How effective are contrastive learning-based approaches for activity-cliff prediction?
- 1University of Florida
Abstract
Activity cliffs, defined as structurally similar molecules with vastly different properties represent a fundamental challenge in modern day drug discovery for property prediction models. While Graph Neural Networks (GNNs) have advanced molecular property prediction, they inherently struggle with this problem due to representation collapse and node over smoothening. In this work, we evaluate the efficacy of incorporating various contrastive learning-based loss functions, including the Supervised Contrastive (SupCon) configurations into several GNN backbones to navigate this structure-activity landscape. Tested across the MoleculeACE benchmarks, the results indicate that while contrastive losses prevent GNN mode collapse to some extent and drastically improve the property-based separation in the embedding space, their impact on absolute predictive accuracy remains highly dataset dependent. Ultimately, these methods offer critical gains in interpretability for mapping optimized lead generations, opening up new directions for models that respect these sharp pharmacological discontinuities.
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BibTeX
@misc{surendran2026effective,
title = {{How effective are contrastive learning-based approaches for activity-cliff prediction?}},
author = {A. Surendran and R. A. Miranda Quintana},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.08.750257},
url = {https://www.biorxiv.org/content/10.64898/2026.09.08.750257v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - How effective are contrastive learning-based approaches for activity-cliff prediction?
AU - A. Surendran
AU - R. A. Miranda Quintana
PY - 2026
DA - 2026/09/08
PB - bioRxiv
DO - 10.64898/2026.09.08.750257
UR - https://www.biorxiv.org/content/10.64898/2026.09.08.750257v1
AB - Activity cliffs, defined as structurally similar molecules with vastly different properties represent a fundamental challenge in modern day drug discovery for property prediction models. While Graph Neural Networks (GNNs) have advanced molecular property prediction, they inherently struggle with this problem due to representation collapse and node over smoothening. In this work, we evaluate the efficacy of incorporating various contrastive learning-based loss functions, including the Supervised Contrastive (SupCon) configurations into several GNN backbones to navigate this structure-activity landscape. Tested across the MoleculeACE benchmarks, the results indicate that while contrastive losses prevent GNN mode collapse to some extent and drastically improve the property-based separation in the embedding space, their impact on absolute predictive accuracy remains highly dataset dependent. Ultimately, these methods offer critical gains in interpretability for mapping optimized lead generations, opening up new directions for models that respect these sharp pharmacological discontinuities.
ER -