Persistent cycles, especially the minimal ones, are useful geometric features functioning as augmentations for the intervals in the purely topological persistence diagrams (also termed as barcodes). In our earlier work, we showed that computing minimal 1-dimensional persistent cycles (persistent 1-cycles) for finite intervals is NP-hard while the same for infinite intervals is polynomially tractable. In this paper, we address this problem for general dimensions with @math coefficients. In addition to proving that it is NP-hard to compute minimal persistent d-cycles (d>1) for both types of intervals given arbitrary simplicial complexes, we identify two interesting cases which are polynomially tractable. These two cases assume the complex to be a certain generalization of manifolds which we term as weak pseudomanifolds. For finite intervals from the d-th persistence diagram of a weak (d+1)-pseudomanifold, we utilize the fact that persistent cycles of such intervals are null-homologous and reduce the problem to a minimal cut problem. Since the same problem for infinite intervals is NP-hard, we further assume the weak (d+1)-pseudomanifold to be embedded in @math so that the complex has a natural dual graph structure and the problem reduces to a minimal cut problem. Experiments with both algorithms on scientific data indicate that the minimal persistent cycles capture various significant features of the data.
We describe the first algorithms to compute minimum cuts in surface-embedded graphs in near-linear time. Given an undirected graph embedded on an orientable surface of genus g, with two specified vertices s and t, our algorithm computes a minimum (s,t)-cut in gO(g) n log n time. Except for the special case of planar graphs, for which O(n log n)-time algorithms have been known for more than 20 years, the best previous time bounds for finding minimum cuts in embedded graphs follow from algorithms for general sparse graphs. A slight generalization of our minimum-cut algorithm computes a minimum-cost subgraph in every Z2-homology class. We also prove that finding a minimum-cost subgraph homologous to a single input cycle is NP -hard. We describe simple greedy algorithms to construct the shortest set of loops that generates either the fundamental group (with a given basepoint) or the first homology group (over any fixed coefficient field) of any oriented 2-manifold. In particular, we show that the shortest set of loops that generate the fundamental group of any oriented combinatorial 2-manifold, with any given basepoint, can be constructed in O(n log n) time using a straightforward application of Dijkstra's shortest path algorithm. This solves an open problem of Colin de Verdiere and Lazarus. Inference of topological and geometric attributes of a hidden manifold from its point data is a fundamental problem arising in many scientific studies and engineering applications. In this paper we present an algorithm to compute a set of loops from a point data that presumably sample a smooth manifold M ⊂ Rd. These loops approximate a shortest basis of the one dimensional homology group H1(M) over coefficients in finite field Z2. Previous results addressed the issue of computing the rank of the homology groups from point data, but there is no result on approximating the shortest basis of a manifold from its point sample. In arriving our result, we also present a polynomial time algorithm for computing a shortest basis of H1 (Κ) for any finite simplicial complex Κ whose edges have non-negative weights. Given a simplicial complex with weights on its simplices, and a nontrivial cycle on it, we are interested in finding the cycle with minimal weight which is homologous to the given one. Assuming that the homology is defined with integer ( @math ) coefficients, we show the following (Theorem 5.2): For a finite simplicial complex @math of dimension greater than @math , the boundary matrix @math is totally unimodular if and only if @math is torsion-free for all pure subcomplexes @math in @math of dimensions @math and @math , respectively, where @math . Because of the total unimodularity of the boundary matrix, we can solve the optimization problem, which is inherently an integer programming problem, as a linear program and obtain an integer solution. Thus, the problem of finding optimal cycles in a given homology class can be solved in polynomial time. This result is surprising in the backdrop of a recent result which says that the problem is NP-hard under @math coefficients which, being a field, is in general easier to deal with. Our result implies, among other things, that one can compute in polynomial time an optimal @math -cycle in a given homology class for any triangulation of an orientable compact @math -manifold or for any finite simplicial complex embedded in @math . Our optimization approach can also be used for various related problems, such as finding an optimal chain homologous to a given one when these are not cycles. Our result can also be viewed as providing a topological characterization of total unimodularity. We develop a method for measuring homology classes. This involves two problems. First, we define the size of a homology class, using ideas from relative homology. Second, we define an optimal basis of a homology group to be the basis whose elements' size have the minimal sum. We provide a greedy algorithm to compute the optimal basis and measure classes in it. The algorithm runs in O(@bn^3log^2n) time, where n is the size of the simplicial complex and @b is the Betti number of the homology group. Finally, we prove the stability of our result. The algorithm can be adapted to measure any given class. We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the Z2 field.