TY - GEN
T1 - Directional Message Passing on Molecular Graphs via Synthetic Coordinates
AU - Klicpera, Johannes
AU - Yeshwanth, Chandan
AU - Günnemann, Stephan
N1 - Publisher Copyright:
© 2021 Neural information processing systems foundation. All rights reserved.
PY - 2021
Y1 - 2021
N2 - Graph neural networks that leverage coordinates via directional message passing have recently set the state of the art on multiple molecular property prediction tasks. However, they rely on atom position information that is often unavailable, and obtaining it is usually prohibitively expensive or even impossible. In this paper we propose synthetic coordinates that enable the use of advanced GNNs without requiring the true molecular configuration. We propose two distances as synthetic coordinates: Distance bounds that specify the rough range of molecular configurations, and graph-based distances using a symmetric variant of personalized PageRank. To leverage both distance and angular information we propose a method of transforming normal graph neural networks into directional MPNNs. We show that with this transformation we can reduce the error of a normal graph neural network by 55% on the ZINC benchmark. We furthermore set the state of the art on ZINC and coordinate-free QM9 by incorporating synthetic coordinates in the SMP and DimeNet++ models. Our implementation is available online. 1.
AB - Graph neural networks that leverage coordinates via directional message passing have recently set the state of the art on multiple molecular property prediction tasks. However, they rely on atom position information that is often unavailable, and obtaining it is usually prohibitively expensive or even impossible. In this paper we propose synthetic coordinates that enable the use of advanced GNNs without requiring the true molecular configuration. We propose two distances as synthetic coordinates: Distance bounds that specify the rough range of molecular configurations, and graph-based distances using a symmetric variant of personalized PageRank. To leverage both distance and angular information we propose a method of transforming normal graph neural networks into directional MPNNs. We show that with this transformation we can reduce the error of a normal graph neural network by 55% on the ZINC benchmark. We furthermore set the state of the art on ZINC and coordinate-free QM9 by incorporating synthetic coordinates in the SMP and DimeNet++ models. Our implementation is available online. 1.
UR - http://www.scopus.com/inward/record.url?scp=85131022289&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:85131022289
T3 - Advances in Neural Information Processing Systems
SP - 15421
EP - 15433
BT - Advances in Neural Information Processing Systems 34 - 35th Conference on Neural Information Processing Systems, NeurIPS 2021
A2 - Ranzato, Marc'Aurelio
A2 - Beygelzimer, Alina
A2 - Dauphin, Yann
A2 - Liang, Percy S.
A2 - Wortman Vaughan, Jenn
PB - Neural information processing systems foundation
T2 - 35th Conference on Neural Information Processing Systems, NeurIPS 2021
Y2 - 6 December 2021 through 14 December 2021
ER -