In this position paper, we argue that when hypergraphs are used to capture multi-way local relations of data, their resulting topological features describe global behaviour. Consequently, these features capture complex correlations that can then serve as high fidelity inputs to autoencoder-driven anomaly detection pipelines. We propose two such potential pipelines for cybersecurity data, one that uses an autoencoder directly to determine network intrusions, and one that de-noises input data for a persistent homology system, PHANTOM. We provide heuristic justification for the use of the methods described therein for an intrusion detection pipeline for cyber data. We conclude by showing a small example over synthetic cyber attack data.