A General-Purpose Molecular Foundation Model Transfers Across Diverse Olfactory Tasks

arXiv:2608.25893v1 Announce Type: new Abstract: Foundation models have transformed molecular property prediction, yet it remains unclear whether a molecular foundation model, fine-tuned on a single canonical olfactory prediction task, can learn representations that transfer across diverse machine olfaction problems. We investigate this question by fine-tuning Uni-Mol2 on the GS-LF benchmark for multi-label odor descriptor prediction and evaluating the resulting model, without additional deep-learning training, on four complementary downstream settings: cross-dataset odor descriptor prediction, odorous-versus-odorless classification, enantiomer evaluation, and odor mixture discriminability. The fine-tuned model matches or exceeds the performance of the state-of-the-art olfaction-specific baseline on the primary GS-LF benchmark and consistently transfers across these downstream evaluations. The enantiomer analysis further shows that three-dimensional molecular representations distinguish mirror-image molecules in a way that two-dimensional graph models fundamentally cannot, although accurately predicting the perceptual consequences of stereochemistry remains an open challenge. Together, these results support a train-once, transfer-across-tasks paradigm for machine olfaction and suggest that chemically pretrained molecular representations provide a strong foundation for transferable olfactory prediction.

Abstract:Foundation models have transformed molecular property prediction, yet it remains unclear whether a molecular foundation model, fine-tuned on a single canonical olfactory prediction task, can learn representations that transfer across diverse machine olfaction problems. We investigate this question by fine-tuning Uni-Mol2 on the GS-LF benchmark for multi-label odor descriptor prediction and evaluating the resulting model, without additional deep-learning training, on four complementary downstream settings: cross-dataset odor descriptor prediction, odorous-versus-odorless classification, enantiomer evaluation, and odor mixture discriminability. The fine-tuned model matches or exceeds the performance of the state-of-the-art olfaction-specific baseline on the primary GS-LF benchmark and consistently transfers across these downstream evaluations. The enantiomer analysis further shows that three-dimensional molecular representations distinguish mirror-image molecules in a way that two-dimensional graph models fundamentally cannot, although accurately predicting the perceptual consequences of stereochemistry remains an open challenge. Together, these results support a train-once, transfer-across-tasks paradigm for machine olfaction and suggest that chemically pretrained molecular representations provide a strong foundation for transferable olfactory prediction.

18 pages, 6 figures. Supplementary information included

Machine Learning (cs.LG)

arXiv:2608.25893 [cs.LG]

(or arXiv:2608.25893v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2608.25893 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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A General-Purpose Molecular Foundation Model Transfers Across Diverse Olfactory Tasks

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