The sublevel Flood bifiltration: towards scalable 2-parameter persistent homology

Persistence-based topological optimization deforms a point cloud $X \subset \mathbb{R}^d$ by minimizing objectives of the form $L(X) = \ell(\mathrm{Dgm}(X))$, where $\mathrm{Dgm}(X)$ is a persistence diagram. In practice, optimization is limited by two coupled issues: persistent homology is typically computed on subsamples, and the resulting topological gradients are highly sparse, with only a few anchor points receiving nonzero updates. Motivated by diffeomorphic interpolation, which extends sparse gradients to smooth ambient vector fields via Reproducing Kernel Hilbert Space (RKHS) interpolation, we propose a more scalable pipeline that improves both subsampling and gradient extension. We introduce subsampling via random slicing, a lightweight scheme that promotes iteration-wise geometric coverage and mitigates density bias. We further replace the costly kernel solve with a fast Nadaraya-Watson (NW) Gaussian convolution, producing a globally defined smooth update field at a fraction of the computational cost, while being more suited for topological optimization tasks. We provide theoretical guarantees for NW smoothing, including anchor approximation bounds and global Lipschitz estimates. Experiments in $2$D and $3$D show that combining random slicing with NW smoothing yields consistent speedups and improved objective values over other baselines on common persistence losses.

We propose persistent discrete homology as a tool for topological data analysis and discuss its advantages over the existing methods. In particular, we provide empirical evidence that persistent discrete homology is more noise-resistant than persistent homology of the Vietoris-Rips complex for data coming from non-metric settings.

We introduce a data-analysis framework based on filtrations of finite topological spaces. Starting from a finite metric data set, we construct a sequence of coarsening topologies on the same set of points. These topologies give persistence modules and barcodes in the usual way, but they also retain information that is lost when the filtration is reduced to homology. At each level one can examine, for example, which points are topologically indistinguishable, how their minimal neighbourhoods overlap, how connected components merge, and how these features change from one level to the next. We develop the basic theory of these filtrations, establish stability results under suitable hypotheses, and give practical constructions starting directly from a distance matrix. We then study what can be learned from the resulting finite topologies. On synthetic data with known clusters of different shapes, sizes, and densities, we examine how these regions appear among the finite-topological structures and how they merge as the topology coarsens. We also study what happens when points that become uncovered early in the construction are removed and the analysis is repeated. For one-dimensional homology, we use paths in the finite-topological structure to locate cycles and to examine how their appearance is related to the geometry of the data. We finally apply these ideas to two real data sets with quite different structures. On the Paul15 single-cell data, we use the evolving finite topology to examine fine cellular states, their overlaps and relations, their assembly into larger groups, and the effect of removing points that connect these structures. On COIL20, where images of an object are sampled through a full rotation, we study how the cyclic organization of the images is reflected in the finite-topological evolution and in the associated one-dimensional homology.