Molecular Representation Matters: Comparative Evaluation of Fingerprints, RDKit Descriptors, and Hashing Effects
Abstract
). We further evaluate how the choice of hash function used during fingerprint construction affects representation quality and identify that noncryptographic hashing preserves locality and leads to better and more consistent outcomes than cryptographic hashing (SHA-256). This work provides mechanistic insights into how different molecular representations encode structural and physicochemical information, highlighting the merits and limits of descriptors for learning quantum-chemical properties. This offers practical guidance for selecting molecular representations and hashing strategies in designing and establishing pipelines for the artificial intelligence study of chemistry.
Fields of Study & Subjects
Computational Drug Discovery Methods
Machine Learning in Materials Science
Graph theory and applications
Publication details
- Journal / source
- The Journal of Physical Chemistry Letters
- Publisher
- American Chemical Society (ACS)
- Volume
- 17
- Issue
- 7
- Pages
- 1960–1971
- Publication date
- 7 February 2026
- Language
- EN