Topological data analysis and its main method, persistent homology, provide a toolkit for computing topological information of high-dimensional and noisy data sets. Kernels for one-parameter persistent homology have been established to connect persistent homology with machine learning techniques with applicability on shape analysis, recognition and classification. We contribute a kernel construction for multi-parameter persistence by integrating a one-parameter kernel weighted along straight lines. We prove that our kernel is stable and efficiently computable, which establishes a theoretical connection between topological data analysis and machine learning for multivariate data analysis.
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http://dx.doi.org/10.1016/j.cagx.2019.100005 | DOI Listing |
Background: Our study aims to understand how network resolution scale impacts the association between topological features in the brain network and Alzheimer's disease (AD) outcomes. In particular, we examine persistence homological cycles, derived from DTI and fMRI neuroimaging. We study subjects in various stages of AD progression.
View Article and Find Full Text PDFBiol Imaging
November 2024
Biological Image Analysis Unit, Institut Pasteur, Université Paris Cité, Paris, France.
We develop a novel method for image segmentation of 3D confocal microscopy images of emerging hematopoietic stem cells. The method is based on the theory of persistent homology and uses an optimal threshold to select the most persistent cycles in the persistence diagram. This enables the segmentation of the image's most contrasted and representative shapes.
View Article and Find Full Text PDFMetal-organic frameworks (MOFs) are porous, crystalline materials with high surface area, adjustable porosity, and structural tunability, making them ideal for diverse applications. However, traditional experimental and computational methods have limited scalability and interpretability, hindering effective exploration of MOF structure-property relationships. To address these challenges, we introduce, for the first time, a category-specific topological learning (CSTL), which combines algebraic topology with chemical insights for robust property prediction.
View Article and Find Full Text PDFNovel multiplexed spatial proteomics imaging platforms expose the spatial architecture of cells in the tumor microenvironment (TME). The diverse cell population in the TME, including its spatial context, has been shown to have important clinical implications, correlating with disease prognosis and treatment response. The accelerating implementation of spatial proteomic technologies motivates new statistical models to test if cell-level images associate with patient-level endpoints.
View Article and Find Full Text PDFMol Biol Evol
January 2025
Universite Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, F-69622, France.
Phylogenetic inference is mainly based on sequence analysis and requires reliable alignments. This can be challenging, especially when sequences are highly divergent. In this context, the use of three-dimensional protein structures is a promising alternative.
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