphic descriptors for predicting FH. Relative to existing DEM-based approaches, this method is innovative, as it relies on the combination of three characteristics: (1) simple multivariate models, (2) a set of exclusively DEM-based descriptors as input, and (3) an existing FH map as reference information. First, the methods are applied to northern Italy, represented with the MERIT DEM (∼90m resolution), and second, to the whole of Italy, represented with the EU-DEM (25m resolution). The results show that multivariate approaches may (a) significantly enhance flood-prone areas delineation relative to a selected univariate one, (b) provide accurate predictions of expected inundation depths, (c) produce encouraging results in extrapolation, (d) complete the information of imperfect reference maps, and (e) conveniently convert binary maps into continuous representation of FH.

Data-driven Signal Processing per Jamming Detection in Sistemi Satellitari

In questo elaborato vengono analizzate differenti tecniche per la detection di jammer attivi e costanti in una comunicazione satellitare in uplink. Osservando un numero limitato di campioni ricevuti si vuole identificare la presenza di un jammer. A tal fine sono stati implementati i seguenti classificatori binari: support vector machine (SVM), multilayer perceptron (MLP), spectrum guarding e autoencoder. Questi algoritmi di apprendimento automatico dipendono dalle features che ricevono in ingresso, per questo motivo è stata posta particolare attenzione alla loro scelta. A tal fine, sono state confrontate le accuratezze ottenute dai detector addestrati utilizzando differenti tipologie di informazione come: i segnali grezzi nel tempo, le statistical features, le trasformate wavelet e lo spettro ciclico. I pattern prodotti dall’estrazione di queste features dai segnali satellitari possono avere dimensioni elevate, quindi, prima della detection, vengono utilizzati i seguenti algoritmi per la riduzione della dimensionalità: principal component analysis (PCA) e linear discriminant analysis (LDA). Lo scopo di tale processo non è quello di eliminare le features meno rilevanti, ma combinarle in modo da preservare al massimo l’informazione, evitando problemi di overfitting e underfitting. Le simulazioni numeriche effettuate hanno evidenziato come lo spettro ciclico sia in grado di fornire le features migliori per la detection producendo però pattern di dimensioni elevate, per questo motivo è stato necessario l’utilizzo di algoritmi di riduzione della dimensionalità. In particolare, l'algoritmo PCA è stato in grado di estrarre delle informazioni migliori rispetto a LDA, le cui accuratezze risentivano troppo del tipo di jammer utilizzato nella fase di addestramento. Infine, l’algoritmo che ha fornito le prestazioni migliori è stato il Multilayer Perceptron che ha richiesto tempi di addestramento contenuti e dei valori di accuratezza elevati.

Iberian peninsula ecosystem carbon fluxes: a model-data integration study

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia do Ambiente pela Universidade Nova de Lisboa,Faculdade de Ciências e Tecnologia

Modelling Z→ττ processes in ATLAS with τ-embedded Z→μμ data

This paper describes the concept, technical realisation and validation of a largely data-driven method to model events with Z→ττ decays. In Z→μμ events selected from proton-proton collision data recorded at s√=8 TeV with the ATLAS experiment at the LHC in 2012, the Z decay muons are replaced by τ leptons from simulated Z→ττ decays at the level of reconstructed tracks and calorimeter cells. The τ lepton kinematics are derived from the kinematics of the original muons. Thus, only the well-understood decays of the Z boson and τ leptons as well as the detector response to the τ decay products are obtained from simulation. All other aspects of the event, such as the Z boson and jet kinematics as well as effects from multiple interactions, are given by the actual data. This so-called τ-embedding method is particularly relevant for Higgs boson searches and analyses in ττ final states, where Z→ττ decays constitute a large irreducible background that cannot be obtained directly from data control samples.

Environmental data mining and modeling based on machine learning algorithms and geostatistics

The paper presents some contemporary approaches to spatial environmental data analysis. The main topics are concentrated on the decision-oriented problems of environmental spatial data mining and modeling: valorization and representativity of data with the help of exploratory data analysis, spatial predictions, probabilistic and risk mapping, development and application of conditional stochastic simulation models. The innovative part of the paper presents integrated/hybrid model-machine learning (ML) residuals sequential simulations-MLRSS. The models are based on multilayer perceptron and support vector regression ML algorithms used for modeling long-range spatial trends and sequential simulations of the residuals. NIL algorithms deliver non-linear solution for the spatial non-stationary problems, which are difficult for geostatistical approach. Geostatistical tools (variography) are used to characterize performance of ML algorithms, by analyzing quality and quantity of the spatially structured information extracted from data with ML algorithms. Sequential simulations provide efficient assessment of uncertainty and spatial variability. Case study from the Chernobyl fallouts illustrates the performance of the proposed model. It is shown that probability mapping, provided by the combination of ML data driven and geostatistical model based approaches, can be efficiently used in decision-making process. (C) 2003 Elsevier Ltd. All rights reserved.

Efficient estimation using the characteristic function : theory and applications with high frequency data

The attached file is created with Scientific Workplace Latex

THEORETICAL STUDIES ON THE METHODS OF RECONSTRUCTING PHYLOGENETIC TREES FROM DNA SEQUENCE DATA (MOLECULAR EVOLUTION, HOMINOID EVOLUTION, COMPUTER SIMULATION)

(1) A mathematical theory for computing the probabilities of various nucleotide configurations is developed, and the probability of obtaining the correct phylogenetic tree (model tree) from sequence data is evaluated for six phylogenetic tree-making methods (UPGMA, distance Wagner method, transformed distance method, Fitch-Margoliash's method, maximum parsimony method, and compatibility method). The number of nucleotides (m*) necessary to obtain the correct tree with a probability of 95% is estimated with special reference to the human, chimpanzee, and gorilla divergence. m* is at least 4,200, but the availability of outgroup species greatly reduces m* for all methods except UPGMA. m* increases if transitions occur more frequently than transversions as in the case of mitochondrial DNA. (2) A new tree-making method called the neighbor-joining method is proposed. This method is applicable either for distance data or character state data. Computer simulation has shown that the neighbor-joining method is generally better than UPGMA, Farris' method, Li's method, and modified Farris method on recovering the true topology when distance data are used. A related method, the simultaneous partitioning method, is also discussed. (3) The maximum likelihood (ML) method for phylogeny reconstruction under the assumption of both constant and varying evolutionary rates is studied, and a new algorithm for obtaining the ML tree is presented. This method gives a tree similar to that obtained by UPGMA when constant evolutionary rate is assumed, whereas it gives a tree similar to that obtained by the maximum parsimony tree and the neighbor-joining method when varying evolutionary rate is assumed. ^

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.

A Novel Nonparametric Density Estimator

We present a novel nonparametric density estimator and a new data-driven bandwidth selection method with excellent properties. The approach is in- spired by the principles of the generalized cross entropy method. The pro- posed density estimation procedure has numerous advantages over the tra- ditional kernel density estimator methods. Firstly, for the first time in the nonparametric literature, the proposed estimator allows for a genuine incor- poration of prior information in the density estimation procedure. Secondly, the approach provides the first data-driven bandwidth selection method that is guaranteed to provide a unique bandwidth for any data. Lastly, simulation examples suggest the proposed approach outperforms the current state of the art in nonparametric density estimation in terms of accuracy and reliability.

Análise do desempenho da tecnologia 4G LTE

O objectivo deste trabalho passa pelo desenvolvimento de uma ferramenta de simulação dinâmica de recursos rádio em LTE no sentido descendente, com recurso à Framework OMNeT++. A ferramenta desenvolvida permite realizar o planeamento das estações base, simulação e análise de resultados. São descritos os principais aspectos da tecnologia de acesso rádio, designadamente a arquitectura da rede, a codificação, definição dos recursos rádio, os ritmos de transmissão suportados ao nível de canal e o mecanismo de controlo de admissão. Foi definido o cenário de utilização de recursos rádio que inclui a definição de modelos de tráfego e de serviços orientados a pacotes e circuitos. Foi ainda considerado um cenário de referência para a verificação e validação do modelo de simulação. A simulação efectua-se ao nível de sistema, suportada por um modelo dinâmico, estocástico e orientado por eventos discretos de modo a contemplar os diferentes mecanismos característicos da tecnologia OFDMA. Os resultados obtidos permitem a análise de desempenho dos serviços, estações base e sistema ao nível do throughput médio da rede, throughput médio por eNodeB e throughput médio por móvel para além de permitir analisar o contributo de outros parâmetros designadamente, largura de banda, raio de cobertura, perfil dos serviços, esquema de modulação, entre outros. Dos resultados obtidos foi possível verificar que, considerando um cenário com estações base com raio de cobertura de 100 m obteve-se um throughput ao nível do utilizador final igual a 4.69494 Mbps, ou seja, 7 vezes superior quando comparado a estações base com raios de cobertura de 200m.

Improving discovery in the life sciences using semantic Web technologies and linked data: design principles for life sciences knowledge organization systems

Dissertation presented to obtain the Ph.D degree in Bioinformatics

Combining data mining and evolutionary computation for multi-criteria optimization of earthworks

Earthworks tasks aim at levelling the ground surface at a target construction area and precede any kind of structural construction (e.g., road and railway construction). It is comprised of sequential tasks, such as excavation, transportation, spreading and compaction, and it is strongly based on heavy mechanical equipment and repetitive processes. Under this context, it is essential to optimize the usage of all available resources under two key criteria: the costs and duration of earthwork projects. In this paper, we present an integrated system that uses two artificial intelligence based techniques: data mining and evolutionary multi-objective optimization. The former is used to build data-driven models capable of providing realistic estimates of resource productivity, while the latter is used to optimize resource allocation considering the two main earthwork objectives (duration and cost). Experiments held using real-world data, from a construction site, have shown that the proposed system is competitive when compared with current manual earthwork design.

Measurement of the top-quark mass in the fully hadronic decay channel from ATLAS data at s√=7 TeV

The mass of the top quark is measured in a data set corresponding to 4.6 fb−1 of proton--proton collisions with centre-of-mass energy s√=7 TeV collected by the ATLAS detector at the LHC. Events consistent with hadronic decays of top--antitop quark pairs with at least six jets in the final state are selected. The substantial background from multijet production is modelled with data-driven methods that utilise the number of identified b-quark jets and the transverse momentum of the sixth leading jet, which have minimal correlation. The top-quark mass is obtained from template fits to the ratio of three-jet to dijet mass. The three-jet mass is calculated from the three jets of a top-quark decay. Using these three jets the dijet mass is obtained from the two jets of the W boson decay. The top-quark mass obtained from this fit is thus less sensitive to the uncertainty in the energy measurement of the jets. A binned likelihood fit yields a top-quark mass of mt = 175.1 ± 1.4 (stat.) ± 1.2 (syst.) GeV.