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1. Robust Persistence Diagrams using Reproducing Kernels

   Vishwanath, Siddharth; Fukumizu, Kenji; Kuriki, Satoshi and (January 2020, Advances in neural information processing systems)

   Larochelle, H.; Ranzato, M.; Hadsell, R.; Balcan, M.F.; and Lin, H. (Ed.)

   Persistent homology has become an important tool for extracting geometric and topological features from data, whose multi-scale features are summarized in a persistence diagram. From a statistical perspective, however, persistence diagrams are very sensitive to perturbations in the input space. In this work, we develop a framework for constructing robust persistence diagrams from superlevel filtrations of robust density estimators constructed using reproducing kernels. Using an analogue of the influence function on the space of persistence diagrams, we establish the proposed framework to be less sensitive to outliers. The robust persistence diagrams are shown to be consistent estimators in the bottleneck distance, with the convergence rate controlled by the smoothness of the kernel — this, in turn, allows us to construct uniform confidence bands in the space of persistence diagrams. Finally, we demonstrate the superiority of the proposed approach on benchmark datasets. 

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2. Bayesian topological signal processing

   https://doi.org/10.3934/dcdss.2021084  

   Oballe, Christopher; Cherne, Alan; Boothe, Dave; Kerick, Scott; Franaszczuk, Piotr J.; Maroulas, Vasileios (January 2021, Discrete & Continuous Dynamical Systems - S)

   Topological data analysis encompasses a broad set of techniques that investigate the shape of data. One of the predominant tools in topological data analysis is persistent homology, which is used to create topological summaries of data called persistence diagrams. Persistent homology offers a novel method for signal analysis. Herein, we aid interpretation of the sublevel set persistence diagrams of signals by 1) showing the effect of frequency and instantaneous amplitude on the persistence diagrams for a family of deterministic signals, and 2) providing a general equation for the probability density of persistence diagrams of random signals via a pushforward measure. We also provide a topologically-motivated, efficiently computable statistical descriptor analogous to the power spectral density for signals based on a generalized Bayesian framework for persistence diagrams. This Bayesian descriptor is shown to be competitive with power spectral densities and continuous wavelet transforms at distinguishing signals with different dynamics in a classification problem with autoregressive signals. 

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3. Learning Simplicial Complexes from Persistence Diagrams

   Belton, Robin Lynne; Fasy, Brittany Terese; Mertz, Rostik; Micka, Samuel; Millman, David L.; Salinas, Daniel; Schenfisch, Anna; Schupbach, Jordan; Williams, Lucia (August 2018, Canadian Conference on Computational Geometry)

   Topological Data Analysis (TDA) studies the “shape” of data. A common topological descriptor is the persistence diagram, which encodes topological features in a topological space at different scales. Turner, Mukherjee, and Boyer showed that one can reconstruct a simplicial complex embedded in R^3 using persistence diagrams generated from all possible height filtrations (an uncountably infinite number of directions). In this paper, we present an algorithm for reconstructing plane graphs K = (V, E) in R^2, i.e., a planar graph with vertices in general position and a straight-line embedding, from a quadratic number height filtrations and their respective persistence diagrams. 

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4. Learning Simplicial Complexes from Persistence Diagrams

   Robin Lynne Belton, Brittany Terese (July 2018, CCCG '18: Thirtieth Canadian Conference on Computational Geometry)

   Topological Data Analysis (TDA) studies the shape of data. A common topological descriptor is the persistence diagram, which encodes topological features in a topological space at different scales. Turner, Mukeherjee, and Boyer showed that one can reconstruct a simplicial complex embedded in R^3 using persistence diagrams generated from all possible height filtrations (an uncountably infinite number of directions). In this paper, we present an algorithm for reconstructing plane graphs K=(V,E) in R^2 , i.e., a planar graph with vertices in general position and a straight-line embedding, from a quadratic number height filtrations and their respective persistence diagrams. 

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5. Learning metrics for persistence-based summaries and applications for graph classification

   Zhao, Qi; Wang, Yusu (November 2019, 33rd Conf. Neural Information Processing Systems (NeuRIPS))

   Recently a new feature representation framework based on a topological tool called persistent homology (and its persistence diagram summary) has gained much momentum. A series of methods have been developed to map a persistence diagram to a vector representation so as to facilitate the downstream use of machine learning tools. In these approaches, the importance (weight) of different persistence features are usually pre-set. However often in practice, the choice of the weight-functions hould depend on the nature of the specific data at hand. It is thus highly desirable to learn a best weight-function (and thus metric for persistence diagrams) from labelled data. We study this problem and develop a new weighted kernel, called WKPI, for persistence summaries, as well as an optimization framework to learn the weight (and thus kernel). We apply the learned kernel to the challenging task of graph classification, and show that our WKPI-based classification framework obtains similar or (sometimes significantly) better results than the best results from a range of previous graph classification frameworks on benchmark datasets. 

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