@unpublished{21051, abstract = {In this work, we introduce and study what we believe is an intriguing and, to the best of our knowledge, previously unknown connection between two areas in computational topology, topological data analysis (TDA) and knot theory. Given a function from a topological space to $\mathbb{R}$, TDA provides tools to simplify and study the importance of topological features: in particular, the $l^{th}$-dimensional persistence diagram encodes the $l$-homology in the sublevel set as the function value increases as a set of points in the plane. Given a continuous one-parameter family of such functions, we can combine the persistence diagrams into an object known as a vineyard, which track the evolution of points in the persistence diagram. If we further restrict that family of functions to be periodic, we identify the two ends of the vineyard, yielding a closed vineyard. This allows the study of monodromy, which in this context means that following the family of functions for a period permutes the set of points in a non-trivial way. In this work, given a link and value $l$, we construct a topological space and periodic family of functions such that the closed $l$-vineyard contains this link. This shows that vineyards are topologically as rich as one could possibly hope. Importantly, it has at least two immediate consequences: First, monodromy of any periodicity can occur in a $l$-vineyard, answering a variant of a question by [Arya et al 2024]. To exhibit this, we also reformulate monodromy in a more geometric way, which may be of interest in itself. Second, distinguishing vineyards is likely to be difficult given the known difficulty of knot and link recognition, which have strong connections to many NP-hard problems.}, author = { Chambers, Erin and Fillmore, Christopher D and Stephenson, Elizabeth R and Wintraecken, Mathijs}, booktitle = {arXiv}, title = {{Braiding vineyards}}, doi = {10.48550/ARXIV.2504.11203}, year = {2026}, } @inbook{21056, abstract = {In this work, we introduce and study what we believe is an intriguing, and, to the best of our knowledge, previously unknown connection between two fundamental areas in computational topology, namely topological data analysis (TDA) and knot theory. Given a function from a topological space to ℝ, TDA provides tools to simplify and study the importance of topological features: in particular, the 𝑙^𝑡⁢ℎ-dimensional persistence diagram encodes the topological changes (or 𝑙-homology) in the sublevel set as the function value increases into a set of points in the plane. Given a continuous one parameter family of such functions, we can combine the persistence diagrams into an object known as a vineyard, which tracks the evolution of points in the persistence diagram as the function changes. If we further restrict that family of functions to be periodic, we identify the two ends of the vineyard, yielding a closed vineyard. This allows the study of monodromy, which in this context means that following the family of functions for a period permutes the set of points in a non-trivial way. Recent work has studied monodromy in the directional persistent homology transform, demonstrating some interesting connections between an input shape and monodromy in the persistent homology transform for 0-dimensional homology embedded in ℝ^2. In this work, given a link and a value 𝑙, we construct a topological space (based on the given link) and periodic family of functions on this space (based on the Euclidean distance function), such that the closed 𝑙-vineyard contains this link. This shows that vineyards are topologically as rich as one could possibly hope, suggesting many future directions of work. Importantly, it has at least two immediate consequences we explicitly point out: 1. Monodromy of any periodicity can occur in a 𝑙-vineyard for any 𝑙. This answers a variant of a question by Arya and collaborators. To exhibit this as a consequence of our first main result we also reformulate monodromy in a more geometric way, which may be of interest in itself. 2. Topologically distinguishing closed vineyards is likely to be difficult (from a complexity theory as well as from a practical perspective) because of the difficulty of knot and link recognition, which have strong connections to many NP-hard problems.}, author = {Chambers, Erin W. and Fillmore, Christopher D and Stephenson, Elizabeth R and Wintraecken, Mathijs}, booktitle = {Proceedings of the 2026 Annual ACM-SIAM Symposium on Discrete Algorithms}, editor = {Green Larsen, Kasper and Saha, Barna}, pages = {6240--6263}, publisher = {Society for Industrial and Applied Mathematics}, title = {{Braiding Vineyards}}, doi = {10.1137/1.9781611978971.225}, year = {2026}, } @article{20260, abstract = {The medial axis of a set consists of the points in the ambient space without a unique closest point in the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a skeleton topologically equivalent to the original set. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities, various prunings of the medial axis have been proposed in the computational geometry community. Here, we examine one type of pruning, called burning. Because of the good experimental results it was hoped that the burning method of simplifying the medial axis would be stable. In this work, we show a simple example that dashes such hopes. Based on Bing’s house with two rooms, we demonstrate an isotopy of a shape where the medial axis goes from collapsible to non-collapsible. More precisely, we consider the standard deformation retract from the closed ball to Bing’s house with two rooms, but stop just short of the point where Bing’s house becomes two dimensional. This way we obtain an isotopy from the 3-ball to a thickened version of Bing’s house. Under this isotopy, the medial axis goes from collapsible to non-collapsible. We stress that this isotopy can be made generic, in the sense of singularity theory, as developed by Arnol’d and Thom.}, author = {Chambers, Erin Wolf and Fillmore, Christopher D and Stephenson, Elizabeth R and Wintraecken, Mathijs}, issn = {2730-9657}, journal = {La Matematica}, pages = {811--828}, publisher = {Springer Nature}, title = {{Burning or collapsing the medial axis is unstable}}, doi = {10.1007/s44007-025-00170-0}, volume = {4}, year = {2025}, } @inproceedings{20658, abstract = {The medial axis of a smoothly embedded surface in R^3 consists of all points for which the Euclidean distance function on the surface has at least two global minima. We generalize this notion to the mid-sphere axis, which consists of all points for which the Euclidean distance function has two interchanging saddles that swap their partners in the pairing by persistent homology. It offers a discrete-algebraic multi-scale approach to computing ridge-like structures on the surface. As a proof of concept, an algorithm that computes stair-case approximations of the mid-sphere axis is provided.}, author = {Edelsbrunner, Herbert and Stephenson, Elizabeth R and Thoresen, Martin H}, booktitle = {4th International Joint Conference on Discrete Geometry and Mathematical Morphology}, isbn = {9783032095435}, issn = {1611-3349}, location = {Groningen, The Netherlands}, pages = {133--147}, publisher = {Springer Nature}, title = {{The mid-sphere cousin of the medial axis transform}}, doi = {10.1007/978-3-032-09544-2_10}, volume = {16296}, year = {2025}, } @inproceedings{17170, abstract = {In this article we extend and strengthen the seminal work by Niyogi, Smale, and Weinberger on the learning of the homotopy type from a sample of an underlying space. In their work, Niyogi, Smale, and Weinberger studied samples of C² manifolds with positive reach embedded in ℝ^d. We extend their results in the following ways: - As the ambient space we consider both ℝ^d and Riemannian manifolds with lower bounded sectional curvature. - In both types of ambient spaces, we study sets of positive reach - a significantly more general setting than C² manifolds - as well as general manifolds of positive reach. - The sample P of a set (or a manifold) 𝒮 of positive reach may be noisy. We work with two one-sided Hausdorff distances - ε and δ - between P and 𝒮. We provide tight bounds in terms of ε and δ, that guarantee that there exists a parameter r such that the union of balls of radius r centred at the sample P deformation-retracts to 𝒮. We exhibit their tightness by an explicit construction. We carefully distinguish the roles of δ and ε. This is not only essential to achieve tight bounds, but also sensible in practical situations, since it allows one to adapt the bound according to sample density and the amount of noise present in the sample separately.}, author = {Attali, Dominique and Kourimska, Hana and Fillmore, Christopher D and Ghosh, Ishika and Lieutier, André and Stephenson, Elizabeth R and Wintraecken, Mathijs}, booktitle = {40th International Symposium on Computational Geometry}, isbn = {9783959773164}, issn = {1868-8969}, location = {Athens, Greece}, pages = {11:1--11:19}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of euclidean spaces and of Riemannian manifolds}}, doi = {10.4230/LIPIcs.SoCG.2024.11}, volume = {293}, year = {2024}, } @inproceedings{18097, abstract = {In our companion paper "Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of Euclidean spaces and of Riemannian manifolds" we gave optimal bounds (in terms of the two one-sided Hausdorff distances) on a sample P of an input shape 𝒮 (either manifold or general set with positive reach) such that one can infer the homotopy of 𝒮 from the union of balls with some radius centred at P, both in Euclidean space and in a Riemannian manifold of bounded curvature. The construction showing the optimality of the bounds is not straightforward. The purpose of this video is to visualize and thus elucidate said construction in the Euclidean setting.}, author = {Attali, Dominique and Kourimska, Hana and Fillmore, Christopher D and Ghosh, Ishika and Lieutier, Andre and Stephenson, Elizabeth R and Wintraecken, Mathijs}, booktitle = {40th International Symposium on Computational Geometry}, isbn = {9783959773164}, location = {Athens, Greece}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{The ultimate frontier: An optimality construction for homotopy inference (media exposition)}}, doi = {10.4230/LIPIcs.SoCG.2024.87}, volume = {293}, year = {2024}, } @phdthesis{14226, abstract = {We introduce the notion of a Faustian interchange in a 1-parameter family of smooth functions to generalize the medial axis to critical points of index larger than 0. We construct and implement a general purpose algorithm for approximating such generalized medial axes.}, author = {Stephenson, Elizabeth R}, issn = {2791-4585}, pages = {43}, publisher = {Institute of Science and Technology Austria}, title = {{Generalizing medial axes with homology switches}}, doi = {10.15479/at:ista:14226}, year = {2023}, } @inproceedings{11428, abstract = {The medial axis of a set consists of the points in the ambient space without a unique closest point on the original set. Since its introduction, the medial axis has been used extensively in many applications as a method of computing a topologically equivalent skeleton. Unfortunately, one limiting factor in the use of the medial axis of a smooth manifold is that it is not necessarily topologically stable under small perturbations of the manifold. To counter these instabilities various prunings of the medial axis have been proposed. Here, we examine one type of pruning, called burning. Because of the good experimental results, it was hoped that the burning method of simplifying the medial axis would be stable. In this work we show a simple example that dashes such hopes based on Bing’s house with two rooms, demonstrating an isotopy of a shape where the medial axis goes from collapsible to non-collapsible.}, author = {Chambers, Erin and Fillmore, Christopher D and Stephenson, Elizabeth R and Wintraecken, Mathijs}, booktitle = {38th International Symposium on Computational Geometry}, editor = {Goaoc, Xavier and Kerber, Michael}, isbn = {978-3-95977-227-3}, issn = {1868-8969}, location = {Berlin, Germany}, pages = {66:1--66:9}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{A cautionary tale: Burning the medial axis is unstable}}, doi = {10.4230/LIPIcs.SoCG.2022.66}, volume = {224}, year = {2022}, } @article{12307, abstract = {Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences.}, author = {Shipman, Barbara A. and Stephenson, Elizabeth R}, issn = {1935-4053}, journal = {PRIMUS}, keywords = {Education, General Mathematics}, number = {5}, pages = {593--609}, publisher = {Taylor & Francis}, title = {{Tangible topology through the lens of limits}}, doi = {10.1080/10511970.2021.1872750}, volume = {32}, year = {2022}, } @article{10754, abstract = {Targeting dysregulated Ca2+ signaling in cancer cells is an emerging chemotherapy approach. We previously reported that store-operated Ca2+ entry (SOCE) blockers, such as RP4010, are promising antitumor drugs for esophageal cancer. As a tyrosine kinase inhibitor (TKI), afatinib received FDA approval to be used in targeted therapy for patients with EGFR mutation-positive cancers. While preclinical studies and clinical trials have shown that afatinib has benefits for esophageal cancer patients, it is not known whether a combination of afatinib and RP4010 could achieve better anticancer effects. Since TKI can alter intracellular Ca2+ dynamics through EGFR/phospholipase C-γ pathway, in this study, we evaluated the inhibitory effect of afatinib and RP4010 on intracellular Ca2+ oscillations in KYSE-150, a human esophageal squamous cell carcinoma cell line, using both experimental and mathematical simulations. Our mathematical simulation of Ca2+ oscillations could fit well with experimental data responding to afatinib or RP4010, both separately or in combination. Guided by simulation, we were able to identify a proper ratio of afatinib and RP4010 for combined treatment, and such a combination presented synergistic anticancer-effect evidence by experimental measurement of intracellular Ca2+ and cell proliferation. This intracellular Ca2+ dynamic-based mathematical simulation approach could be useful for a rapid and cost-effective evaluation of combined targeting therapy drugs.}, author = {Chang, Yan and Funk, Marah and Roy, Souvik and Stephenson, Elizabeth R and Choi, Sangyong and Kojouharov, Hristo V. and Chen, Benito and Pan, Zui}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, number = {3}, publisher = {MDPI}, title = {{Developing a mathematical model of intracellular Calcium dynamics for evaluating combined anticancer effects of afatinib and RP4010 in esophageal cancer}}, doi = {10.3390/ijms23031763}, volume = {23}, year = {2022}, }