Related papers: Inference of Ancestral Recombination Graphs throug…

Topological Data Analysis (TDA) is the collection of mathematical tools that capture the structure of shapes in data. Despite computational topology and computational geometry, the utilization of TDA in time series and signal processing is…

Topological Data Analysis (TDA) combines computational topology and data science to extract and analyze intrinsic topological and geometric structures in data set in a metric space. While the persistent homology (PH), a widely used tool in…

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such…

Graphs have become a crucial way to represent large, complex and often temporal datasets across a wide range of scientific disciplines. However, when graphs are used as input to machine learning models, this rich temporal information is…

Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…

Topological data analysis (TDA) provides insight into data shape. The summaries obtained by these methods are principled global descriptions of multi-dimensional data whilst exhibiting stable properties such as robustness to deformation and…

Topological Data Analysis (TDA) gives practioners the ability to analyse the global structure of cybersecurity data. We use TDA for anomaly detection in host-based logs collected with the open-source Logging Made Easy (LME) project. We…

Topological data analysis (TDA), while abstract, allows a characterization of time-series data obtained from nonlinear and complex dynamical systems. Though it is surprising that such an abstract measure of structure - counting pieces and…

Topological Data Analysis (TDA) involves techniques of analyzing the underlying structure and connectivity of data. However, traditional methods like persistent homology can be computationally demanding, motivating the development of neural…

Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…

Topological Data Analysis (TDA) has emerged as a powerful framework for extracting robust, multiscale, and interpretable features from complex molecular data for artificial intelligence (AI) modeling and topological deep learning (TDL).…

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample.…

Topological data analysis (TDA) is a rapidly evolving field in applied mathematics and data science that leverages tools from topology to uncover robust, shape-driven insights in complex datasets. The main workhorse is persistent homology,…

Topological Data Analysis (TDA) is a novel, and relatively new approach to analysing high-dimensional data sets. It does this by focussing on global properties like the shape and connectivity of the data giving it a significant advantage…

The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…

Graph embeddings play a critical role in graph representation learning, allowing machine learning models to explore and interpret graph-structured data. However, existing methods often rely on opaque, high-dimensional embeddings, limiting…

In this study, we present and analyze a framework for geometric and topological estimation for mapping of unknown environments. We consider agents mimicking motion behaviors of cyborg insects, known as biobots, and exploit coordinate-free…

Topological Data Analysis (TDA) is a rising field of computational topology in which the topological structure of a data set can be observed by persistent homology. By considering a sequence of sublevel sets, one obtains a filtration that…

Topological Data Analysis (TDA) can broadly be described as a collection of data analysis methods that find structure in data. This includes: clustering, manifold estimation, nonlinear dimension reduction, mode estimation, ridge estimation…

Advancing the discovery of prognostic cancer biomarkers is crucial for comprehending disease mechanisms, refining treatment plans, and improving patient outcomes. This study introduces Weighted Gene Topological Data Analysis (WGTDA), an…