6,019 research outputs found

    Inter-individual variation of the human epigenome & applications

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    Bayesian spline-based hidden Markov models with applications to actimetry data and sleep analysis

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    B-spline-based hidden Markov models employ B-splines to specify the emission distributions, offering a more flexible modeling approach to data than conventional parametric HMMs. We introduce a Bayesian framework for inference, enabling the simultaneous estimation of all unknown model parameters including the number of states. A parsimonious knot configuration of the B-splines is identified by the use of a trans-dimensional Markov chain sampling algorithm, while model selection regarding the number of states can be performed based on the marginal likelihood within a parallel sampling framework. Using extensive simulation studies, we demonstrate the superiority of our methodology over alternative approaches as well as its robustness and scalability. We illustrate the explorative use of our methods for data on activity in animals, that is whitetip-sharks. The flexibility of our Bayesian approach also facilitates the incorporation of more realistic assumptions and we demonstrate this by developing a novel hierarchical conditional HMM to analyse human activity for circadian and sleep modeling. Supplementary materials for this article are available online

    Integrating expert-based objectivist and nonexpert-based subjectivist paradigms in landscape assessment

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    This thesis explores the integration of objective and subjective measures of landscape aesthetics, particularly focusing on crowdsourced geo-information. It addresses the increasing importance of considering public perceptions in national landscape governance, in line with the European Landscape Convention's emphasis on public involvement. Despite this, national landscape assessments often remain expert-centric and top-down, facing challenges in resource constraints and limited public engagement. The thesis leverages Web 2.0 technologies and crowdsourced geographic information, examining correlations between expert-based metrics of landscape quality and public perceptions. The Scenic-Or-Not initiative for Great Britain, GIS-based Wildness spatial layers, and LANDMAP dataset for Wales serve as key datasets for analysis. The research investigates the relationships between objective measures of landscape wildness quality and subjective measures of aesthetics. Multiscale geographically weighted regression (MGWR) reveals significant correlations, with different wildness components exhibiting varying degrees of association. The study suggests the feasibility of incorporating wildness and scenicness measures into formal landscape aesthetic assessments. Comparing expert and public perceptions, the research identifies preferences for water-related landforms and variations in upland and lowland typologies. The study emphasizes the agreement between experts and non-experts on extreme scenic perceptions but notes discrepancies in mid-spectrum landscapes. To overcome limitations in systematic landscape evaluations, an integrative approach is proposed. Utilizing XGBoost models, the research predicts spatial patterns of landscape aesthetics across Great Britain, based on the Scenic-Or-Not initiatives, Wildness spatial layers, and LANDMAP data. The models achieve comparable accuracy to traditional statistical models, offering insights for Landscape Character Assessment practices and policy decisions. While acknowledging data limitations and biases in crowdsourcing, the thesis discusses the necessity of an aggregation strategy to manage computational challenges. Methodological considerations include addressing the modifiable areal unit problem (MAUP) associated with aggregating point-based observations. The thesis comprises three studies published or submitted for publication, each contributing to the understanding of the relationship between objective and subjective measures of landscape aesthetics. The concluding chapter discusses the limitations of data and methods, providing a comprehensive overview of the research

    Deep generative models for network data synthesis and monitoring

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    Measurement and monitoring are fundamental tasks in all networks, enabling the down-stream management and optimization of the network. Although networks inherently have abundant amounts of monitoring data, its access and effective measurement is another story. The challenges exist in many aspects. First, the inaccessibility of network monitoring data for external users, and it is hard to provide a high-fidelity dataset without leaking commercial sensitive information. Second, it could be very expensive to carry out effective data collection to cover a large-scale network system, considering the size of network growing, i.e., cell number of radio network and the number of flows in the Internet Service Provider (ISP) network. Third, it is difficult to ensure fidelity and efficiency simultaneously in network monitoring, as the available resources in the network element that can be applied to support the measurement function are too limited to implement sophisticated mechanisms. Finally, understanding and explaining the behavior of the network becomes challenging due to its size and complex structure. Various emerging optimization-based solutions (e.g., compressive sensing) or data-driven solutions (e.g. deep learning) have been proposed for the aforementioned challenges. However, the fidelity and efficiency of existing methods cannot yet meet the current network requirements. The contributions made in this thesis significantly advance the state of the art in the domain of network measurement and monitoring techniques. Overall, we leverage cutting-edge machine learning technology, deep generative modeling, throughout the entire thesis. First, we design and realize APPSHOT , an efficient city-scale network traffic sharing with a conditional generative model, which only requires open-source contextual data during inference (e.g., land use information and population distribution). Second, we develop an efficient drive testing system — GENDT, based on generative model, which combines graph neural networks, conditional generation, and quantified model uncertainty to enhance the efficiency of mobile drive testing. Third, we design and implement DISTILGAN, a high-fidelity, efficient, versatile, and real-time network telemetry system with latent GANs and spectral-temporal networks. Finally, we propose SPOTLIGHT , an accurate, explainable, and efficient anomaly detection system of the Open RAN (Radio Access Network) system. The lessons learned through this research are summarized, and interesting topics are discussed for future work in this domain. All proposed solutions have been evaluated with real-world datasets and applied to support different applications in real systems

    Capsule networks with residual pose routing

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    Capsule networks (CapsNets) have been known difficult to develop a deeper architecture, which is desirable for high performance in the deep learning era, due to the complex capsule routing algorithms. In this article, we present a simple yet effective capsule routing algorithm, which is presented by a residual pose routing. Specifically, the higher-layer capsule pose is achieved by an identity mapping on the adjacently lower-layer capsule pose. Such simple residual pose routing has two advantages: 1) reducing the routing computation complexity and 2) avoiding gradient vanishing due to its residual learning framework. On top of that, we explicitly reformulate the capsule layers by building a residual pose block. Stacking multiple such blocks results in a deep residual CapsNets (ResCaps) with a ResNet-like architecture. Results on MNIST, AffNIST, SmallNORB, and CIFAR-10/100 show the effectiveness of ResCaps for image classification. Furthermore, we successfully extend our residual pose routing to large-scale real-world applications, including 3-D object reconstruction and classification, and 2-D saliency dense prediction. The source code has been released on https://github.com/liuyi1989/ResCaps

    Genomic resources for a historical collection of cultivated two-row European spring barley genotypes

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    Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.</p

    Online semi-supervised learning in non-stationary environments

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    Existing Data Stream Mining (DSM) algorithms assume the availability of labelled and balanced data, immediately or after some delay, to extract worthwhile knowledge from the continuous and rapid data streams. However, in many real-world applications such as Robotics, Weather Monitoring, Fraud Detection Systems, Cyber Security, and Computer Network Traffic Flow, an enormous amount of high-speed data is generated by Internet of Things sensors and real-time data on the Internet. Manual labelling of these data streams is not practical due to time consumption and the need for domain expertise. Another challenge is learning under Non-Stationary Environments (NSEs), which occurs due to changes in the data distributions in a set of input variables and/or class labels. The problem of Extreme Verification Latency (EVL) under NSEs is referred to as Initially Labelled Non-Stationary Environment (ILNSE). This is a challenging task because the learning algorithms have no access to the true class labels directly when the concept evolves. Several approaches exist that deal with NSE and EVL in isolation. However, few algorithms address both issues simultaneously. This research directly responds to ILNSE’s challenge in proposing two novel algorithms “Predictor for Streaming Data with Scarce Labels” (PSDSL) and Heterogeneous Dynamic Weighted Majority (HDWM) classifier. PSDSL is an Online Semi-Supervised Learning (OSSL) method for real-time DSM and is closely related to label scarcity issues in online machine learning. The key capabilities of PSDSL include learning from a small amount of labelled data in an incremental or online manner and being available to predict at any time. To achieve this, PSDSL utilises both labelled and unlabelled data to train the prediction models, meaning it continuously learns from incoming data and updates the model as new labelled or unlabelled data becomes available over time. Furthermore, it can predict under NSE conditions under the scarcity of class labels. PSDSL is built on top of the HDWM classifier, which preserves the diversity of the classifiers. PSDSL and HDWM can intelligently switch and adapt to the conditions. The PSDSL adapts to learning states between self-learning, micro-clustering and CGC, whichever approach is beneficial, based on the characteristics of the data stream. HDWM makes use of “seed” learners of different types in an ensemble to maintain its diversity. The ensembles are simply the combination of predictive models grouped to improve the predictive performance of a single classifier. PSDSL is empirically evaluated against COMPOSE, LEVELIW, SCARGC and MClassification on benchmarks, NSE datasets as well as Massive Online Analysis (MOA) data streams and real-world datasets. The results showed that PSDSL performed significantly better than existing approaches on most real-time data streams including randomised data instances. PSDSL performed significantly better than ‘Static’ i.e. the classifier is not updated after it is trained with the first examples in the data streams. When applied to MOA-generated data streams, PSDSL ranked highest (1.5) and thus performed significantly better than SCARGC, while SCARGC performed the same as the Static. PSDSL achieved better average prediction accuracies in a short time than SCARGC. The HDWM algorithm is evaluated on artificial and real-world data streams against existing well-known approaches such as the heterogeneous WMA and the homogeneous Dynamic DWM algorithm. The results showed that HDWM performed significantly better than WMA and DWM. Also, when recurring concept drifts were present, the predictive performance of HDWM showed an improvement over DWM. In both drift and real-world streams, significance tests and post hoc comparisons found significant differences between algorithms, HDWM performed significantly better than DWM and WMA when applied to MOA data streams and 4 real-world datasets Electric, Spam, Sensor and Forest cover. The seeding mechanism and dynamic inclusion of new base learners in the HDWM algorithms benefit from the use of both forgetting and retaining the models. The algorithm also provides the independence of selecting the optimal base classifier in its ensemble depending on the problem. A new approach, Envelope-Clustering is introduced to resolve the cluster overlap conflicts during the cluster labelling process. In this process, PSDSL transforms the centroids’ information of micro-clusters into micro-instances and generates new clusters called Envelopes. The nearest envelope clusters assist the conflicted micro-clusters and successfully guide the cluster labelling process after the concept drifts in the absence of true class labels. PSDSL has been evaluated on real-world problem ‘keystroke dynamics’, and the results show that PSDSL achieved higher prediction accuracy (85.3%) and SCARGC (81.6%), while the Static (49.0%) significantly degrades the performance due to changes in the users typing pattern. Furthermore, the predictive accuracies of SCARGC are found highly fluctuated between (41.1% to 81.6%) based on different values of parameter ‘k’ (number of clusters), while PSDSL automatically determine the best values for this parameter

    Life on a scale:Deep brain stimulation in anorexia nervosa

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    Anorexia nervosa (AN) is a severe psychiatric disorder marked by low body weight, body image abnormalities, and anxiety and shows elevated rates of morbidity, comorbidity and mortality. Given the limited availability of evidence-based treatments, there is an urgent need to investigate new therapeutic options that are informed by the disorder’s underlying neurobiological mechanisms. This thesis represents the first study in the Netherlands and one of a limited number globally to evaluate the efficacy, safety, and tolerability of deep brain stimulation (DBS) in the treatment of AN. DBS has the advantage of being both reversible and adjustable. Beyond assessing the primary impact of DBS on body weight, psychological parameters, and quality of life, this research is novel in its comprehensive approach. We integrated evaluations of efficacy with critical examinations of the functional impact of DBS in AN, including fMRI, electroencephalography EEG, as well as endocrinological and metabolic assessments. Furthermore, this work situates AN within a broader theoretical framework, specifically focusing on its manifestation as a form of self-destructive behavior. Finally, we reflect on the practical, ethical and philosophical aspects of conducting an experimental, invasive procedure in a vulnerable patient group. This thesis deepens our understanding of the neurobiological underpinnings of AN and paves the way for future research and potential clinical applications of DBS in the management of severe and enduring AN

    Socioeconomic implications of adverse birth outcomes

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    In the following chapters, I present research on potential risk factors for adverse birth outcomes and their implications for the socioeconomic status of the newborn in later life. Beyond that, I study the economic consequences for the parents of a newborn child with adverse birth outcomes. Except for the second chapter, all chapters have an applied econometric approach and statistically analyse observational data from Germany and the United Kingdom. The analyses are interdisciplinary and focus on the explanation of them assumptions required to causally interpret the results and address the limitations of the analyses.New Opportunities for Research Funding Agency Cooperation in Europe (NORFACE)/Life Course Dynamics after Preterm Birth: Protective Factors for Social and Educational Transitions, Health, and Prosperity (PremLife)/462-16-040/E
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