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Register a new userTopological Data Analysis for Object Data
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Added by
Peter Bubenik
Publication date
2018
fields
Mathematical Statistics
and research's language is
English
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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 persistence landscapes to vectorize object data and perform statistical analysis. We apply to this pipeline to some biological images that were previously shown to be challenging to study using shape theory. 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.
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Topological Data Analysis (TDA) is a rapidly growing field, which studies methods for learning underlying topological structures present in complex data representations. TDA methods have found recent success in extracting useful geometric structures for a wide range of applications, including protein classification, neuroscience, and time-series analysis. However, in many such applications, one is also interested in sequentially detecting changes in this topological structure. We propose a new method called Persistence Diagram based Change-Point (PD-CP), which tackles this problem by integrating the widely-used persistence diagrams in TDA with recent developments in nonparametric change-point detection. The key novelty in PD-CP is that it leverages the distribution of points on persistence diagrams for online detection of topological changes. We demonstrate the effectiveness of PD-CP in an application to solar flare monitoring.
We introduce giotto-tda, a Python library that integrates high-performance topological data analysis with machine learning via a scikit-learn-compatible API and state-of-the-art C++ implementations. The librarys ability to handle various types of data is rooted in a wide range of preprocessing techniques, and its strong focus on data exploration and interpretability is aided by an intuitive plotting API. Source code, binaries, examples, and documentation can be found at https://github.com/giotto-ai/giotto-tda.
We develop a novel exploratory tool for non-Euclidean object data based on data depth, extending the celebrated Tukeys depth for Euclidean data. The proposed metric halfspace depth, applicable to data objects in a general metric space, assigns to data points depth values that characterize the centrality of these points with respect to the distribution and provides an interpretable center-outward ranking. Desirable theoretical properties that generalize standard depth properties postulated for Euclidean data are established for the metric halfspace depth. The depth median, defined as the deepest point, is shown to have high robustness as a location descriptor both in theory and in simulation. We propose an efficient algorithm to approximate the metric halfspace depth and illustrate its ability to adapt to the intrinsic data geometry. The metric halfspace depth was applied to an Alzheimers disease study, revealing group differences in the brain connectivity, modeled as covariance matrices, for subjects in different stages of dementia. Based on phylogenetic trees of 7 pathogenic parasites, our proposed metric halfspace depth was also used to construct a meaningful consensus estimate of the evolutionary history and to identify potential outlier trees.
The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galapagos Islands.
In this article, we show how the recent statistical techniques developed in Topological Data Analysis for the Mapper algorithm can be extended and leveraged to formally define and statistically quantify the presence of topological structures coming from biological phenomena in datasets of CCC contact maps.
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