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Persistent homology, a central tool of topological data analysis, provides invariants of data called barcodes (also known as persistence diagrams). A barcode is simply a multiset of real intervals. Recent work of Edelsbrunner, Jablonski,…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
The persistence barcode is a topological descriptor of data that plays a fundamental role in topological data analysis. Given a filtration of data, the persistence barcode tracks the evolution of its homology groups. In this paper, we…
We introduce a new feature map for barcodes that arise in persistent homology computation. The main idea is to first realize each barcode as a path in a convenient vector space, and to then compute its path signature which takes values in…
We propose a study of multipartite entanglement through persistent homology, a tool used in topological data analysis. In persistent homology, a 1-parameter filtration of simplicial complexes called persistence complex is used to reveal…
We introduce "quantum barcodes," a theoretical framework that applies persistent homology to classify topological phases in quantum many-body systems. By mapping quantum states to classical data points through strategic observable…
Time-delay embedding is a fundamental technique in Topological Data Analysis (TDA) for reconstructing the phase space dynamics of time-series data. Persistent homology effectively identifies global topological features, such as loops…
We discuss and review recent developments in the area of applied algebraic topology, such as persistent homology and barcodes. In particular, we discuss how these are related to understanding more about manifold learning from random point…
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…
Persistent homology is a popular technique in topological data analysis that tracks the lifespans of homological features in a nested sequence of spaces. This data is typically presented in a multi-set called a persistence diagram or a…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
The persistence barcode is a topological descriptor of data that plays a fundamental role in topological data analysis. Given a filtration of the space of data, a persistence barcode tracks the evolution of its homological features. In this…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
Persistent homology provides information about the lifetime of homology classes along a filtration of cell complexes. Persistence barcode is a graphical representation of such information. A filtration might be determined by time in a set…
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…
We propose a novel method for topological analysis of unweighted graphs which is based on \textit{persistent homology}. The proposed method maps the input graph to a complete weighted graph where the weighting function maps each edge to a…
Studying distributed computing through the lens of algebraic topology has been the source of many significant breakthroughs during the last two decades, especially in the design of lower bounds or impossibility results for deterministic…
The genealogy at a single locus of a constant size $N$ population in equilibrium is given by the well-known Kingman's coalescent. When considering multiple loci under recombination, the ancestral recombination graph encodes the genealogies…
Topological data analysis is an emerging area in exploratory data analysis and data mining. Its main tool, persistent homology, has become a popular technique to study the structure of complex, high-dimensional data. In this paper, we…