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Register a new userPersistent topology for natural data analysis - A survey
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Authors
Massimo Ferri
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Natural data offer a hard challenge to data analysis. One set of tools is being developed by several teams to face this difficult task: Persistent topology. After a brief introduction to this theory, some applications to the analysis and classification of cells, lesions, music pieces, gait, oil and gas reservoirs, cyclones, galaxies, bones, brain connections, languages, handwritten and gestured letters are shown.
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The musical realm is a promising area in which to expect to find nontrivial topological structures. This paper describes several kinds of metrics on musical data, and explores the implications of these metrics in two ways: via techniques of classical topology where the metric space of all-possible musical data can be described explicitly, and via modern data-driven ideas of persistent homology which calculates the Betti-number bar-codes of individual musical works. Both analyses are able to recover three well known topological structures in music: the circle of notes (octave-reduced scalar structures), the circle of fifths, and the rhythmic repetition of timelines. Applications to a variety of musical works (for example, folk music in the form of standard MIDI files) are presented, and the bar codes show many interesting features. Examples show that individual pieces may span the complete space (in which case the classical and the data-driven analyses agree), or they may span only part of the space.
Persistent Topology studies topological features of shapes by analyzing the lower level sets of suitable functions, called filtering functions, and encoding the arising information in a parameterized version of the Betti numbers, i.e. the ranks of persistent homology groups. Initially introduced by considering real-valued filtering functions, Persistent Topology has been subsequently generalized to a multidimensional setting, i.e. to the case of $R^n$-valued filtering functions, leading to studying the ranks of multidimensional homology groups. In particular, a multidimensional matching distance has been defined, in order to compare these ranks. The definition of the multidimensional matching distance is based on foliating the domain of the ranks of multidimensional homology groups by a collection of half-planes, and hence it formally depends on a subset of $R^ntimesR^n$ inducing a parameterization of these half-planes. It happens that it is possible to choose this subset in an infinite number of different ways. In this paper we show that the multidimensional matching distance is actually invariant with respect to such a choice.
Utilizing Visualization-oriented Natural Language Interfaces (V-NLI) as a complementary input modality to direct manipulation for visual analytics can provide an engaging user experience. It enables users to focus on their tasks rather than worrying about operating the interface to visualization tools. In the past two decades, leveraging advanced natural language processing technologies, numerous V-NLI systems have been developed both within academic research and commercial software, especially in recent years. In this article, we conduct a comprehensive review of the existing V-NLIs. In order to classify each paper, we develop categorical dimensions based on a classic information visualization pipeline with the extension of a V-NLI layer. The following seven stages are used: query understanding, data transformation, visual mapping, view transformation, human interaction, context management, and presentation. Finally, we also shed light on several promising directions for future work in the community.
We use persistent homology to build a quantitative understanding of large complex systems that are driven far-from-equilibrium; in particular, we analyze image time series of flow field patterns from numerical simulations of two important problems in fluid dynamics: Kolmogorov flow and Rayleigh-Benard convection. For each image we compute a persistence diagram to yield a reduced description of the flow field; by applying different metrics to the space of persistence diagrams, we relate characteristic features in persistence diagrams to the geometry of the corresponding flow patterns. We also examine the dynamics of the flow patterns by a second application of persistent homology to the time series of persistence diagrams. We demonstrate that persistent homology provides an effective method both for quotienting out symmetries in families of solutions and for identifying multiscale recurrent dynamics. Our approach is quite general and it is anticipated to be applicable to a broad range of open problems exhibiting complex spatio-temporal behavior.
In this paper we introduce the persistent magnitude, a new numerical invariant of (sufficiently nice) graded persistence modules. It is a weighted and signed count of the bars of the persistence module, in which a bar of the form $[a,b)$ in degree $d$ is counted with weight $(e^{-a}-e^{-b})$ and sign $(-1)^d$. Persistent magnitude has good formal properties, such as additivity with respect to exact sequences and compatibility with tensor products, and has interpretations in terms of both the associated graded functor, and the Laplace transform. Our definition is inspired by Otters notion of blurred magnitude homology: we show that the magnitude of a finite metric space is precisely the persistent magnitude of its blurred magnitude homology. Turning this result on its head, we obtain a strategy for turning existing persistent homology theories into new numerical invariants by applying the persistent magnitude. We explore this strategy in detail in the case of persistent homology of Morse functions, and in the case of Rips homology.
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