MOES-Pred: Molecular Structural Representation Learning by Adaptive Energy-Sentinel Vibration for Generalized Property Prediction

Abstract (source: OpenReview · © authors)

Predicting molecular properties from three-dimensional structures is fundamentally hindered by limited labeled data. While researchers have adapted self-supervised pre-training techniques from computer vision and natural language processing to address this scarcity, these approaches frequently neglect the intrinsic physical principles unique to molecular systems. From a physical perspective, denoising pre-training can be formally proven equivalent to learning molecular force fields. However, existing methods indiscriminately apply uniform noise across all molecules, thereby introducing systematic bias into the modeling of molecular distributions. To mitigate this issue, we introduce MOES-Pred, a denoising pre-training framework featuring an energy sentinel mechanism that dynamically tailors noise perturbations to individual molecules. Leveraging chemical prior knowledge, our molecule-specific noising strategies enhance conformational sampling coverage and improve distribution modeling fidelity. Extensive experiments show that MOES-Pred surpasses mainstream approaches in both force prediction and downstream quantum chemical property prediction, demonstrating substantial improvements.

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