128,879 research outputs found
Integration and visualisation of clinical-omics datasets for medical knowledge discovery
In recent decades, the rise of various omics fields has flooded life sciences with unprecedented amounts of high-throughput data, which have transformed the way biomedical research is conducted. This trend will only intensify in the coming decades, as the cost of data acquisition will continue to decrease. Therefore, there is a pressing need to find novel ways to turn this ocean of raw data into waves of information and finally distil those into drops of translational medical knowledge. This is particularly challenging because of the incredible richness of these datasets, the humbling complexity of biological systems and the growing abundance of clinical metadata, which makes the integration of disparate data sources even more difficult.
Data integration has proven to be a promising avenue for knowledge discovery in biomedical research. Multi-omics studies allow us to examine a biological problem through different lenses using more than one analytical platform. These studies not only present tremendous opportunities for the deep and systematic understanding of health and disease, but they also pose new statistical and computational challenges. The work presented in this thesis aims to alleviate this problem with a novel pipeline for omics data integration.
Modern omics datasets are extremely feature rich and in multi-omics studies this complexity is compounded by a second or even third dataset. However, many of these features might be completely irrelevant to the studied biological problem or redundant in the context of others. Therefore, in this thesis, clinical metadata driven feature selection is proposed as a viable option for narrowing down the focus of analyses in biomedical research.
Our visual cortex has been fine-tuned through millions of years to become an outstanding pattern recognition machine. To leverage this incredible resource of the human brain, we need to develop advanced visualisation software that enables researchers to explore these vast biological datasets through illuminating charts and interactivity. Accordingly, a substantial portion of this PhD was dedicated to implementing truly novel visualisation methods for multi-omics studies.Open Acces
Development of method of matched morphological filtering of biomedical signals and images
Formalized approach to the analysis of biomedical signals and images with locally concentrated features is developed on the basis of matched morphological filtering taking into account the useful signal models that allowed generalizing the existing methods of digital processing and analysis of biomedical signals and images with locally concentrated features. The proposed matched morphological filter has been adapted to solve such problems as localization of the searched structural elements on biomedical signals with locally concentrated features, estimation of the irregular background aimed at the visualization quality improving of biological objects on X-ray biomedical images, pathologic structures selection on mammogram. The efficiency of the proposed methods of matched morphological filtration of biomedical signals and images with locally concentrated features is proved by experiments
Making visible the invisible through the analysis of acknowledgements in the humanities
Purpose: Science is subject to a normative structure that includes how the
contributions and interactions between scientists are rewarded. Authorship and
citations have been the key elements within the reward system of science,
whereas acknowledgements, despite being a well-established element in scholarly
communication, have not received the same attention. This paper aims to put
forward the bearing of acknowledgements in the humanities to bring to the
foreground contributions and interactions that, otherwise, would remain
invisible through traditional indicators of research performance.
Design/methodology/approach: The study provides a comprehensive framework to
understanding acknowledgements as part of the reward system with a special
focus on its value in the humanities as a reflection of intellectual
indebtedness. The distinctive features of research in the humanities are
outlined and the role of acknowledgements as a source of contributorship
information is reviewed to support these assumptions.
Findings: Peer interactive communication is the prevailing support thanked in
the acknowledgements of humanities, so the notion of acknowledgements as
super-citations can make special sense in this area. Since single-authored
papers still predominate as publishing pattern in this domain, the study of
acknowledgements might help to understand social interactions and intellectual
influences that lie behind a piece of research and are not visible through
authorship.
Originality/value: Previous works have proposed and explored the prevailing
acknowledgement types by domain. This paper focuses on the humanities to show
the role of acknowledgements within the reward system and highlight publication
patterns and inherent research features which make acknowledgements
particularly interesting in the area as reflection of the socio-cognitive
structure of research.Comment: 14 page
Predictive biometrics: A review and analysis of predicting personal characteristics from biometric data
Interest in the exploitation of soft biometrics information has continued to develop over the last decade or so. In comparison with traditional biometrics, which focuses principally on person identification, the idea of soft biometrics processing is to study the utilisation of more general information regarding a system user, which is not necessarily unique. There are increasing indications that this type of data will have great value in providing complementary information for user authentication. However, the authors have also seen a growing interest in broadening the predictive capabilities of biometric data, encompassing both easily definable characteristics such as subject age and, most recently, `higher level' characteristics such as emotional or mental states. This study will present a selective review of the predictive capabilities, in the widest sense, of biometric data processing, providing an analysis of the key issues still adequately to be addressed if this concept of predictive biometrics is to be fully exploited in the future
Signal2Image Modules in Deep Neural Networks for EEG Classification
Deep learning has revolutionized computer vision utilizing the increased
availability of big data and the power of parallel computational units such as
graphical processing units. The vast majority of deep learning research is
conducted using images as training data, however the biomedical domain is rich
in physiological signals that are used for diagnosis and prediction problems.
It is still an open research question how to best utilize signals to train deep
neural networks.
In this paper we define the term Signal2Image (S2Is) as trainable or
non-trainable prefix modules that convert signals, such as
Electroencephalography (EEG), to image-like representations making them
suitable for training image-based deep neural networks defined as `base
models'. We compare the accuracy and time performance of four S2Is (`signal as
image', spectrogram, one and two layer Convolutional Neural Networks (CNNs))
combined with a set of `base models' (LeNet, AlexNet, VGGnet, ResNet, DenseNet)
along with the depth-wise and 1D variations of the latter. We also provide
empirical evidence that the one layer CNN S2I performs better in eleven out of
fifteen tested models than non-trainable S2Is for classifying EEG signals and
we present visual comparisons of the outputs of the S2Is.Comment: 4 pages, 2 figures, 1 table, EMBC 201
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