Forthcoming events in this series


Fri, 10 Jun 2022
15:00
L3

Directed networks through simplicial paths and Hochschild homology

Henri Riihimäki
(KTH Royal Institute of Technology)
Abstract

Directed graphs are a model for various phenomena in the
sciences. In topological data analysis particularly the advent of
applying topological tools to networks of brain neurons has spawned
interest in constructing topological spaces out of digraphs, developing
computational tools for obtaining topological information, and using
these to understand networks. At the end of the day, (homological)
computations of the spaces reveal something about the geometric
realisation, thereby losing the directionality information.

However, digraphs can also be associated with path algebras. We can now
consider applying Hochschild homology to extract information, hopefully
obtaining something more refined in terms of the combinatorics of the
directed edges and paths in the digraph. Unfortunately, Hochschild
homology tends to vanish beyond degree 1. We can overcome this by
considering different higher paths of simplices, and thus introduce
Hochschild homology of digraphs in higher degrees. Moreover, this
procedure gives an implementable persistence pipeline for network
analysis. This is a joint work with Luigi Caputi.

Fri, 03 Jun 2022
15:00
L3

Projected barcodes : a new class of invariants and distances for multi-parameter persistence modules

Nicolas Berkouk
(École Polytechnique Fédérale de Lausanne (EPFL))
Abstract

In this talk, we will present a new class of invariants of multi-parameter persistence modules : \emph{projected barcodes}. Relying on Grothendieck's six operations for sheaves, projected barcodes are defined as derived pushforwards of persistence modules onto $\R$ (which can be seen as sheaves on a vector space in a precise sense). We will prove that the well-known fibered barcode is a particular instance of projected barcodes. Moreover, our construction is able to distinguish persistence modules that have the same fibered barcodes but are not isomorphic. We will present a systematic study of the stability of projected barcodes. Given F a subset of the 1-Lipschitz functions, this leads us to define a new class of well-behaved distances between persistence modules, the  F-Integral Sheaf Metrics (F-ISM), as the supremum over p in F of the bottleneck distance of the projected barcodes by p of two persistence modules. 

In the case where M is the collection in all degrees of the sublevel-sets persistence modules of a function f : X -> R^n, we prove that the projected barcode of M by a linear map p : R^n \to R is nothing but the collection of sublevel-sets barcodes of the post-composition of f by p. In particular, it can be computed using already existing softwares, without having to compute entirely M. We also provide an explicit formula for the gradient with respect to p of the bottleneck distance between projected barcodes, allowing to use a gradient ascent scheme of approximation for the linear ISM. This is joint work with François Petit.

 

Fri, 20 May 2022

15:00 - 16:00
L3

Approximating Persistent Homology for Large Datasets

Anthea Monod
(Imperial College London)
Abstract

Persistent homology is an important methodology from topological data analysis which adapts theory from algebraic topology to data settings and has been successfully implemented in many applications. It produces a statistical summary in the form of a persistence diagram, which captures the shape and size of the data. Despite its widespread use, persistent homology is simply impossible to implement when a dataset is very large. In this talk, I will address the problem of finding a representative persistence diagram for prohibitively large datasets. We adapt the classical statistical method of bootstrapping, namely, drawing and studying smaller multiple subsamples from the large dataset. We show that the mean of the persistence diagrams of subsamples—taken as a mean persistence measure computed from the subsamples—is a valid approximation of the true persistent homology of the larger dataset. We give the rate of convergence of the mean persistence diagram to the true persistence diagram in terms of the number of subsamples and size of each subsample. Given the complex algebraic and geometric nature of persistent homology, we adapt the convexity and stability properties in the space of persistence diagrams together with random set theory to achieve our theoretical results for the general setting of point cloud data. We demonstrate our approach on simulated and real data, including an application of shape clustering on complex large-scale point cloud data.

 

This is joint work with Yueqi Cao (Imperial College London).

Fri, 13 May 2022

15:00 - 16:00
L2

Non-Euclidean Data Analysis (and a lot of questions)

John Aston
(University of Cambridge)
Abstract

The statistical analysis of data which lies in a non-Euclidean space has become increasingly common over the last decade, starting from the point of view of shape analysis, but also being driven by a number of novel application areas. However, while there are a number of interesting avenues this analysis has taken, particularly around positive definite matrix data and data which lies in function spaces, it has increasingly raised more questions than answers. In this talk, I'll introduce some non-Euclidean data from applications in brain imaging and in linguistics, but spend considerable time asking questions, where I hope the interaction of statistics and topological data analysis (understood broadly) could potentially start to bring understanding into the applications themselves.

Fri, 06 May 2022

15:00 - 16:00
L4

Applied Topology TBC

Bernadette Stolz
(University of Oxford, Mathematical Institute)
Fri, 29 Apr 2022

15:00 - 16:00
L4

Signed barcodes for multiparameter persistence

Magnus Botnan
(Free University of Amsterdam)
Abstract

Moving from persistent homology in one parameter to multiparameter persistence comes at a significant increase in complexity. In particular, the notion of a barcode does not generalize straightforwardly. However, in this talk, I will show how it is possible to assign a unique barcode to a multiparameter persistence module if one is willing to take Z-linear combinations of intervals. The theoretical discussion will be complemented by numerical experiments. This is joint work with Steffen Oppermann and Steve Oudot.

Fri, 04 Mar 2022

15:00 - 16:00
L6

Open questions on protein topology in its natural environment.

Christopher Prior
(Durham University)
Abstract

Small angle x-ray scattering is one of the most flexible and readily available experimental methods for obtaining information on the structure of proteins in solution. In the advent of powerful predictive methods such as the alphaFold and rossettaFold algorithms, this information has become increasingly in demand, owing to the need to characterise the more flexible and varying components of proteins which resist characterisation by these and more standard experimental techniques. To deal with structures about little of which is known a parsimonious method of representing the tertiary fold of a protein backbone as a discrete curve has been developed. It represents the fundamental local Ramachandran constraints through a pair of parameters and is able to generate millions of potentially realistic protein geometries in a short space of time. The data obtained from these methods provides a treasure trove of information on the potential range of topological structures available to proteins, which is much more constrained that that available to self-avoiding walks, but still far more complex than currently understood from existing data. I will introduce this method and its considerations then attempt to pose some questions I think topological data analysis might help answer. Along the way I will ask why roadies might also help give us some insight….

Fri, 25 Feb 2022

15:00 - 16:00
L6

Homotopy, Homology, and Persistent Homology using Cech’s Closure Spaces

Peter Bubenik
(University of Florida)
Abstract

We use Cech closure spaces, also known as pretopological spaces, to develop a uniform framework that encompasses the discrete homology of metric spaces, the singular homology of topological spaces, and the homology of (directed) clique complexes, along with their respective homotopy theories. We obtain nine homology and six homotopy theories of closure spaces. We show how metric spaces and more general structures such as weighted directed graphs produce filtered closure spaces. For filtered closure spaces, our homology theories produce persistence modules. We extend the definition of Gromov-Hausdorff distance to filtered closure spaces and use it to prove that our persistence modules and their persistence diagrams are stable. We also extend the definitions Vietoris-Rips and Cech complexes to closure spaces and prove that their persistent homology is stable.

This is joint work with Nikola Milicevic.

Fri, 11 Feb 2022

15:00 - 16:00
L2

Topology-Based Graph Learning

Bastian Rieck
(Helmholtz Zentrum München)
Abstract

Topological data analysis is starting to establish itself as a powerful and effective framework in machine learning , supporting the analysis of neural networks, but also driving the development of novel algorithms that incorporate topological characteristics. As a problem class, graph representation learning is of particular interest here, since graphs are inherently amenable to a topological description in terms of their connected components and cycles. This talk will provide
an overview of how to address graph learning tasks using machine learning techniques, with a specific focus on how to make such techniques 'topology-aware.' We will discuss how to learn filtrations for graphs and how to incorporate topological information into modern graph neural networks, resulting in provably more expressive algorithms. This talk aims to be accessible to an audience of TDA enthusiasts; prior knowledge of machine learning is helpful but not required.

Fri, 04 Feb 2022

11:00 - 12:00
L6

Computing the Extended Persistent Homology Transform of binary images

Katharine Turner
(Australian National University)
Further Information

PLEASE NOTE this seminar will be at 11am instead of 3pm.

Abstract

The Persistent Homology Transform, and the Euler Characteristic Transform are topological analogs of the Radon transform that can be used in statsistical shape analysis. In this talk I will consider an interesting variant called the Extended Persistent Homology Transform (XPHT) which replaces the normal persistent homology with extended persistent homology. We are particularly interested in the application of the XPHT to binary images. This paper outlines an algorithm for efficient calculation of the XPHT exploting relationships between the PHT of the boundary curves to the XPHT of the foreground.

Fri, 28 Jan 2022

15:00 - 16:00
L6

Topological Tools for Signal Processing

Sarah Tymochko
(Michigan State University)
Abstract

Topological data analysis (TDA) is a field with tools to quantify the shape of data in a manner that is concise and robust using concepts from algebraic topology. Persistent homology, one of the most popular tools in TDA, has proven useful in applications to time series data, detecting shape that changes over time and quantifying features like periodicity. In this talk, I will present two applications using tools from TDA to study time series data: the first using zigzag persistence, a generalization of persistent homology, to study bifurcations in dynamical systems and the second, using the shape of weighted, directed networks to distinguish periodic and chaotic behavior in time series data.

Fri, 21 Jan 2022

15:00 - 16:00
L6

A Multivariate CLT for Dissociated Sums with Applications to Random Complexes

Tadas Temčinas
(Mathematical Institute)
Abstract

Acyclic partial matchings on simplicial complexes play an important role in topological data analysis by facilitating efficient computation of (persistent) homology groups. Here we describe probabilistic properties of critical simplex counts for such matchings on clique complexes of Bernoulli random graphs. In order to accomplish this goal, we generalise the notion of a dissociated sum to a multivariate setting and prove an abstract multivariate central limit theorem using Stein's method. As a consequence of this general result, we are able to extract central limit theorems not only for critical simplex counts, but also for generalised U-statistics (and hence for clique counts in Bernoulli random graphs) as well as simplex counts in the link of a fixed simplex in a random clique complex.

Fri, 10 Dec 2021

15:00 - 16:00
Virtual

A topological approach to signatures

Darrick Lee
(EPFL)
Abstract

The path signature is a characterization of paths that originated in Chen's iterated integral cochain model for path spaces and loop spaces. More recently, it has been used to form the foundations of rough paths in stochastic analysis, and provides an effective feature map for sequential data in machine learning. In this talk, we return to the topological foundations in Chen's construction to develop generalizations of the signature.

Fri, 26 Nov 2021

15:00 - 16:00
Virtual

Morse inequalities for the Koszul complex of multi-persistence

Claudia Landi
(University of Modena and Reggio Emilia)
Abstract

In this talk, I'll present inequalities bounding the number of critical cells in a filtered cell complex on the one hand, and the entries of the Betti tables of the multi-parameter persistence modules of such filtrations on the other hand. Using the Mayer-Vietoris spectral sequence we first obtain strong and weak Morse inequalities involving the above quantities, and then we improve the weak inequalities achieving a sharp lower bound for the number of critical cells. Furthermore, we prove a sharp upper bound for the minimal number of critical cells, expressed again in terms of the entries of Betti tables. This is joint work with Andrea Guidolin (KTH, Stockholm). The full paper is posted online as arxiv:2108.11427.

Fri, 05 Nov 2021

15:00 - 16:00
Virtual

Why should one care about metrics on (multi) persistent modules?

Wojciech Chacholski
(KTH)
Abstract

What do we use metrics on persistent modules for? Is it only to asure  stability of some constructions? 

In my talk I will describe why I care about such metrics, show how to construct a rich space of them and illustrate how  to use

them for analysis. 

Fri, 29 Oct 2021

15:00 - 16:00
Virtual

Modeling shapes and fields: a sheaf theoretic perspective

Sayan Mukherjee
(Duke University)
Abstract

We will consider modeling shapes and fields via topological and lifted-topological transforms. 

Specifically, we show how the Euler Characteristic Transform and the Lifted Euler Characteristic Transform can be used in practice for statistical analysis of shape and field data. The Lifted Euler Characteristic is an alternative to the. Euler calculus developed by Ghrist and Baryshnikov for real valued functions. We also state a moduli space of shapes for which we can provide a complexity metric for the shapes. We also provide a sheaf theoretic construction of shape space that does not require diffeomorphisms or correspondence. A direct result of this sheaf theoretic construction is that in three dimensions for meshes, 0-dimensional homology is enough to characterize the shape.

Fri, 22 Oct 2021

15:00 - 16:00
Virtual

Combinatorial Laplacians in data analysis: applications in genomics

Pablo Camara
(University of Pennsylvania)
Further Information

Pablo G. Cámara is an Assistant Professor of Genetics at the University of Pennsylvania and a faculty member of the Penn Institute for Biomedical Informatics. He received a Ph.D. in Theoretical Physics in 2006 from Universidad Autónoma de Madrid. He performed research in string theory for several years, with postdoctoral appointments at Ecole Polytechnique, the European Organization for Nuclear Research (CERN), and University of Barcelona. Fascinated by the extremely interesting and fundamental open questions in biology, in 2014 he shifted his research focus into problems in quantitative biology, and joined the groups of Dr. Rabadan, at Columbia University, and Dr. Levine, at the Institute for Advanced Study (Princeton). Building upon techniques from applied topology and statistics, he has devised novel approaches to the inference of ancestral recombination, human recombination mapping, the study of cancer heterogeneity, and the analysis of single-cell RNA-sequencing data from dynamic and heterogeneous cellular populations.

Abstract

One of the prevailing paradigms in data analysis involves comparing groups of samples to statistically infer features that discriminate them. However, many modern applications do not fit well into this paradigm because samples cannot be naturally arranged into discrete groups. In such instances, graph techniques can be used to rank features according to their degree of consistency with an underlying metric structure without the need to cluster the samples. Here, we extend graph methods for feature selection to abstract simplicial complexes and present a general framework for clustering-independent analysis. Combinatorial Laplacian scores take into account the topology spanned by the data and reduce to the ordinary Laplacian score when restricted to graphs. We show the utility of this framework with several applications to the analysis of gene expression and multi-modal cancer data. Our results provide a unifying perspective on topological data analysis and manifold learning approaches to the analysis of point clouds.

Fri, 15 Oct 2021

15:00 - 16:00

Exemplars of Sheaf Theory in TDA

Justin Curry
(University of Albany)
Abstract

In this talk I will present four case studies of sheaves and cosheaves in topological data analysis. The first two are examples of (co)sheaves in the small:

(1) level set persistence---and its efficacious computation via discrete Morse theory---and,

(2) decorated merge trees and Reeb graphs---enriched topological invariants that have enhanced classification power over traditional TDA methods. The second set of examples are focused on (co)sheaves in the large:

(3) understanding the space of merge trees as a stratified map to the space of barcodes and

(4) the development of a new "sheaf of sheaves" that organizes the persistent homology transform over different shapes.

Fri, 04 Jun 2021

15:00 - 16:00
Virtual

Topological and geometric analysis of graphs - Yusu Wang

Yusu Wang
(University of San Diego)
Abstract

In recent years, topological and geometric data analysis (TGDA) has emerged as a new and promising field for processing, analyzing and understanding complex data. Indeed, geometry and topology form natural platforms for data analysis, with geometry describing the ''shape'' behind data; and topology characterizing / summarizing both the domain where data are sampled from, as well as functions and maps associated with them. In this talk, I will show how topological (and geometric ideas) can be used to analyze graph data, which occurs ubiquitously across science and engineering. Graphs could be geometric in nature, such as road networks in GIS, or relational and abstract. I will particularly focus on the reconstruction of hidden geometric graphs from noisy data, as well as graph matching and classification. I will discuss the motivating applications, algorithm development, and theoretical guarantees for these methods. Through these topics, I aim to illustrate the important role that topological and geometric ideas can play in data analysis.