Statistical analysis on object data presents many challenges. Basic summaries such as means and variances are difficult to compute. We apply ideas from topology to study object data. We present a framework for using death vectors and persistence landscapes to vectorize object data and perform statistical analysis. We apply this method to some common leaf images that were previously shown to be challenging to compare using a 3D shape techniques. Surprisingly, the most persistent features are shown to be “topological noise” and the statistical analysis depends on the less persistent features which we refer to as the “geometric signal”. We also describe the first steps to a new approach to using topology for object data analysis, which applies topology to distributions on object spaces. We introduce a new Frechet-Morse function technique for probability distribution on a compact object space, extending the Frechet means lo a larger number of location parameters, including Frechet antimeans. An example of 3D data analysis to distinguish two flowers using the new location parameters associated with a Veronese-Whitney (VW) embedding of random projective shapes of 3D configurations extracted from a set of pairs of their digital camera images is also given here.
Our approach and results are closely related to work by (2016) @cite_22 , who also applied TDA to object data. In their case they considered brain artery structures extracted from magnetic resonance images and applied persistence homology, which was encoded in vectors by the order statistic on the most persistent points in the persistence diagram. Also, closely related is work by Kovacev- (2016) @cite_28 who applied persistent homology and persistence landscapes to protein structure data.
@cite_28 @cite_22
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Persistent homology captures the evolution of topological features of a model as a parameter changes. The most commonly used summary statistics of persistent homology are the barcode and the persistence diagram. Another summary statistic, the persistence landscape, was recently introduced by Bubenik. It is a functional summary, so it is easy to calculate sample means and variances, and it is straightforward to construct various test statistics. Implementing a permutation test we detect conformational changes between closed and open forms of the maltose-binding protein, a large biomolecule consisting of 370 amino acid residues. Furthermore, persistence landscapes can be applied to machine learning methods. A hyperplane from a support vector machine shows the clear separation between the closed and open proteins conformations. Moreover, because our approach captures dynamical properties of the protein our results may help in identifying residues susceptible to ligand binding; we show that the majority of active site residues and allosteric pathway residues are located in the vicinity of the most persistent loop in the corresponding filtered Vietoris-Rips complex. This finding was not observed in the classical anisotropic network model. Persistence diagrams, which summarize the birth and death of homological features extracted from data, are employed as stable signatures for applications in image analysis and other areas. Besides simply considering the multiset of intervals included in a persistence diagram, some applications need to find representative cycles for the intervals. In this paper, we address the problem of computing these representative cycles, termed as persistent 1-cycles. The definition of persistent cycles is based on the interval module decomposition of persistence modules, which reveals the structure of persistent homology. After showing that the computation of the optimal persistent 1-cycles is NP-hard, we propose an alternative set of meaningful persistent 1-cycles that can be computed with an efficient polynomial time algorithm. We also inspect the stability issues of the optimal persistent 1-cycles and the persistent 1-cycles computed by our algorithm with the observation that the perturbations of both cannot be properly bounded. We design a software which applies our algorithm to various datasets. Experiments on 3D point clouds, mineral structures, and images show the effectiveness of our algorithm in practice. Topological data analysis (TDA) is an emerging mathematical concept for characterizing shapes in complex data. In TDA, persistence diagrams are widely recognized as a useful descriptor of data, and can distinguish robust and noisy topological properties. This paper proposes a kernel method on persistence diagrams to develop a statistical framework in TDA. The proposed kernel satisfies the stability property and provides explicit control on the effect of persistence. Furthermore, the method allows a fast approximation technique. The method is applied into practical data on proteins and oxide glasses, and the results show the advantage of our method compared to other relevant methods on persistence diagrams. This work introduces a new dataset and framework for the exploration of topological data analysis (TDA) techniques applied to time-series data. We examine the end-toend TDA processing pipeline for persistent homology applied to time-delay embeddings of time series – embeddings that capture the underlying system dynamics from which time series data is acquired. In particular, we consider stability with respect to time series length, the approximation accuracy of sparse filtration methods, and the discriminating ability of persistence diagrams as a feature for learning. We explore these properties across a wide range of time-series datasets spanning multiple domains for single source multi-segment signals as well as multi-source single segment signals. Our analysis and dataset captures the entire TDA processing pipeline and includes time-delay embeddings, persistence diagrams, topological distance measures, as well as kernels for similarity learning and classification tasks for a broad set of time-series data sources. We outline the TDA framework and rationale behind the dataset and provide insights into the role of TDA for time-series analysis as well as opportunities for new work.