Search results for "Pairwise comparison"
showing 10 items of 82 documents
Linking species interactions with phylogenetic and functional distance in European bird assemblages at broad spatial scales
2017
Aim Understanding the relative contribution of different species interactions in shaping community assembly has been a pivotal aim in community ecology. Biotic interactions are acknowledged to be important at local scales, although their signal is assumed to weaken over longer distances. We examine the relationship between positive, neutral and negative pairwise bird abundance distributions and the phylogenetic and functional distance between these pairs after first controlling for habitat associations. Location France and Finland. Time period 1984 to 2011 (Finland), 2001 to 2012 (France). Major Taxa studied Birds. Methods We used results from French and Finnish land bird monitoring program…
Quantifying and addressing the prevalence and bias of study designs in the environmental and social sciences
2020
Building trust in science and evidence-based decision-making depends heavily on the credibility of studies and their findings. Researchers employ many different study designs that vary in their risk of bias to evaluate the true effect of interventions or impacts. Here, we empirically quantify, on a large scale, the prevalence of different study designs and the magnitude of bias in their estimates. Randomised designs and controlled observational designs with pre-intervention sampling were used by just 23% of intervention studies in biodiversity conservation, and 36% of intervention studies in social science. We demonstrate, through pairwise within-study comparisons across 49 environmental da…
Consistent Clustering of Elements in Large Pairwise Comparison Matrices
2018
[EN] In multi-attribute decision making the number of decision elements under consideration may be huge, especially for complex, real-world problems. Typically these elements are clustered and then the clusters organized hierarchically to reduce the number of elements to be simultaneously handled. These decomposition methodologies are intended to bring the problem within the cognitive ability of decision makers. However, such methodologies have disadvantages, and it may happen that such a priori clustering is not clear, and/or the problem has previously been addressed without any grouping action. This is the situation for the case study we address, in which a panel of experts gives opinions…
Decorous combinatorial lower bounds for row layout problems
2020
Abstract In this paper we consider the Double-Row Facility Layout Problem (DRFLP). Given a set of departments and pairwise transport weights between them the DRFLP asks for a non-overlapping arrangement of the departments along both sides of a common path such that the weighted sum of the center-to-center distances between the departments is minimized. Despite its broad applicability in factory planning, only small instances can be solved to optimality in reasonable time. Apart from this even deriving good lower bounds using existing integer programming formulations and branch-and-cut methods is a challenging problem. We focus here on deriving combinatorial lower bounds which can be compute…
Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures
2016
This is a post-peer-review, pre-copyedit version of an article published in IEEE Transactions on Parallel and Distributed Systems. The final authenticated version is available online at: http://dx.doi.org/10.1109/TPDS.2015.2460247. [Abstract] Development of new methods to detect pairwise epistasis, such as SNP-SNP interactions, in Genome-Wide Association Studies is an important task in bioinformatics as they can help to explain genetic influences on diseases. As these studies are time consuming operations, some tools exploit the characteristics of different hardware accelerators (such as GPUs and Xeon Phi coprocessors) to reduce the runtime. Nevertheless, all these approaches are not able t…
The colored longest common prefix array computed via sequential scans
2018
Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the computation of statistics of the sequences in the dataset. Such computations become impractical in internal memory when very large collections of long sequences are considered. In this paper, we present a new conceptual data structure, the colored longest common prefix array (cLCP), that allows to efficiently tackle several problems with an alignment-free approach. In fact, we show that such a data structure can be computed via sequential scans in semi-exter…
Some awkward issues on pairwise comparison matrices
2017
Many decision-making techniques use pairwise comparisons (PCs) elicited by one or more stakeholders involved in a given corresponding decision-making process. In very complex problems, the number of criteria or options to be compared may be too large, thus limiting PC applicability to large-scale decision problems due to the so-called curse of dimensionality, that is, a large number of pairwise comparisons need to be produced from a decision maker. For example, in AHP, Saaty [1] recommends that to obtain a reasonable and consistent PC matrix, the number of comparing elements should be at most seven. In [2] and [3], arguing on limitations of the human capabilities, the maximum number of elem…
The Right Job and the Job Right: Novelty, Impact and Journal Stratification in Science
2018
Though Science is traditionally associated with creative behavior, concerns have been raised on its professional procedures being sufficiently open to innovative research. Thanks to a new measurement of novelty based on the frequencies of pairwise combinations of article keywords calculated on the set of all research articles published from 1999 to 2013 in the journals referenced by the WoS (more than ten million papers), we find no evidence of shrinking novelty in science over that period. Novel contributions are more often performed in larger teams that span more institutional boundaries and geographic areas. High novelty increases citations by more than forty percent and the odds of a “b…
Products of pairwise totally permutable groups
2003
[EN] In this paper finite groups factorized as products of pairwise totally permutable subgroups are studied in the framework of Fitting classes
CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA
2011
Pyrosequencing technologies are frequently used for sequencing the 16S rRNA marker gene for metagenomic studies of microbial communities. Computing a pairwise genetic distance matrix from the produced reads is an important but highly time consuming task. In this paper, we present a parallelized tool (called CRiSPy) for scalable pairwise genetic distance matrix computation and clustering that is based on the processing pipeline of the popular ESPRIT software package. To achieve high computational efficiency, we have designed massively parallel CUDA algorithms for pairwise k-mer distance and pairwise genetic distance computation. We have also implemented a memory-efficient sparse matrix clust…