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Concept# Topological data analysis

Résumé

In applied mathematics, topological data analysis (TDA) is an approach to the analysis of datasets using techniques from topology. Extraction of information from datasets that are high-dimensional, incomplete and noisy is generally challenging. TDA provides a general framework to analyze such data in a manner that is insensitive to the particular metric chosen and provides dimensionality reduction and robustness to noise. Beyond this, it inherits functoriality, a fundamental concept of modern mathematics, from its topological nature, which allows it to adapt to new mathematical tools.
The initial motivation is to study the shape of data. TDA has combined algebraic topology and other tools from pure mathematics to allow mathematically rigorous study of "shape". The main tool is persistent homology, an adaptation of homology to point cloud data. Persistent homology has been applied to many types of data across many fields. Moreover, its mathematical foundation is also of theoretical i

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Persistent homology

:See homology for an introduction to the notation.
Persistent homology is a method for computing topological features of a space at different spatial resolutions. More persistent features are detect

Homologie (mathématiques)

En mathématiques, l'homologie est une manière générale d'associer une séquence d'objets algébriques tels que des groupes abéliens ou des modules à d'autres objets mathématiques tels que des espaces t

Simplicial homology

In algebraic topology, simplicial homology is the sequence of homology groups of a simplicial complex. It formalizes the idea of the number of holes of a given dimension in the complex. This generaliz

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ME-371: Discretization methods in fluids

Ce cours présente une introduction aux méthodes d'approximation utilisées pour la simulation numérique en mécanique des fluides.
Les concepts fondamentaux sont présentés dans le cadre de la méthode des différences finies puis étendus à celles des éléments finis et spectraux.

DH-405: Foundations of digital humanities

This course gives an introduction to the fundamental concepts and methods of the Digital Humanities, both from a theoretical and applied point of view. The course introduces the Digital Humanities circle of processing and interpretation, from data acquisition to new understandings.

MATH-688: Reading group in applied topology I

The subject of this reading group is Ginerstra Bianconi's book "Higher-order networks - an introduction to simplicial complexes". Participants will take turns presenting chapters, then leading a discussion of the contents. In the last session, the author will give a guest lecture.

In this thesis, we investigate the inverse problem of trees and barcodes from a combinatorial, geometric, probabilistic and statistical point of view.Computing the persistent homology of a merge tree yields a barcode B. Reconstructing a tree from B involves gluing the branches back together. We are able to define combinatorial equivalence classes of merge trees and barcodes that allow us to completely solve this inverse problem. A barcode can be associated with an element in the symmetric group, and the number of trees with the same barcode, the tree realization number, depends only on the permutation type. We compare these combinatorial definitions of barcodes and trees to those of phylogenetic trees, thus describing the subtle differences between these spaces. The result is a clear combinatorial distinction between the phylogenetic tree space and the merge tree space.The representation of a barcode by a permutation not only gives a formula for the tree realization number, but also opens the door to deeper connections between inverse problems in topological data analysis, group theory, and combinatorics.Based on the combinatorial classes of barcodes, we construct a stratification of the barcode space. We define coordinates that partition the space of barcodes into regions indexed by the averages and the standard deviations of birth and death times and by the permutation type of a barcode. By associating to a barcode the coordinates of its region, we define a new invariant of barcodes.These equivalence classes define a stratification of the space of barcodes with n bars where the strata are indexed by the symmetric group on n letters and its parabolic subgroups.We study the realization numbers computed from barcodes with uniform permutation type (i.e., drawn from the uniform distribution on the symmetric group) and establish a fundamental null hypothesis for this invariant. We show that the tree realization number can be used as a statistic to distinguish distributions of trees by comparing neuronal trees to random barcode distributions.

The field of computational topology has developed many powerful tools to describe the shape of data, offering an alternative point of view from classical statistics. This results in a variety of complex structures that are not always directly amenable for machine learning tasks. We develop theory and algorithms to produce computable representations of simplicial or cell complexes, potentially equipped with additional information such as signals and multifiltrations. The common goal of the topics discussed in this thesis is to find reduced representations of these often high dimensional and complex structures to better visualize, transform or formulate theoretical results about them. We extend the well known graph learning algorithm node2vec to simplicial complexes, a higher dimensional analogue of graphs. To this end we propose a way to define random walks on simplicial complexes, which we then use to design an extension of node2vec called k-simplex2vec, producing a representation of the simplices in a Euclidean space. Furthermore, the study of this method leads to interesting questions about robustness of graph and simplicial learning methods. In the case of graphs, we study node2vec embeddings arising from different parameter sets, analysing their quality and stability using various measures. In the topic of signal processing, we explore how discrete Morse theory can be used for compression and reconstruction of cell complexes equipped with signals. In particular we study the effect of the compression of a complex on the Hodge decomposition of its signals. We study how the signal changes through compression and reconstruction by introducing a topological reconstruction error, showing in particular that part of the Hodge decomposition is preserved. Moreover, we prove that any deformation retract over R can be expressed as a Morse deformation retract in a well-chosen basis, thus extending the reconstruction results to any deformation retract. In addition, we introduce an algorithm to minimize the loss induced by the reconstruction of a compressed signal. Finally, we use discrete Morse theory to compute an invariant of multi-parameter persistent homology, the rank invariant. We can restrict a multi-parameter persistence module to a one- dimensional persistence module along any line of positive slope and compute the one-dimensional analogue of the rank invariant, namely the barcode. Through a discrete Morse matching we can determine critical values in the multifiltration, which in turn allows us to identify equivalence classes of lines in the parameter space. In our main result, we explain how to compute the barcode along any given line of an equivalence class given the barcode along a representative line. This provides a way to fiber the rank invariant according to the critical values of a discrete Morse matching and to perform computations in the corresponding one-dimensional module, which is much better understood.

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Digital images enable quantitative analysis of material properties at micro and macro length scales, but choosing an appropriate resolution when acquiring the image is challenging. A high resolution means longer image acquisition and larger data requirements for a given sample, but if the resolution is too low, significant information may be lost. This paper studies the impact of changes in resolution on persistent homology, a tool from topological data analysis that provides a signature of structure in an image across all length scales. Given prior information about a function, the geometry of an object, or its density distribution at a given resolution, we provide methods to select the coarsest resolution yielding results within an acceptable tolerance. We present numerical case studies for an illustrative synthetic example and samples from porous materials where the theoretical bounds are unknown.