Analysis of Atom-level pretraining with QM data for Graph Neural Networks Molecular property models

Jose Arjona-Medina, Ramil Nugmanov

Keywords: Drug Discovery, Graph Neural Networks, Molecular property predictions, QSAR

TL;DR: This paper shows how atom-level pretraining with quantum mechanics data enhances the generalization and robustness of molecular representations in QSAR models.

Abstract:

Despite the rapid and significant advancements in deep learning for Quantitative Structure-Activity Relationship (QSAR) models, the challenge of learning robust molecular representations that effectively generalize in real-world scenarios to novel compounds remains an elusive and unresolved task.

This study examines how atom-level pretraining with quantum mechanics (QM) data can mitigate violations of assumptions regarding the distributional similarity between training and test data and therefore improve performance and generalization in downstream tasks.

In the public dataset Therapeutics Data Commons (TDC), we show how pretraining on atom-level QM improves performance overall and makes the activation of the features distributes more Gaussian-like which results in a representation that is more robust to distribution shifts.

To the best of our knowledge, this is the first time that hidden state molecular representations are analyzed to compare the effects of molecule-level and atom-level pretraining on QM data.

Submission Number: 56