2,696 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

    The AddACO: A bio-inspired modified version of the ant colony optimization algorithm to solve travel salesman problems

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    The Travel Salesman Problem (TSP) consists in finding the minimal-length closed tour that connects the entire group of nodes of a given graph. We propose to solve such a combinatorial optimization problem with the AddACO algorithm: it is a version of the Ant Colony Optimization method that is characterized by a modified probabilistic law at the basis of the exploratory movement of the artificial insects. In particular, the ant decisional rule is here set to amount in a linear convex combination of competing behavioral stimuli and has therefore an additive form (hence the name of our algorithm), rather than the canonical multiplicative one. The AddACO intends to address two conceptual shortcomings that characterize classical ACO methods: (i) the population of artificial insects is in principle allowed to simultaneously minimize/maximize all migratory guidance cues (which is in implausible from a biological/ecological point of view) and (ii) a given edge of the graph has a null probability to be explored if at least one of the movement trait is therein equal to zero, i.e., regardless the intensity of the others (this in principle reduces the exploratory potential of the ant colony). Three possible variants of our method are then specified: the AddACO-V1, which includes pheromone trail and visibility as insect decisional variables, and the AddACO-V2 and the AddACO-V3, which in turn add random effects and inertia, respectively, to the two classical migratory stimuli. The three versions of our algorithm are tested on benchmark middle-scale TPS instances, in order to assess their performance and to find their optimal parameter setting. The best performing variant is finally applied to large-scale TSPs, compared to the naive Ant-Cycle Ant System, proposed by Dorigo and colleagues, and evaluated in terms of quality of the solutions, computational time, and convergence speed. The aim is in fact to show that the proposed transition probability, as long as its conceptual advantages, is competitive from a performance perspective, i.e., if it does not reduce the exploratory capacity of the ant population w.r.t. the canonical one (at least in the case of selected TSPs). A theoretical study of the asymptotic behavior of the AddACO is given in the appendix of the work, whose conclusive section contains some hints for further improvements of our algorithm, also in the perspective of its application to other optimization problems

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    MECHANICAL ENERGY HARVESTER FOR POWERING RFID SYSTEMS COMPONENTS: MODELING, ANALYSIS, OPTIMIZATION AND DESIGN

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    Finding alternative power sources has been an important topic of study worldwide. It is vital to find substitutes for finite fossil fuels. Such substitutes may be termed renewable energy sources and infinite supplies. Such limitless sources are derived from ambient energy like wind energy, solar energy, sea waves energy; on the other hand, smart cities megaprojects have been receiving enormous amounts of funding to transition our lives into smart lives. Smart cities heavily rely on smart devices and electronics, which utilize small amounts of energy to run. Using batteries as the power source for such smart devices imposes environmental and labor cost issues. Moreover, in many cases, smart devices are in hard-to-access places, making accessibility for disposal and replacement difficult. Finally, battery waste harms the environment. To overcome these issues, vibration-based energy harvesters have been proposed and implemented. Vibration-based energy harvesters convert the dynamic or kinetic energy which is generated due to the motion of an object into electric energy. Energy transduction mechanisms can be delivered based on piezoelectric, electromagnetic, or electrostatic methods; the piezoelectric method is generally preferred to the other methods, particularly if the frequency fluctuations are considerable. In response, piezoelectric vibration-based energy harvesters (PVEHs), have been modeled and analyzed widely. However, there are two challenges with PVEH: the maximum amount of extractable voltage and the effective (operational) frequency bandwidth are often insufficient. In this dissertation, a new type of integrated multiple system comprised of a cantilever and spring-oscillator is proposed to improve and develop the performance of the energy harvester in terms of extractable voltage and effective frequency bandwidth. The new energy harvester model is proposed to supply sufficient energy to power low-power electronic devices like RFID components. Due to the temperature fluctuations, the thermal effect over the performance of the harvester is initially studied. To alter the resonance frequency of the harvester structure, a rotating element system is considered and analyzed. In the analytical-numerical analysis, Hamilton’s principle along with Galerkin’s decomposition approach are adopted to derive the governing equations of the harvester motion and corresponding electric circuit. It is observed that integration of the spring-oscillator subsystem alters the boundary condition of the cantilever and subsequently reforms the resulting characteristic equation into a more complicated nonlinear transcendental equation. To find the resonance frequencies, this equation is solved numerically in MATLAB. It is observed that the inertial effects of the oscillator rendered to the cantilever via the restoring force effects of the spring significantly alter vibrational features of the harvester. Finally, the voltage frequency response function is analytically and numerically derived in a closed-from expression. Variations in parameter values enable the designer to mutate resonance frequencies and mode shape functions as desired. This is particularly important, since the generated energy from a PVEH is significant only if the excitation frequency coming from an external source matches the resonance (natural) frequency of the harvester structure. In subsequent sections of this work, the oscillator mass and spring stiffness are considered as the design parameters to maximize the harvestable voltage and effective frequency bandwidth, respectively. For the optimization, a genetic algorithm is adopted to find the optimal values. Since the voltage frequency response function cannot be implemented in a computer algorithm script, a suitable function approximator (regressor) is designed using fuzzy logic and neural networks. The voltage function requires manual assistance to find the resonance frequency and cannot be done automatically using computer algorithms. Specifically, to apply the numerical root-solver, one needs to manually provide the solver with an initial guess. Such an estimation is accomplished using a plot of the characteristic equation along with human visual inference. Thus, the entire process cannot be automated. Moreover, the voltage function encompasses several coefficients making the process computationally expensive. Thus, training a supervised machine learning regressor is essential. The trained regressor using adaptive-neuro-fuzzy-inference-system (ANFIS) is utilized in the genetic optimization procedure. The optimization problem is implemented, first to find the maximum voltage and second to find the maximum widened effective frequency bandwidth, which yields the optimal oscillator mass value along with the optimal spring stiffness value. As there is often no control over the external excitation frequency, it is helpful to design an adaptive energy harvester. This means that, considering a specific given value of the excitation frequency, energy harvester system parameters (oscillator mass and spring stiffness) need to be adjusted so that the resulting natural (resonance) frequency of the system aligns with the given excitation frequency. To do so, the given excitation frequency value is considered as the input and the system parameters are assumed as outputs which are estimated via the neural network fuzzy logic regressor. Finally, an experimental setup is implemented for a simple pure cantilever energy harvester triggered by impact excitations. Unlike the theoretical section, the experimental excitation is considered to be an impact excitation, which is a random process. The rationale for this is that, in the real world, the external source is a random trigger. Harmonic base excitations used in the theoretical chapters are to assess the performance of the energy harvester per standard criteria. To evaluate the performance of a proposed energy harvester model, the input excitation type consists of harmonic base triggers. In summary, this dissertation discusses several case studies and addresses key issues in the design of optimized piezoelectric vibration-based energy harvesters (PVEHs). First, an advanced model of the integrated systems is presented with equation derivations. Second, the proposed model is decomposed and analyzed in terms of mechanical and electrical frequency response functions. To do so, analytic-numeric methods are adopted. Later, influential parameters of the integrated system are detected. Then the proposed model is optimized with respect to the two vital criteria of maximum amount of extractable voltage and widened effective (operational) frequency bandwidth. Corresponding design (influential) parameters are found using neural network fuzzy logic along with genetic optimization algorithms, i.e., a soft computing method. The accuracy of the trained integrated algorithms is verified using the analytical-numerical closed-form expression of the voltage function. Then, an adaptive piezoelectric vibration-based energy harvester (PVEH) is designed. This final design pertains to the cases where the excitation (driving) frequency is given and constant, so the desired goal is to match the natural frequency of the system with the given driving frequency. In this response, a regressor using neural network fuzzy logic is designed to find the proper design parameters. Finally, the experimental setup is implemented and tested to report the maximum voltage harvested in each test execution

    Proceedings of SIRM 2023 - The 15th European Conference on Rotordynamics

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    It was our great honor and pleasure to host the SIRM Conference after 2003 and 2011 for the third time in Darmstadt. Rotordynamics covers a huge variety of different applications and challenges which are all in the scope of this conference. The conference was opened with a keynote lecture given by Rainer Nordmann, one of the three founders of SIRM “Schwingungen in rotierenden Maschinen”. In total 53 papers passed our strict review process and were presented. This impressively shows that rotordynamics is relevant as ever. These contributions cover a very wide spectrum of session topics: fluid bearings and seals; air foil bearings; magnetic bearings; rotor blade interaction; rotor fluid interactions; unbalance and balancing; vibrations in turbomachines; vibration control; instability; electrical machines; monitoring, identification and diagnosis; advanced numerical tools and nonlinearities as well as general rotordynamics. The international character of the conference has been significantly enhanced by the Scientific Board since the 14th SIRM resulting on one hand in an expanded Scientific Committee which meanwhile consists of 31 members from 13 different European countries and on the other hand in the new name “European Conference on Rotordynamics”. This new international profile has also been emphasized by participants of the 15th SIRM coming from 17 different countries out of three continents. We experienced a vital discussion and dialogue between industry and academia at the conference where roughly one third of the papers were presented by industry and two thirds by academia being an excellent basis to follow a bidirectional transfer what we call xchange at Technical University of Darmstadt. At this point we also want to give our special thanks to the eleven industry sponsors for their great support of the conference. On behalf of the Darmstadt Local Committee I welcome you to read the papers of the 15th SIRM giving you further insight into the topics and presentations

    AI: Limits and Prospects of Artificial Intelligence

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    The emergence of artificial intelligence has triggered enthusiasm and promise of boundless opportunities as much as uncertainty about its limits. The contributions to this volume explore the limits of AI, describe the necessary conditions for its functionality, reveal its attendant technical and social problems, and present some existing and potential solutions. At the same time, the contributors highlight the societal and attending economic hopes and fears, utopias and dystopias that are associated with the current and future development of artificial intelligence

    Low-Thrust Optimal Escape Trajectories from Lagrangian Points and Quasi-Periodic Orbits in a High-Fidelity Model

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    L'abstract è presente nell'allegato / the abstract is in the attachmen

    Asymptotics of stochastic learning in structured networks

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    Advances and Applications of DSmT for Information Fusion. Collected Works, Volume 5

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    This fifth volume on Advances and Applications of DSmT for Information Fusion collects theoretical and applied contributions of researchers working in different fields of applications and in mathematics, and is available in open-access. The collected contributions of this volume have either been published or presented after disseminating the fourth volume in 2015 in international conferences, seminars, workshops and journals, or they are new. The contributions of each part of this volume are chronologically ordered. First Part of this book presents some theoretical advances on DSmT, dealing mainly with modified Proportional Conflict Redistribution Rules (PCR) of combination with degree of intersection, coarsening techniques, interval calculus for PCR thanks to set inversion via interval analysis (SIVIA), rough set classifiers, canonical decomposition of dichotomous belief functions, fast PCR fusion, fast inter-criteria analysis with PCR, and improved PCR5 and PCR6 rules preserving the (quasi-)neutrality of (quasi-)vacuous belief assignment in the fusion of sources of evidence with their Matlab codes. Because more applications of DSmT have emerged in the past years since the apparition of the fourth book of DSmT in 2015, the second part of this volume is about selected applications of DSmT mainly in building change detection, object recognition, quality of data association in tracking, perception in robotics, risk assessment for torrent protection and multi-criteria decision-making, multi-modal image fusion, coarsening techniques, recommender system, levee characterization and assessment, human heading perception, trust assessment, robotics, biometrics, failure detection, GPS systems, inter-criteria analysis, group decision, human activity recognition, storm prediction, data association for autonomous vehicles, identification of maritime vessels, fusion of support vector machines (SVM), Silx-Furtif RUST code library for information fusion including PCR rules, and network for ship classification. Finally, the third part presents interesting contributions related to belief functions in general published or presented along the years since 2015. These contributions are related with decision-making under uncertainty, belief approximations, probability transformations, new distances between belief functions, non-classical multi-criteria decision-making problems with belief functions, generalization of Bayes theorem, image processing, data association, entropy and cross-entropy measures, fuzzy evidence numbers, negator of belief mass, human activity recognition, information fusion for breast cancer therapy, imbalanced data classification, and hybrid techniques mixing deep learning with belief functions as well

    20th SC@RUG 2023 proceedings 2022-2023

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