This thesis proposes a combinatorial generalization of a nilpotent operator on a vector space. The resulting object is highly natural, with basic connections to a variety of fields in pure mathematics, engineering, and the sciences. For the purpose of exposition we focus the discussion of applications on homological algebra and computation, with additional remarks in lattice theory, linear algebra, and abelian categories. For motivation, we recall that the methods of algebraic topology have driven remarkable progress in the qualitative study of large, noisy bodies of data over the past 15 years. A primary tool in Topological Data Analysis [TDA] is the homological persistence module, which leverages categorical structure to compare algebraic shape descriptors across multiple scales of measurement. Our principle application to computation is a novel algorithm to calculate persistent homology which, in certain cases, improves the state of the art by several orders of magnitude. Included are novel results in discrete, spectral, and algebraic Morse theory, and on the strong maps of matroid theory. The defining theme throughout is interplay between the combinatorial theory matroids and the algebraic theory of categories. The nature of these interactions is remarkably simple, but their consequences in homological algebra, quiver theory, and combinatorial optimization represent new and widely open fields for interaction between the disciplines.
We present a parallelizable algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by G ", which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we improve the performance through parallelized computation. Nonlinear dimensionality reduction (NLDR) algorithms such as Isomap, LLE and Laplacian Eigenmaps address the problem of representing high-dimensional nonlinear data in terms of low-dimensional coordinates which represent the intrinsic structure of the data. This paradigm incorporates the assumption that real-valued coordinates provide a rich enough class of functions to represent the data faithfully and efficiently. On the other hand, there are simple structures which challenge this assumption: the circle, for example, is one-dimensional but its faithful representation requires two real coordinates. In this work, we present a strategy for constructing circle-valued functions on a statistical data set. We develop a machinery of persistent cohomology to identify candidates for significant circle-structures in the data, and we use harmonic smoothing and integration to obtain the circle-valued coordinate functions themselves. We suggest that this enriched class of coordinate functions permits a precise NLDR analysis of a broader range of realistic data sets. The persistence diagram of a filtered simplicial complex is usually computed by reducing the boundary matrix of the complex. We introduce a simple optimization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new algorithm which yields to sub-cubic asymptotic bounds under certain assumptions. Combining concepts from topology and algorithms, this book delivers what its title promises: an introduction to the field of computational topology. Starting with motivating problems in both mathematics and computer science and building up from classic topics in geometric and algebraic topology, the third part of the text advances to persistent homology. This point of view is critically important in turning a mostly theoretical field of mathematics into one that is relevant to a multitude of disciplines in the sciences and engineering. The main approach is the discovery of topology through algorithms. The book is ideal for teaching a graduate or advanced undergraduate course in computational topology, as it develops all the background of both the mathematical and algorithmic aspects of the subject from first principles. Thus the text could serve equally well in a course taught in a mathematics department or computer science department. We approach the problem of the computation of persistent homology for large datasets by a divide-and-conquer strategy. Dividing the total space into separate but overlapping components, we are able to limit the total memory residency for any part of the computation, while not degrading the overall complexity much. Locally computed persistence information is then merged from the components and their intersections using a spectral sequence generalizing the Mayer-Vietoris long exact sequence. We describe the Mayer-Vietoris spectral sequence and give details on how to compute with it. This allows us to merge local homological data into the global persistent homology. Furthermore, we detail how the classical topology constructions inherent in the spectral sequence adapt to a persistence perspective, as well as describe the techniques from computational commutative algebra necessary for this extension. The resulting computational scheme suggests a parallelization scheme, and we discuss the communication steps involved in this scheme. Furthermore, the computational scheme can also serve as a guideline for which parts of the boundary matrix manipulation need to co-exist in primary memory at any given time allowing for stratified memory access in single-core computation. The spectral sequence viewpoint also provides easy proofs of a homology nerve lemma as well as a persistent homology nerve lemma. In addition, the algebraic tools we develop to approch persistent homology provide a purely algebraic formulation of kernel, image and cokernel persistence (D. Cohen-Steiner, H. Edelsbrunner, J. Harer, and D. Morozov. Persistent homology for kernels, images, and cokernels. In Proceedings of the twentieth Annual ACM-SIAM Symposium on Discrete Algorithms, pages 1011-1020. Society for Industrial and Applied Mathematics, 2009.) We consider sequences of absolute and relative homology and cohomology groups that arise naturally for a filtered cell complex. We establish algebraic relationships between their persistence modules, and show that they contain equivalent information. We explain how one can use the existing algorithm for persistent homology to process any of the four modules, and relate it to a recently introduced persistent cohomology algorithm. We present experimental evidence for the practical efficiency of the latter algorithm. Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically -- as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems, we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (10^9) elements within seconds on a cluster with 32 nodes using less than 10GB of memory per node.