1,721,021 research outputs found
Thallinger, Gerhard: Messung und Analyse von zeit- und ortsabhängigen Raumimpulsantworten
No full textGraz, Univ. für Musik und darstellende Kunst, Diplomarb., 200
ONT Base-calling mitjançant l'aprenentatge profund
No full text[ES] La secuenciación de nanoporos ha evolucionado durante las últimas cuatro décadas y Oxford Nanopore Technologies la convirtió en una tecnología viable, que está disponible comercialmente desde 2015. Uno de los muchos pasos cruciales en la secuenciación de ONT es la llamada de base donde los cambios actuales (garabatos) medidos por el dispositivo MinION durante el paso de la hebra de ADN a través del poro se convierte en la secuencia de nucleótidos real. Se han propuesto varios enfoques basados en redes neuronales (NN) [7-11], que difieren en precisión y velocidad. El objetivo general de esta tesis de licenciatura es describir la arquitectura de red neuronal (NNA) de los diferentes enfoques y compararlos utilizando datos de secuenciación ONT adquiridos recientemente de diferentes tipos de poros. En concreto, se debe lograr lo siguiente:
1. Familiarícese con la secuenciación de ONT, el aprendizaje profundo en general y los diferentes NNA utilizados para la llamada de base de ONT en particular.
2. Configure un entorno de desarrollo que incluya Guppy (versión 3.30 y la más reciente), fast-bonito, Heron and Osprey, samtools, minimap2, BLAST y SeqKit.
3. Describa las NNA de los llamadores de base en términos de arquitectura, nodos de entrada, capas, nodos por capa, nodos de salida y número total de parámetros en la NN.
4. Evaluar la velocidad de los diferentes enfoques utilizando los datos de los experimentos de secuenciación ONT recientes de diferentes tipos de celdas de flujo. Trate de crear un modelo matemático para estimar el tiempo total de llamada de base para los diferentes tipos de celdas de flujo y llamadas de base en función de un tiempo de configuración, la cantidad de lecturas y su duración utilizando diferentes conjuntos de datos de muestreo descendente.
5. Evaluar la precisión de la llamada de base asignando las lecturas a un genoma de referencia de la especie secuenciada y utilizando samtools para determinar la tasa de error. Estratifique los errores en desajustes, eliminaciones, inserciones y errores en tramos de homopolímero.
6. Resumir el trabajo y los resultados en una tesis escrita[EN] In the field of biological research, an essential procedure involves
sequencing, which encompasses the precise determination of the sequence
of nucleotides within DNA or RNA molecules. Nanopore sequencing
technology, pioneered by Oxford Nanopore Technologies (ONT), is
founded on the concept of guiding DNA or RNA molecules through a
minute pore while monitoring changes in electrical current as each
nucleotide traverses the pore. In the ONT sequencing process, a critical
bottleneck arises during basecalling, a technique that converts the raw
electrical current data collected by a sequencing instrument into the
corresponding nucleotide sequence. To address this challenge, numerous
basecalling algorithms have been proposed for ONT data, many of which
rely on neural networks (NN). These algorithms vary in terms of accuracy
and speed. To evaluate the performance of these basecallers, we conducted
tests using raw data obtained from the organism Pichia pastoris. Specifically,
we assessed version 6.4.8 of Guppy, version 0.3.2 of Dorado, and their
modified basecalling algorithms across different models (fast, high
accuracy, and super accuracy), in addition to Heron and Osprey.
Subsequently, the results were aligned with a reference genome and
analyzed to determine various characteristics, such as runtime and error
rates. The findings revealed that the modified basecalling algorithms
exhibited nearly identical results compared to the unmodified version
across all models, although with a slight increase in runtime. Guppy
demonstrated the lowest error rates for all models. The model with the most
pronounced differences was the super accuracy with a 0.062 error rate
average that came at the cost of longer execution times getting to around 18
hours. Dorado, on the other hand, exhibited reduced error rates with
around 0.096 for the same model (so not as reduced as Guppy) with
significantly lower runtimes particularly in the hac (35 minutes) and sup
models (2 hours 15 minutes). Osprey could be compared to the fast model
of the other basecallers, taking around 5 minutes and presenting an average
error rate of 0.128 that did not surpass the performance of Dorado’s (0.124)
or Guppy’s (0.114) fast model. Unfortunately, Heron was unable to assess
due to significant installation issues that proved challenging to resolve.Paredes De Isla, J. (2023). ONT Base-calling using Deep Learning. Universitat Politècnica de València. https://riunet.upv.es/handle/10251/197884TFG
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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