Search results for "Reference"
showing 10 items of 2491 documents
Consensus among preference rankings: a new weighted correlation coefficient for linear and weak orderings
2021
AbstractPreference data are a particular type of ranking data where some subjects (voters, judges,...) express their preferences over a set of alternatives (items). In most real life cases, some items receive the same preference by a judge, thus giving rise to a ranking with ties. An important issue involving rankings concerns the aggregation of the preferences into a “consensus”. The purpose of this paper is to investigate the consensus between rankings with ties, taking into account the importance of swapping elements belonging to the top (or to the bottom) of the ordering (position weights). By combining the structure of $$\tau _x$$ τ x proposed by Emond and Mason (J Multi-Criteria Decis…
Overall Objective Priors
2015
In multi-parameter models, reference priors typically depend on the parameter or quantity of interest, and it is well known that this is necessary to produce objective posterior distributions with optimal properties. There are, however, many situations where one is simultaneously interested in all the parameters of the model or, more realistically, in functions of them that include aspects such as prediction, and it would then be useful to have a single objective prior that could safely be used to produce reasonable posterior inferences for all the quantities of interest. In this paper, we consider three methods for selecting a single objective prior and study, in a variety of problems incl…
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study
2019
Abstract Motivation Metagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome. Results To address this problem, we developed a novel clustering approach called ‘metagenomic clustering by reference library’ (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed ‘signatures’, are iteratively clustered in a greedy fashion, re…
A new position weight correlation coefficient for consensus ranking process without ties
2019
Preference data represent a particular type of ranking data where a group of people gives their preferences over a set of alternatives. The traditional metrics between rankings do not take into account the importance of swapping elements similar among them (element weights) or elements belonging to the top (or to the bottom) of an ordering (position weights). Following the structure of the τx proposed by Emond and Mason and the class of weighted Kemeny–Snell distances, a proper rank correlation coefficient is defined for measuring the correlation among weighted position rankings without ties. The one‐to‐one correspondence between the weighted distance and the rank correlation coefficient ho…
Weighted distance-based trees for ranking data
2017
Within the framework of preference rankings, the interest can lie in finding which predictors and which interactions are able to explain the observed preference structures, because preference decisions will usually depend on the characteristics of both the judges and the objects being judged. This work proposes the use of a univariate decision tree for ranking data based on the weighted distances for complete and incomplete rankings, and considers the area under the ROC curve both for pruning and model assessment. Two real and well-known datasets, the SUSHI preference data and the University ranking data, are used to display the performance of the methodology.
Adaptive reference-free compression of sequence quality scores
2014
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and hence are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full reso…
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files
2021
[Motivation]: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user’s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences’ analysis.
A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data
2015
Abstract Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available appli…
On the problem of finding a suitable distribution of students to universities in Germany
2009
For many years, the problem of how to distribute students to the various universities in Germany according to the preferences of the students has remained unsolved. Various approaches, like the centralized method to let a central agency organize the distribution to the various universities or the decentralized method to let the students apply directly at their preferred universities, turned out to lead to a significant fraction of frustrated students ending up at universities not being on their preference list or even not having a place to study at all. With our centralized approach, we are able to decrease the fraction of frustrated students as well as the bureaucratic expenses for applica…
Improving the speed estimation by load torque estimation in induction motor drives: an MRAS and NUIO approach
2021
This paper proposes the application of the NUIO inside a FOC induction motor drive for the simultaneous estimation of the load torque and the rotor speed. The idea is to estimate at first the speed with the current model in parallel with a reference model developed on the basis of the voltage model of the induction machine. Then, the estimated speed is given as input to a nonlinear unknown input observer (NUIO) to estimate the load torque. This estimation is then used to correct the previous estimation of the speed. Simulation and experimental results confirm the goodness of the method for an extended range of speed and different load torque, and they confirm the reduction of error in trans…