Computing Topological Persistence for Simplicial Maps

Algorithms for persistent homology and zigzag persistent homology are well-studied for persistence modules where homomorphisms are induced by inclusion maps. In this paper, we propose a practical algorithm for computing persistence under $\mathbb{Z}_2$ coefficients for a sequence of general simplicial maps and show how these maps arise naturally in some applications of topological data analysis. First, we observe that it is not hard to simulate simplicial maps by inclusion maps but not necessarily in a monotone direction. This, combined with the known algorithms for zigzag persistence, provides an algorithm for computing the persistence induced by simplicial maps. Our main result is that the above simple minded approach can be improved for a sequence of simplicial maps given in a monotone direction. A simplicial map can be decomposed into a set of elementary inclusions and vertex collapses--two atomic operations that can be supported efficiently with the notion of simplex annotations for computing persistent homology. A consistent annotation through these atomic operations implies the maintenance of a consistent cohomology basis, hence a homology basis by duality. While the idea of maintaining a cohomology basis through an inclusion is not new, maintaining them through a vertex collapse is new, which constitutes an important atomic operation for simulating simplicial maps. Annotations support the vertex collapse in addition to the usual inclusion quite naturally. Finally, we exhibit an application of this new tool in which we approximate the persistence diagram of a filtration of Rips complexes where vertex collapses are used to tame the blow-up in size.Comment: This is the revised and full version of the paper that is going to appear in the Proceedings of 30th Annual Symposium on Computational Geometr

Dist2Cycle: A Simplicial Neural Network for Homology Localization

Simplicial complexes can be viewed as high dimensional generalizations of graphs that explicitly encode multi-way ordered relations between vertices at different resolutions, all at once. This concept is central towards detection of higher dimensional topological features of data, features to which graphs, encoding only pairwise relationships, remain oblivious. While attempts have been made to extend Graph Neural Networks (GNNs) to a simplicial complex setting, the methods do not inherently exploit, or reason about, the underlying topological structure of the network. We propose a graph convolutional model for learning functions parametrized by the $k$-homological features of simplicial complexes. By spectrally manipulating their combinatorial $k$-dimensional Hodge Laplacians, the proposed model enables learning topological features of the underlying simplicial complexes, specifically, the distance of each $k$-simplex from the nearest "optimal" $k$-th homology generator, effectively providing an alternative to homology localization.Comment: 9 pages, 5 figure

Homological scaffold via minimal homology bases

The homological scaffold leverages persistent homology to construct a topologically sound summary of a weighted network. However, its crucial dependency on the choice of representative cycles hinders the ability to trace back global features onto individual network components, unless one provides a principled way to make such a choice. In this paper, we apply recent advances in the computation of minimal homology bases to introduce a quasi-canonical version of the scaffold, called minimal, and employ it to analyze data both real and in silico. At the same time, we verify that, statistically, the standard scaffold is a good proxy of the minimal one for sufficiently complex networks

Computing multiparameter persistent homology through a discrete Morse-based approach

Persistent homology allows for tracking topological features, like loops, holes and their higher-dimensional analogues, along a single-parameter family of nested shapes. Computing descriptors for complex data characterized by multiple parameters is becoming a major challenging task in several applications, including physics, chemistry, medicine, and geography. Multiparameter persistent homology generalizes persistent homology to allow for the exploration and analysis of shapes endowed with multiple filtering functions. Still, computational constraints prevent multiparameter persistent homology to be a feasible tool for analyzing large size data sets. We consider discrete Morse theory as a strategy to reduce the computation of multiparameter persistent homology by working on a reduced dataset. We propose a new preprocessing algorithm, well suited for parallel and distributed implementations, and we provide the first evaluation of the impact of multiparameter persistent homology on computations

Persistent Laplacians: properties, algorithms and implications

We present a thorough study of the theoretical properties and devise efficient algorithms for the \emph{persistent Laplacian}, an extension of the standard combinatorial Laplacian to the setting of pairs (or, in more generality, sequences) of simplicial complexes $K \hookrightarrow L$, which was recently introduced by Wang, Nguyen, and Wei. In particular, in analogy with the non-persistent case, we first prove that the nullity of the $q$-th persistent Laplacian $\Delta_q^{K,L}$ equals the $q$-th persistent Betti number of the inclusion $(K \hookrightarrow L)$. We then present an initial algorithm for finding a matrix representation of $\Delta_q^{K,L}$, which itself helps interpret the persistent Laplacian. We exhibit a novel relationship between the persistent Laplacian and the notion of Schur complement of a matrix which has several important implications. In the graph case, it both uncovers a link with the notion of effective resistance and leads to a persistent version of the Cheeger inequality. This relationship also yields an additional, very simple algorithm for finding (a matrix representation of) the $q$-th persistent Laplacian which in turn leads to a novel and fundamentally different algorithm for computing the $q$-th persistent Betti number for a pair $(K,L)$ which can be significantly more efficient than standard algorithms. Finally, we study persistent Laplacians for simplicial filtrations and present novel stability results for their eigenvalues. Our work brings methods from spectral graph theory, circuit theory, and persistent homology together with a topological view of the combinatorial Laplacian on simplicial complexes