Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search

Nearest neighbor-based similarity searching is a common task in chemistry, with notable use cases in drug discovery. Yet, some of the most commonly used approaches for this task still leverage a brute-force approach. In practice this can be computationally costly and overly time-consuming, due in part to the sheer size of modern chemical databases. Previous computational advancements for this task have generally relied on improvements to hardware or dataset-specific tricks that lack generalizability. Approaches that leverage lower-complexity searching algorithms remain …

cases chemistry cs.ir cs.lg discovery drug discovery embeddings low part practice search searching use cases