Convolutional Networks on Graphs for Learning Molecular Fingerprints

Duvenaud, D., Maclaurin, D., Aguilera-Iparraguirre, J., Gómez-Bombarelli, R., Hirzel, T. D., Aspuru-Guzik, A., & Adams, R. P. (2015). Convolutional Networks on Graphs for Learning Molecular Fingerprints. Advances in Neural Information Processing Systems (NIPS) 28.

We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.

  @conference{duvenaud2015fingerprints,
  year = {2015},
  author = {Duvenaud, David and Maclaurin, Dougal and Aguilera-Iparraguirre, Jorge and G\'{o}mez-Bombarelli, Rafael and Hirzel, Timothy D. and Aspuru-Guzik, Alan and Adams, Ryan P.},
  title = {Convolutional Networks on Graphs for Learning Molecular Fingerprints},
  booktitle = {Advances in Neural Information Processing Systems (NIPS) 28},
  note = {arXiv:1509.09292 [stat.ML]},
  keywords = {NIPS, chemistry, deep learning}
}