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Register a new userOn Computing a Center Persistence Diagram
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Added by
Binhai Zhu
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Throughout this paper, a persistence diagram ${cal P}$ is composed of a set $P$ of planar points (each corresponding to a topological feature) above the line $Y=X$, as well as the line $Y=X$ itself, i.e., ${cal P}=Pcup{(x,y)|y=x}$. Given a set of persistence diagrams ${cal P}_1,...,{cal P}_m$, for the data reduction purpose, one way to summarize their topological features is to compute the {em center} ${cal C}$ of them first under the bottleneck distance. We consider two discre
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Graphs model real-world circumstances in many applications where they may constantly change to capture the dynamic behavior of the phenomena. Topological persistence which provides a set of birth and death pairs for the topological features is one instrument for analyzing such changing graph data. However, standard persistent homology defined over a growing space cannot always capture such a dynamic process unless shrinking with deletions is also allowed. Hence, zigzag persistence which incorporates both insertions and deletions of simplices is more appropriate in such a setting. Unlike standard persistence which admits nearly linear-time algorithms for graphs, such results for the zigzag version improving the general $O(m^omega)$ time complexity are not known, where $omega< 2.37286$ is the matrix multiplication exponent. In this paper, we propose algorithms for zigzag persistence on graphs which run in near-linear time. Specifically, given a filtration with $m$ additions and deletions on a graph with $n$ vertices and edges, the algorithm for $0$-dimension runs in $O(mlog^2 n+mlog m)$ time and the algorithm for 1-dimension runs in $O(mlog^4 n)$ time. The algorithm for $0$-dimension draws upon another algorithm designed originally for pairing critical points of Morse functions on $2$-manifolds. The algorithm for $1$-dimension pairs a negative edge with the earliest positive edge so that a $1$-cycle containing both edges resides in all intermediate graphs. Both algorithms achieve the claimed time complexity via dynamic graph data structures proposed by Holm et al. In the end, using Alexander duality, we extend the algorithm for $0$-dimension to compute the $(p-1)$-dimensional zigzag persistence for $mathbb{R}^p$-embedded complexes in $O(mlog^2 n+mlog m+nlog n)$ time.
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.
Given a simple polygon $P$ and a set $Q$ of points contained in $P$, we consider the geodesic $k$-center problem where we want to find $k$ points, called emph{centers}, in $P$ to minimize the maximum geodesic distance of any point of $Q$ to its closest center. In this paper, we focus on the case for $k=2$ and present the first exact algorithm that efficiently computes an optimal $2$-center of $Q$ with respect to the geodesic distance in $P$.
For a polygonal domain with $h$ holes and a total of $n$ vertices, we present algorithms that compute the $L_1$ geodesic diameter in $O(n^2+h^4)$ time and the $L_1$ geodesic center in $O((n^4+n^2 h^4)alpha(n))$ time, respectively, where $alpha(cdot)$ denotes the inverse Ackermann function. No algorithms were known for these problems before. For the Euclidean counterpart, the best algorithms compute the geodesic diameter in $O(n^{7.73})$ or $O(n^7(h+log n))$ time, and compute the geodesic center in $O(n^{11}log n)$ time. Therefore, our algorithms are significantly faster than the algorithms for the Euclidean problems. Our algorithms are based on several interesting observations on $L_1$ shortest paths in polygonal domains.
An algorithm is presented that constructs an acyclic partial matching on the cells of a given simplicial complex from a vector-valued function defined on the vertices and extended to each simplex by taking the least common upper bound of the values on its vertices. The resulting acyclic partial matching may be used to construct a reduced filtered complex with the same multidimensional persistent homology as the original simplicial complex filtered by the sublevel sets of the function. Numerical tests show that in practical cases the rate of reduction in the number of cells achieved by the algorithm is substantial. This promises to be useful for the computation of multidimensional persistent homology of simplicial complexes filtered by sublevel sets of vector-valued functions.
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