From High Dimensions to Human Insight: Exploring Dimensionality Reduction for Chemical Space Visualization

Dimensionality reduction is an important exploratory data analysis method that allows high-dimensional data to be represented in a human-interpretable lower-dimensional space. It is extensively applied in the analysis of chemical libraries, where chemical structure data - represented as high-dimensional feature vectors-are transformed into 2D or 3D chemical space maps. In this paper, commonly used dimensionality reduction techniques - Principal Component Analysis (PCA), t-Distributed Stochastic Neighbor Embedding (t-SNE), Uniform Manifold Approximation and Projection (UMAP), and Generative Topographic Mapping (GTM) - are evaluated in terms of neighborhood preservation and visualization capability of sets of small molecules from the ChEMBL database.