8,463 research outputs found

    Bayesian networks for disease diagnosis: What are they, who has used them and how?

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    A Bayesian network (BN) is a probabilistic graph based on Bayes' theorem, used to show dependencies or cause-and-effect relationships between variables. They are widely applied in diagnostic processes since they allow the incorporation of medical knowledge to the model while expressing uncertainty in terms of probability. This systematic review presents the state of the art in the applications of BNs in medicine in general and in the diagnosis and prognosis of diseases in particular. Indexed articles from the last 40 years were included. The studies generally used the typical measures of diagnostic and prognostic accuracy: sensitivity, specificity, accuracy, precision, and the area under the ROC curve. Overall, we found that disease diagnosis and prognosis based on BNs can be successfully used to model complex medical problems that require reasoning under conditions of uncertainty.Comment: 22 pages, 5 figures, 1 table, Student PhD first pape

    Vegetation responses to variations in climate: A combined ordinary differential equation and sequential Monte Carlo estimation approach

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    Vegetation responses to variation in climate are a current research priority in the context of accelerated shifts generated by climate change. However, the interactions between environmental and biological factors still represent one of the largest uncertainties in projections of future scenarios, since the relationship between drivers and ecosystem responses has a complex and nonlinear nature. We aimed to develop a model to study the vegetation’s primary productivity dynamic response to temporal variations in climatic conditions as measured by rainfall, temperature and radiation. Thus, we propose a new way to estimate the vegetation response to climate via a non-autonomous version of a classical growth curve, with a time-varying growth rate and carrying capacity parameters according to climate variables. With a Sequential Monte Carlo Estimation to account for complexities in the climate-vegetation relationship to minimize the number of parameters. The model was applied to six key sites identified in a previous study, consisting of different arid and semiarid rangelands from North Patagonia, Argentina. For each site, we selected the time series of MODIS NDVI, and climate data from ERA5 Copernicus hourly reanalysis from 2000 to 2021. After calculating the time series of the a posteriori distribution of parameters, we analyzed the explained capacity of the model in terms of the linear coefficient of determination and the parameters distribution variation. Results showed that most rangelands recorded changes in their sensitivity over time to climatic factors, but vegetation responses were heterogeneous and influenced by different drivers. Differences in this climate-vegetation relationship were recorded among different cases: (1) a marginal and decreasing sensitivity to temperature and radiation, respectively, but a high sensitivity to water availability; (2) high and increasing sensitivity to temperature and water availability, respectively; and (3) a case with an abrupt shift in vegetation dynamics driven by a progressively decreasing sensitivity to water availability, without any changes in the sensitivity either to temperature or radiation. Finally, we also found that the time scale, in which the ecosystem integrated the rainfall phenomenon in terms of the width of the window function used to convolve the rainfall series into a water availability variable, was also variable in time. This approach allows us to estimate the connection degree between ecosystem productivity and climatic variables. The capacity of the model to identify changes over time in the vegetation-climate relationship might inform decision-makers about ecological transitions and the differential impact of climatic drivers on ecosystems.Estación Experimental Agropecuaria BarilocheFil: Bruzzone, Octavio Augusto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; ArgentinaFil: Bruzzone, Octavio Augusto. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; ArgentinaFil: Perri, Daiana Vanesa. Instituto Nacional de Tecnologia Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Área de Recursos Naturales; ArgentinaFil: Perri, Daiana Vanesa. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; ArgentinaFil: Easdale, Marcos Horacio. Instituto Nacional de Tecnologia Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Área de Recursos Naturales; ArgentinaFil: Easdale, Marcos Horacio. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentin

    Assessing performance of artificial neural networks and re-sampling techniques for healthcare datasets.

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    Re-sampling methods to solve class imbalance problems have shown to improve classification accuracy by mitigating the bias introduced by differences in class size. However, it is possible that a model which uses a specific re-sampling technique prior to Artificial neural networks (ANN) training may not be suitable for aid in classifying varied datasets from the healthcare industry. Five healthcare-related datasets were used across three re-sampling conditions: under-sampling, over-sampling and combi-sampling. Within each condition, different algorithmic approaches were applied to the dataset and the results were statistically analysed for a significant difference in ANN performance. The combi-sampling condition showed that four out of the five datasets did not show significant consistency for the optimal re-sampling technique between the f1-score and Area Under the Receiver Operating Characteristic Curve performance evaluation methods. Contrarily, the over-sampling and under-sampling condition showed all five datasets put forward the same optimal algorithmic approach across performance evaluation methods. Furthermore, the optimal combi-sampling technique (under-, over-sampling and convergence point), were found to be consistent across evaluation measures in only two of the five datasets. This study exemplifies how discrete ANN performances on datasets from the same industry can occur in two ways: how the same re-sampling technique can generate varying ANN performance on different datasets, and how different re-sampling techniques can generate varying ANN performance on the same dataset

    Learning disentangled speech representations

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    A variety of informational factors are contained within the speech signal and a single short recording of speech reveals much more than the spoken words. The best method to extract and represent informational factors from the speech signal ultimately depends on which informational factors are desired and how they will be used. In addition, sometimes methods will capture more than one informational factor at the same time such as speaker identity, spoken content, and speaker prosody. The goal of this dissertation is to explore different ways to deconstruct the speech signal into abstract representations that can be learned and later reused in various speech technology tasks. This task of deconstructing, also known as disentanglement, is a form of distributed representation learning. As a general approach to disentanglement, there are some guiding principles that elaborate what a learned representation should contain as well as how it should function. In particular, learned representations should contain all of the requisite information in a more compact manner, be interpretable, remove nuisance factors of irrelevant information, be useful in downstream tasks, and independent of the task at hand. The learned representations should also be able to answer counter-factual questions. In some cases, learned speech representations can be re-assembled in different ways according to the requirements of downstream applications. For example, in a voice conversion task, the speech content is retained while the speaker identity is changed. And in a content-privacy task, some targeted content may be concealed without affecting how surrounding words sound. While there is no single-best method to disentangle all types of factors, some end-to-end approaches demonstrate a promising degree of generalization to diverse speech tasks. This thesis explores a variety of use-cases for disentangled representations including phone recognition, speaker diarization, linguistic code-switching, voice conversion, and content-based privacy masking. Speech representations can also be utilised for automatically assessing the quality and authenticity of speech, such as automatic MOS ratings or detecting deep fakes. The meaning of the term "disentanglement" is not well defined in previous work, and it has acquired several meanings depending on the domain (e.g. image vs. speech). Sometimes the term "disentanglement" is used interchangeably with the term "factorization". This thesis proposes that disentanglement of speech is distinct, and offers a viewpoint of disentanglement that can be considered both theoretically and practically

    Mathematical models to evaluate the impact of increasing serotype coverage in pneumococcal conjugate vaccines

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    Of over 100 serotypes of Streptococcus pneumoniae, only 7 were included in the first pneumo- coccal conjugate vaccine (PCV). While PCV reduced the disease incidence, in part because of a herd immunity effect, a replacement effect was observed whereby disease was increasingly caused by serotypes not included in the vaccine. Dynamic transmission models can account for these effects to describe post-vaccination scenarios, whereas economic evaluations can enable decision-makers to compare vaccines of increasing valency for implementation. This thesis has four aims. First, to explore the limitations and assumptions of published pneu- mococcal models and the implications for future vaccine formulation and policy. Second, to conduct a trend analysis assembling all the available evidence for serotype replacement in Europe, North America and Australia to characterise invasive pneumococcal disease (IPD) caused by vaccine-type (VT) and non-vaccine-types (NVT) serotypes. The motivation behind this is to assess the patterns of relative abundance in IPD cases pre- and post-vaccination, to examine country-level differences in relation to the vaccines employed over time since introduction, and to assess the growth of the replacement serotypes in comparison with the serotypes targeted by the vaccine. The third aim is to use a Bayesian framework to estimate serotype-specific invasiveness, i.e. the rate of invasive disease given carriage. This is useful for dynamic transmission modelling, as transmission is through carriage but a majority of serotype-specific pneumococcal data lies in active disease surveillance. This is also helpful to address whether serotype replacement reflects serotypes that are more invasive or whether serotypes in a specific location are equally more invasive than in other locations. Finally, the last aim of this thesis is to estimate the epidemiological and economic impact of increas- ing serotype coverage in PCVs using a dynamic transmission model. Together, the results highlight that though there are key parameter uncertainties that merit further exploration, divergence in serotype replacement and inconsistencies in invasiveness on a country-level may make a universal PCV suboptimal.Open Acces

    Addressing infrastructure challenges posed by the Harwich Formation through understanding its geological origins

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    Variable deposits known to make up the sequence of the Harwich Formation in London have been the subject of ongoing uncertainty within the engineering industry. Current stratigraphical subdivisions do not account for the systematic recognition of individual members in unexposed ground where recovered material is usually disturbed - fines are flushed out during the drilling process and loose materials are often lost or mixed with the surrounding layers. Most engineering problems associated with the Harwich Formation deposits are down to their unconsolidated nature and irregular cementation within layers. The consequent engineering hazards are commonly reflected in high permeability, raised groundwater pressures, ground settlements - when found near the surface and poor stability - when exposed during excavations or tunnelling operations. This frequently leads to sudden design changes or requires contingency measures during construction. All of these can result in damaged equipment, slow progress, and unforeseen costs. This research proposes a facies-based approach where the lithological facies assigned were identified based on reinterpretation of available borehole data from various ground investigations in London, supported by visual inspection of deposits in-situ and a selection of laboratory testing including Particle Size Distribution, Optical and Scanning Electron Microscopy and X-ray Diffraction analyses. Two ground models were developed as a result: 1st a 3D geological model (MOVE model) of the stratigraphy found within the study area that explores the influence of local structural processes controlling/affecting these sediments pre-, syn- and post- deposition and 2nd a sequence stratigraphic model (Dionisos Flow model) unveiling stratal geometries of facies at various stages of accretion. The models present a series of sediment distribution maps, localised 3D views and cross-sections that aim to provide a novel approach to assist the geotechnical industry in predicting the likely distribution of the Harwich Formation deposits, decreasing the engineering risks associated with this stratum.Open Acces

    Unraveling the effect of sex on human genetic architecture

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    Sex is arguably the most important differentiating characteristic in most mammalian species, separating populations into different groups, with varying behaviors, morphologies, and physiologies based on their complement of sex chromosomes, amongst other factors. In humans, despite males and females sharing nearly identical genomes, there are differences between the sexes in complex traits and in the risk of a wide array of diseases. Sex provides the genome with a distinct hormonal milieu, differential gene expression, and environmental pressures arising from gender societal roles. This thus poses the possibility of observing gene by sex (GxS) interactions between the sexes that may contribute to some of the phenotypic differences observed. In recent years, there has been growing evidence of GxS, with common genetic variation presenting different effects on males and females. These studies have however been limited in regards to the number of traits studied and/or statistical power. Understanding sex differences in genetic architecture is of great importance as this could lead to improved understanding of potential differences in underlying biological pathways and disease etiology between the sexes and in turn help inform personalised treatments and precision medicine. In this thesis we provide insights into both the scope and mechanism of GxS across the genome of circa 450,000 individuals of European ancestry and 530 complex traits in the UK Biobank. We found small yet widespread differences in genetic architecture across traits through the calculation of sex-specific heritability, genetic correlations, and sex-stratified genome-wide association studies (GWAS). We further investigated whether sex-agnostic (non-stratified) efforts could potentially be missing information of interest, including sex-specific trait-relevant loci and increased phenotype prediction accuracies. Finally, we studied the potential functional role of sex differences in genetic architecture through sex biased expression quantitative trait loci (eQTL) and gene-level analyses. Overall, this study marks a broad examination of the genetics of sex differences. Our findings parallel previous reports, suggesting the presence of sexual genetic heterogeneity across complex traits of generally modest magnitude. Furthermore, our results suggest the need to consider sex-stratified analyses in future studies in order to shed light into possible sex-specific molecular mechanisms

    Optical coherence tomography methods using 2-D detector arrays

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    Optical coherence tomography (OCT) is a non-invasive, non-contact optical technique that allows cross-section imaging of biological tissues with high spatial resolution, high sensitivity and high dynamic range. Standard OCT uses a focused beam to illuminate a point on the target and detects the signal using a single photodetector. To acquire transverse information, transversal scanning of the illumination point is required. Alternatively, multiple OCT channels can be operated in parallel simultaneously; parallel OCT signals are recorded by a two-dimensional (2D) detector array. This approach is known as Parallel-detection OCT. In this thesis, methods, experiments and results using three parallel OCT techniques, including full -field (time-domain) OCT (FF-OCT), full-field swept-source OCT (FF-SS-OCT) and line-field Fourier-domain OCT (LF-FD-OCT), are presented. Several 2D digital cameras of different formats have been used and evaluated in the experiments of different methods. With the LF-FD-OCT method, photography equipment, such as flashtubes and commercial DSLR cameras have been equipped and tested for OCT imaging. The techniques used in FF-OCT and FF-SS-OCT are employed in a novel wavefront sensing technique, which combines OCT methods with a Shack-Hartmann wavefront sensor (SH-WFS). This combination technique is demonstrated capable of measuring depth-resolved wavefront aberrations, which has the potential to extend the applications of SH-WFS in wavefront-guided biomedical imaging techniques
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