Comparing dimensionality reduction methods for local structural identification in colloidal systems.

Quantifying local structures in self-assembled systems is a central challenge in soft matter and materials science. When no a priori knowledge of the relevant structures is available, traditional order parameters often fall short. Unsupervised machine learning provides a convenient route to autonomously uncover structural motifs directly from particle configurations. In this work, we systematically compare three popular dimensionality reduction techniques, principal component analysis, autoencoders, and uniform manifold approximation and projection (UMAP), for classifying local environments in self-assembled systems. We first apply these methods to fluid and crystal configurations of hard and charged spheres. Thereafter, we apply it to an icosahedral arrangement of spheres that self-assembled in spherical confinement, both from simulations and from experiments. We demonstrate that UMAP consistently outperforms the other methods in capturing complex structural features, offering a robust tool for structural classification without supervision.