🍩 Database of Original & NonTheoretical Uses of Topology
(found 7 matches in 0.00117s)


Using Persistent Homology to Reveal Hidden Information in Neural Data (2015)
Gard Spreemann, Benjamin Dunn, Magnus Bakke Botnan, Nils A. BaasAbstract
We propose a method, based on persistent homology, to uncover topological properties of a priori unknown covariates of neuron activity. Our input data consist of spike train measurements of a set of neurons of interest, a candidate list of the known stimuli that govern neuron activity, and the corresponding state of the animal throughout the experiment performed. Using a generalized linear model for neuron activity and simple assumptions on the effects of the external stimuli, we infer away any contribution to the observed spike trains by the candidate stimuli. Persistent homology then reveals useful information about any further, unknown, covariates. 
Homological Scaffold via Minimal Homology Bases (2021)
Marco Guerra, Alessandro De Gregorio, Ulderico Fugacci, Giovanni Petri, Francesco VaccarinoAbstract
The homological scaffold leverages persistent homology to construct a topologically sound summary of a weighted network. However, its crucial dependency on the choice of representative cycles hinders the ability to trace back global features onto individual network components, unless one provides a principled way to make such a choice. In this paper, we apply recent advances in the computation of minimal homology bases to introduce a quasicanonical version of the scaffold, called minimal, and employ it to analyze data both real and in silico. At the same time, we verify that, statistically, the standard scaffold is a good proxy of the minimal one for sufficiently complex networks. 
Topological Data Analysis of C. Elegans Locomotion and Behavior (2021)
Ashleigh Thomas, Kathleen Bates, Alex Elchesen, Iryna Hartsock, Hang Lu, Peter BubenikAbstract
Video of nematodes/roundworms was analyzed using persistent homology to study locomotion and behavior. In each frame, an organism's body posture was represented by a highdimensional vector. By concatenating points in fixedduration segments of this time series, we created a sliding window embedding (sometimes called a time delay embedding) where each point corresponds to a sequence of postures of an organism. Persistent homology on the points in this time series detected behaviors and comparisons of these persistent homology computations detected variation in their corresponding behaviors. We used average persistence landscapes and machine learning techniques to study changes in locomotion and behavior in varying environments. 
Reviews: Topological Distances and Losses for Brain Networks (2021)
Moo K. Chung, Alexander Smith, Gary ShiuAbstract
Almost all statistical and machine learning methods in analyzing brain networks rely on distances and loss functions, which are mostly Euclidean or matrix norms. The Euclidean or matrix distances may fail to capture underlying subtle topological differences in brain networks. Further, Euclidean distances are sensitive to outliers. A few extreme edge weights may severely affect the distance. Thus it is necessary to use distances and loss functions that recognize topology of data. In this review paper, we survey various topological distance and loss functions from topological data analysis (TDA) and persistent homology that can be used in brain network analysis more effectively. Although there are many recent brain imaging studies that are based on TDA methods, possibly due to the lack of method awareness, TDA has not taken as the mainstream tool in brain imaging field yet. The main purpose of this paper is provide the relevant technical survey of these powerful tools that are immediately applicable to brain network data. 
The Growing Topology of the C. Elegans Connectome (2020)
Alec Helm, Ann S. Blevins, Danielle S. BassettAbstract
Probing the developing neural circuitry in Caenorhabditis elegans has enhanced our understanding of nervous systems. The C. elegans connectome, like those of other species, is characterized by a rich club of densely connected neurons embedded within a smallworld architecture. This organization of neuronal connections, captured by quantitative network statistics, provides insight into the system's capacity to perform integrative computations. Yet these network measures are limited in their ability to detect weakly connected motifs, such as topological cavities, that may support the systems capacity to perform segregated computations. We address this limitation by using persistent homology to track the evolution of topological cavities in the growing C. elegans connectome throughout neural development, and assess the degree to which the growing connectomes topology is resistant to biological noise. We show that the developing connectome topology is both relatively robust to changes in neuron birth times and not captured by similar growth models. Additionally, we quantify the consequence of a neurons specific birth time and ask if this metric tracks other biological properties of neurons. Our results suggest that the connectomes growing topology is a robust feature of the developing connectome that is distinct from other network properties, and that the growing topology is particularly sensitive to the exact birth times of a small set of predominantly motor neurons. By utilizing novel measurements that track biological features, we anticipate that our study will be helpful in the construction of more accurate models of neuronal development in C. elegans 
Quantifying Genetic Innovation: Mathematical Foundations for the Topological Study of Reticulate Evolution (2020)
Michael Lesnick, Raúl Rabadán, Daniel I. S. RosenbloomAbstract
A topological approach to the study of genetic recombination, based on persistent homology, was introduced by Chan, Carlsson, and Rabadán in 2013. This associates a sequence of signatures called barcodes to genomic data sampled from an evolutionary history. In this paper, we develop theoretical foundations for this approach. First, we present a novel formulation of the underlying inference problem. Specifically, we introduce and study the novelty profile, a simple, stable statistic of an evolutionary history which not only counts recombination events but also quantifies how recombination creates genetic diversity. We propose that the (hitherto implicit) goal of the topological approach to recombination is the estimation of novelty profiles. We then study the problem of obtaining a lower bound on the novelty profile using barcodes. We focus on a lowrecombination regime, where the evolutionary history can be described by a directed acyclic graph called a galled tree, which differs from a tree only by isolated topological defects. We show that in this regime, under a complete sampling assumption, the \$1\textasciicircum\mathrm\st\\$ barcode yields a lower bound on the novelty profile, and hence on the number of recombination events. For \$i\textgreater1\$, the \$i\textasciicircum\\mathrm\th\\\$ barcode is empty. In addition, we use a stability principle to strengthen these results to ones which hold for any subsample of an arbitrary evolutionary history. To establish these results, we describe the topology of the VietorisRips filtrations arising from evolutionary histories indexed by galled trees. As a step towards a probabilistic theory, we also show that for a random history indexed by a fixed galled tree and satisfying biologically reasonable conditions, the intervals of the \$1\textasciicircum\\mathrm\st\\\$ barcode are independent random variables. Using simulations, we explore the sensitivity of these intervals to recombination.