Search results for "Jaccard index"
showing 10 items of 15 documents
Macrophyte and macroinvertebrate patterns in unimpacted mountain rivers of two European ecoregions
2017
The aim of the study was to compare the patterns of development of macrophytes and macroinvertebrates in different types of reference mountain rivers. The study is based on reference river sites surveyed throughout the mountains in Poland and Slovakia in two European ecoregions (9—Central Highlands, 10—The Carpathians). A wide range of environmental variables were estimated, including water chemistry, hydromorphology, geology, and the spatial factor. Based on the Jaccard index, macrophyte and macroinvertebrate variation was confirmed between four mountain and upland river types. It was found that the biological diversification is mainly influenced by geological and associated chemical facto…
Replication of fMRI group activations in the neuroimaging battery for the Mainz Resilience Project (MARP)
2020
Abstract Motivated by the recent replicability crisis we tested replicability of functional magnetic resonance imaging (fMRI) group activations in two independent samples. An identical behavioral and fMRI test battery for the longitudinal investigation of stress resilience mechanisms was developed for the Mainz Resilience Project (MARP) and conducted in a discovery (N = 54) and a replication sample (N = 103). The test battery consisted of a stress reactivity task, a reward sensitivity task, a fear conditioning and extinction paradigm, two volitional reappraisal tasks and an emotional interference inhibition task. Replicability of group activations was tested with the Jaccard index and the I…
TESTING SIMILARITY COEFFICIENTS FOR ANALYSIS OF THE FOSSIL RECORD USING CLUSTERING METHODS: THE PALAEOZOIC FLORA AS A STUDY CASE
2020
This paper reports a global methodological approach based on the similarity and clustering methods of the Palaeozoic plant fossil record using a comparative approach between two similarity measures: the Jacard and Raup-Crick Coefficients. The results show that although the Raup-Crick Coefficients clearly have the potential for providing more robust results, the consequences of the extinction processes are better reflected in the similarity analysis based on the Jaccard Coefficients. On the other hand, the cluster analysis based on UPGMA algorithm shows four robust clusters and reveals new evidence for the singularity of Mississippian flora. Finally, the results obtained reveal that similari…
Amplified fragment length polymorphisms and sequence data in the phylogenetic analysis of polyploids: multiple origins of Veronica cymbalaria (Planta…
2007
Summary • The origin of polyploid Veronica cymbalaria (Plantaginaceae) was investigated using DNA sequence data and amplified fragment length polymorphism (AFLP) fingerprints to reveal the parentage of this taxon. The use of AFLP fingerprints in phylogenetic analysis is problematic and various methods have therefore been compared. • DNA sequence data (for the internal transcribed spacer (ITS) region and the plastid trnL-F region (trnL intron, 3’exon, and trnL-F spacer)) and polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the ITS region suggested a reliable hypothesis for the evolution of the V. cymbalaria complex. This hypothesis allowed evaluation …
Probabilistic quantum clustering
2020
Abstract Quantum Clustering is a powerful method to detect clusters with complex shapes. However, it is very sensitive to a length parameter that controls the shape of the Gaussian kernel associated with a wave function, which is employed in the Schrodinger equation with the role of a density estimator. In addition, linking data points into clusters requires local estimates of covariance which requires further parameters. This paper proposes a Bayesian framework that provides an objective measure of goodness-of-fit to the data, to optimise the adjustable parameters. This also quantifies the probabilities of cluster membership, thus partitioning the data into a specific number of clusters, w…
A non-parametric segmentation methodology for oral videocapillaroscopic images
2014
We aim to describe a new non-parametric methodology to support the clinician during the diagnostic process of oral videocapillaroscopy to evaluate peripheral microcirculation. Our methodology, mainly based on wavelet analysis and mathematical morphology to preprocess the images, segments them by minimizing the within-class luminosity variance of both capillaries and background. Experiments were carried out on a set of real microphotographs to validate this approach versus handmade segmentations provided by physicians. By using a leave-one-patient-out approach, we pointed out that our methodology is robust, according to precision-recall criteria (average precision and recall are equal to 0.9…
A 3D deep learning approach based on Shape Prior for automatic segmentation of myocardial diseases
2020
Accurate three-dimensional (3D) cardiac segmentation from late gadolinium enhancement (LGE)-MRI plays a critical role in designing a structure of reference for diagnosing many cardiac pathologies such as ischemia, myocarditis and myocardial infarction. This segmentation is however still a non-trivial task, due to the motion artifacts during acquisition, and heterogeneous intensity distributions. In this study, we develop a fully 3D automated model based on deep neural networks (DNN) for LGE-MRI myocardial pathologies (scar and No-reflow tissues) segmentation in a new expert annotated dataset. Considering that damaged tissue constitutes a small area of the whole LGE-MRI, we concentrated on m…
Gamma Knife treatment planning: MR brain tumor segmentation and volume measurement based on unsupervised Fuzzy C-Means clustering
2015
Nowadays, radiation treatment is beginning to intensively use MRI thanks to its greater ability to discriminate healthy and diseased soft-tissues. Leksell Gamma Knife® is a radio-surgical device, used to treat different brain lesions, which are often inaccessible for conventional surgery, such as benign or malignant tumors. Currently, the target to be treated with radiation therapy is contoured with slice-by-slice manual segmentation on MR datasets. This approach makes the segmentation procedure time consuming and operator-dependent. The repeatability of the tumor boundary delineation may be ensured only by using automatic or semiautomatic methods, supporting clinicians in the treatment pla…
Classification of Spanish Mosquitoes in Functional Groups
2011
Abstract We present a classification of Spanish mosquitoes according to their different life cycles. The bio-ecological parameters analyzed in our study were oviposition sites, overwintering stages, preferred hosts, and number of generations per year for each species. The results revealed 13 different functional groups. To assess the validity and robustness of the classification system, we analyzed the data from an intensive sampling carried out over a period of 4 years (2005–08) in eastern Spain. In this area, 9 of the 13 functional groups were found. The Jaccard cluster and the principal components analysis (between-group analysis method) revealed 3 different mosquito groups: the tree hol…
Reference standard space hippocampus labels according to the European Alzheimer's Disease Consortium–Alzheimer's Disease Neuroimaging Initiative harm…
2017
Abstract Introduction A harmonized protocol (HarP) for manual hippocampal segmentation on magnetic resonance imaging (MRI) has recently been developed by an international European Alzheimer's Disease Consortium–Alzheimer's Disease Neuroimaging Initiative project. We aimed at providing consensual certified HarP hippocampal labels in Montreal Neurological Institute (MNI) standard space to serve as reference in automated image analyses. Methods Manual HarP tracings on the high-resolution MNI152 standard space template of four expert certified HarP tracers were combined to obtain consensual bilateral hippocampus labels. Utility and validity of these reference labels is demonstrated in a simple …