11,289 research outputs found

    Computational Analyses of Metagenomic Data

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    Metagenomics studies the collective microbial genomes extracted from a particular environment without requiring the culturing or isolation of individual genomes, addressing questions revolving around the composition, functionality, and dynamics of microbial communities. The intrinsic complexity of metagenomic data and the diversity of applications call for efficient and accurate computational methods in data handling. In this thesis, I present three primary projects that collectively focus on the computational analysis of metagenomic data, each addressing a distinct topic. In the first project, I designed and implemented an algorithm named Mapbin for reference-free genomic binning of metagenomic assemblies. Binning aims to group a mixture of genomic fragments based on their genome origin. Mapbin enhances binning results by building a multilayer network that combines the initial binning, assembly graph, and read-pairing information from paired-end sequencing data. The network is further partitioned by the community-detection algorithm, Infomap, to yield a new binning result. Mapbin was tested on multiple simulated and real datasets. The results indicated an overall improvement in the common binning quality metrics. The second and third projects are both derived from ImMiGeNe, a collaborative and multidisciplinary study investigating the interplay between gut microbiota, host genetics, and immunity in stem-cell transplantation (SCT) patients. In the second project, I conducted microbiome analyses for the metagenomic data. The workflow included the removal of contaminant reads and multiple taxonomic and functional profiling. The results revealed that the SCT recipients' samples yielded significantly fewer reads with heavy contamination of the host DNA, and their microbiomes displayed evident signs of dysbiosis. Finally, I discussed several inherent challenges posed by extremely low levels of target DNA and high levels of contamination in the recipient samples, which cannot be rectified solely through bioinformatics approaches. The primary goal of the third project is to design a set of primers that can be used to cover bacterial flagellin genes present in the human gut microbiota. Considering the notable diversity of flagellins, I incorporated a method to select representative bacterial flagellin gene sequences, a heuristic approach based on established primer design methods to generate a degenerate primer set, and a selection method to filter genes unlikely to occur in the human gut microbiome. As a result, I successfully curated a reduced yet representative set of primers that would be practical for experimental implementation

    Displacement and the Humanities: Manifestos from the Ancient to the Present

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    This is the final version. Available on open access from MDPI via the DOI in this recordThis is a reprint of articles from the Special Issue published online in the open access journal Humanities (ISSN 2076-0787) (available at: https://www.mdpi.com/journal/humanities/special_issues/Manifestos Ancient Present)This volume brings together the work of practitioners, communities, artists and other researchers from multiple disciplines. Seeking to provoke a discourse around displacement within and beyond the field of Humanities, it positions historical cases and debates, some reaching into the ancient past, within diverse geo-chronological contexts and current world urgencies. In adopting an innovative dialogic structure, between practitioners on the ground - from architects and urban planners to artists - and academics working across subject areas, the volume is a proposition to: remap priorities for current research agendas; open up disciplines, critically analysing their approaches; address the socio-political responsibilities that we have as scholars and practitioners; and provide an alternative site of discourse for contemporary concerns about displacement. Ultimately, this volume aims to provoke future work and collaborations - hence, manifestos - not only in the historical and literary fields, but wider research concerned with human mobility and the challenges confronting people who are out of place of rights, protection and belonging

    Energy storage design and integration in power systems by system-value optimization

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    Energy storage can play a crucial role in decarbonising power systems by balancing power and energy in time. Wider power system benefits that arise from these balancing technologies include lower grid expansion, renewable curtailment, and average electricity costs. However, with the proliferation of new energy storage technologies, it becomes increasingly difficult to identify which technologies are economically viable and how to design and integrate them effectively. Using large-scale energy system models in Europe, the dissertation shows that solely relying on Levelized Cost of Storage (LCOS) metrics for technology assessments can mislead and that traditional system-value methods raise important questions about how to assess multiple energy storage technologies. Further, the work introduces a new complementary system-value assessment method called the market-potential method, which provides a systematic deployment analysis for assessing multiple storage technologies under competition. However, integrating energy storage in system models can lead to the unintended storage cycling effect, which occurs in approximately two-thirds of models and significantly distorts results. The thesis finds that traditional approaches to deal with the issue, such as multi-stage optimization or mixed integer linear programming approaches, are either ineffective or computationally inefficient. A new approach is suggested that only requires appropriate model parameterization with variable costs while keeping the model convex to reduce the risk of misleading results. In addition, to enable energy storage assessments and energy system research around the world, the thesis extended the geographical scope of an existing European opensource model to global coverage. The new build energy system model ‘PyPSA-Earth’ is thereby demonstrated and validated in Africa. Using PyPSA-Earth, the thesis assesses for the first time the system value of 20 energy storage technologies across multiple scenarios in a representative future power system in Africa. The results offer insights into approaches for assessing multiple energy storage technologies under competition in large-scale energy system models. In particular, the dissertation addresses extreme cost uncertainty through a comprehensive scenario tree and finds that, apart from lithium and hydrogen, only seven energy storage are optimizationrelevant technologies. The work also discovers that a heterogeneous storage design can increase power system benefits and that some energy storage are more important than others. Finally, in contrast to traditional methods that only consider single energy storage, the thesis finds that optimizing multiple energy storage options tends to significantly reduce total system costs by up to 29%. The presented research findings have the potential to inform decision-making processes for the sizing, integration, and deployment of energy storage systems in decarbonized power systems, contributing to a paradigm shift in scientific methodology and advancing efforts towards a sustainable future

    Multidisciplinary perspectives on Artificial Intelligence and the law

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    This open access book presents an interdisciplinary, multi-authored, edited collection of chapters on Artificial Intelligence (‘AI’) and the Law. AI technology has come to play a central role in the modern data economy. Through a combination of increased computing power, the growing availability of data and the advancement of algorithms, AI has now become an umbrella term for some of the most transformational technological breakthroughs of this age. The importance of AI stems from both the opportunities that it offers and the challenges that it entails. While AI applications hold the promise of economic growth and efficiency gains, they also create significant risks and uncertainty. The potential and perils of AI have thus come to dominate modern discussions of technology and ethics – and although AI was initially allowed to largely develop without guidelines or rules, few would deny that the law is set to play a fundamental role in shaping the future of AI. As the debate over AI is far from over, the need for rigorous analysis has never been greater. This book thus brings together contributors from different fields and backgrounds to explore how the law might provide answers to some of the most pressing questions raised by AI. An outcome of the Católica Research Centre for the Future of Law and its interdisciplinary working group on Law and Artificial Intelligence, it includes contributions by leading scholars in the fields of technology, ethics and the law.info:eu-repo/semantics/publishedVersio

    A revisited branch-and-cut algorithm for large-scale orienteering problems

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    The orienteering problem is a route optimization problem which consists of finding a simple cycle that maximizes the total collected profit subject to a maximum distance limitation. In the last few decades, the occurrence of this problem in real-life applications has boosted the development of many heuristic algorithms to solve it. However, during the same period, not much research has been devoted to the field of exact algorithms for the orienteering problem. The aim of this work is to develop an exact method which is able to obtain the optimum in a wider set of instances than with previous methods, or to improve the lower and upper bounds in its disability. We propose a revisited version of the branch-and-cut algorithm for the orienteering problem which includes new contributions in the separation algorithms of inequalities stemming from the cycle problem, in the separation loop, in the variables pricing, and in the calculation of the lower and upper bounds of the problem. Our proposal is compared to three state-of-the-art algorithms on 258 benchmark instances with up to 7397 nodes. The computational experiments show the relevance of the designed components where 18 new optima, 76 new best-known solutions and 85 new upper-bound values were obtained

    1st Design Factory Global Network Research Conference ‘Designing the Future’ 5-6 October 2022

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    DFGN.R 2022 -Designing the Future - is the first research conference organised by the Design Factory Global Network. The open event offers the opportunity for all like-minded educators, designers and researchers to share their insights and inspire others on education, methods, practices and ecosystems of co-creation and innovation. The DFGN.R conference is a two-day event hosted on-site in Leeuwarden, the Netherlands. The conference is organized alongside International Design Factory Week 2022, the annual gathering of DFGN members. This year's conference is organized in collaboration with Aalto University from Helsinki Finland and hosted by the NHL Stenden University of Applied Sciences

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Approximations for the Steiner Multicycle Problem

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    The Steiner Multicycle problem consists of, given a complete graph, a weight function on its vertices, and a collection of pairwise disjoint non-unitary sets called terminal sets, finding a minimum weight collection of vertex-disjoint cycles in the graph such that, for every terminal set, all of its vertices are in a same cycle of the collection. This problem generalizes the Traveling Salesman problem and therefore is hard to approximate in general. On the practical side, it models a collaborative less-than-truckload problem with pickup and delivery locations. Using an algorithm for the Survivable Network Design problem and T -joins, we obtain a 3-approximation for the metric case, improving on the previous best 4-approximation. Furthermore, we present an (11/9)-approximation for the particular case of the Steiner Multicycle in which each edge weight is 1 or 2. This algorithm can be adapted to obtain a (7/6)-approximation when every terminal set contains at least 4 vertices. Finally, we devise an O(lg n)-approximation algorithm for the asymmetric version of the problem

    Quantum Alternating Operator Ansatz (QAOA) beyond low depth with gradually changing unitaries

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    The Quantum Approximate Optimization Algorithm and its generalization to Quantum Alternating Operator Ansatz (QAOA) is a promising approach for applying quantum computers to challenging problems such as combinatorial optimization and computational chemistry. In this paper, we study the underlying mechanisms governing the behavior of QAOA circuits beyond shallow depth in the practically relevant setting of gradually varying unitaries. We use the discrete adiabatic theorem, which complements and generalizes the insights obtained from the continuous-time adiabatic theorem primarily considered in prior work. Our analysis explains some general properties that are conspicuously depicted in the recently introduced QAOA performance diagrams. For parameter sequences derived from continuous schedules (e.g. linear ramps), these diagrams capture the algorithm's performance over different parameter sizes and circuit depths. Surprisingly, they have been observed to be qualitatively similar across different performance metrics and application domains. Our analysis explains this behavior as well as entails some unexpected results, such as connections between the eigenstates of the cost and mixer QAOA Hamiltonians changing based on parameter size and the possibility of reducing circuit depth without sacrificing performance

    Deeply Rational Machines -- What the History of Philosophy Can Teach Us about the Future of Artificial Intelligence -- Sample Chapter 1 -- "Moderate Empiricism and Machine Learning"

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    This book provides a framework for thinking about foundational philosophical questions surrounding the use of deep artificial neural networks (“deep learning”) to achieve artificial intelligence. Specifically, it links recent breakthroughs in deep learning to classical empiricist philosophy of mind. In recent assessments of deep learning’s current capabilities and future potential, prominent scientists have cited historical figures from the perennial philosophical debate between nativism and empiricism, which primarily concerns the origins of abstract knowledge. These empiricists were generally faculty psychologists; that is, they argued that the extraction of abstract knowledge from perceptual experience involves the active engagement of general psychological faculties—such as perception, memory, imagination, attention, and empathy. This book explains how recent headline-grabbing deep learning achievements were enabled by adding functionality to these networks that model forms of processing attributed to these faculties by philosophers such as Aristotle, Ibn Sina (Avicenna), John Locke, David Hume, William James, and Sophie de Grouchy. It illustrates the utility of this interdisciplinary connection by showing how it can provide benefits to both philosophy and computer science: computer scientists can continue to mine the history of philosophy for ideas and aspirational targets to hit on the way to building more robustly rational artificial agents, and philosophers can see how some of the historical empiricists’ most ambitious speculations can now be realized in specific computational systems
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