6,781 research outputs found

    Undergraduate Catalog of Studies, 2023-2024

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    Exploring missing heritability in neurodevelopmental disorders:Learning from regulatory elements

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    In this thesis, I aimed to solve part of the missing heritability in neurodevelopmental disorders, using computational approaches. Next to the investigations of a novel epilepsy syndrome and investigations aiming to elucidate the regulation of the gene involved, I investigated and prioritized genomic sequences that have implications in gene regulation during the developmental stages of human brain, with the goal to create an atlas of high confidence non-coding regulatory elements that future studies can assess for genetic variants in genetically unexplained individuals suffering from neurodevelopmental disorders that are of suspected genetic origin

    A Survey on Forensics and Compliance Auditing for Critical Infrastructure Protection

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    The broadening dependency and reliance that modern societies have on essential services provided by Critical Infrastructures is increasing the relevance of their trustworthiness. However, Critical Infrastructures are attractive targets for cyberattacks, due to the potential for considerable impact, not just at the economic level but also in terms of physical damage and even loss of human life. Complementing traditional security mechanisms, forensics and compliance audit processes play an important role in ensuring Critical Infrastructure trustworthiness. Compliance auditing contributes to checking if security measures are in place and compliant with standards and internal policies. Forensics assist the investigation of past security incidents. Since these two areas significantly overlap, in terms of data sources, tools and techniques, they can be merged into unified Forensics and Compliance Auditing (FCA) frameworks. In this paper, we survey the latest developments, methodologies, challenges, and solutions addressing forensics and compliance auditing in the scope of Critical Infrastructure Protection. This survey focuses on relevant contributions, capable of tackling the requirements imposed by massively distributed and complex Industrial Automation and Control Systems, in terms of handling large volumes of heterogeneous data (that can be noisy, ambiguous, and redundant) for analytic purposes, with adequate performance and reliability. The achieved results produced a taxonomy in the field of FCA whose key categories denote the relevant topics in the literature. Also, the collected knowledge resulted in the establishment of a reference FCA architecture, proposed as a generic template for a converged platform. These results are intended to guide future research on forensics and compliance auditing for Critical Infrastructure Protection.info:eu-repo/semantics/publishedVersio

    Flood dynamics derived from video remote sensing

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    Flooding is by far the most pervasive natural hazard, with the human impacts of floods expected to worsen in the coming decades due to climate change. Hydraulic models are a key tool for understanding flood dynamics and play a pivotal role in unravelling the processes that occur during a flood event, including inundation flow patterns and velocities. In the realm of river basin dynamics, video remote sensing is emerging as a transformative tool that can offer insights into flow dynamics and thus, together with other remotely sensed data, has the potential to be deployed to estimate discharge. Moreover, the integration of video remote sensing data with hydraulic models offers a pivotal opportunity to enhance the predictive capacity of these models. Hydraulic models are traditionally built with accurate terrain, flow and bathymetric data and are often calibrated and validated using observed data to obtain meaningful and actionable model predictions. Data for accurately calibrating and validating hydraulic models are not always available, leaving the assessment of the predictive capabilities of some models deployed in flood risk management in question. Recent advances in remote sensing have heralded the availability of vast video datasets of high resolution. The parallel evolution of computing capabilities, coupled with advancements in artificial intelligence are enabling the processing of data at unprecedented scales and complexities, allowing us to glean meaningful insights into datasets that can be integrated with hydraulic models. The aims of the research presented in this thesis were twofold. The first aim was to evaluate and explore the potential applications of video from air- and space-borne platforms to comprehensively calibrate and validate two-dimensional hydraulic models. The second aim was to estimate river discharge using satellite video combined with high resolution topographic data. In the first of three empirical chapters, non-intrusive image velocimetry techniques were employed to estimate river surface velocities in a rural catchment. For the first time, a 2D hydraulicvmodel was fully calibrated and validated using velocities derived from Unpiloted Aerial Vehicle (UAV) image velocimetry approaches. This highlighted the value of these data in mitigating the limitations associated with traditional data sources used in parameterizing two-dimensional hydraulic models. This finding inspired the subsequent chapter where river surface velocities, derived using Large Scale Particle Image Velocimetry (LSPIV), and flood extents, derived using deep neural network-based segmentation, were extracted from satellite video and used to rigorously assess the skill of a two-dimensional hydraulic model. Harnessing the ability of deep neural networks to learn complex features and deliver accurate and contextually informed flood segmentation, the potential value of satellite video for validating two dimensional hydraulic model simulations is exhibited. In the final empirical chapter, the convergence of satellite video imagery and high-resolution topographical data bridges the gap between visual observations and quantitative measurements by enabling the direct extraction of velocities from video imagery, which is used to estimate river discharge. Overall, this thesis demonstrates the significant potential of emerging video-based remote sensing datasets and offers approaches for integrating these data into hydraulic modelling and discharge estimation practice. The incorporation of LSPIV techniques into flood modelling workflows signifies a methodological progression, especially in areas lacking robust data collection infrastructure. Satellite video remote sensing heralds a major step forward in our ability to observe river dynamics in real time, with potentially significant implications in the domain of flood modelling science

    Computational Analyses of Metagenomic Data

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    Metagenomics studies the collective microbial genomes extracted from a particular environment without requiring the culturing or isolation of individual genomes, addressing questions revolving around the composition, functionality, and dynamics of microbial communities. The intrinsic complexity of metagenomic data and the diversity of applications call for efficient and accurate computational methods in data handling. In this thesis, I present three primary projects that collectively focus on the computational analysis of metagenomic data, each addressing a distinct topic. In the first project, I designed and implemented an algorithm named Mapbin for reference-free genomic binning of metagenomic assemblies. Binning aims to group a mixture of genomic fragments based on their genome origin. Mapbin enhances binning results by building a multilayer network that combines the initial binning, assembly graph, and read-pairing information from paired-end sequencing data. The network is further partitioned by the community-detection algorithm, Infomap, to yield a new binning result. Mapbin was tested on multiple simulated and real datasets. The results indicated an overall improvement in the common binning quality metrics. The second and third projects are both derived from ImMiGeNe, a collaborative and multidisciplinary study investigating the interplay between gut microbiota, host genetics, and immunity in stem-cell transplantation (SCT) patients. In the second project, I conducted microbiome analyses for the metagenomic data. The workflow included the removal of contaminant reads and multiple taxonomic and functional profiling. The results revealed that the SCT recipients' samples yielded significantly fewer reads with heavy contamination of the host DNA, and their microbiomes displayed evident signs of dysbiosis. Finally, I discussed several inherent challenges posed by extremely low levels of target DNA and high levels of contamination in the recipient samples, which cannot be rectified solely through bioinformatics approaches. The primary goal of the third project is to design a set of primers that can be used to cover bacterial flagellin genes present in the human gut microbiota. Considering the notable diversity of flagellins, I incorporated a method to select representative bacterial flagellin gene sequences, a heuristic approach based on established primer design methods to generate a degenerate primer set, and a selection method to filter genes unlikely to occur in the human gut microbiome. As a result, I successfully curated a reduced yet representative set of primers that would be practical for experimental implementation

    On the Generation of Realistic and Robust Counterfactual Explanations for Algorithmic Recourse

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    This recent widespread deployment of machine learning algorithms presents many new challenges. Machine learning algorithms are usually opaque and can be particularly difficult to interpret. When humans are involved, algorithmic and automated decisions can negatively impact people’s lives. Therefore, end users would like to be insured against potential harm. One popular way to achieve this is to provide end users access to algorithmic recourse, which gives end users negatively affected by algorithmic decisions the opportunity to reverse unfavorable decisions, e.g., from a loan denial to a loan acceptance. In this thesis, we design recourse algorithms to meet various end user needs. First, we propose methods for the generation of realistic recourses. We use generative models to suggest recourses likely to occur under the data distribution. To this end, we shift the recourse action from the input space to the generative model’s latent space, allowing to generate counterfactuals that lie in regions with data support. Second, we observe that small changes applied to the recourses prescribed to end users likely invalidate the suggested recourse after being nosily implemented in practice. Motivated by this observation, we design methods for the generation of robust recourses and for assessing the robustness of recourse algorithms to data deletion requests. Third, the lack of a commonly used code-base for counterfactual explanation and algorithmic recourse algorithms and the vast array of evaluation measures in literature make it difficult to compare the per formance of different algorithms. To solve this problem, we provide an open source benchmarking library that streamlines the evaluation process and can be used for benchmarking, rapidly developing new methods, and setting up new experiments. In summary, our work contributes to a more reliable interaction of end users and machine learned models by covering fundamental aspects of the recourse process and suggests new solutions towards generating realistic and robust counterfactual explanations for algorithmic recourse

    Statistical analysis of grouped text documents

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    L'argomento di questa tesi sono i modelli statistici per l'analisi dei dati testuali, con particolare attenzione ai contesti in cui i campioni di testo sono raggruppati. Quando si ha a che fare con dati testuali, il primo problema è quello di elaborarli, per renderli compatibili dal punto di vista computazionale e metodologico con i metodi matematici e statistici prodotti e continuamente sviluppati dalla comunità scientifica. Per questo motivo, la tesi passa in rassegna i metodi esistenti per la rappresentazione analitica e l'elaborazione di campioni di dati testuali, compresi i "Vector Space Models", le "rappresentazioni distribuite" di parole e documenti e i "contextualized embeddings". Questa rassegna comporta la standardizzazione di una notazione che, anche all'interno dello stesso approccio di rappresentazione, appare molto eterogenea in letteratura. Vengono poi esplorati due domini di applicazione: i social media e il turismo culturale. Per quanto riguarda il primo, viene proposto uno studio sull'autodescrizione di gruppi diversi di individui sulla piattaforma StockTwits, dove i mercati finanziari sono gli argomenti dominanti. La metodologia proposta ha integrato diversi tipi di dati, sia testuali che variabili categoriche. Questo studio ha agevolato la comprensione sul modo in cui le persone si presentano online e ha trovato stutture di comportamento ricorrenti all'interno di gruppi di utenti. Per quanto riguarda il turismo culturale, la tesi approfondisce uno studio condotto nell'ambito del progetto "Data Science for Brescia - Arts and Cultural Places", in cui è stato addestrato un modello linguistico per classificare le recensioni online scritte in italiano in quattro aree semantiche distinte relative alle attrazioni culturali della città di Brescia. Il modello proposto permette di identificare le attrazioni nei documenti di testo, anche quando non sono esplicitamente menzionate nei metadati del documento, aprendo così la possibilità di espandere il database relativo a queste attrazioni culturali con nuove fonti, come piattaforme di social media, forum e altri spazi online. Infine, la tesi presenta uno studio metodologico che esamina la specificità di gruppo delle parole, analizzando diversi stimatori di specificità di gruppo proposti in letteratura. Lo studio ha preso in considerazione documenti testuali raggruppati con variabile di "outcome" e variabile di gruppo. Il suo contributo consiste nella proposta di modellare il corpus di documenti come una distribuzione multivariata, consentendo la simulazione di corpora di documenti di testo con caratteristiche predefinite. La simulazione ha fornito preziose indicazioni sulla relazione tra gruppi di documenti e parole. Inoltre, tutti i risultati possono essere liberamente esplorati attraverso un'applicazione web, i cui componenti sono altresì descritti in questo manoscritto. In conclusione, questa tesi è stata concepita come una raccolta di studi, ognuno dei quali suggerisce percorsi di ricerca futuri per affrontare le sfide dell'analisi dei dati testuali raggruppati.The topic of this thesis is statistical models for the analysis of textual data, emphasizing contexts in which text samples are grouped. When dealing with text data, the first issue is to process it, making it computationally and methodologically compatible with the existing mathematical and statistical methods produced and continually developed by the scientific community. Therefore, the thesis firstly reviews existing methods for analytically representing and processing textual datasets, including Vector Space Models, distributed representations of words and documents, and contextualized embeddings. It realizes this review by standardizing a notation that, even within the same representation approach, appears highly heterogeneous in the literature. Then, two domains of application are explored: social media and cultural tourism. About the former, a study is proposed about self-presentation among diverse groups of individuals on the StockTwits platform, where finance and stock markets are the dominant topics. The methodology proposed integrated various types of data, including textual and categorical data. This study revealed insights into how people present themselves online and found recurring patterns within groups of users. About the latter, the thesis delves into a study conducted as part of the "Data Science for Brescia - Arts and Cultural Places" Project, where a language model was trained to classify Italian-written online reviews into four distinct semantic areas related to cultural attractions in the Italian city of Brescia. The model proposed allows for the identification of attractions in text documents, even when not explicitly mentioned in document metadata, thus opening possibilities for expanding the database related to these cultural attractions with new sources, such as social media platforms, forums, and other online spaces. Lastly, the thesis presents a methodological study examining the group-specificity of words, analyzing various group-specificity estimators proposed in the literature. The study considered grouped text documents with both outcome and group variables. Its contribution consists of the proposal of modeling the corpus of documents as a multivariate distribution, enabling the simulation of corpora of text documents with predefined characteristics. The simulation provided valuable insights into the relationship between groups of documents and words. Furthermore, all its results can be freely explored through a web application, whose components are also described in this manuscript. In conclusion, this thesis has been conceived as a collection of papers. It aimed to contribute to the field with both applications and methodological proposals, and each study presented here suggests paths for future research to address the challenges in the analysis of grouped textual data

    Dataflow Programming and Acceleration of Computationally-Intensive Algorithms

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    The volume of unstructured textual information continues to grow due to recent technological advancements. This resulted in an exponential growth of information generated in various formats, including blogs, posts, social networking, and enterprise documents. Numerous Enterprise Architecture (EA) documents are also created daily, such as reports, contracts, agreements, frameworks, architecture requirements, designs, and operational guides. The processing and computation of this massive amount of unstructured information necessitate substantial computing capabilities and the implementation of new techniques. It is critical to manage this unstructured information through a centralized knowledge management platform. Knowledge management is the process of managing information within an organization. This involves creating, collecting, organizing, and storing information in a way that makes it easily accessible and usable. The research involved the development textual knowledge management system, and two use cases were considered for extracting textual knowledge from documents. The first case study focused on the safety-critical documents of a railway enterprise. Safety is of paramount importance in the railway industry. There are several EA documents including manuals, operational procedures, and technical guidelines that contain critical information. Digitalization of these documents is essential for analysing vast amounts of textual knowledge that exist in these documents to improve the safety and security of railway operations. A case study was conducted between the University of Huddersfield and the Railway Safety Standard Board (RSSB) to analyse EA safety documents using Natural language processing (NLP). A graphical user interface was developed that includes various document processing features such as semantic search, document mapping, text summarization, and visualization of key trends. For the second case study, open-source data was utilized, and textual knowledge was extracted. Several features were also developed, including kernel distribution, analysis offkey trends, and sentiment analysis of words (such as unique, positive, and negative) within the documents. Additionally, a heterogeneous framework was designed using CPU/GPU and FPGAs to analyse the computational performance of document mapping

    Analysis and Design of Non-Orthogonal Multiple Access (NOMA) Techniques for Next Generation Wireless Communication Systems

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    The current surge in wireless connectivity, anticipated to amplify significantly in future wireless technologies, brings a new wave of users. Given the impracticality of an endlessly expanding bandwidth, there’s a pressing need for communication techniques that efficiently serve this burgeoning user base with limited resources. Multiple Access (MA) techniques, notably Orthogonal Multiple Access (OMA), have long addressed bandwidth constraints. However, with escalating user numbers, OMA’s orthogonality becomes limiting for emerging wireless technologies. Non-Orthogonal Multiple Access (NOMA), employing superposition coding, serves more users within the same bandwidth as OMA by allocating different power levels to users whose signals can then be detected using the gap between them, thus offering superior spectral efficiency and massive connectivity. This thesis examines the integration of NOMA techniques with cooperative relaying, EXtrinsic Information Transfer (EXIT) chart analysis, and deep learning for enhancing 6G and beyond communication systems. The adopted methodology aims to optimize the systems’ performance, spanning from bit-error rate (BER) versus signal to noise ratio (SNR) to overall system efficiency and data rates. The primary focus of this thesis is the investigation of the integration of NOMA with cooperative relaying, EXIT chart analysis, and deep learning techniques. In the cooperative relaying context, NOMA notably improved diversity gains, thereby proving the superiority of combining NOMA with cooperative relaying over just NOMA. With EXIT chart analysis, NOMA achieved low BER at mid-range SNR as well as achieved optimal user fairness in the power allocation stage. Additionally, employing a trained neural network enhanced signal detection for NOMA in the deep learning scenario, thereby producing a simpler signal detection for NOMA which addresses NOMAs’ complex receiver problem
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