Search Results for author: Heather A. Harrington

Found 16 papers, 8 papers with code

Algebraic network reconstruction of discrete dynamical systems

no code implementations5 Dec 2022 Heather A. Harrington, Mike Stillman, Alan Veliz-Cuba

We present a computational algebra solution to reverse engineering the network structure of discrete dynamical systems from data.

Stability of topological descriptors for neuronal morphology

no code implementations16 Nov 2022 David Beers, Heather A. Harrington, Alain Goriely

These results guarantee that persistence images of topological morphology descriptors are stable against the same set of perturbations and reliable.

Multiscale methods for signal selection in single-cell data

1 code implementation15 Jun 2022 Renee S. Hoekzema, Lewis Marsh, Otto Sumray, Thomas M. Carroll, Xin Lu, Helen M. Byrne, Heather A. Harrington

Analysis of single-cell transcriptomics often relies on clustering cells and then performing differential gene expression (DGE) to identify genes that vary between these clusters.

Barcodes distinguish morphology of neuronal tauopathy

no code implementations7 Apr 2022 David Beers, Despoina Goniotaki, Diane P. Hanger, Alain Goriely, Heather A. Harrington

We introduce {topological morphology functions}, a class of functions similar to Sholl functions, that can be recovered from the associated topological morphology descriptor.

Algebra, Geometry and Topology of ERK Kinetics

no code implementations1 Dec 2021 Lewis Marsh, Emilie Dufresne, Helen M. Byrne, Heather A. Harrington

The MEK/ERK signalling pathway is involved in cell division, cell specialisation, survival and cell death.

Topological Approximate Bayesian Computation for Parameter Inference of an Angiogenesis Model

1 code implementation26 Aug 2021 Thomas Thorne, Paul D. W. Kirk, Heather A. Harrington

Here we focus on recent work using topological data analysis to study different regimes of parameter space for a well-studied model of angiogenesis.

Topological Data Analysis

Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis

1 code implementation2 Jan 2021 John T. Nardini, Bernadette J. Stolz, Kevin B. Flores, Heather A. Harrington, Helen M. Byrne

Here we simulate the Anderson-Chaplain model of angiogenesis at different parameter values and quantify the vessel architectures of the resulting synthetic data.

Topological Data Analysis

Multiscale Topology Characterises Dynamic Tumour Vascular Networks

1 code implementation19 Aug 2020 Bernadette J. Stolz, Jakob Kaeppler, Bostjan Markelc, Franziska Mech, Florian Lipsmeier, Ruth J. Muschel, Helen M. Byrne, Heather A. Harrington

Advances in imaging techniques enable high resolution 3D visualisation of vascular networks over time and reveal abnormal structural features such as twists and loops, and their quantification is an active area of research.

Topological Data Analysis

Geometric anomaly detection in data

1 code implementation25 Aug 2019 Bernadette J. Stolz, Jared Tanner, Heather A. Harrington, Vidit Nanda

This paper describes the systematic application of local topological methods for detecting interfaces and related anomalies in complicated high-dimensional data.

Algebraic Topology Algebraic Geometry 57N80

Topological Data Analysis of Task-Based fMRI Data from Experiments on Schizophrenia

no code implementations22 Sep 2018 Bernadette J. Stolz, Tegan Emerson, Satu Nahkuri, Mason A. Porter, Heather A. Harrington

With these tools, which allow one to characterize topological invariants such as loops in high-dimensional data, we are able to gain understanding into low-dimensional structures in networks in a way that complements traditional approaches that are based on pairwise interactions.

Community Detection Time Series +1

Sampling real algebraic varieties for topological data analysis

1 code implementation21 Feb 2018 Emilie Dufresne, Parker B. Edwards, Heather A. Harrington, Jonathan D. Hauenstein

Topological data analysis (TDA) provides a growing body of tools for computing geometric and topological information about spaces from a finite sample of points.

Algebraic Topology Algebraic Geometry Numerical Analysis

Stratifying multiparameter persistent homology

no code implementations24 Aug 2017 Heather A. Harrington, Nina Otter, Hal Schenck, Ulrike Tillmann

A fundamental tool in topological data analysis is persistent homology, which allows extraction of information from complex datasets in a robust way.

Algebraic Topology Commutative Algebra 55B55, 68U05, 68Q17, 13P25 (primary)

A roadmap for the computation of persistent homology

1 code implementation30 Jun 2015 Nina Otter, Mason A. Porter, Ulrike Tillmann, Peter Grindrod, Heather A. Harrington

We give a friendly introduction to PH, navigate the pipeline for the computation of PH with an eye towards applications, and use a range of synthetic and real-world data sets to evaluate currently available open-source implementations for the computation of PH.

Algebraic Topology Computational Geometry Data Analysis, Statistics and Probability Quantitative Methods

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