Measuring Chemical LLM robustness to molecular representations: a SMILES variation-based framework.

ABSTRACT: The recent integration of natural language processing into chemistry has advanced drug discovery. Molecule representations in language models (LMs) are crucial to enhance chemical understanding. We explored the ability of models to match the same chemical structures despite their different representations. Recognizing the same substance in different representations is an important component of emulating the understanding of how chemistry works. We propose Augmented Molecular Retrieval (AMORE), a flexible zero-shot framework for the assessment of chemistry LMs of different natures. The framework is based on SMILES augmentations that maintain a foundational chemical structure. The proposed method facilitates the similarity between the embedding representations of the molecule, its SMILES var

SUBMITTER: Ganeeva V 

PROVIDER: S-EPMC12574305 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature