Browsing by Subject "Optimization"

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  • Vuoriheimo, Tomi (Helsingfors universitet, 2017)
    Accelerator mass spectrometry (AMS) is a technique developed from mass spectrometry and it is able to measure single very rare isotopes from samples with detection capability down to one atom in 10^16. It uses an accelerator system to accelerate the atoms and molecules to break molecular bonds for precise single isotope detection. This thesis describes the optimization of University of Helsinki's AMS system to detect the rare radioactive isotope 14C from CO2 gas samples. Using AMS to detect radiocarbon is a precise and fast way to conduct radiocarbon dating with minimal sample sizes. Solid graphite samples have been in use before but as the ion source has been adopted to use also gaseous CO2 samples, optimizations must be made to maximize the carbon current and ionization efficiency for efficient 14C detection. Parameters optimized include cesium oven temperature, CO2 flow, carrier gas helium flow and their dependencies with each other. Both carbon current and ionization efficiency is looked at in the optimizations. The results are analyzed and discussed for further optimizations or actual measurements with gas. Ionization occurring in the ion source can be understood better with the results. Standard samples of CO2 were measured to determine the background and precision of the AMS system in gas use by comparing the results with literature. The current system was found to have tolerable background of 1.5% of the standard and the Fraction modern value of actual sample was 2.4% higher than values from literature. Ideas to improve background were discussed. A new theory of negative-ion formation in a cesium sputtering ion source by John S. Vogel is reviewed and taken into account in the discussion of optimization. Utilizing the theory, possible future upgrades to improve the ionization efficiency are presented such as cathode material choices to reduce competitive ionization and cesium excitation by laser.
  • Somervuo, Panu; Koskinen, Patrik; Mei, Peng; Holm, Liisa; Auvinen, Petri; Paulin, Lars (2018)
    Background: Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, the samples are binned by identifying the barcode sequence within each sequence read. In order to tolerate sequencing errors, barcodes should be sufficiently apart from each other in sequence space. An additional constraint due to both nucleotide usage and basecalling accuracy is that the proportion of different nucleotides should be in balance in each barcode position. The number of samples to be mixed in each sequencing run may vary and this introduces a problem how to select the best subset of available barcodes at sequencing core facility for each sequencing run. There are plenty of tools available for de novo barcode design, but they are not suitable for subset selection. Results: We have developed a tool which can be used for three different tasks: 1) selecting an optimal barcode set from a larger set of candidates, 2) checking the compatibility of user-defined set of barcodes, e.g. whether two or more libraries with existing barcodes can be combined in a single sequencing pool, and 3) augmenting an existing set of barcodes. In our approach the selection process is formulated as a minimization problem. We define the cost function and a set of constraints and use integer programming to solve the resulting combinatorial problem. Based on the desired number of barcodes to be selected and the set of candidate sequences given by user, the necessary constraints are automatically generated and the optimal solution can be found. The method is implemented in C programming language and web interface is available at http://ekhidna2.biocenter.helsinki.fi/barcosel. Conclusions: Increasing capacity of sequencing platforms raises the challenge of mixing barcodes. Our method allows the user to select a given number of barcodes among the larger existing barcode set so that both sequencing errors are tolerated and the nucleotide balance is optimized. The tool is easy to access via web browser.
  • Somervuo, Panu; Koskinen, Patrik; Mei, Peng; Holm, Liisa; Auvinen, Petri; Paulin, Lars (BioMed Central, 2018)
    Abstract Background Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, the samples are binned by identifying the barcode sequence within each sequence read. In order to tolerate sequencing errors, barcodes should be sufficiently apart from each other in sequence space. An additional constraint due to both nucleotide usage and basecalling accuracy is that the proportion of different nucleotides should be in balance in each barcode position. The number of samples to be mixed in each sequencing run may vary and this introduces a problem how to select the best subset of available barcodes at sequencing core facility for each sequencing run. There are plenty of tools available for de novo barcode design, but they are not suitable for subset selection. Results We have developed a tool which can be used for three different tasks: 1) selecting an optimal barcode set from a larger set of candidates, 2) checking the compatibility of user-defined set of barcodes, e.g. whether two or more libraries with existing barcodes can be combined in a single sequencing pool, and 3) augmenting an existing set of barcodes. In our approach the selection process is formulated as a minimization problem. We define the cost function and a set of constraints and use integer programming to solve the resulting combinatorial problem. Based on the desired number of barcodes to be selected and the set of candidate sequences given by user, the necessary constraints are automatically generated and the optimal solution can be found. The method is implemented in C programming language and web interface is available at http://ekhidna2.biocenter.helsinki.fi/barcosel . Conclusions Increasing capacity of sequencing platforms raises the challenge of mixing barcodes. Our method allows the user to select a given number of barcodes among the larger existing barcode set so that both sequencing errors are tolerated and the nucleotide balance is optimized. The tool is easy to access via web browser.
  • Koponen, Lari M.; Nieminen, Jaakko O.; Mutanen, Tuomas P.; Stenroos, Matti; Ilmoniemi, Risto J. (2017)
    Background: Transcranial magnetic stimulation (TMS) allows focal, non-invasive stimulation of the cortex. A TMS pulse is inherently weakly coupled to the cortex; thus, magnetic stimulation requires both high current and high voltage to reach sufficient intensity. These requirements limit, for example, the maximum repetition rate and the maximum number of consecutive pulses with the same coil due to the rise of its temperature. Objective: To develop methods to optimise, design, and manufacture energy-efficient TMS coils in realistic head geometry with an arbitrary overall coil shape. Methods: We derive a semi-analytical integration scheme for computing the magnetic field energy of an arbitrary surface current distribution, compute the electric field induced by this distribution with a boundary element method, and optimise a TMS coil for focal stimulation. Additionally, we introduce a method for manufacturing such a coil by using Litz wire and a coil former machined from polyvinyl chloride. Results: We designed, manufactured, and validated an optimised TMS coil and applied it to brain stimulation. Our simulations indicate that this coil requires less than half the power of a commercial figure-of-eight coil, with a 41% reduction due to the optimised winding geometry and a partial contribution due to our thinner coil former and reduced conductor height. With the optimised coil, the resting motor threshold of abductor pollicis brevis was reached with the capacitor voltage below 600 V and peak current below 3000 A. Conclusion: The described method allows designing practical TMS coils that have considerably higher efficiency than conventional figure-of-eight coils. (C) 2017 Elsevier Inc. All rights reserved.
  • Holma, Maija; Lindroos, Marko; Romakkaniemi, Atso; Oinonen, Soile (2019)
  • Pozza, Matteo; Rao, Ashwin; Lugones, Diego. F.; Tarkoma, Sasu (2021)
    Network function (NF) developers have traditionally prioritized performance when creating new packet processing capabilities. This was usually driven by a market demand for highly available solutions with differentiating features running at line rate, even at the expense of flexibility and tightly-coupled monolithic designs. Today, however, the market advantage is achieved by providing more features in shorter development cycles and quickly deploying them in different operating environments. In fact, network operators are increasingly adopting continuous software delivery practices as well as new architectural styles (e.g., microservices) to decouple functionality and accelerate development. A key challenge in revisiting NF design is state management, which is usually highly optimized for a deployment by carefully selecting the underlying data store. Therefore, migrating to a data store that suits a different use case is time-consuming as it requires code refactoring and adaptation to new application programming interfaces, APIs. As a result, refactoring NF software for different environments can take up to months, reducing the pace at which new features and upgrades can be deployed in production networks. In this paper, we demonstrate experimentally that it is feasible to introduce an abstraction layer to decouple NF state management from the data store adopted while still approaching line-rate performance. We present FlexState, a state management system that exposes data store functionality as configuration options, which reduces code refactoring efforts. Experiments show that FlexState achieves significant flexibility in optimizing the state management, and accelerates deployment on new scenarios while preserving performance and scalability.
  • Li, Tong; Braud, Tristan; Li, Yong; Hui, Pan (2021)
    The current explosion of video traffic compels service providers to deploy caches at edge networks. Nowadays, most caching systems store data with a high programming voltage corresponding to the largest possible ‘expiry date’, typically on the order of years, which maximizes the cache damage. However, popular videos rarely exhibit lifecycles longer than a couple of months. Consequently, the programming voltage can instead be adapted to fit the lifecycle and mitigate the cache damage accordingly. In this paper, we propose LiA-cache, a Lifecycle-Aware caching policy for online videos. LiA-cache finds both near-optimal caching retention times and cache eviction policies by optimizing traffic delivery cost and cache damage cost conjointly. We first investigate temporal patterns of video access from a real-world dataset covering 10 million online videos collected by one of the largest mobile network operators in the world. We next cluster the videos based on their access lifecycles and integrate the clustering into a general model of the caching system. Specifically, LiA-cache analyzes videos and caches them depending on their cluster label. Compared to other popular policies in real-world scenarios, LiA-cache can reduce cache damage up to 90%, while keeping a cache hit ratio close to a policy purely relying on video popularity.