Dynamic Bayesian networks (DBNs) are a widely used framework for modeling systems whose probabilistic structure evolves over time. Standard inference methods focus on local conditional distributions and can miss larger-scale patterns in how dependencies between variables organize and change over time. We introduce a topological approach to this problem. To each DBN we associate a time-varying graph, called a Dynamic Bayesian Graph (DBG), by assigning to each edge a strength that measures variation in its conditional dependence across parent configurations, and retaining edges whose strength exceeds a chosen threshold. We show that this construction fits within the dynamic graph framework of Kim and Mémoli, enabling the use of tools from topological data analysis. Applying persistent homology to a DBG produces a barcode, which records the merging and disappearance of connected groups of strongly dependent variables over time. We prove that this barcode is stable: small perturbations in the conditional probability tables of the DBN lead to small changes in the resulting barcode. This yields a principled and noise-resistant summary of how dependency structure evolves in a dynamic Bayesian network.

Persistence diagrams provide stable, interpretable summaries of geometric and topological structure and are useful for simulation-based inference when low-order statistics miss key information. Yet persistence-based pipelines require hand-chosen filtrations, vectorizations, and compressors, typically without an objective tied to parameter uncertainty. We introduce \textbf{TopoFisher}, a differentiable persistent-homology pipeline that learns topological summaries by maximizing local Gaussian Fisher information. Using simulations near a fiducial parameter, TopoFisher optimizes trainable filtrations, diagram vectorizations, and compressors without posterior samples or supervised regression targets, while retaining stable topological inductive bias. We also give sufficient regularity conditions for the log-determinant Fisher loss to be locally Lipschitz in trainable parameters. Controlled experiments on noisy spirals and Gaussian random fields, where total Fisher information is known, show that TopoFisher recovers much of the available information and outperforms fixed topological vectorizations. Our main results are on weak gravitational lensing, a high-dimensional non-Gaussian cosmological field-inference problem. Learned topological summaries reach higher Fisher information than state-of-the-art cosmological summaries and approach an unconstrained Information Maximising Neural Network baseline with up to $\sim80\times$ fewer parameters. The learned filtrations also generalize better: under simulator shift from lognormal to LPT-based maps it retains most Fisher information, while the neural baseline drops, and in neural posterior estimation they give tighter constraints than the neural baseline, and of state-of-the-art cosmological summaries. These results support Fisher-based topological optimization as a robust, parameter-efficient front end for simulation-based inference.

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}.

Topological data analysis (TDA) delivers invaluable and complementary information on the intrinsic properties of data inaccessible to conventional methods.

Persistent entropy (PE) is an information-theoretic summary statistic of persistence barcodes that has been widely used to detect regime changes in complex systems. Despite its empirical success, a general theoretical understanding of when and why persistent entropy reliably detects phase transitions has remained limited, particularly in stochastic and data-driven settings. In this work, we establish a general, model-independent theorem providing sufficient conditions under which persistent entropy provably separates two phases. We show that persistent entropy exhibits an asymptotically non-vanishing gap across phases. The result relies only on continuity of persistent entropy along the convergent diagram sequence, or under mild regularization, and is therefore broadly applicable across data modalities, filtrations, and homological degrees. To connect asymptotic theory with finite-time computations, we introduce an operational framework based on topological stabilization, defining a topological transition time by stabilizing a chosen topological statistic over sliding windows, and a probability-based estimator of critical parameters within a finite observation horizon. We validate the framework on the Kuramoto synchronization transition, the Vicsek order-to-disorder transition in collective motion, and neural network training dynamics across multiple datasets and architectures. Across all experiments, stabilization of persistent entropy and collapse of variability across realizations provide robust numerical signatures consistent with the theoretical mechanism.