574 research outputs found

    Inter-individual variation of the human epigenome & applications

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    Mobile Device Background Sensors: Authentication vs Privacy

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    The increasing number of mobile devices in recent years has caused the collection of a large amount of personal information that needs to be protected. To this aim, behavioural biometrics has become very popular. But, what is the discriminative power of mobile behavioural biometrics in real scenarios? With the success of Deep Learning (DL), architectures based on Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs), such as Long Short-Term Memory (LSTM), have shown improvements compared to traditional machine learning methods. However, these DL architectures still have limitations that need to be addressed. In response, new DL architectures like Transformers have emerged. The question is, can these new Transformers outperform previous biometric approaches? To answers to these questions, this thesis focuses on behavioural biometric authentication with data acquired from mobile background sensors (i.e., accelerometers and gyroscopes). In addition, to the best of our knowledge, this is the first thesis that explores and proposes novel behavioural biometric systems based on Transformers, achieving state-of-the-art results in gait, swipe, and keystroke biometrics. The adoption of biometrics requires a balance between security and privacy. Biometric modalities provide a unique and inherently personal approach for authentication. Nevertheless, biometrics also give rise to concerns regarding the invasion of personal privacy. According to the General Data Protection Regulation (GDPR) introduced by the European Union, personal data such as biometric data are sensitive and must be used and protected properly. This thesis analyses the impact of sensitive data in the performance of biometric systems and proposes a novel unsupervised privacy-preserving approach. The research conducted in this thesis makes significant contributions, including: i) a comprehensive review of the privacy vulnerabilities of mobile device sensors, covering metrics for quantifying privacy in relation to sensitive data, along with protection methods for safeguarding sensitive information; ii) an analysis of authentication systems for behavioural biometrics on mobile devices (i.e., gait, swipe, and keystroke), being the first thesis that explores the potential of Transformers for behavioural biometrics, introducing novel architectures that outperform the state of the art; and iii) a novel privacy-preserving approach for mobile biometric gait verification using unsupervised learning techniques, ensuring the protection of sensitive data during the verification process

    Inter-individual variation of the human epigenome & applications

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    Genome-wide association studies (GWAS) have led to the discovery of genetic variants influencing human phenotypes in health and disease. However, almost two decades later, most human traits can still not be accurately predicted from common genetic variants. Moreover, genetic variants discovered via GWAS mostly map to the non-coding genome and have historically resisted interpretation via mechanistic models. Alternatively, the epigenome lies in the cross-roads between genetics and the environment. Thus, there is great excitement towards the mapping of epigenetic inter-individual variation since its study may link environmental factors to human traits that remain unexplained by genetic variants. For instance, the environmental component of the epigenome may serve as a source of biomarkers for accurate, robust and interpretable phenotypic prediction on low-heritability traits that cannot be attained by classical genetic-based models. Additionally, its research may provide mechanisms of action for genetic associations at non-coding regions that mediate their effect via the epigenome. The aim of this thesis was to explore epigenetic inter-individual variation and to mitigate some of the methodological limitations faced towards its future valorisation.Chapter 1 is dedicated to the scope and aims of the thesis. It begins by describing historical milestones and basic concepts in human genetics, statistical genetics, the heritability problem and polygenic risk scores. It then moves towards epigenetics, covering the several dimensions it encompasses. It subsequently focuses on DNA methylation with topics like mitotic stability, epigenetic reprogramming, X-inactivation or imprinting. This is followed by concepts from epigenetic epidemiology such as epigenome-wide association studies (EWAS), epigenetic clocks, Mendelian randomization, methylation risk scores and methylation quantitative trait loci (mQTL). The chapter ends by introducing the aims of the thesis.Chapter 2 focuses on stochastic epigenetic inter-individual variation resulting from processes occurring post-twinning, during embryonic development and early life. Specifically, it describes the discovery and characterisation of hundreds of variably methylated CpGs in the blood of healthy adolescent monozygotic (MZ) twins showing equivalent variation among co-twins and unrelated individuals (evCpGs) that could not be explained only by measurement error on the DNA methylation microarray. DNA methylation levels at evCpGs were shown to be stable short-term but susceptible to aging and epigenetic drift in the long-term. The identified sites were significantly enriched at the clustered protocadherin loci, known for stochastic methylation in neurons in the context of embryonic neurodevelopment. Critically, evCpGs were capable of clustering technical and longitudinal replicates while differentiating young MZ twins. Thus, discovered evCpGs can be considered as a first prototype towards universal epigenetic fingerprint, relevant in the discrimination of MZ twins for forensic purposes, currently impossible with standard DNA profiling. Besides, DNA methylation microarrays are the preferred technology for EWAS and mQTL mapping studies. However, their probe design inherently assumes that the assayed genomic DNA is identical to the reference genome, leading to genetic artifacts whenever this assumption is not fulfilled. Building upon the previous experience analysing microarray data, Chapter 3 covers the development and benchmarking of UMtools, an R-package for the quantification and qualification of genetic artifacts on DNA methylation microarrays based on the unprocessed fluorescence intensity signals. These tools were used to assemble an atlas on genetic artifacts encountered on DNA methylation microarrays, including interactions between artifacts or with X-inactivation, imprinting and tissue-specific regulation. Additionally, to distinguish artifacts from genuine epigenetic variation, a co-methylation-based approach was proposed. Overall, this study revealed that genetic artifacts continue to filter through into the reported literature since current methodologies to address them have overlooked this challenge.Furthermore, EWAS, mQTL and allele-specific methylation (ASM) mapping studies have all been employed to map epigenetic variation but require matching phenotypic/genotypic data and can only map specific components of epigenetic inter-individual variation. Inspired by the previously proposed co-methylation strategy, Chapter 4 describes a novel method to simultaneously map inter-haplotype, inter-cell and inter-individual variation without these requirements. Specifically, binomial likelihood function-based bootstrap hypothesis test for co-methylation within reads (Binokulars) is a randomization test that can identify jointly regulated CpGs (JRCs) from pooled whole genome bisulfite sequencing (WGBS) data by solely relying on joint DNA methylation information available in reads spanning multiple CpGs. Binokulars was tested on pooled WGBS data in whole blood, sperm and combined, and benchmarked against EWAS and ASM. Our comparisons revealed that Binokulars can integrate a wide range of epigenetic phenomena under the same umbrella since it simultaneously discovered regions associated with imprinting, cell type- and tissue-specific regulation, mQTL, ageing or even unknown epigenetic processes. Finally, we verified examples of mQTL and polymorphic imprinting by employing another novel tool, JRC_sorter, to classify regions based on epigenotype models and non-pooled WGBS data in cord blood. In the future, we envision how this cost-effective approach can be applied on larger pools to simultaneously highlight regions of interest in the methylome, a highly relevant task in the light of the post-GWAS era.Moving towards future applications of epigenetic inter-individual variation, Chapters 5 and 6 are dedicated to solving some of methodological issues faced in translational epigenomics.Firstly, due to its simplicity and well-known properties, linear regression is the starting point methodology when performing prediction of a continuous outcome given a set of predictors. However, linear regression is incompatible with missing data, a common phenomenon and a huge threat to the integrity of data analysis in empirical sciences, including (epi)genomics. Chapter 5 describes the development of combinatorial linear models (cmb-lm), an imputation-free, CPU/RAM-efficient and privacy-preserving statistical method for linear regression prediction on datasets with missing values. Cmb-lm provide prediction errors that take into account the pattern of missing values in the incomplete data, even at extreme missingness. As a proof-of-concept, we tested cmb-lm in the context of epigenetic ageing clocks, one of the most popular applications of epigenetic inter-individual variation. Overall, cmb-lm offer a simple and flexible methodology with a wide range of applications that can provide a smooth transition towards the valorisation of linear models in the real world, where missing data is almost inevitable. Beyond microarrays, due to its high accuracy, reliability and sample multiplexing capabilities, massively parallel sequencing (MPS) is currently the preferred methodology of choice to translate prediction models for traits of interests into practice. At the same time, tobacco smoking is a frequent habit sustained by more than 1.3 billion people in 2020 and a leading (and preventable) health risk factor in the modern world. Predicting smoking habits from a persistent biomarker, such as DNA methylation, is not only relevant to account for self-reporting bias in public health and personalized medicine studies, but may also allow broadening forensic DNA phenotyping. Previously, a model to predict whether someone is a current, former, or never smoker had been published based on solely 13 CpGs from the hundreds of thousands included in the DNA methylation microarray. However, a matching lab tool with lower marker throughput, and higher accuracy and sensitivity was missing towards translating the model in practice. Chapter 6 describes the development of an MPS assay and data analysis pipeline to quantify DNA methylation on these 13 smoking-associated biomarkers for the prediction of smoking status. Though our systematic evaluation on DNA standards of known methylation levels revealed marker-specific amplification bias, our novel tool was still able to provide highly accurate and reproducible DNA methylation quantification and smoking habit prediction. Overall, our MPS assay allows the technological transfer of DNA methylation microarray findings and models to practical settings, one step closer towards future applications.Finally, Chapter 7 provides a general discussion on the results and topics discussed across Chapters 2-6. It begins by summarizing the main findings across the thesis, including proposals for follow-up studies. It then covers technical limitations pertaining bisulfite conversion and DNA methylation microarrays, but also more general considerations such as restricted data access. This chapter ends by covering the outlook of this PhD thesis, including topics such as bisulfite-free methods, third-generation sequencing, single-cell methylomics, multi-omics and systems biology.<br/

    Object Detection and Classification in the Visible and Infrared Spectrums

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    The over-arching theme of this dissertation is the development of automated detection and/or classification systems for challenging infrared scenarios. The six works presented herein can be categorized into four problem scenarios. In the first scenario, long-distance detection and classification of vehicles in thermal imagery, a custom convolutional network architecture is proposed for small thermal target detection. For the second scenario, thermal face landmark detection and thermal cross-spectral face verification, a publicly-available visible and thermal face dataset is introduced, along with benchmark results for several landmark detection and face verification algorithms. Furthermore, a novel visible-to-thermal transfer learning algorithm for face landmark detection is presented. The third scenario addresses near-infrared cross-spectral periocular recognition with a coupled conditional generative adversarial network guided by auxiliary synthetic loss functions. Finally, a deep sparse feature selection and fusion is proposed to detect the presence of textured contact lenses prior to near-infrared iris recognition

    Computational approaches to Explainable Artificial Intelligence: Advances in theory, applications and trends

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    Deep Learning (DL), a groundbreaking branch of Machine Learning (ML), has emerged as a driving force in both theoretical and applied Artificial Intelligence (AI). DL algorithms, rooted in complex and non-linear artificial neural systems, excel at extracting high-level features from data. DL has demonstrated human-level performance in real-world tasks, including clinical diagnostics, and has unlocked solutions to previously intractable problems in virtual agent design, robotics, genomics, neuroimaging, computer vision, and industrial automation. In this paper, the most relevant advances from the last few years in Artificial Intelligence (AI) and several applications to neuroscience, neuroimaging, computer vision, and robotics are presented, reviewed and discussed. In this way, we summarize the state-of-the-art in AI methods, models and applications within a collection of works presented at the 9 International Conference on the Interplay between Natural and Artificial Computation (IWINAC). The works presented in this paper are excellent examples of new scientific discoveries made in laboratories that have successfully transitioned to real-life applications

    Data simulation in deep learning-based human recognition

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    Human recognition is an important part of perception systems, such as those used in autonomous vehicles or robots. These systems often use deep neural networks for this purpose, which rely on large amounts of data that ideally cover various situations, movements, visual appearances, and interactions. However, obtaining such data is typically complex and expensive. In addition to raw data, labels are required to create training data for supervised learning. Thus, manual annotation of bounding boxes, keypoints, orientations, or actions performed is frequently necessary. This work addresses whether the laborious acquisition and creation of data can be simplified through targeted simulation. If data are generated in a simulation, information such as positions, dimensions, orientations, surfaces, and occlusions are already known, and appropriate labels can be generated automatically. A key question is whether deep neural networks, trained with simulated data, can be applied to real data. This work explores the use of simulated training data using examples from the field of pedestrian detection for autonomous vehicles. On the one hand, it is shown how existing systems can be improved by targeted retraining with simulation data, for example to better recognize corner cases. On the other hand, the work focuses on the generation of data that hardly or not occur at all in real standard datasets. It will be demonstrated how training data can be generated by targeted acquisition and combination of motion data and 3D models, which contain finely graded action labels to recognize even complex pedestrian situations. Through the diverse annotation data that simulations provide, it becomes possible to train deep neural networks for a wide variety of tasks with one dataset. In this work, such simulated data is used to train a novel deep multitask network that brings together diverse, previously mostly independently considered but related, tasks such as 2D and 3D human pose recognition and body and orientation estimation

    Infrared Image Super-Resolution: Systematic Review, and Future Trends

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    Image Super-Resolution (SR) is essential for a wide range of computer vision and image processing tasks. Investigating infrared (IR) image (or thermal images) super-resolution is a continuing concern within the development of deep learning. This survey aims to provide a comprehensive perspective of IR image super-resolution, including its applications, hardware imaging system dilemmas, and taxonomy of image processing methodologies. In addition, the datasets and evaluation metrics in IR image super-resolution tasks are also discussed. Furthermore, the deficiencies in current technologies and possible promising directions for the community to explore are highlighted. To cope with the rapid development in this field, we intend to regularly update the relevant excellent work at \url{https://github.com/yongsongH/Infrared_Image_SR_SurveyComment: Submitted to IEEE TNNL

    Data-centric Design and Training of Deep Neural Networks with Multiple Data Modalities for Vision-based Perception Systems

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    224 p.Los avances en visión artificial y aprendizaje automático han revolucionado la capacidad de construir sistemas que procesen e interpreten datos digitales, permitiéndoles imitar la percepción humana y abriendo el camino a un amplio rango de aplicaciones. En los últimos años, ambas disciplinas han logrado avances significativos,impulsadas por los progresos en las técnicas de aprendizaje profundo(deep learning). El aprendizaje profundo es una disciplina que utiliza redes neuronales profundas (DNNs, por sus siglas en inglés) para enseñar a las máquinas a reconocer patrones y hacer predicciones basadas en datos. Los sistemas de percepción basados en el aprendizaje profundo son cada vez más frecuentes en diversos campos, donde humanos y máquinas colaboran para combinar sus fortalezas.Estos campos incluyen la automoción, la industria o la medicina, donde mejorar la seguridad, apoyar el diagnóstico y automatizar tareas repetitivas son algunos de los objetivos perseguidos.Sin embargo, los datos son uno de los factores clave detrás del éxito de los algoritmos de aprendizaje profundo. La dependencia de datos limita fuertemente la creación y el éxito de nuevas DNN. La disponibilidad de datos de calidad para resolver un problema específico es esencial pero difícil de obtener, incluso impracticable,en la mayoría de los desarrollos. La inteligencia artificial centrada en datos enfatiza la importancia de usar datos de alta calidad que transmitan de manera efectiva lo que un modelo debe aprender. Motivada por los desafíos y la necesidad de los datos, esta tesis formula y valida cinco hipótesis sobre la adquisición y el impacto de los datos en el diseño y entrenamiento de las DNNs.Específicamente, investigamos y proponemos diferentes metodologías para obtener datos adecuados para entrenar DNNs en problemas con acceso limitado a fuentes de datos de gran escala. Exploramos dos posibles soluciones para la obtención de datos de entrenamiento, basadas en la generación de datos sintéticos. En primer lugar, investigamos la generación de datos sintéticos utilizando gráficos 3D y el impacto de diferentes opciones de diseño en la precisión de los DNN obtenidos. Además, proponemos una metodología para automatizar el proceso de generación de datos y producir datos anotados variados, mediante la replicación de un entorno 3D personalizado a partir de un archivo de configuración de entrada. En segundo lugar, proponemos una red neuronal generativa(GAN) que genera imágenes anotadas utilizando conjuntos de datos anotados limitados y datos sin anotaciones capturados en entornos no controlados
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