Persistent Homology: A Pedagogical Introduction with Biological ApplicationsAurelie Jodelle Kemme, Collins Amburo Agyingi
Persistent Homology (PH) is a fundamental tool in computational topology, designed to uncover the intrinsic geometric and topological features of data across multiple scales. Originating within the broader framework of Topological Data Analysis (TDA), PH has found diverse applications ranging from protein structure and knot analysis to financial domains such as Bitcoin behaviour and stock market dynamics. Despite its growing relevance, there remains a lack of accessible resources that bridge the gap between theoretical foundations and practical implementation for beginners. This paper offers a clear and comprehensive introduction to persistent homology, guiding readers from core concepts to real-world applications. Specifically, we illustrate the methodology through the analysis of a 3-1 supercoiled DNA structure. The paper is tailored for readers without prior exposure to algebraic topology, aiming to demystify persistent homology and foster its broader adoption in data analysis tasks.
Reduction Algorithms for Persistence Diagrams of Networks: CoralTDA and PrunITCuneyt Gurcan Akcora, Murat Kantarcioglu, Yulia R. Gel, Baris Coskunuzer
Topological data analysis (TDA) delivers invaluable and complementary information on the intrinsic properties of data inaccessible to conventional methods. However, high computational costs remain the primary roadblock hindering the successful application of TDA in real-world studies, particularly with machine learning on large complex networks. Indeed, most modern networks such as citation, blockchain, and online social networks often have hundreds of thousands of vertices, making the application of existing TDA methods infeasible. We develop two new, remarkably simple but effective algorithms to compute the exact persistence diagrams of large graphs to address this major TDA limitation. First, we prove that $(k+1)$-core of a graph $\mathcal{G}$ suffices to compute its $k^{th}$ persistence diagram, $PD_k(\mathcal{G})$. Second, we introduce a pruning algorithm for graphs to compute their persistence diagrams by removing the dominated vertices. Our experiments on large networks show that our novel approach can achieve computational gains up to 95%. The developed framework provides the first bridge between the graph theory and TDA, with applications in machine learning of large complex networks. Our implementation is available at https://github.com/cakcora/PersistentHomologyWithCoralPrunit
Topological Anomaly Detection in Dynamic Multilayer Blockchain NetworksDorcas Ofori-Boateng, Ignacio Segovia Dominguez, Murat Kantarcioglu, Cuneyt G. Akcora · 5 authors
Motivated by the recent surge of criminal activities with cross-cryptocurrency trades, we introduce a new topological perspective to structural anomaly detection in dynamic multilayer networks. We postulate that anomalies in the underlying blockchain transaction graph that are composed of multiple layers are likely to also be manifested in anomalous patterns of the network shape properties. As such, we invoke the machinery of clique persistent homology on graphs to systematically and efficiently track evolution of the network shape and, as a result, to detect changes in the underlying network topology and geometry. We develop a new persistence summary for multilayer networks, called stacked persistence diagram, and prove its stability under input data perturbations. We validate our new topological anomaly detection framework in application to dynamic multilayer networks from the Ethereum Blockchain and the Ripple Credit Network, and demonstrate that our stacked PD approach substantially outperforms state-of-art techniques.