We study the grokking phenomenon through the lens of topology. Using persistent homology on point clouds derived from the embedding matrices of a range of models trained on modular arithmetic with varying primes, we identify a clear and consistent topological signature of grokking: a sharp increase in both the maximum and total persistence of first homology ($H_1$). Persistence diagrams reveal the emergence of a dominant long-lived topological feature together with increasingly structured secondary features, reflecting the underlying cyclic structure of the task. Compared to existing spectral and geometric diagnostics -- specifically, Fourier analysis and local intrinsic dimension -- persistent homology provides a unified geometric and topological characterization of representation learning, capturing both local and global multi-scale structure. Ablations across data regimes and control settings show that these topological transitions are tied to generalization rather than memorization. Our results suggest that persistent homology offers a principled and interpretable framework for analyzing how neural networks internalize latent structure during training.

We present a unified pipeline for univariate time series classification via complex networks and persistent homology. A time series is mapped to a graph through one of five constructions across three families--visibility (natural and horizontal visibility graphs), transition, and proximity--and the graph is converted to a dissimilarity matrix from which a Vietoris-Rips filtration yields persistence diagrams. These diagrams are vectorized into fixed-length features through persistence landscapes and topological summary statistics. By standardizing the downstream processing, differences in classification performance are attributable to the network construction and distance metric alone. Experiments on twelve UCR benchmarks show that (i) no single construction dominates: the optimal graph type depends on the signal's discriminative structure; (ii) the graph distance metric is a first-order design choice, with diffusion distance uniformly outperforming shortest-path alternatives; and (iii) persistence-based features degrade gracefully under noise, consistent with the classical stability theorem of persistent homology.

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

Persistent homology (PH) encodes global information, such as cycles, and is thus increasingly integrated into graph neural networks (GNNs). PH methods in GNNs typically traverse an increasing sequence of subgraphs. In this work, we first expose limitations of this inclusion procedure. To remedy these shortcomings, we analyze contractions as a principled topological operation, in particular, for graph representation learning. We study the persistence of contraction sequences, which we call Contraction Homology (CH). We establish that forward PH and CH differ in expressivity. We then introduce Hourglass Persistence, a class of topological descriptors that interleave a sequence of inclusions and contractions to boost expressivity, learnability, and stability. We also study related families parametrized by two paradigms. We also discuss how our framework extends to simplicial and cellular networks. We further design efficient algorithms that are pluggable into end-to-end differentiable GNN pipelines, enabling consistent empirical improvements over many PH methods across standard real-world graph datasets. Code is available at \href{https://github.com/Aalto-QuML/Hourglass}{this https URL}.

We propose a topological framework for the detection of Hopf bifurcations directly from time series, based on persistent homology applied to phase space reconstructions via Takens embedding within the framework of Topological Data Analysis. The central idea is that changes in the dynamical regime are reflected in the emergence or disappearance of a dominant one-dimensional homological features in the reconstructed attractor. To quantify this behavior, we introduce a simple and interpretable scalar topological functional defined as the maximum persistence of homology classes in dimension one. This functional is used to construct a computable criterion for identifying critical parameters in families of dynamical systems without requiring knowledge of the underlying equations. The proposed approach is validated on representative systems of increasing complexity, showing consistent detection of the bifurcation point. The results support the interpretation of dynamical transitions as topological phase transitions and demonstrate the potential of topological data analysis as a model-free tool for the quantitative analysis of nonlinear time series.

Computational topology provides a tool, persistent homology, to extract quantitative descriptors from structured objects (images, graphs, point clouds, etc). These descriptors can then be involved in optimization problems, typically as a way to incorporate topological priors or to regularize machine learning models. This is usually achieved by minimizing adequate, topologically-informed losses based on these descriptors, which, in turn, naturally raises theoretical and practical questions about the possibility of optimizing such loss functions using gradient-based algorithms. This has been an active research field in the topological data analysis community over the last decade, and various techniques have been developed to enable optimization of persistence-based loss functions with gradient descent schemes. This survey presents the current state of this field, covering its theoretical foundations, the algorithmic aspects, and showcasing practical uses in several applications. It includes a detailed introduction to persistence theory and, as such, aims at being accessible to mathematicians and data scientists newcomers to the field. It is accompanied by an open-source library which implements the different approaches covered in this survey, providing a convenient playground for researchers to get familiar with the field.

We introduce graphcodes, a novel multi-scale summary of the topological properties of a dataset that is based on the well-established theory of persistent homology. Graphcodes handle datasets that are filtered along two real-valued scale parameters. Such multi-parameter topological summaries are usually based on complicated theoretical foundations and difficult to compute; in contrast, graphcodes yield an informative and interpretable summary and can be computed as efficient as one-parameter summaries. Moreover, a graphcode is simply an embedded graph and can therefore be readily integrated in machine learning pipelines using graph neural networks. We describe such a pipeline and demonstrate that graphcodes achieve better classification accuracy than state-of-the-art approaches on various datasets.

Augmenting these graph models with topological features via persistent homology (PH) has gained prominence, but identifying the class of attributed graphs that PH can recognize remains open. We introduce a novel concept of color-separating sets to provide a complete resolution to this important problem.