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So3krates: Equivariant attention for interactions on arbitrary length-scales in molecular systems

About

The application of machine learning methods in quantum chemistry has enabled the study of numerous chemical phenomena, which are computationally intractable with traditional ab-initio methods. However, some quantum mechanical properties of molecules and materials depend on non-local electronic effects, which are often neglected due to the difficulty of modeling them efficiently. This work proposes a modified attention mechanism adapted to the underlying physics, which allows to recover the relevant non-local effects. Namely, we introduce spherical harmonic coordinates (SPHCs) to reflect higher-order geometric information for each atom in a molecule, enabling a non-local formulation of attention in the SPHC space. Our proposed model So3krates - a self-attention based message passing neural network - uncouples geometric information from atomic features, making them independently amenable to attention mechanisms. Thereby we construct spherical filters, which extend the concept of continuous filters in Euclidean space to SPHC space and serve as foundation for a spherical self-attention mechanism. We show that in contrast to other published methods, So3krates is able to describe non-local quantum mechanical effects over arbitrary length scales. Further, we find evidence that the inclusion of higher-order geometric correlations increases data efficiency and improves generalization. So3krates matches or exceeds state-of-the-art performance on popular benchmarks, notably, requiring a significantly lower number of parameters (0.25 - 0.4x) while at the same time giving a substantial speedup (6 - 14x for training and 2 - 11x for inference) compared to other models.

J. Thorben Frank, Oliver T. Unke, Klaus-Robert M\"uller• 2022

Related benchmarks

TaskDatasetResultRank
Molecular property predictionMD17 Malondialdehyde 1k (train)
Force MAE (kcal/mol/Å)0.147
7
Molecular property predictionMD17 Aspirin 1k (train)
Force MAE0.236
7
Molecular property predictionMD17 Naphthalene (1k train points)
Force MAE (kcal/mol/Å)0.074
7
Molecular property predictionMD17 Salicylic Acid 1k (train)
Force MAE (kcal/mol/Å)0.145
7
Molecular property predictionMD17 Toluene (1k train points)
Force MAE (kcal/mol/Å)0.073
7
Molecular property predictionMD17 Uracil 1k (train)
Force MAE (kcal/mol/Å)0.111
7
Molecular property predictionMD17 Ethanol (1k train)
Force MAE (kcal/mol/Å)0.096
7
Interatomic Potential PredictionC10H2 / C10H2+ (test)
Energy RMSE (meV/atom)0.113
6
Interatomic Potential PredictionNa8/9Cl8+ (test)
Energy RMSE (meV/atom)0.455
6
Energy and force predictionQM7-X known molecules unknown conformations full
Energy MAE15.228
6
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