Search results for "Abstract"
showing 10 items of 1959 documents
Multiple testing in candidate gene situations: a comparison of classical, discrete, and resampling-based procedures.
2011
In candidate gene association studies, usually several elementary hypotheses are tested simultaneously using one particular set of data. The data normally consist of partly correlated SNP information. Every SNP can be tested for association with the disease, e.g., using the Cochran-Armitage test for trend. To account for the multiplicity of the test situation, different types of multiple testing procedures have been proposed. The question arises whether procedures taking into account the discreteness of the situation show a benefit especially in case of correlated data. We empirically evaluate several different multiple testing procedures via simulation studies using simulated correlated SN…
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…
Community detection algorithm evaluation with ground-truth data
2018
International audience; Community structure is of paramount importance for the understanding of complex networks. Consequently, there is a tremendous effort in order to develop efficient community detection algorithms. Unfortunately, the issue of a fair assessment of these algorithms is a thriving open question. If the ground-truth community structure is available, various clustering-based metrics are used in order to compare it versus the one discovered by these algorithms. However, these metrics defined at the node level are fairly insensitive to the variation of the overall community structure. To overcome these limitations, we propose to exploit the topological features of the ‘communit…
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…
Stochastic Learning for SAT- Encoded Graph Coloring Problems
2010
The graph coloring problem (GCP) is a widely studied combinatorial optimization problem due to its numerous applications in many areas, including time tabling, frequency assignment, and register allocation. The need for more efficient algorithms has led to the development of several GC solvers. In this paper, the authors introduce a team of Finite Learning Automata, combined with the random walk algorithm, using Boolean satisfiability encoding for the GCP. The authors present an experimental analysis of the new algorithm’s performance compared to the random walk technique, using a benchmark set containing SAT-encoding graph coloring test sets.
Analyzing Temperature Effects on Mortality Within theREnvironment: The Constrained Segmented Distributed Lag Parameterization
2010
Here we present and discuss the R package modTempEff including a set of functions aimed at modelling temperature effects on mortality with time series data. The functions fit a particular log linear model which allows to capture the two main features of mortality- temperature relationships: nonlinearity and distributed lag effect. Penalized splines and segmented regression constitute the core of the modelling framework. We briefly review the model and illustrate the functions throughout a simulated dataset.
Ranking Scientific Journals Via Latent Class Models for Polytomous Item Response Data
2015
Summary We propose a model-based strategy for ranking scientific journals starting from a set of observed bibliometric indicators that represent imperfect measures of the unobserved ‘value’ of a journal. After discretizing the available indicators, we estimate an extended latent class model for polytomous item response data and use the estimated model to cluster journals. We illustrate our approach by using the data from the Italian research evaluation exercise that was carried out for the period 2004–2010, focusing on the set of journals that are considered relevant for the subarea statistics and financial mathematics. Using four bibliometric indicators (IF, IF5, AIS and the h-index), some…
Study Design in Causal Models
2014
The causal assumptions, the study design and the data are the elements required for scientific inference in empirical research. The research is adequately communicated only if all of these elements and their relations are described precisely. Causal models with design describe the study design and the missing-data mechanism together with the causal structure and allow the direct application of causal calculus in the estimation of the causal effects. The flow of the study is visualized by ordering the nodes of the causal diagram in two dimensions by their causal order and the time of the observation. Conclusions on whether a causal or observational relationship can be estimated from the coll…
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…
Comparative Evaluation of Community Detection Algorithms: A Topological Approach
2012
International audience; Community detection is one of the most active fields in complex networks analysis, due to its potential value in practical applications. Many works inspired by different paradigms are devoted to the development of algorithmic solutions allowing to reveal the network structure in such cohesive subgroups. Comparative studies reported in the literature usually rely on a performance measure considering the community structure as a partition (Rand Index, Normalized Mutual information, etc.). However, this type of comparison neglects the topological properties of the communities. In this article, we present a comprehensive comparative study of a representative set of commu…