36 research outputs found

    A machine learning approach to the unsupervised segmentation of mitochondria in subcellular electron microscopy data

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    Recent advances in cellular and subcellular microscopy demonstrated its potential towards unravelling the mechanisms of various diseases at the molecular level. The biggest challenge in both human- and computer-based visual analysis of micrographs is the variety of nanostructures and mitochondrial morphologies. The state-of-the-art is, however, dominated by supervised manual data annotation and early attempts to automate the segmentation process were based on supervised machine learning techniques which require large datasets for training. Given a minimal number of training sequences or none at all, unsupervised machine learning formulations, such as spectral dimensionality reduction, are known to be superior in detecting salient image structures. This thesis presents three major contributions developed around the spectral clustering framework which is proven to capture perceptual organization features. Firstly, we approach the problem of mitochondria localization. We propose a novel grouping method for the extracted line segments which describes the normal mitochondrial morphology. Experimental findings show that the clusters obtained successfully model the inner mitochondrial membrane folding and therefore can be used as markers for the subsequent segmentation approaches. Secondly, we developed an unsupervised mitochondria segmentation framework. This method follows the evolutional ability of human vision to extrapolate salient membrane structures in a micrograph. Furthermore, we designed robust non-parametric similarity models according to Gestaltic laws of visual segregation. Experiments demonstrate that such models automatically adapt to the statistical structure of the biological domain and return optimal performance in pixel classification tasks under the wide variety of distributional assumptions. The last major contribution addresses the computational complexity of spectral clustering. Here, we introduced a new anticorrelation-based spectral clustering formulation with the objective to improve both: speed and quality of segmentation. The experimental findings showed the applicability of our dimensionality reduction algorithm to very large scale problems as well as asymmetric, dense and non-Euclidean datasets

    CRIS-IR 2006

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    The recognition of entities and their relationships in document collections is an important step towards the discovery of latent knowledge as well as to support knowledge management applications. The challenge lies on how to extract and correlate entities, aiming to answer key knowledge management questions, such as; who works with whom, on which projects, with which customers and on what research areas. The present work proposes a knowledge mining approach supported by information retrieval and text mining tasks in which its core is based on the correlation of textual elements through the LRD (Latent Relation Discovery) method. Our experiments show that LRD outperform better than other correlation methods. Also, we present an application in order to demonstrate the approach over knowledge management scenarios.Fundação para a Ciência e a Tecnologia (FCT) Denmark's Electronic Research Librar

    The 11th Conference of PhD Students in Computer Science

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    Concepts in Action

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    This open access book is a timely contribution in presenting recent issues, approaches, and results that are not only central to the highly interdisciplinary field of concept research but also particularly important to newly emergent paradigms and challenges. The contributors present a unique, holistic picture for the understanding and use of concepts from a wide range of fields including cognitive science, linguistics, philosophy, psychology, artificial intelligence, and computer science. The chapters focus on three distinct points of view that lie at the core of concept research: representation, learning, and application. The contributions present a combination of theoretical, experimental, computational, and applied methods that appeal to students and researchers working in these fields

    Proceedings of the 9th International Workshop on Information Retrieval on Current Research Information Systems

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    The recognition of entities and their relationships in document collections is an important step towards the discovery of latent knowledge as well as to support knowledge management applications. The challenge lies on how to extract and correlate entities, aiming to answer key knowledge management questions, such as; who works with whom, on which projects, with which customers and on what research areas. The present work proposes a knowledge mining approach supported by information retrieval and text mining tasks in which its core is based on the correlation of textual elements through the LRD (Latent Relation Discovery) method. Our experiments show that LRD outperform better than other correlation methods. Also, we present an application in order to demonstrate the approach over knowledge management scenarios

    Concepts in Action

    Get PDF
    This open access book is a timely contribution in presenting recent issues, approaches, and results that are not only central to the highly interdisciplinary field of concept research but also particularly important to newly emergent paradigms and challenges. The contributors present a unique, holistic picture for the understanding and use of concepts from a wide range of fields including cognitive science, linguistics, philosophy, psychology, artificial intelligence, and computer science. The chapters focus on three distinct points of view that lie at the core of concept research: representation, learning, and application. The contributions present a combination of theoretical, experimental, computational, and applied methods that appeal to students and researchers working in these fields

    Advances in knowledge discovery and data mining Part II

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    19th Pacific-Asia Conference, PAKDD 2015, Ho Chi Minh City, Vietnam, May 19-22, 2015, Proceedings, Part II</p

    Recent Developments in Smart Healthcare

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    Medicine is undergoing a sector-wide transformation thanks to the advances in computing and networking technologies. Healthcare is changing from reactive and hospital-centered to preventive and personalized, from disease focused to well-being centered. In essence, the healthcare systems, as well as fundamental medicine research, are becoming smarter. We anticipate significant improvements in areas ranging from molecular genomics and proteomics to decision support for healthcare professionals through big data analytics, to support behavior changes through technology-enabled self-management, and social and motivational support. Furthermore, with smart technologies, healthcare delivery could also be made more efficient, higher quality, and lower cost. In this special issue, we received a total 45 submissions and accepted 19 outstanding papers that roughly span across several interesting topics on smart healthcare, including public health, health information technology (Health IT), and smart medicine

    Applications of Molecular Dynamics simulations for biomolecular systems and improvements to density-based clustering in the analysis

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    Molecular Dynamics simulations provide a powerful tool to study biomolecular systems with atomistic detail. The key to better understand the function and behaviour of these molecules can often be found in their structural variability. Simulations can help to expose this information that is otherwise experimentally hard or impossible to attain. This work covers two application examples for which a sampling and a characterisation of the conformational ensemble could reveal the structural basis to answer a topical research question. For the fungal toxin phalloidin—a small bicyclic peptide—observed product ratios in different cyclisation reactions could be rationalised by assessing the conformational pre-organisation of precursor fragments. For the C-type lectin receptor langerin, conformational changes induced by different side-chain protonations could deliver an explanation of the pH-dependency in the protein’s calcium-binding. The investigations were accompanied by the continued development of a density-based clustering protocol into a respective software package, which is generally well applicable for the use case of extracting conformational states from Molecular Dynamics data
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