Undersampling Techniques for Nonlinear Chemical Space Visualization

The visualization of high-dimensional chemical space is a critical tool for understanding molecular diversity, structure-property relationships, and for guiding compound selection. However, the performance of non-linear dimensionality reduction (DR) techniques like t-Stochastic Neighborhood Embedding (t-SNE), Uniform Manifold Approximation and Projection (UMAP), and Generative Topographic Mapping (GTM) are often susceptible to the choice of hyperparameters, along with the high cost of their training for large datasets. In this study, we investigated the effect of undersampling methods on the choice of hyperparameter selection for these non-linear dimensionality reduction methods. Our results demonstrate that selecting small representative subsets of chemical data not only reduces computational costs associated with hyperparameter training but also serves as an innovative means to train non-linear DR methods, leading to projections that better preserve the local structure within the chemical space.