Over the last decade merge trees have been proven to support a plethora of visualization and analysis tasks since they effectively abstract complex datasets. This paper describes the ExTreeM-Algorithm: A scalable algorithm for the computation of merge trees via extremum graphs. The core idea of ExTreeM is to first derive the extremum graph G of an input scalar field f defined on a cell complex K, and subsequently compute the unaugmented merge tree of f on G instead of K; which are equivalent. Any merge tree algorithm can be carried out significantly faster on G, since K in general contains substantially more cells than G. To further speed up computation, ExTreeM includes a tailored procedure to derive merge trees of extremum graphs. The computation of the fully augmented merge tree, i.e., a merge tree domain segmentation of K, can then be performed in an optional post-processing step. All steps of ExTreeM consist of procedures with high parallel efficiency, and we provide a formal proof of its correctness. Our experiments, performed on publicly available datasets, report a speedup of up to one order of magnitude over the state-of-the-art algorithms included in the TTK and VTK-m software libraries, while also requiring significantly less memory and exhibiting excellent scaling behavior.
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http://dx.doi.org/10.1109/TVCG.2023.3326526 | DOI Listing |
Yi Chuan
December 2024
Belt and Road Research Center for Forensic Molecular Anthropology, Gansu University of Political Science and Law, Lanzhou 730000, China.
The Yugur people represent one of the ethnic groups residing within the Hexi Corridor, distinguishable by their small population size, linguistic diversity, intricate ancestral components, serving as a quintessential exemplar of the populations inhabiting this corridor. There are still many controversial issues in the academic community regarding the origin, migration, and formation process of the Yugur. In this study, we explored the formation process of the Yugur from the perspective of molecular anthropology, based on the paternal genetic characteristics of the Yugur people.
View Article and Find Full Text PDFSci Rep
December 2024
College of Science and Technology, Ningbo University, Cixi, 315300, China.
Clustering plays a crucial role in data mining and pattern recognition, but the interpretation of clustering results is often challenging. Existing interpretation methods usually lack an intuitive and accurate description of irregular shapes and high dimensional datas. This paper proposes a novel clustering explanation method based on a Multi-HyperRectangle(MHR), for extracting post hoc explanations of clustering results.
View Article and Find Full Text PDFGenes (Basel)
October 2024
Center of Genomics and Bioinformatics, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.
Accurate phylogenetic tree construction for species without reference genomes often relies on de novo transcriptome assembly to identify single-copy orthologous genes. However, challenges such as whole-genome duplication (WGD), heterozygosity, gene duplication, and loss can hinder the selection of these genes, leading to limited data for constructing reliable species trees. To address these issues, we developed a new analytical pipeline, OHDLF (Orthologous Haploid Duplication and Loss Filter), which filters orthologous genes from transcript data and adapts parameter settings based on genomic characteristics for further phylogenetic tree construction.
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November 2024
Department of Financial Technologies, Financial University Under the Government of the Russian Federation, Moscow, 125993, Russia.
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