Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userComputing Zigzag Persistence on Graphs in Near-Linear Time
176
0
0.0
(
0
)
Added by
Tao Hou
Publication date
2021
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
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.
rate research
Read More
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.
In standard persistent homology, a persistent cycle born and dying with a persistence interval (bar) associates the bar with a concrete topological representative, which provides means to effectively navigate back from the barcode to the topological space. Among the possibly many, optimal persistent cycles bring forth further information due to having guaranteed quality. However, topological features usually go through variations in the lifecycle of a bar which a single persistent cycle may not capture. Hence, for persistent homology induced from PL functions, we propose levelset persistent cycles consisting of a sequence of cycles that depict the evolution of homological features from birth to death. Our definition is based on levelset zigzag persistence which involves four types of persistence intervals as opposed to the two types in standard persistence. For each of the four types, we present a polynomial-time algorithm computing an optimal sequence of levelset persistent $p$-cycles for the so-called weak $(p+1)$-pseudomanifolds. Given that optimal cycle problems for homology are NP-hard in general, our results are useful in practice because weak pseudomanifolds do appear in applications. Our algorithms draw upon an idea of relating optimal cycles to min-cuts in a graph that we exploited earlier for standard persistent cycles. Note that levelset zigzag poses non-trivial challenges for the approach because a sequence of optimal cycles instead of a single one needs to be computed in this case.
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
Reeb graphs are widely used in a range of fields for the purposes of analyzing and comparing complex spaces via a simpler combinatorial object. Further, they are closely related to extended persistence diagrams, which largely but not completely encode the information of the Reeb graph. In this paper, we investigate the effect on the persistence diagram of a particular continuous operation on Reeb graphs; namely the (truncated) smoothing operation. This construction arises in the context of the Reeb graph interleaving distance, but separately from that viewpoint provides a simplification of the Reeb graph which continuously shrinks small loops. We then use this characterization to initiate the study of inverse problems for Reeb graphs using smoothing by showing which paths in persistence diagram space (commonly known as vineyards) can be realized by a path in the space of Reeb graphs via these simple operations. This allows us to solve the inverse problem on a certain family of piecewise linear vineyards when fixing an initial Reeb graph.
Computation of persistent homology of simplicial representations such as the Rips and the Cv{e}ch complexes do not efficiently scale to large point clouds. It is, therefore, meaningful to devise approximate representations and evaluate the trade-off between their efficiency and effectiveness. The lazy witness complex economically defines such a representation using only a few selected points, called landmarks. Topological data analysis traditionally considers a point cloud in a Euclidean space. In many situations, however, data is available in the form of a weighted graph. A graph along with the geodesic distance defines a metric space. This metric space of a graph is amenable to topological data analysis. We discuss the computation of persistent homologies on a weighted graph. We present a lazy witness complex approach leveraging the notion of $epsilon$-net that we adapt to weighted graphs and their geodesic distance to select landmarks. We show that the value of the $epsilon$ parameter of the $epsilon$-net provides control on the trade-off between choice and number of landmarks and the quality of the approximate simplicial representation. We present three algorithms for constructing an $epsilon$-net of a graph. We comparatively and empirically evaluate the efficiency and effectiveness of the choice of landmarks that they induce for the topological data analysis of different real-world graphs.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
